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RRS Discovery Cruise DY017, 20 Oct

1. mctd 02b m This script can replicate and apply the oxygen hysteresis correction that can also be implemented in the seabird software The user must choose whether to include or omit the hysteresis correction For DY017 the oxygen hysteresis correction was applied in the seabird software and omitted in the script mctd 02b input DYOI7 Output ctd DYOI7 24hz nc mctd 03 m averages the 24Hz data to 1Hz and calculates derived variables e g salinity potential temperature etc input DYOI7 24hz nc Output ctd DYOI7 NNN Ihz nc ctd DYO17 NNN psal nc 01 m creates an empty file based on template file dcs DYO17 varlist csv which will later hold info on start and end of up and down casts 52 input dcs DYOI7 varlist csv Output dcs DYOI7 NNN nc mdcs 02 m Calculates position of deepest datapoint in CTD file and adds information time scan number position to the dcs file input dcs DYOI7 Output dcs DYOI7 NNN nc At this point the user must manually obtain the first and last good data points in each CTD profile This is done via 03g m which is a graphical interface which allows the user to choose the first and last good points of data in the downcast and upcast respectively After both points have been identified the scan numbers are saved to the dcs file Generally the first good data point is the shallowest data point
2. eve ie Reb e ee da dee node discern res 115 References oie teda ituri ga a Read 116 Page intentionally left blank Preface The data presented in this Cruise Report are provisional and should not be used or reproduced without permission In some cases they are fully calibrated and in other cases not Further details can be obtained from the originators see Scientific Reports In due course the full data set will be lodged with the British Oceanographic Data Centre ACKNOWLEDGMENTS We thank the Master the officers and the crew of RRS Discovery for their excellent support and assistance throughout the cruise particularly given the technical problems experienced Excellent support was provided by NMFSS staff on board and also prior to departure SCIENTIFIC PERSONNEL ALLEN Stephanie BEATON John BENSON Jeff BIRCHILL Antony BURRIS James CARR Nealy CLARGO Nikki DANIELS Chris HARTMAN Sue HEMSLEY Victoria JONES Sam KIVIMAER Caroline LEADBEATER Andrew McNIELL Jack MILNE Angela MUNNS Lucie PAINTER Stuart Principal Scientist RUSIECKA Dagamara SALT Leslie SHERRING Alan SIEMERING Beatrix SIMS Richard SPINGYS Carl WOODS Julie NOC OBE PhD SAMS NOC NMFSS U PLYMOUTH PhD NOC NMFSS U LIVERPOOL PhD NIOZ NOC OBE PhD NOC OBE NOC OBE PhD SAMS PhD NOC OBE NOC NMFSS NOC NMFSS U PLYMOUTH NOC OBE PhD NOC OBE NOC OES KIEL PhD SBR NOC NMFSS SAMS Ph
3. Flow Ctrl EnsCyc PngCyc Binry Ser Rec gt CF11101 gt RN RTADI gt cs Appendix C Sample Iridium email gt From NOC Iridium Moorings lt Iridium Moorings noc ac uk gt gt Date 29 October 2014 14 18 28 GMT gt NOCS NMFSS SM lt nocs_nmfss_sm noc ac uk gt dr400 noc ac uk lt dr400 noc ac uk gt stuart cunningham sams ac uk lt stuart cunningham sams ac uk gt colin griffiths sams ac uk lt colin griffiths sams ac uk gt john beaton sams ac uk lt john beaton sams ac uk gt mark inall sams ac uk lt mark inall sams ac uk gt gt Subject FW SBD Msg From Unit 300434060 123920 gt From sbdservice sbd iridium com SMTP SBDSERVICE SBD IRIDIUM COM gt Sent Wednesday October 29 2014 2 11 47 PM gt To NOC Iridium Moorings gt Subject SBD Msg From Unit 300434060123920 gt Auto forwarded by a Rule gt gt MOMSN 28 gt MTMSN 0 gt Time of Session UTC Wed Oct 29 14 11 47 2014 gt Session Status 00 Transfer OK gt Message Size bytes 67 gt gt Unit Location Lat 57 21276 Long 9 17922 gt CEPradius 6 103 Near Surface Ocean Profiler Measurements Richard Sims Method Measurements of near surface gradients were collected using the Near Surface Ocean Profiler NSOP Figure 12 The method is the same as used during DY026 An instrument cage containing two CTD models Valeport Seabird giving measurements of temperature salinity depth and fluorescenc
4. Specifications EA640_data_sheet_Ir pdf Location dy _data_disc cruise_reports instrument_data_sheets EK60 Multi Frequency Echosounder Fish Finder The EK60 has 18 38 70 120 200 and 333 kHz transducers fitted to the starboard drop keel Equipment to calibrate the system is carried onboard Specifications Ek60_brochure_english_reduced pdf Location dy _data_disc cruise_reports instrument_data_sheets Kongsberg Simrad 5016 Synchronisation Unit K Sync 39 Running several acoustic systems simultaneously on ships with several acoustic instruments can cause interference between the systems which may reduce the data quality This unit and associated software lets you synchronise the pings of different acoustic equipment providing that they operate at different frequencies This system lets the SST control the timing of the instruments and by controlling the triggering of each instrument s transmission Specifications Operator Manual pdf Location dyf data disc cruise reports instrument data sheets k sync Sonardyne Transponder Beacons amp Software There are two hull mounted transponders on the RRS Discovery The Starboard side USBL is a 7000 directional bis head for improved performance in deeper water the Port side USBL is a 5000 standard head The USBL transponder spars are extensible amp retractable and project more or less vertically down from the aft half of the hull between the Drop Keels and t
5. At station C2 58 4 02N 8 0 72W we deployed the stainless steel CTD CTD015 and the air sea buoy BUOY002 forgoing an opportunity to deploy the titanium CTD due to time constraints and a desire to ensure sampling of deeper stations along Transect C Extensive cloud covered the site and also brought with it light rain which made sampling the CTD a less than pleasant task A moderate swell still invaded the site but wind speeds were noticeably down on recent days allowing us to work comfortably The buoy deployment was a success with no repeat of the electronics failure that terminated deployment BUOY001 early On arrival at station C3 58 5 95N 8 25 05W we proceeded to deploy sample and stow the titanium CTD CTD016 and steel CTD CTD017 systems before moving on to station C4 We arrived at station C4 58 13 407N 8 49 914W at 22050 and deployed titanium CTD018 and steel CTD s CTD019 These deployments were complete by 2300 when the plankton net was also deployed NET004 before leaving this station for station C5 On arrival at station C5 58 17 33N 9 14 88W at 0115 the titanium CTD was deployed CTD020 This was successfully recovered by 0230 During the deployment of the stainless 18 steel CTD however the deep tow cable jumped in the sheath and was crushed terminating the deployment We were fortunate that this happened as the CTD was being raised from the deck for deployment rather than when at depth Unfortunately this halt
6. To average the ADCP data over 2 minutes the routine ave for calib m is called with the arguments 0575 sgl ping av time set to 120 seconds ref uplim ref lowlim and which prdid fix ave for calib m This routine is a reduced version of average pings m see 4 4 13 including only variables required by calib points bt m The possibility of missing out ping ensembles in the averaging process when several ENX files exist in a file sequence is ignored here for more about that issue see 4 4 13 After the averaging a check is done whether bottom track velocities are available or not If all bottom velocities are NaNs the routine stops and returns to the main program 75 The principle used is based on a comparison of ADCP bottom track data and GPS tracks The bottom velocity recorded by the ADCP should be the same as the GPS derived ship velocity Therefore the value GPS ship speed ADCP bottom track speed gives the scaling factor to adjust ADCP velocities and GPS ship heading ADCP bottom track heading is the misalignment angle As velocities from bottom tracking are crucial for the calibration ping ensembles with NaNs in either zonal or meridional bottom velocity are discharged The ship velocity is derived from navigation data 0575 sgl ping nav and which prdid fix sets which fix is used Ship velocity is then calculated as in ship vel m as distance in east and northward direction divided by time difference The criteria potent
7. 01 20 00 Time per Ping min sec sec 100 TS 14 10 20 17 46 18 Time Set yr mon day hour min sec WD 111 100 000 gt SYSTEM Data Out Vel Cor Amp PG St P0 P1 P2 P3 Blank After Transmit cm Number of depth cells 1 128 Pings per Ensemble 0 16384 Depth Cell Size cm Mode 1 Ambiguity Vel cm s radial System Control Data Recovery and Testing Commands 100 AC Output Active Fluxgate amp Tilt Calibration data AF Field calibrate to remove hard soft iron error AR Restore factory fluxgate calibration data AX Examine compass performance AZ Zero pressure reading CB 411 Serial Port Control Baud Par Stop CP Polled Mode 0 NORMAL 1 POLLED CZ Power Down Instrument FC Clear Fault Log FD Display Fault Log OL Display Features List PA Pre Deployment Tests PC 1 Beam Continuity PC2 Sensor Data PSO System Configuration PS3 Transformation Matrices RR Recorder Directory RF Recorder Space used free bytes RY Upload Re
8. Day 296 Conditions overnight were calm with greatly reduced wind speeds and we awoke to find patchy skies and the occasional sunny period as we finished our transit through the Little Minch The forecast for the next 48 hours was promising but changeable and though wind speeds were predicted to increase to GF6 8 as we rounded the corner of the Isle of Lewis conditions looked promising for our first day of science We arrived at station A1 58 60N 5 80W at 1020 and deployed the titanium CTD CTD002 for the trace metal measurements This was followed at 1104 by the stainless steel CTD CTD003 at 1228 by the plankton net NET001 and finally the air sea buoy BUOY001 at 1323 As is usual at the first station a few delays were encountered including failure of the buoy electronics which terminated the deployment early but otherwise all sampled as planned We departed for station A2 at 1500 On arrival at station A2 58 48 027N 6 11 618W at 1700 we proceeded to deploy the titanium CTD CTD004 and the stainless CTD CTD005 Both deployments were problem free and we departed for station A3 at 1930 Wind speeds increased to GF8 on passage to station A3 and work was temporarily delayed on arrival at 2120 Conditions sadly did not improve and no further work was possible overnight when gt 40 knot south westerly winds and an 8 m swell impacted the work site Friday Oct 24 Day 297 Conditions had improved by breakfast time with winds of
9. Prior to the deployment of the air sea buoy BUOY004 electrical problems were identified with the buoy winch system Rather than lose the station we deployed the instrument package via the starboard davit crane which seemed to be a successful alternative deployment method A nice sunset was observed by all onboard at 1650 the first of the cruise before we deployed the titanium CTD CTD039 and the plankton net NETO11 Station completed by 2130 we then proceeded south to station F7 Saturday Nov 1 Day 305 On arrival at station F7 at 0515 56 07 298N 10 29 928W it was noted that the wind speed had increased to F7 The stainless CTD CTD040 was deployed at 0530 but at a depth of only 285 m weather conditions deteriorated rapidly due to an incoming squall and the bridge ordered a halt to the deployment and the recovery of the CTD package We maintained station for an hour before deciding to abandon this station and move on to station F6 We arrived at station F6 at 0850 56 07 29N 10 06 01W but weather conditions were still too poor to work By 1000 the wind was blowing a steady F5 but the swell seemed to have increased We maintained position at this station until 1800 when we deployed the steel CTD CTD041 This was followed by a plankton net NET012 Information received overnight from Rolls Royce Norway suggests that the deep tow winch may be usable We arrived at station F5 at 2300 and deployed the steel CTD CTD042 a
10. correct offset m Using the helper routine uvrot n this routine scales the water and bottom track velocities and corrects them for misalignment From the main routine the arguments OS75 sgl ping misalignment xb and amplitude xb are passed on or b depending on whether the current file ensemble is in narrow or broadband mode The horizontal velocities are multiplied by the scaling factor amplitude xb and rotated by the specified misalignment angle misalignment xb The heading is adjusted by subtracting the misalignment angle The modified structure OS75 sgl ping is returned to the main routine ship vel m The routine is called with the arguments 0575 sgl ping and which prdid fix The latter decides which navigation fix is used for the calculation of the ship velocity either 1 or txy2 With the help of the routine sw_dist m from the CSIRO Seawater toolbox the distance and the direction between the fixes is calculated and then converted to distance in east and northward direction in meters and time difference in seconds Dividing distance by time difference results in ship velocity in m s which is written to OS75 sgl ping ship velocity If bottom tracking was on the horizontal bottom track velocities OS75 sgl ping bt vel 1 2 should contain values other than NaN If that is the case the ship velocity is set to OS75 sgl ping bt vel 1 2 The structure OS75 sgl ping is then handed back to the main routine vel clean ship vel m Thi
11. 18 21 22 0 23 12 3 5 7 9 10 12 14 15 16 17 18 22 24 6 1 2 7 8 12 15 25 0 26 12 1 3 5 7 9 11 13 15 17 19 21 21 27 5 1 7 13 17 21 28 5 1 11 13 15 17 29 4 3 535 T5 30 0 3l 6 1 3 5 10 15 19 32 6 1 559 15 17 21 33 0 34 6 1 5 7 9 17 19 35 0 36 4 8 10 13 15 37 12 1 3 5 7 9 11 13 15 17 19 21 23 38 12 1 3 5 7 8 9 11 12 14 15 16 19 39 0 40 0 41 12 1 3 5 7 9 11 12 13 14 15 17 19 42 5 1 5 7 14 20 43 0 44 4 2 10 18 20 45 0 46 12 1 3 5 7 9 11 13 15 17 19 21 23 47 0 48 6 1 5 7 9 11 13 49 6 1 3 7 11 15 19 50 4 3 11 23 24 51 3 1 6 15 52 4 2 8 21 24 53 0 54 0 55 0 56 12 1 3 5 7 9 11 12 13 15 17 19 21 Table 6 Summary of all sampling for dissolved oxygen 88 Dissolved Inorganic Carbon Total Alkalinity Nikki Clargo Sue Hartman Caroline Kivim e Lesley Salt Methodology Sampling and analysis for carbonate system parameters broadly followed the standard operating procedures outlined by Dickson et al 2007 Water samples of 0 6 L were collected from the CTD niskin bottles into borosilicate sample bottles with plastic caps using tygon tubing Samples were collected from every station occupied during the cruise except F7 where no bottles were fired Samples were collected from the stainless steel CTD except on station C5 G4 and G5 where only the titanium CTD was deployed In general one duplicate sample was collecte
12. Frequency 2 Pressure Digiquartz with TC Serial number 129735 Calibrated on 12 March 2014 CI 6 064446e 004 C2 6 966022e 001 C3 1 971200e 002 DI 2 882500e 002 D2 0 000000e 000 Tl 3 029590e 001 T2 6 713679e 005 T3 4 165400e 006 T4 0 000000e 000 T5 0 000000e 000 Slope 1 00000000 Offset 0 00000 AD590M 1 279181e 002 AD590B 8 821250e 000 30 4 Frequency 3 Temperature 2 Serial number 03P 5785 Calibrated on 6 May 2014 G 4 33666977e 003 H 6 27870652 004 1 95435025e 005 J 1 44731780e 006 FO 1000 000 Slope 1 00000000 Offset 0 0000 5 Frequency 4 Conductivity 2 Serial number 04C 4143 Calibrated on 25 February 2014 G 9 80210332e 000 H 1 32372648e 000 I 5 61268048e 004 J 1 06763091e 004 CTcor 3 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 6 A D voltage 0 Oxygen SBE 43 Serial number 43 2055 Calibrated on 2 May 2014 Equation Sea Bird Soc 3 65900e 001 Offset 7 06100e 001 A 2 57000e 003 B 1 30080e 004 C 2 23610e 006 E 3 60000e 002 Tau20 1 46000e 000 DI 1 92634e 004 D2 4 64803e 002 HI 3 30000e 002 H2 5 00000e 003 H3 1 45000 003 7 A D voltage 1 Free 8 A D voltage 2 Free 9 A D voltage 3 Free 10 A D voltage 4 Altimeter Serial number 62679 Calibrated on 27 March 2014 Scale factor 15 000 Offset 0 000 11 A D voltage 5 Turbidity Meter WET
13. It can only generate data in above a minimum wind speed of 3ms It detects open wave spectra Sea state is calculated from detected backscatter of p wave sea clutter in real time The system detects wavelengths from 15 m 600 m and covers periods from 4 sec 20 seconds At coastal sites WaMoS II can only measure the spatial wave field beyond the wave breaking zone There is a WaMoS computer in the Met Lab where it stores processed radar images Data is logged in WaMoS s own format Summary wave information is available in one of the ASCII files generated 41 Specifications WaMoSII geninfo 2010 pdf Location dyf f data disc cruise reports instrument data sheets wamos Manufacturer http www oceanwaves org NMESS SurfMet Surface Water System and Meteorological Monitoring System SurfMet comprises two sets of scientific instruments Meteorological and Surface Water Sampling along with ADCs and a PC hosting SurfMet data conversion software that passes data to the Data Systems for event logging Meteorological Instruments Met The Meteorological part of the system comprises a range of instruments located near the forward mast about 10 metres above sea level Table 1 The instrument called the measures o calculate Vaisala HMP45A Temperature Thermal radiation and water Sunlight Ambient air temperature and amp Humidity Sensor vapour Air Relative humidity Gill Windsonic Anemometer Ultrason
14. NET006 All activities were inboard by 0700 and we departed for station D4 57 37 18N 9 23 45W at the shelf edge arriving at 0840 whence we deployed the titanium CTD CTD025 stainless steel CTD CTD026 and plankton net NET007 Due to pumping problems the trace metal tow fish was recovered and inspected This revealed that the plastic sampling tube had been forcibly withdrawn into the tow fish by the force of the flow of water and that the screw holding the nose cone in place was dangerously loose and almost certainly would have fallen off in the near future Remedial action was undertaken and the fish readied for redeployment at the next opportunity Due to loss of time at the last station during transit to station D4 and the need to have daylight during the deployment of the ADCP mooring we broke survey after station D4 and headed south to the proposed mooring site A last minute change in position to a shallower inshore site 750 m water depth saw the mooring provisionally located at 57 06 09N 9 20 15W The benthic mooring MOOR001 was released at the surface at 1531 and sinking at a rate of 50 m min arrived at the sea bed 15 minutes later The release signal was sent at 1602 to allow recovery of the buoyancy parachute Unfortunately the release did not work as planned and the buoyancy and acoustic release did not disengage cleanly from the lander After several minutes of repeated range finding during which time the depth range remained
15. NOTE BEAM 4 MISSING commence test run of VMADCP around Land s end and thru Irish Sea Ro ine daily processing Routine daily processing END BOTTOM TRACK START WATER TRACK Ro ine daily processing Restarted to try to solve data screening problem END WATER TRACK START BOTTOM TRACK Closed to check ADCP setup nothing altered Routine daily processing Remaining 3 beams noted as very short range and flaky Noticeable now in deep water Routine daily processing Routine daily processing Routine daily processing CLOSED TO INSTALL ALTERNATE DECK UNIT attempt to resolve beam 4 dropout RESTARTED USING ALTERNATE DECK UNIT Beam 4 dropout appears to be resolved NOTE file 002 breaks the processing Date var wroing length Routine daily processing 2 D Routine daily processing e D Routine daily processing Routine e D ily processing file skipped as restarted to try to improve poor penetration Routine e D ily processing Routine ex D ily processing List of OS75 raw data files collected during DY017 84 OS150 Raw Data Files Filename 18 47 OS150 DY017000 000000 18 49 09150 DY017000 000000 18 49 09150 DY017001 000000 19 53 OS150 DY017001 000000 19 53 OS150 DY017002 000000 15 42 OS150 DY017002 000000 15 42 OS150 DY017003 000000 11 03 OS150 DY017003 000000 11 03 09150 DY017004 000000 20 31 05150 DY017004 000000 20 34 05150 DY017005 000000 08 39 05150 DY01700
16. Ni Cu Zn Cd and Pb in seawater using high resolution magnetic sector inductively coupled mass spectrometry HR ICP MS Analytica Chimica Acta 665 200 207 Obata H H Karatani and E Nakayama 1993 Automated Determination of Iron in Seawater by Chelating Resin Concentration and Chemiluminescence Detection Analytical Chemistry 65 1524 1528 Resing J A and C I Measures 1994 Fluorometric determination of Al in seawater by flow injection analysis with in line preconcentration Analytical Chemistry 66 22 4105 4111 Sheridan C C C Lee S G Wakeham and J K B Bishop 2002 Suspended particle organic composition and cycling in surface and midwaters of the equatorial Pacific Ocean Deep Sea Research Part I 49 1983 2008 doi 10 1016 S0967 0637 02 001 18 8 Souza A J J H Simpson M Harikrishnan and J Malarkey 2001 Flow structure and seasonality in the Hebridean slope current Oceanologica Acta 24 Supplementary S63 S76 Strickland J D H and T R Parsons 1972 Fisheries Research Board of Canada Tria J E C V Butler P R Haddad and A R Bowie 2007 Determination of aluminium in natural water samples Analytica Chimica Acta 588 153 165 Turnewitsch R B M Springer K Kiriakoulakis J C Vilas J Ar stegui G A Wolff F Peine S Werk Graf and J Waniek 2007 Approaching the true concentration of particulate organic carbon in seawater the relative methodological importance of artific
17. tracking on for the steam through the Irish Sea to the Malin Shelf to provide a calibration period in shallow waters then switch it off for the rest of the cruise However when it was switched off in shallow waters it was found that the VMDAS processing no longer stripped the seabed reflection from the data resulting in profiles with echoes and interference below the seabed We therefore kept bottom tracking switched on for the rest of the cruise Not sure whether this is to be expected there is a strip seabed data tickbox in the setup panels but as this was not enabled in previous cruises we decided not to venture into the unknown Output data format The filenames of the VmDas data are of the general structure CRUISE xxx yyyyyy END where CRUISE is the name set in the recording tab of VmDas see above xxx is the number set in the same tab and changed before every restart of recording and yyyyyy is a number automatically set by VmDas starting at 0 and increasing when the file size becomes larger than max size and a new file is created END is the filename extension denoting the different files that are created for each recording The following list shows all the different file types that were created during DYO017 and their content ENR binary raw ADCP data file STA binary average ADCP data using the short time period specified in VmDas Data Options LTA binary average ADCP data using the long time period specified in V
18. 2014 0 12 08075 DYO 2014 09 21 08075 DYO 2014 09 21 08075 DYO 2014 09 05 09075 DYO 2014 09 05 09075 DYO 2014 09 40 09075 DYO 2014 1 20 05075 DYO 2014 07 42 08075 DYO 2014 07 42 08075 DYO 2014 20 05075 DYO 2014 20 05075 DYO 2014 1 00 05075 DYO 2014 1 00 05075 DYO 2014 40 05075 DYO 2014 40 05075 DYO 2014 08 25 09075 DYO 2014 08 25 09075 DYO 2014 08 20 09075 DYO 2014 08 20 09075 DYO 2014 09 30 09075 DYO T003 0000 T003 0000 7004 0000 7004 0000 005 0000 005 0000 006 0000 006 0000 T007 0000 T007 0000 008 0000 008 0000 009 0000 009 0000 0 0 0 0 0 0 0 0 0 0 0 0 n 0 0 0 0 n 0 0 0 0000 0 0000 1 0000 1 0000 2 0000 2 0000 3 0000 3 0000 4 0000 4 0000 5 0000 5 0000 6 0000 6 0000 7 0000 7 0000 8 0000 8 0000 9 0000 9 0000 7020 0000 7020 0000 7022 0000 1022 0000 1023 0000 1023 0000 7024 0000 7024 0000 5 c5 c5 c5 c5 c5 c5 5 c5 c5 c5 c5 c5 5 c5 5 05 File open closed opened closed opened closed opened closed opened closed opened closed opened closed opened closed opened closed opened closed opened closed opened closed 0 c 0 c 0 c 0 c 0 c 0 c 0 c 0 c 0 c 0 c pened osed pened osed pened osed pened osed pened osed pened osed pened osed pened osed pened osed pened osed Comments
19. 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 3 Frequency 2 Pressure Digiquartz with TC Serial number 100898 Calibrated on 6 January 2012 CI 4 405863e 004 C2 6 206030e 002 C3 1 337540e 002 DI 3 669100e 002 D2 0 000000e 000 TI 2 990734 001 2 3 493620e 004 T3 4 061200e 006 T4 3 043880e 009 T5 0 000000e 000 Slope 0 99995000 Offset 1 59900 AD590M 1 288520e 002 AD590B 8 271930e 000 4 Frequency 3 Temperature 2 Serial number 03P 5495 Calibrated on 18 October 2013 G 4 38224202e 003 H 6 31062233e 004 I 2 03280217e 005 J 1 58958907e 006 FO 1000 000 Slope 1 00000000 Offset 0 0000 5 Frequency 4 Conductivity 2 Serial number 04C 3874 Calibrated on 24 October 2013 G 1 05028427e 001 H 1 38920147e 000 I 1 01866557e 003 J 1 39949777e 004 CTcor 3 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 6 A D voltage 0 Oxygen SBE 43 Serial number 43 1624 Calibrated on 17 May 2013 Equation Sea Bird 32 Soc 5 26900e 001 Offset 5 08100e 001 A 3 06370e 003 B 1 92500e 004 C 2 78720e 006 E 3 60000e 002 Tau20 1 43000e 000 DI 1 92634e 004 D2 4 64803e 002 HI 3 30000e 002 H2 5 00000e 003 H3 1 45000e 003 7 A D voltage 1 Free 8 A D voltage 2 PAR Irradiance Biospherical Licor Serial number 70510 Calibrated on 1 March 2013 M 1 00000
20. Adu sina Advcosa 77 Values for A and phi are written to the array alpha together with relevant heading navigation and velocity data and alpha is handed back to the main routine calc wt m After alpha has been created in calib points wt m it is passed on to this subroutine Here average median and standard deviation for phi and A are calculated and written to cal file wt The average or the median should then be used during the second run of OS75_DY017 m for misalignment and amplitude correction Several plots of the misalignment and the scaling are also produced and stored in adcp correction stats ps calib_calc_bt m During the first run of OS75_DY017 m the misalignment angle and the scaling factor which are to be used for the second run are calculated here In the second run the results for phi and A should be closer to zero and one respectively than before The arguments handed over are cal file which specifies the file with the calibration point data cruise misalignment xb and amplitude xb which are used for the plots created in this routine After cal file is read in scaling factors and misalignment angles outside the interval average standard deviation are sorted out From the remaining points the average the median and the standard deviation for A and phi are calculated and added to the structure cal The median is less affected by outliers which might have survived the screening in calib points
21. All titanium casts Primary Conductivity Sensor SBE 4C 4C 4138 Ti Fl All titanium casts Digiquartz Pressure sensor Paroscientific 129735 F2 All titanium casts Secondary Temperature Sensor SBE 3P 3P 5785 Ti F3 All titanium casts Secondary Conductivity Sensor SBE 4C 4C 4143 Ti F4 All titanium casts Primary Pump SBE 5T 5T 3088 n a titanium casts Secondary Pump SBEST 5T 3090 n a titanium casts 32 60380 0805 All titanium casts 24 way Carousel SBE 32 Ti n a Dissolved Oxygen Sensor SBE 43 43 2055 VO All titanium casts Altimeter Benthos 916T 62679 v4 All titanium casts Light Scattering Sensor WETLabs BBRTD BBRTD 758R V5 All titanium casts CTG Alphatracka All titanium casts Transmissometer MKII 161049 V6 CTG Aquatracka All titanium casts Fluorometer MKIII 088244 V7 10L Water Samplers OTE TMF 1T 24T n a All titanium casts 35 RRS Discovery Instrumentation Overview Jack McNeill Introduction The new RRS Discovery is broadly similar to the RRS James Cook and has a similar arrangement of instruments and sensors Figure 2 As Discovery is a new ship this summary provides a brief overview of what s on board where it is what it does what its inputs and outputs are and gives an indication of where to get more information External Internal Greening EP notation Plug in Laboratories Laboratories Sampling Winch Suite Ballast Water ctp t Platform Bilge Water Treatment DP1 Fwd Communications V Sat
22. GF4 6 allowing a cautious deployment of the stainless steel CTD CTD006 at station A3 58 57 583N 6 30 002W at 0852 The weather conditions were forecast to remain fairly constant with winds of GF4 6 throughout the day We departed for station A4 at 0955 We arrived on station A4 59 11 92N 6 56 82W at 1300 and deployed both CTD systems CTD007 amp CTD008 A little time was lost on station due to necessary checks of the winch scrolling system but otherwise conditions were amenable to the task at hand A large long period swell from the southwest was noticeable heralding the approach of yet another North Atlantic low pressure system which is predicted to bring with it significant wind speeds and swell Our plan now is to head for safety behind the Isle of Lewis after completing Line A We departed station A4 at 1600 and headed further northwest towards station A5 arriving at 1810 We deployed the titanium CTD CTD009 59 24 05N 720 66W undertaking a full profile to 1000 m and recovered the package at 2054 Delays were encountered during this deployment as a minor problem with the metal free winch scrolling system was identified and 17 rectified The stainless steel CTD was deployed at 2138 CTD010 59 23 86N 7 19 59W and recovered at 2310 At this point the decision was made to abandon station A6 and we returned to the Isle of Lewis to wait out the approaching storm Saturday Oct 25 Day 298 We arrived in Broad Bay at 0830 on the e
23. In the convoluted path through this code l m not sure whether one or both is seen by the QC routines so it s best to change both After the first run to correct for the angle and the scaling set the variables to the mean median mode or whichever value is preferred and run OS75 DY017 m again The Mean median and standard deviation are displayed in the plot adcp calib calc ps The commented out values used on DYO17 should give a ballpark value for Discovery To keep track of which values were used it is a good idea to note down which file sequences require which correction factors That is all that should be set All that needs to be done then is 1 Put raw files into data_in folder Note the Matlab suite only requires NIR N2R and ENX files to run just make sure you get the whole file sequence on DY017 max file size was set at 10 Mb after which a new file was started by the VMDAS 2 Run OS75 DY017 m 3 Check which values for misalignment angle and scaling factor are derived 4 Set misalignment and amplitude in OS75 DY017 m to these values Note setting these values other than 1 and 0 invokes some additional statistical routines which increase the processing time 5 Run 0575 DYO017 m again Existence of files in data processed and data_in folders If the program encounters files or plots of the current working name in the data_processed folder it skips much of the processing assu
24. MV PhINS KB Seapath 330 CNAV 3050 OceanWaves WaMos DartCom Polar Ingester NESSCo V Sat Thrane amp Thrane Sailor 500 Fleet BroadBand e Instrumentation DartCom Live pCO SWS Underway amp Met Platform instrumentation 44 Requested Services 150 kHz hull mounted ADCP system Hydroacoustics 75 kHz hull mounted ADCP system Hydroacoustics Meteorology monitoring package SurfMet Pumped sea water sampling system SurfMet Sea surface monitoring system SurfMet Ship scientific computing systems Ship Scientific Datasystems Data Acquisition Performance times given are in UTC Ship Scientific Data systems Data was logged and converted into NetCDF file format by the TechSAS datalogger The format of the NetCDF files is given in the file NMFSS NetCDF Description Discovery docx The instruments logged are given in DYO17 Ship fitted information sheet DY docx Data was additionally logged in the RVS Level C format which is also described in NMFSS NetCDF Description Discovery docx Position amp Attitude GPS and attitude measurement systems were run throughout the cruise Kongsberg Seapath 330 The Seapath is the vessel s primary GPS it outputs the position of the ship s common reference point in the gravity meter room Seapath position and attitude was used by the EM710 EM122 and SBP120 Applanix POSMV The POSMV is the secondary scientific GPS and is used on the SSDS displays around the vessel TechS
25. NET004 26 0 100 Y C6 CTD021 28 10 50 90 22 23 24 Y C7 CTD023 30 10 50 100 20 22 24 NET005 31 0 100 Y D5 CTD024 32 10 50 75 21 22 24 NET006 33 0 80 Y D4 CTD026 35 10 30 60 13 19 23 NETO007 36 0 60 Y DI CTD029 41 10 50 100 5 13 23 NETO008 42 0 100 Y El CTD031 44 10 50 60 8 12 20 9 45 0 60 Y E3 CTD034 49 10 30 50 16 19 24 NETO010 50 0 50 Y E6 CTD037 53 20 40 60 21 2223 Y E5 CTD038 54 10 50 70 18 19 23 NETO11 55 0 70 Y F6 CTD041 59 20 60 90 15 16 20 NETO12 60 0 100 Y F5 CTD042 61 10 20 50 22 23 24 F4 CTD043 61 10 20 50 20 22 24 NETO013 63 0 50 Y CTD049 68 20 38 75 5 15 20 NETO14 69 0 80 Y Gl CTD050 70 10 30 60 1 13 21 NET015 7 0 60 Y CTD054 G5 Titanium 77 25 50 70 13 15 16 16 78 0 70 G6 CTD056 81 50 87 92 16 17 19 NETO017 82 0 100 Y Table 13 Summary of sampling activities Notes Stormy weather conditions disrupted sampling On the 25 and 26 of October the RRS Discovery sheltered in Broad Bay near Stornoway on the east side of Lewis to avoid adverse weather conditions At this location Lat 58 16 18566N Lon 6 13 18440W an additional underway sample was taken and sampled for phytoplankton community chlorophyll a and CARD fish Labelled as station X Strong winds often made deployment and recovery of net samples difficult Winds and surface currents often pushed the net sidewards Consequently the length of rope deployment might not be indicative
26. Pseudo nitzschia on the Scottish west coast The area of the Malin shelf and shelf edge is of interest for this project as it was suggested to be a spot for overwintering seed populations of harmful phytoplankton To determine this phytoplankton community and chlorophyll data were collected from different depths within the surface layer via CTD cast Additional CARD fish samples were also collected for the PhD student Ruth Patterson also based at SAMS Samples were collected between the 20 10 2014 and 6 11 14 on board the RRS Discovery and taken back to SAMS for further analysis A summary of sampling activities is presented in Table 13 Methods 105 sample bottles and filtration equipment were rinsed with sample water before use Phytoplankton community structure The phytoplankton community structure will be assessed via microscopy analysis of Lugol s samples collected during the cruise For this purpose 60 ml water samples were collected from the underway seawater supply 5m deep passed through a 5mm filter and from three depths in the surface mixed layer sampled by the stainless steel CTD from 20L bottles until 28 October and from 10L bottles thereafter At one occasion at station G5 water samples were taken from the titanium CTD Sampled depths were different for each station and determined by the fluorescence profile Samples were taken at depth were peaks in fluorescence were seen and at the depth on which fluorescence started
27. TESTS XILINX Interrupts IRQ3 IRQ3 IRQ3 PASS Wide Bandwidth RRA TL FE Narrow Bandwidth PASS RSSI PASS Transmit esses RRA TLE SENSOR TESTS H W PASS gt RS ERR 005 EXTRA PARAMETERS ENCOUNTERED gt 1 BEAM CONTINUITY TEST When prompted to do so vigorously rub the selected beam s face If a beam does not PASS the test send any character to the ADCP to automatically select the next beam Collecting Statistical Data 26 26 31 28 Rub Beam PASS Rub Beam 2 PASS Rub Beam 3 PASS Rub Beam 4 PASS gt CZ Powering Down Appendix B ADCP program log file gt gt gt gt gt gt Function starting 10 26 14 15 28 06 gt gt gt gt gt gt BREAK Wakeup B WorkHorse Broadband ADCP Version 50 40 Teledyne RD Instruments c 1996 2010 All Rights Reserved gt CR1 Parameters set to FACTORY defaults gt CQ255 gt CF11101 gt EAO gt EBO gt EDO gt ES35 gt EX11111 102 gt EZ1111111 2WAS0 gt gt WD111100000 gt WF704 gt WN50 gt WP30 gt WS1600 gt WV175 gt 1 00 00 00 gt 14 10 26 16 00 00 gt TP02 00 00 gt CK Parameters saved as USER defaults gt The command CS is not allowed in this command file It has been ignored gt The following commands are generated by this program gt CF CF 11101
28. TRBM s internal releases s n 899 amp 1326 to confirm realistic ranges and correct horizontal orientations Instrument serial numbers AL 500 TRBM s n J14110 001 99 Teledyne RDI 75KHz ADCP Ixsea AR861 acoustic release Ixsea AR861 acoustic release Ixsea AR861 acoustic release Novatech strobe beacon Novatech Iridium beacon 29 10 2014 s n 20467 512Mb memory card s n 899 A 1A7A R 1A55D 1A49 s n 1326 A 18B4R 1855 D 1849 s n 1916 A 090DR 0955 D 0949 no serial number s n M00146 IMEI 300434060123920 on at 1405 One email alert was received from the Iridium beacon at 1418 prior to deployment Recovery The anticipated recovery date for this mooring is June 2015 Appendix A ADCP pre deployment test BREAK Wakeup B WorkHorse Broadband ADCP Version 50 40 Teledyne RD Instruments c 1996 2010 Rights Reserved gt DEPLOY Deployment Commands CF 11111 TE 01 00 00 00 Flow Ctrl EnsCyc PngCyc Binry Ser Rec Keep Parameters as USER Defaults Retrieve Parameters 0 USER 1 FACTORY Start Deployment Heading Alignment 1 100 deg Heading Bias 1 100 deg Transducer Depth 0 65535 dm Salinity 0 40 pp thousand Coord Transform Xform Type Tilts 3 Bm Map Sensor Source C D H P R S T Recorder ErAsE Set Deployment Name Time per Ensemble hrs min sec sec 100 TF kk kk kk Time of First Ping yr mon day hour min sec TP
29. Table 15 Summary of sampling for total dissolvable and dissolved trace metal measurements Ligands Dagmara Rusiecka Objectives Understanding the biogeochemistry of Fe requires the ability to measure its oceanic chemical speciation Fe is present in seawater as chelates with strong metal binding organic ligands Bruland amp Lohan 2004 which dramatically influences its chemical behaviour These ligands have a stabilising influence preventing inorganic precipitation e g Liu and Millero 2002 and increasing the availability of metals for biological uptake They are therefore an important component in understanding the cycling and distribution of Fe in any system Ligand samples will therefore be collected at selected stations along the cruise Sampling protocol On recovery of the Ti rosette the OTE bottles were transferred into a clean sampling laboratory where they were immediately sampled for oxygen nutrients salinity and total dissolvable elements before being pressurised to approximately 7 psi with 0 2 filtered air using an oil free compressor After the collection of particulate samples see section on Particulate Trace Metals a Sartobran 300 Sartorius filter capsule 0 2 was used to collect filtered seawater samples into clean LDPE sample bottles Bottles and caps were rinsed 3 times with the filtered sample before being filled All samples were double bagged and stored unacidified at 20 C until analysis Samples
30. TiT ng T E X 2 H 1 gt o o 5 n 1 0 1000 2000 3000 4000 5000 6000 Sampnum Bottle oxy CTD oxy umol 127 0 1 i 1 i 0 1000 2000 3000 4000 5000 6000 Sampnum Pressure db Pressure db Pressure db 500 1000 1500 2000 r p E o EE c qui 20 15 10 5 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 500 1000 1500 2000 5 500 1000 1500 2000 F 2500 Bottle oxy CTD oxy umol L Bottle oxy CTD oxy umol L Figure 5 Summary of CTD oxygen calibrations Panels a and c show temporal oxygen residuals for the stainless and titanium CTD systems respectively whilst panels b and d show the vertical pressure residuals Panels E and F show final residuals after calibration Vertical blue lines in panel f indicate 2 umol L offset range Surfmet underway data Stuart Painter Continued problems with the surfmet TSG system during DYO17 were thought to have rendered all underway data streams unusable Provisional examination of the data however suggests that some underway salinity and temperature data may be recoverable but no other data stream will be functional This will be investigated post cruise 59 Vessel mounted ADCP VMADCP processing using an RDI OS75 RDI OS150 and PosMV positioning Sam Jones Ada
31. after the CTD has soaked and all pumps are on and the last good data point is the last data point for which there is good oxygen salinity temperature and conductivity data input DYOI7 psal nc Output dcs DYOI7 ctd all part2 m Another batch script which calls a variety of mstar routines including metd_04 m extracts downcast data using information in dcs file and averages to 2db intervals input ctd_DYO17_NNN_psal nc Output ctd DYOI7 NNN 2db nc mdcs 04 m adds positions of profile start bottom and end from the navigation file into dcs file input dcs DYOI7 Output dcs DYOI7 NNN nc mfir_Ol m create mstar NetCDF file with info from SeaBird bottle bl file input Seabird bottle bl file Output fir DYOI7 mfir 02 m add time from CTD file to firing information file input fir DYOI7 Output fir DYOI7 time nc mfir 03 m Locate and extract CTD data from upcast and paste into fir file input fir DYO17 time nc Output fir DYOI7 NNN ctd nc ctd DYOI7 NNN psal nc mfir 04 Paste CTD data from fir file into sample file input fir DYOI7 ctd nc Output sam DYOI7 NNN nc mwin 01 m create NetCDF file to hold winch data extracted from Techsas NetCDF files 53 input Techsas NetCDF file Output win DYO17 NNN nc mwin_03 m Merges winch data onto fir file input win DYOI7 Output fir DYOI7 NNN wi
32. and most of the scientific party re emerged after a broken nights sleep Only minor displacement of equipment due to ship movement was reported from the scientific labs with one exception One of the working benches in the Deck Lab supporting a fume hood had partially collapsed overnight due to the continuous rocking motion of the ship Complete collapse of this particular bench was only averted due to the fortuitous placement of another piece of scientific equipment that acted as a brace Remedial repair work was quickly undertaken by the crew in the morning and whilst all other benches were checked for similar signs of collapse none were found to be at risk Nevertheless precautions were taken to avoid this from happening by bracing benches where possible It is troubling that so many of the benches were found to wobble with light pressure applied and in the opinion of this PSO this is only likely to worsen over time possibly leading to collapse when supporting heavy equipment particularly during high seas These particular benches do not appear to be well made Poor weather conditions remained throughout the day with a drop in wind speed to GF6 by early afternoon however our progress north has been slowed due to the unfavourable conditions Once in the Irish Sea and in the lee of Ireland the sea state dropped and by early evening conditions were greatly improved Wednesday Oct 22 Day 295 Conditions were fairly calm overnight and into Wednesda
33. and this core is bonded to the armouring in the termination to avoid any induced voltage The two remaining cores green and the other brown translucent sheath are used as the 250VDC and 250VDC from Main Lab to termination RR ODIM MFW RG58 BNC cable of 15m length installed in JB47 next to RR ODIM MFCTD to connect to Junction Box Stationary in RR ODIM container NB This is a temporary cable amp connection as the RR supplied Epic style connector and cable cannot be located Replacement connector ordered from RR via RR representative on board during DY008 but none has been delivered as yet to best of knowledge Junction Box Rotary not wired by RR to umbilical nor was the slip ring wired to the Junction Box Stationary This was completed prior to sailing by NMPFSS staff using 2 5m of 4 core 0 82mm 2 stranded tinned copper wire left in place by RR post repair NB Because of restricted space and access to the Rotary Junction Box these connections are unlikely to be field serviceable once the vessel has sailed All BNC interconnecting and terminated cables megger to 2999 MOhms The four cores were then meggered to 2999 MOhms following with each pair shorted to measure internal resistance Values for each pair varied from 198 Ohms to 202 Ohms not comparable to the expected manufacturer s maximum of 162 Ohms for the present umbilical length of 4250m but within SBE recommended seacable maximum resistance of 350 Ohms The umbilical w
34. bt m and calib calc bt m and should therefore be used as correction value in the second run Before returning to the main routine a plot showing the distribution of the misalignment angles and the scaling factors and their temporal evolution is produced After returning to the main program the plot is written to the file adcp calib calc ps b mask m OS75 ave ping and bindepth are passed on to this routine Here a mask is created using the bottom range bt range With this mask velocity data below 8696 of the bottom range water depth is set to NaN The structure containing the modified velocity fields is returned to the main routine abs vel m OS75 ping and bindepth are handed over from the main routine In order to derive absolute water velocities independent of the ship movement the east and northward ship velocity is added to the horizontal water velocity OS75 ave ping vel The same is done for the velocity in the reference layer OS75 ave ping ref vel The resulting absolute velocities the navigation data and the depth array set to bindepth are handed back to the main routine within the structure OS75 abs Helper routines julian m sw dist m uvrot m rot fun l m mfilter m These routines are called on various occasions during the processing sw dist m is part of the CSIRO Seawater toolbox Overview of output files CRUISE xxx yyyyyy raw mat Note there are a few instances where structures in the OS150 outp
35. by forcing a commensurate reduction in water requirements but thankfully did not stop any planned science Resolution of the technical problems with the deep tow winch are ongoing as part of the wider resolution of winch problems Other issues which do require further investigation however concern 1 The underway surfmet instrumentation suite which was not working at the start of the cruise and provided no sensible or usable data during the cruise Despite efforts to unravel the wiring and debug software no solution was found Given the poor weather experienced during parts of DY017 this loss of data will likely prove detrimental to the scientific objectives 2 The benches in many of the scientific spaces do not look suitable for supporting heavy scientific instrumentation as the collapse of one bench supporting a fume hood on Oct 21 demonstrated Further remedial work and or replacement may be needed 3 Internet communications were particularly poor for most people on board In many instances people had more success using their mobile phones than their laptops for accessing email Although more of an annoyance than a major problem the comms on Discovery appear worse than on the predecessor ship Some improvement was made very late in the cruise but some participants were unable to access their email for the duration of the cruise which they consider to be unsatisfactory 4 The OS75 ADCP experienced a few problems early in the cruise and was o
36. collected A total of 49 speciation samples were collected at 9 stations as detailed in Table 16 112 Station Samples collected from separate depths Al 3 A2 3 A4 6 AS 10 Bl 3 Cl 3 x 2 duplicates C3 5 C4 6 C5 7 Table 16 Summary of ligand sampling Sample analysis The concentrations and conditional stability of Fe ligands Fe soluble inorganic Fe and free aqueous Fe will be measured at NOCS GEOMAR by competitive ligand exchange cathodic stripping voltammetry CLE CSV with the ligand TAC Croot and Johansson 2000 Particulate trace metals Angela Milne and Antony Birchill Objectives Particulate trace metals may occur in several forms including stable refractory phases or as coatings on surfaces that can be rapidly recycled Particulate behaviour is metal specific with for instance the majority of particulate Fe occurring in refractory phases while Zn is primarily associated with more labile phases Hurst amp Bruland 2005 Few studies have concurrently measured trace elements in both the dissolved and particulate phases Furthermore labile particulate trace metals which are biologically available could be considerably higher than the dissolved phase Berger et al 2008 Assessment of total biologically available trace elements may thus require the determination of both dissolved and labile particulate metal phases Lam amp Bishop 2008 A step towards a quantitative description of the cycling of t
37. in the sample bottle volumes Each sample was fixed immediately using 1 ml of manganese chloride and 1 ml of alkaline iodide The samples were shaken thoroughly and then left to settle before being shaken again Samples were typically analysed within a few hours of collection but in cases where samples were collected overnight analysis could have occurred up to 12 hours after collection samples were analysed following the procedure outlined in Holley and Hydes 1995 Samples were first acidified with 1 ml of sulphuric acid immediately before titration against sodium thiosulphate and continuously stirred using a magnetic stirrer The Winkler whole bottle titration method with amperometric endpoint detection Culberson and Huang 1987 using a Metrohm titrino was used to determine the oxygen concentration The normality of the sodium thiosulphate titrant was checked every few days using a potassium iodate standard This was done four times throughout the cruise Thiosulphate standardisation was carried out by adding 10 ml of 5 N iodate solution after the other reagents had been added in reverse order to a sample of milli Q water Results from this standardisation check were used in the calculation of final dissolved oxygen concentrations The volume of sodium thiosulphate needed to titrate the 10 ml potassium iodate standard can be seen in Figure 7 The amount of dissolved oxygen in the reagents was also checked by performing a blank correcti
38. in the ocean Due to its low solubility iron can be a limiting factor for the growth of phytoplankton in the open ocean as well as in coastal seas de Baar et al 1990 Hutchins and Bruland 1998 Martin and Fitzwater 1988 It has become evident that the atmosphere Duce and Tindale 1991 rivers De Baar and de Jong 2001 hydrothermal activity Tagliabue et al 2010 Klunder et al 2011 and advection of shelf derived sediment to the open ocean Bucciarelli et al 2001 Lam and Bishop 2008 are significant transport pathways for iron to the ocean Fe fluxes from shelf seas to the open ocean are poorly constrained although estimates indicate they 109 could be 2 10 times higher than atmospheric inputs Elrod et al 2004 and thus potentially be a major contributor to the oceanic Fe cycle Shelf edge biogeochemical processes that result in Fe export to the ocean are not well understood and key questions remain about the magnitude and significance of Fe fluxes from the shelf to the open ocean We aim to investigate and quantify the supply and transport of iron in the shelf region off the North West of Scotland Sampling protocol On recovery the 10 L OTE bottles were transferred into a clean sampling laboratory where they were immediately sampled for oxygen nutrients salinity and total dissolvable iron before being pressurised to approximately 7 psi with 0 2 filtered air using an oil free compressor After the collection of particulat
39. of calibration points speed heading and range 1 x number of calibration points vel number of bins x 2 x number of calibration points array of east and northward velocity heading 1 x number of cal points array heading from N1R data nav structure containing txy1 data at the calibration points ship speed ship heading 1 x number of cal points arrays scaling phi scaling factor and misalignment angle at each calibration point 1 x number of cal points array intervals stats for each interval of successive calibration points see description of routine calib points bt m mode 1 x number of cal points array 1 or 10 for each calibration point depending on broadband or narrowband mode which file number of cal points x 16 character array with file name of the file the calibration point is from stat structure with values for the scaling factor a and the misalignment angle phi as calculated in the routine calib calc bt m the values stored here after the first run of the main routine OS75 DYO017 m are the ones that should be used for the second run Only one file for all file sequences processed in a run is created CRUISE cal points wt mat If no bottom track data is available calibration is done using water track For this the array alpha is created From data in alpha the misalignment angle phi and the scaling factor scaling are derived and alpha phi and scaling are stored in t
40. output is the position of the ship s common reference point the cross on the top of the POSMV MRU in the gravity room Specifications Posmv_datasheet pdf Location dyf data disc cruise reports instrument data sheets 37 Kongsberg Seapath DPS330 Secondary Science GNSS and Attitude Sensor This is a secondary Science GNSS and attitude sensor The position output is the position of the ship s common reference point the cross on the top of the POSMV MRU in the Gravity Meter Room Specifications Seapath330 pdf Location dyf data disc cruise reports instrument data sheets iXSea PhINS Photonic Inertial Navigation System A surface inertial navigation system that uses a FOG Fibre Optic Gyro to output accurate position attitude and velocity data Specifications br phins 2013 06 web pdf Location dy data disc cruise reports instrument data sheets CNav 3050 GPS GLONASS Galileo GNSS GNSS and RTCM Satellite Corrections Receiver The position output is the position of the antenna This GPS is not referenced to any other systems It is primarily used to provide RTCM differential corrections to the other GPS systems Please note that the position output is the position of the antenna This GPS is not referenced to any other systems Specifications CNav3050Brochure pdf Location dy _data_disc cruise_reports instrument_data_sheets Hydroacoustics RRS Discovery has both vessel mounted and smaller deployable tr
41. pitch and roll Checksum modulo 65536 checksum sum of all bytes in the output buffer excluding the checksum If data storing by VmDas is interrupted by e g a software crash and or the data files are not closed properly by VmDas the checksum can be incorrect and the check in the post processing can fail 65 Note The date recorded by VmDas is given as Julian day VmDas takes Ist Jan to be day no different from the ship clock and the other data logging systems Navigation data in the VmDas output files There two NMEA nav feeds into the VmDas software The stream is normally written to the NIR files the NMEA2 stream to the N2R files They are also included in the binary ENX data files NMEA2 gives the messages used by the processing software In both files a message from VmDas is stored in the PADCP line at every ADCP ping Note Depending on the way the feeds to VMDAS are configured the data relevant to the Matlab routines pitch roll heading etc may be either stored in the NIR or N2R files so this is an important thing to check In DYOI7 the file read in was N2R To change the file read by the post processing software amend the variable extension in read nmea att disc2 m The line headings containing this data also vary depending on the device and software used to supply the nav data This version of the post processing only reads the PADCP and PRDID messages The PRDID header might change but
42. prdid fix OS75 sgl ping nav txyl or 2 is checked for time first row longitude second row and latitude third row duplicates The number of rejected data cycles is printed on screen and saved as bad and good number of data cycles number of rejected cycles in the file CRUISE bad nav mat The rejected data cycles are then removed from 0575 sgl ping and the structure handed back to the main routine include disc2 m Arguments passed on to this routine are OS75 sgl ping add to ensnum for the correction of ensemble numbers see below and which prdid fix If no file CRUISE xxx 000000 att mat exists yet in the processed data directory i e the navigation data in the N2R files has not been read yet OS75 sgl ping is passed on to read nmea att disc2 m which is called to read the N2R files read nmea att disc2 imm Works on the new Discovery file output Also versions named Jer and jc The routine goes through all N2R files in a file sequence The number of lines to be read in one go is limited to a maximum of 160000 the loop will go on until all lines are read The text in the N2R file is read into a matrix Then lines containing the PADCP or the PRDID string are extracted If two PADCP lines are consecutive the first of them is discharged no attitude data available for this ping ensemble From the PRDID lines the one following the PADCP line are extracted the others discharged Pitch roll and heading are read from th
43. removed from the oven parafilm was applied as a lid and the samples stored Note Ashed GFF filters were first pre treated in a 10 HCL bath for 24 hours and then transferred to a Milli Q bath for 12hours emptied and then applied to another Milli Q bath for a further 12 hours Biogenic Silica BSi 500ml of seawater was filtered onto 0 8um polycarbonate filters with a MF300 backing filter Once filtering was completed the filter was rinsed with pH adjusted Milli Q folded in quarter and stored in a labelled a 15ml centrifuge tube The label denoted the unique sample number described below JDay of collection time of CTD deployment and volume of sample 94 seawater that was filtered Samples were placed in an oven set at 50 60 C for 8 12 hours with the lid off When removed from the oven the lid was secured on the sample and stored Particulate Inorganic Carbonate PIC 500ml of seawater was filtered onto 0 8um polycarbonate filter with a MF300 backing filter Once filtering was completed the filter was rinsed with pH adjusted Milli Q and stored in a labelled 50ml centrifuge tube The label denoted the unique sample number described below JDay of collection time of CTD deployment and volume of sample seawater that was filtered Samples were placed in an oven set at 50 60 C for 8 12 hours with the lid off When removed from the oven the lid was secured on the sample and stored Note Samples from stations Al were filtered using 0 4 m p
44. the main deck lab and filtered in a similar fashion This was usually undertaken when the weather prevented the deployment of the CTD rosette Filtering of samples Particulate Organic Carbon POC Particulate Organic Nitrogen PON Between 750ml and 1000ml of seawater was filtered onto an ashed GFF 0 7m filter When filtering was complete the filter was rinsed with 1 HCL and then pre filtered seawater The filter was then stored in a labelled cryovial The label denoted the unique sample number described below JDay of collection time of CTD deployment and volume of sample seawater that was filtered Samples were placed in an oven set at 50 60 C for 8 12 hours with the lid removed When removed from the oven the lid was secured and the cryovial stored Note Pre filtered seawater was produced during the transit to the Outer Herbrides by collecting underway seawater and filtering it first through ashed GFF filter and then again through a 0 4 polycarbonate filter Particulate Organic Phosphate POP Between 750ml 1000ml of seawater was filtered onto pre treated GFF 0 7m filters When filtering was complete the filter was removed and stored in non pre combusted glass tubes that were labelled The label denoted the unique sample number described below JDay of collection time of CTD deployment and volume of sample seawater that was filtered Samples were placed in an oven set at 50 60 C for 8 12 hours without a covering When
45. the resulting averaged relative velocity The averaged variables are added to the structure OS75 ave ping as are the variables depth and ref bins numbers of the bins in the reference layer The structure is then returned to the main routine average pings m is the last routine called within the loops through all files in a file sequence and through all file sequences specified At the end of the loops the structure OS75 ave ping contains averaged data for all files included in the processing Before the loops are left the array bindepth containing bin depths for each of the averaged velocity profiles is created Next steps are the final part of the calibration blanking the bottom and removing the ship velocity from the ADCP velocity data points If there is no bottom track data available the calibration is done using water track Again the search for possible calibration points is done using 2 minute averages produced by ave for calib m First differences are calculated from the average data for the reference velocities i e the water velocities in the reference layer specified by ref uplim and ref lowlim du and dv and the ship velocities dsu and dsv Of those only differences were considered for when ship speed exceeded 3 m s between ensembles not more than 5000 m or 3600 s apart Using the Matlab function fminsearch m the following function was minimized for phi and A Adu cosa Advsin
46. to decline rapidly often at the mixed layer depth Where weather conditions and time allowed additional samples were collected by deploying a phytoplankton net Due to the dimensions 25cm diameter and 40cm depth and shape of the net it became also known as the Smurf Hat The net was lowered on a dynamar line via the metal free winch gantry The generally windy conditions required a weight of approximately 4 kg on the bottom of the net to keep the net in an upright position and to ensure it sank Depth of net deployment was determined by the fluorescence profile from the CTD cast The depth of rapid fluorescence decline was picked as the maximum depth for the net Sample volume from the net hauls was approximately 60ml samples were fixed with 1 ml Lugol s Iodine solution a minimum of 1 Lugol s by volume is needed to fix a sample which would be 0 6ml for a 60ml sample However 1 ml was chosen due to the minimum size of the pipette Samples were stored in the dark at room temperature and will be returned to SAMS for community analysis using standard sedimentation chamber and light microscopy methodologies An additional 60 ml sample taken from the underway system will be analysed by Ruth Patterson for genetic evidence of the presence of a Azidinium a newly discovered harmful phytoplankton species Chlorophyll a The same depths sampled for community composition were also sampled for chlorophyll a 500 ml water samples were filtered
47. 000 B 0 00000000 Calibration constant 1253 1000000 00000000 Multiplier 1 00000000 Offset 0 08126488 9 A D voltage 3 PAR Irradiance Biospherical Licor 2 Serial number 70520 Calibrated on 3 February 2014 M 1 00000000 B 0 00000000 Calibration constant 17574692442 90000200 Multiplier 1 00000000 Offset 0 05835960 10 A D voltage 4 Altimeter Serial number 59493 Calibrated on 29 November 2012 Scale factor 15 000 Offset 0 000 11 A D voltage 5 Turbidity Meter WET Labs ECO BB Serial number BBRTD 1055 Calibrated on 13 March 2013 ScaleFactor 0 002365 Dark output 0 061000 33 12 A D voltage 6 Transmissometer Chelsea Seatech Serial number 161048 Calibrated on 24 July 2012 M 23 5922 B 0 1151 Path length 0 250 13 A D voltage 7 Fluorometer Chelsea Aqua 3 Serial number 88 2615 124 Calibrated on 19 October 2012 VB 0 277300 VI 1 956300 Vacetone 0 356100 Scale factor 1 000000 Slope 1 000000 Offset 0 000000 Scan length 41 Stainless Steel Frame Sensor Information Manufacturer Serial Casts Used Number Instrument Sensor Model Channel Primary CTD deck unit SBE 11plus 11P 34173 0676 n a casts CTD Underwater Unit SBE 9plus 09P 46253 0869 n a stainless casts Stainless steel 24 way frame NOCS Zubkov 75313 n a All stainless casts Primary Temperature Sensor SBE 3P 3P 4782 FO All stainless casts Prim
48. 1 0 0080 0060 0040 002 0 0 0020 0040 0060 008 0 01 Sampnum Bottle CTD salinity offset Titanium TiT 0 0 08 0 06 0 04 500 gt gt 0 02 0r B 0 02 1000 o 0 04 p 5 0 06 a i 1500 o Oirs o 0 12 a i i 1 1 2000 1 1 i i 1 1 i 0 1000 2000 3000 4000 5000 6000 0 1 0 08 0 06 0 04 0 02 0 0 02 0 04 0 06 0 08 0 1 Sampnum Bottle CTD salinity offset 0 02 0 2 0 01 _5001 ok 5 1000 8 e 0 01 5 1500 0 02 9 amp E 0 08 2000 o en 0 04 i i i 2500 i i i 0 1000 2000 3000 4000 5000 6000 0 01 0 0080 0060 0040 002 0 0 0020 0040 0060 008 0 01 Sampnum Bottle CTD salinity offset Figure 4 Summary of CTD salinity calibrations Panels a and c show temporal salinity residuals for the stainless and titanium CTD systems respectively whilst panels b and d show the vertical pressure residuals Panels E and F show final residuals after calibration Vertical blue lines in panel f indicate 40 002 offset range 58 Stainless Steel StS a Raw data H 2 E amp Calibrated zd m blouse eei eri 4 gt 4 a J H el 11 4 US J gt J Sol 8 0 1000 2000 3000 4000 5000 6000 Sampnum E Titanium
49. 10 985 140 30 10 2014 031 E2 056 52 223 008 30 013 133 30 10 2014 032 E3 056 52 192 009 3 518 200 30 10 2014 034 4 056 52 187 009 17 917 1415 30 10 2014 036 5 056 52 348 009 43 233 1870 31 10 2014 038 91 E6 056 52211 010 5 401 2100 31 10 2014 037 Fl 056 07 177 008 06 149 120 02 11 2014 049 F2 056 7 147 008 30 90 129 02 11 2014 048 F3 056 7 290 008 53 870 139 02 11 2014 046 F4 056 07 156 009 10 609 205 02 11 2014 044 F5 056 07 466 009 42 089 1629 02 11 2014 042 F6 056 7 298 010 5 988 2002 01 11 2014 041 Table 7 Locations of cross shelf edge stations for transects A C E and F approximate water depth metres taken from pressure sensor during CTD casts date sampled and corresponding CTD numter Inorganic Nutrient Analysis Chris Daniels Cruise Objectives My objective on cruise DY017 was to measure the concentrations of the inorganic nutrients TON silicate and phosphate using segmented flow analysis Method Analysis for micro molar concentrations of nitrate and nitrite Total Oxidised Nitrogen or TON phosphate and silicate was undertaken on a Skalar San segmented flow autoanalyser following methods described by Kirkwood 1996 Samples were drawn from Niskin bottles on the CTD into 25ml sterilin coulter counter vials and kept refrigerated at approximately 4 C until analysis which commenced within 24 hours Overall 12 runs
50. 11 2014 307 14 57 55 3669 10 1008 TiT CTD056 G6 03 11 2014 307 17 33 55 3669 10 1009 Sts Table 3 Summary table of CTD deployments during DY017 See Figure 2 for position of CTD stations CTD data processing post cruise addendum All CTD data were processed and calibrated in Matlab using the mstar data processing environment Brian King NOC as has become common on a number of recent NOC led cruises Mstar is an alternative to the Unix based Pstar data processing system that has been heavily used on UK research ships in the past and is entirely based around NetCDF file formats The description below mainly follows similar procedures used by Penny Holliday on JCO86 and Adrian Martin on JC087 SeaBird Data Processing SeaBird Data Processing was restricted to three stages for compatibility with other cruises using mstar Data Conversion Align CTD Cell Thermal Mass Translate This was run with the hysteresis correction for oxygen and ensuring conductivity was in units of mS cm n b The hysteresis correction can also be handled directly in mstar in the script mctd 02b m see below If this option is followed then it is essential that the hysteresis correction is not applied here using a value of 6 sec consistent with prior cruises e g JC86 and JC87 using standard SeaBird recommendations of alpha 0 03 and 1 beta 7 0 for both primary and secondary c
51. 14 303 08 08 56 8755 8 1831 TiT CTD031 El 30 10 2014 303 08 49 56 8755 8 1831 Sts CTD032 E2 30 10 2014 303 11 00 56 8704 8 5002 Sts CTD033 E3 30 10 2014 303 16 10 56 8699 9 0586 TiT CTD034 E3 30 10 2014 303 17 05 56 8699 9 0587 Sts CTD035 4 30 10 2014 303 19 19 56 8698 9 2987 TiT CTD036 4 30 10 2014 303 21 50 56 8698 9 2986 Sts CTD037 E6 31 10 2014 304 07 39 56 8702 10 0928 Sts CTD038 E5 31 10 2014 304 13 40 56 8725 9 7039 Sts CTD039 5 31 10 2014 304 16 10 56 8687 9 696 TiT CTD040 F7 01 11 2014 305 05 30 56 1216 10 4987 StS CTD041 F6 01 11 2014 305 18 12 56 1217 10 0998 Sts CTD042 F5 01 11 2014 305 23 01 56 125 9 7017 StS CTD043 F5 02 11 2014 306 02 03 56 1288 9 7048 TiT CTD044 F4 02 11 2014 306 06 27 56 1193 9 1768 Sts CTD045 F4 02 11 2014 306 07 42 56 1193 9 1768 TiT CTD046 F3 02 11 2014 306 10 00 56 1215 8 8978 StS 50 CTD047 F3 02 11 2014 306 11 08 56 1215 8 8979 TiT CTD048 F2 02 11 2014 306 15 24 56 1191 8 5015 StS CTD049 F1 02 11 2014 306 17 44 56 1196 8 1025 StS CTD050 G1 02 11 2014 306 23 52 55 3706 8 0977 StS CTD051 G2 03 11 2014 307 02 14 55 3687 8 5016 StS CTD052 G3 03 11 2014 307 05 03 55 37 8 8997 StS CTD053 G4 03 11 2014 307 07 30 55 3709 9 303 TiT CTD054 G5 03 11 2014 307 09 51 55 3693 9 7356 TiT CTD055 G6 03
52. 14 297 08 52 58 9597 6 5001 StS CTD007 A4 24 10 2014 297 13 38 59 1962 6 9492 TiT CTD008 A4 24 10 2014 297 14 59 59 1962 6 9493 StS CTD009 5 24 10 2014 297 18 43 59 3977 7 3381 TiT CTD010 5 24 10 2014 297 21 38 59 3971 7 3242 StS CTD011 Bl 27 10 2014 300 03 18 58 4466 7 1935 TiT CTD012 Bl 27 10 2014 300 03 53 58 4466 7 1936 Sts CTD013 Cl 27 10 2014 300 09 17 58 0227 7 7157 TiT CTD014 Cl 27 10 2014 300 09 58 58 0227 7 7157 Sts CTDO15 C2 27 10 2014 300 12 36 58 0804 8 012 Sts CTD016 C3 27 10 2014 300 16 46 58 1492 8 4177 TiT CTD017 C3 27 10 2014 300 17 37 58 1492 8 4177 StS 49 CTD018 C4 27 10 2014 300 21 09 58 2235 8 8319 TiT CTD019 C4 27 10 2014 300 22 08 58 2234 8 8318 Sts CTD020 C5 28 10 2014 301 01 31 58 289 9 248 TiT CTD021 C6 28 10 2014 301 14 10 58 3638 9 6627 StS CTD022 C7 28 10 2014 301 18 47 58 4335 10 0758 TiT CTD023 C7 28 10 2014 301 21 21 58 4334 10 0706 StS CTD024 D5 29 10 2014 302 05 12 57 6261 9 7077 StS CTD025 D4 29 10 2014 302 08 45 57 6196 9 3894 TiT CTD026 D4 29 10 2014 302 10 13 57 6196 9 3895 StS CTD027 D3 29 10 2014 302 21 29 57 6218 8 9006 StS CTD028 D2 29 10 2014 302 23 45 57 6216 8 4999 StS CTD029 D1 30 10 2014 303 01 47 57 6159 8 1855 StS CTD030 El 30 10 20
53. 159 170 Kirkwood D S 1996 Nutrients Practical notes on their determination in seawater In ICES Techniques in Marine Environmental Sciences Report 17 International Council for the Exploration of the Seas Copenhagen 25 pp Klunder M B P Laan R Middag H J W De Baar and J C Van Ooijen 2011 Dissolved iron in the Southern Ocean Atlantic sector Deep Sea Research Part li Topical Studies in Oceanography 58 2678 2694 Lam P J and Bishop 2008 The continental margin is a key source of iron to the HNLC North Pacific Ocean Geophysical Research Letters 35 L07608 Liu X W and F J Millero 2002 The solubility of iron in seawater Marine Chemistry 77 43 54 Llewellyn C A J R Fishwick J C Blackford 2005 Phytoplankton community assemblage in the English Channel a comparison using chlorophyll a derived from HPLC CHEMTAX and carbon described from microscopy cell counts Journal of Plankton Research 277 103 119 Martin J H and S E Fitzwater 1988 Iron deficiency limits phytoplankton growth in the northeast pacific subarctic Nature 331 6154 341 343 117 Mcllvin M R and K L Casciotti 2011 Analytical Chemistry 83 1850 1856 Middag R H J W de Baar P Laan and M B Klunder 2011 Fluvial and hydrothermal input of manganese into the Arctic Ocean Geochimica et Cosmochimica Acta 75 2393 2408 Milne A W Landing M Bizimus and P Morton 2010 Determination of Mn Fe Co
54. 17 10 19 30 21 20 08 20 10 43 13 06 16 00 18 30 23 21 08 48 19 30 02 35 05 15 09 05 11 03 12 18 14 38 16 43 19 07 21 00 23 32 01 20 03 15 04 52 14 00 16 00 18 20 00 02 05 08 07 25 08 34 11 38 15 00 24 Passage to CTD test site off the Isle of Coll 3 generators until 13 00 22 10 14 Clocks retarded 1 hr to GMT S S CTD test deploymente on Deep Tow wire amp deploy Tow Fish Passage to DYO17 start Stn Al SS and MF CTD Plankton Net Near Surface Sampling Buoy Relocate for next station Stn A2 SS and MF CTD Relocate for next station At Stn A3 Waiting on weather Wind 40kts Swell 5 6m Stn A3 SS and MF CTD Tow Fish issues Relocate for next station Stn A4 SS and MF CTD Relocate for next station Stn A5 SS and MF CTD amp test of lander accoustic releases To Broad Bay for shelter Waiting on weather in Broad Bay Return to science line at B1 Stn SS and MF CTD Plankton Net Relocate for next station Stn C1 SS and MF CTD Plankton Net Relocate for next station Stn C2 SS CTD amp Near Surface Sampling Buoy Relocate for next station Stn C3 SS and MF CTD Relocate for next station Stn C4 SS and MF CTD Plankton Net Relocate for next station Stn C5 MF CTD Deep Tow wire jumps out of sheave Wire needs reterminating Relocate for next station On stn at C6 Awaiting retermination and test Stn C6 SS CTD Relocate for next station Stn C7 SS and MF
55. 5 000000 08 39 05150 DY017006 000000 11 17 08150 17006 000000 11 17 09150 017007 000000 13 04 09150 017007 000000 13 04 09150 DY017008 000000 14 43 08150 DY017008 000000 14 43 08150 DY017011 000000 18 39 09150 DY017011 000000 18 43 09150 DY017012 000000 08 54 05150 DY017012 000000 08 54 05150 DY017013 000000 10 12 09150 DY017013 000000 10 12 09150 017014 000000 09 21 05150 DY017014 000000 09 21 05150 DY017015 000000 09 05 05150 017015 000000 09 05 05150 DY017016 000000 09 55 05150 DY017016 000000 09 55 05150 DY017017 000000 07 45 05150 DYO17017 000000 07 45 05150 DY017018 000000 10 20 08150 DY017018 000000 10 20 08150 DY017019 000000 11 00 09150 DY017019 000000 11 00 09150 DY017020 000000 10 40 09150 017020 000000 10 40 09150 DY017020 000000 08 25 05150 17021 000000 08 25 05150 17022 000000 08 20 05150 DY017022 000000 08 20 05150 DY017023 000000 09 30 05150 DY017023 000000 File open closed opened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed pened losed Comments commence Routine dai Routine dai test run of VMADCP around Land s end and thru Irish
56. 60m min to ensure no undue strain or movement of the slip ring cabling and wire assemblies Initial tests with the ROV team Bicotest Cable Tester indicated a fault within the first 100ft of the outboard end of the cable This agreed with previous continuity tests in a very low resistance was measured from the outboard end approximately 5 to 10 Q whilst a figure of approximately 960 was measured from the inboard end with the cable disconnected from the slip ring and all the ships internal wiring The manufacture gives a resistance of 4 90 km for this cable and with 10km of wire on the drum a figure of 96Q is consistent with a fault being very close to one end of the wire 100m of cable was then run off and the cable cut and opened up again The next test with the Cable Tester revealed a healthy wire indicating no further problems with the 10km on the drum As a final confirmation an insulation resistance test was 28 carried out on each core and this resulted in readings in excess of 3000MQ between each core and between each core and the metal armouring A continuity test of each core was then carried out from both ends and a figure of approximately 950 was obtained in every case The slip ring and all other connections were replaced and a final test of the entire system from Main Lab to termination was carried out to ensure no faults Also one core brown translucent sheath is permanently bonded to earth at the Main Lab and in the Winch Room
57. AS and Level C only attitude data from the POSMV was logged A TechSAS data logging module for the iXSea PHINS and Seapath 330 is under development 45 Instrumentation SurfMet Malfunctions in the system led to unreliable data being displayed and logged All SurfMet data from this cruise should be disregarded Extensive efforts have been made to faultfind the system to no avail Please see the separate BODC information sheet dy017 surfmet sensor information sheet docx for details of the sensors used and the calibrations that need to be applied The calibration sheets are included in the directory Ship Systems MetSURFMET calibrations The non toxic water supply was active from YYYYMMDDHHMM to YYYYMMDDHHMM SurfMet Surface Water System Malfunctions in the system led to unreliable data being displayed and logged All SurfMet data from this cruise should be disregarded SurfMet Met Platform System Malfunctions in the system led to unreliable data being displayed and logged All SurfMet data from this cruise should be disregarded SurfMet PC Express Malfunctions in the system led to unreliable data being displayed and logged All SurfMet data from this cruise should be disregarded WaMoS II Wave Radar Not requested but logged occasionally The WAMOS wave radar was run throughout the cruise All data was logged and a summary of its output is given in the PARA ems files Gravity Meter Not installed on the ship for this cr
58. As such quantifying the chemical gradients and fluxes of material both onto and off of the continental shelf in this region is important for the subsequent objectives of understanding the continental shelf carbon pump and the role of the NW European shelf in the global carbon cycle The objectives for DY017 were to map the large scale gradients in dissolved inorganic carbon iron inorganic and organic nutrients across the Hebridean and Malin Shelves Figure 2 of these properties are central to the SSB scientific objectives and subsequent work will relate the distribution of these properties to the circulation of the region including the prominent northward flowing shelf slope current Souza et al 2001 and to model estimates 13 of shelf edge exchange Unlike other activities in the SSB programme which are repeated or on going cruise DYO17 was a one time affair collecting a snap shot of the western shelf during the autumn months a time when the seasonal breakdown of water column stratification occurs 60 N 51 N hy 48 N 15 W 10 W 5 W 0 5 Longitude W Figure 1 Chart showing the main working areas of the Shelf Sea Biogeochemistry programme research cruises in the Celtic Sea previous NERC funded research activities on the western shelf including the Extended Ellett Line red diamonds the Shelf Edge Study blue hexagon FastNet green circle and the approximate working area of the Outer Hebrides p
59. Bottom tracking was enabled for the majority of the cruise though most good calibration data were acquired during the long transits at the beginning and end of the cruise A suite of MATLAB routines were used to perform data screening and transformation to absolute velocities in Earth coordinates A summary of configuration and the processing steps during DY017 is given below OS75 basic VMDAS configuration ADCP Setup Number of bins 60 Bin size 16m Blank distance 8 m 60 Transducer depth 6 m Processing mode low resolution long range recommended by Brian King NOC Bottom track on Ensemble time fast as possible Recording Number start at 1 but allow VMDAS to increment automatically otherwise files are overwritten Max Size 10 Mb rolls over to new sub file automatically Setting the file size to very large can cause it to crash NAV NMEA ship position sources NMEA1 Transform Heading tilt source PRDID NMEA2 Custom NMEA from C RDI VmDas ADCP alignment correction Heading 45 Averaging First time interval 120 seconds Second time interval 600 seconds Data screening All unchecked OS150 basic VMDAS configuration ADCP Setup Number of bins 96 Bin size 4m Blank distance 4 Transducer depth 6 m Processing mode low resolution long range Bottom track on 61 Ensemble time fast as possible Recording Number start at 1 but allow VMDAS to increment automatically otherw
60. C Garbage Disposal 30 knots gusting 40 Band 512kbps minimum knots on beam Enclosed 55 6 7 on beam Overside Handling Systems Lifeboats Performance Winches Cranes amp Gantries Survey amp speed Large Aft amp seit Transit 12 kts Stbd Max Speed 15 kts s L 99 8m B 18 0m D 6 5m t Drop Keels 7 52 total Swath Transducers Hull Bow greed 24 Crew Retractable Azimuth Ser designed to ias 28 Scientists Thruster Thruster Minimise aeration 1D for longevity amp robustness and URN LR 100 A1 Ice 1D LMC UMS IWS EP DP AM NAV1 IBS Research Vessel Figure 3 RRS Discovery instrumentation suite Datalogging amp Data Storage Datalogging software and storage is provided on a platform common to both RRS vessels managed by the NOC RRS Discovery and RRS James Cook TechSAS TechSAS is an integrated technical and scientific sensors acquisition system and is the primary datalogger on both vessels The system allows monitoring and accurate time stamping of each individual instrument with a graphical output TechSAS saves data in the self describing NetCDF Network Common Data Format format that can be easily read via MatLab or using freely available NetCDF libraries TechSAS also broadcasts the logged data across the ship s network in UDP pseudo NMEAO183 1 NMEA like packets Separate NetCDF documentation is available that explains the logged variables 36 RVS Level C Level
61. C is a data management programme written in C for its Sun SPARC environment The Level C system logs the TechSAS UDP packets in the Level C binary format as flat files colloquially known as streams Level C has a number of little programmes inside it that allow the flat files to be viewed edited and exported rapidly in a range of formats e g CSV ASCII text file at custom intervals and averaging periods Another feature is the display of meteorological depth and navigation data as with the SSDS software running on the wall mounted HP touchscreens around the ship The NMFSS Science Systems Technician will be able to generate the necessary reports from the Level C system for you Positioning amp Attitude Sensors The new RRS Discovery has some of the same sensors as the RRS James Cook and some new ones Applanix POS MV V4 Primary Science GNSS and Attitude Sensor A combined GNSS receiver and attitude 1 gyrocompass and conventional motion sensor that provides data about attitude heave position and velocity The GNSS aspect is for use with Multibeam Echosounder systems The POSMV is logged to the TechSAS Datalogger The datalogger produces two files for its configured file period usually 24hrs These files are e POSMVPOS POS NetCDF File Containing Positional Data Heading Latitude Longitude e POSMVATT ATT NetCDF File Containing Attitude data Roll Pitch Heave Please note that the position
62. CTD Plankton Net Relocate for next station Stn D5 SS CTD and Plankton Net Relocate for next station Stn D4 SS and MF CTD Plankton Net Tow Fish recovered Reposition for Lander deployment Flotation package not releasing 30 10 2014 31 10 2014 01 11 2014 02 11 2014 15 00 16 00 18 05 21 24 22 09 23 37 00 22 01 36 02 35 08 00 09 39 10 54 13 44 16 11 18 05 19 05 23 37 01 10 01 30 04 00 04 30 06 30 07 39 10 12 12 10 13 30 21 36 05 00 07 20 08 57 18 12 21 28 23 00 04 20 06 22 08 33 09 38 11 37 13 06 16 15 29 10 2014 29 10 2014 29 10 2014 29 10 2014 29 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 30 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 31 10 2014 01 11 2014 01 11 2014 01 11 2014 01 11 2014 01 11 2014 01 11 2014 02 11 2014 02 11 2014 02 11 2014 02 11 2014 02 11 2014 02 11 2014 02 11 2014 02 11 2014 16 00 18 05 21 24 22 09 23 37 00 22 01 36 02 35 08 00 09 39 10 54 13 44 16 11 18 05 19 05 23 37 01 10 01 30 04 00 04 30 06 30 07 39 10 12 12 10 13 30 21 36 05 00 07 20 08 57 18 12 21 28 23 00 04 20 06 22 08 33 09 38 11 37 13 06 16 15 17 40 25 Lander deployment Lander position calibrated triangulation Tow Fish deployed Relocate
63. D PML PhD U LIVERPOOL PhD NOC NMFSS NOC National Oceanography Centre OBE Ocean Biogeochemistry and Ecosystems NMESS NERC Marine Facilities Sea Systems OES Ocean and Earth Science SBR Station Biologique de Roscoff NIOZ Royal Netherlands Institute for Sea Research U LIVERPOOL University of Liverpool U PLYMOUTH University of Plymouth PML Plymouth Marine Laboratory SAMS Scottish Association for Marine Science SHIP S PERSONNEL GATTI Antonio COX Jo HOOD Michael MACKAY Stewart STOOP Richard O SULLIVAN Geraldine NICHOLSON Gavin McGrath Charles BRAZIER Tom WATTERSON Ian Stuart GREGORY Nathan MINNOCK Mick LAWES Duncan WYTHE Viv WILCOX Simon STIVEY Mark TONER Steve DEAL Dickie SUTTON Lloyd WATERHOUSE Jacqui ORSBORN Jeff VOLOSNUHINA Rita 10 Master Captain Chief Officer 2 Officer Chief Engineer 2 Engineer 3 Engineer 3 Engineer ETO PCO CPO D PO D CPO S ERPO D E S Man 1A S Man 1A S Man 1A S Man 1A Head Chef Chef Steward Asst Steward LIST OF FIGURES Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Chart showing the main working areas of the Shelf Sea Biogeochemistry programme research cruises in the Celtic Sea previous NERC funded research activities on the western shelf including the Extended Ellett Line red diamonds the Sh
64. E 000 000000 zz ave ping mat where only the values in the velocity field are changed Additionally the variable bindepth is included OS75 abs includes xyz number of velocity profiles after averaging vel number of bins x 2 x xyz array of absolute velocity zonal meridional i e horizontal velocities are corrected for ship velocity nav structure containing txyl 3 x xyz array of time decimal Julian days longitude and latitude ref structure with velocity 2 x xyz array average over the reference layer and bins vector containing the depth bins that lie within the reference layer depth number of bins x xyz array bin depths corresponding to the settings used for the velocity profiles DYO017 File generation and calibration 82 Typically a new file was generated daily to keep track of the ADCP behaviour This is good practice as problems with the ADCP can develop which are hard to diagnose using only the VMDAS display Raw data files and processed data files in MATLAB format will be logged with BODC after the cruise the approximate total quantity of data will be 6GB Raw data for the 75 kHz ADCP are divided into around 20 series OS075 DY017003 000000 to OS075 DY017024 000000 with some gaps Raw data for the 150 kHz ADCP are divided into around 20 series OS150 DY017000 000000 to OS150 DY017023 000000 with some gaps Within each series files are subdivided into files of maximum 10MB in size S
65. Labs ECO BB Serial number BBRTD 758R Calibrated on 3 June 2013 ScaleFactor 0 002903 Dark output 0 043100 12 A D voltage 6 Transmissometer Chelsea Seatech Serial number 161049 Calibrated on 20 October 2010 M 23 9408 31 B 0 3507 Path length 0 250 13 A D voltage 7 Fluorometer Chelsea Aqua 3 Serial number 088244 Calibrated on 6 August 2014 VB 0 236800 VI 2 151000 Vacetone 0 305900 Scale factor 1 000000 Slope 1 000000 Offset 0 000000 Scan length 41 Stainless CTD frame Date 10 20 2014 Instrument configuration file C Program Files Sea BirdNSeasaveV7NDYO17NDYOI7 stainless NMEA xmlcon Configuration report for SBE 911plus 917plus CTD Frequency channels suppressed 0 Voltage words suppressed 0 Computer interface RS 232C Deck unit SBE1 plus Firmware Version gt 5 0 Scans to average 11 NMEA position data added Yes NMEA depth data added No NMEA time added No NMEA device connected to deck unit Surface PAR voltage added No Scan time added Yes 1 Frequency 0 Temperature Serial number 03P 4782 Calibrated on 2 July 2013 G 4 34988979e 003 H 6 36411045e 004 I 2 08372334e 005 J 1 75345425e 006 FO 1000 000 Slope 1 00000000 Offset 0 0000 2 Frequency 1 Conductivity Serial number 04C 2231 Calibrated on 2 July 2013 G 1 07805493e 001 H 1 69843332e 000 I 3 58275165e 003 J 3 82993434e 004 CTcor 3
66. Mount showing twin acoustic releases recovery aids and ADCP battery case AL 500 showing three legged bridle and part of buoyancy parachute top The Near Surface Ocean Profiler 11 14 36 58 59 71 87 93 97 98 99 104 LIST OF TABLES Table 1 Table 2 Table 3 Table 4 Table 5 Table 6 Table 7 Table 8 Table 9 Table 10 Table 11 Table 12 Table 13 Table 14 Table 15 Table 16 Table 17 Meteorological instrument suite on RRS Discovery Surface water sampling instrument suite on RRS Discovery Summary table of CTD deployments during DYO017 See Figure 2 for position of CTD stations List of OS75 raw data files collected during DY017 List of OS150 raw data files collected during DY017 Summary of all sampling for dissolved oxygen measurements Locations of cross shelf edge stations for transects A C E and F approximate water depth metres taken from pressure sensor during CTD casts date sampled and corresponding CTD number Labelling code given to each type of analysis Description of CTD sample labelling for sample NA12 Description of underway sample labelling for sample UW1N Summary table of sampling for particulate material Summary of NSOP deployments Summary of phytoplankton sampling activities Summary of sampling for total dissolvable and dissolved iron measurements Summary of sampling for total dissolvable and dissolved trace metal measurements Summary of lig
67. National Oceanography Centre NATURAL ENVIRONMENT RESEARCH COUNCIL National Oceanography Centre Cruise Report No 29 RRS Discovery Cruise DYOI7 20 OCT 06 NOV 2014 Outer Hebrides process cruise Principal Scientist S C Painter 2015 National Oceanography Centre Southampton University of Southampton Waterfront Campus European Way Southampton Hants SOI4 3ZH UK Tel 44 0 23 8059 9237 Email stuart painter noc ac uk O National Oceanography Centre 2015 DOCUMENT DATA SHEET AUTHOR PUBLICATION PAINTER SC etal DATE 2015 TITLE RRS Discovery Cruise DY017 20 Oct 05 Nov 2014 Outer Hebrides process cruise REFERENCE Southampton UK National Oceanography Centre Southampton 118pp National Oceanography Centre Cruise Report No 29 ABSTRACT The continental shelf region immediately west of the UK and North of Ireland is thought to be a key region for the exchange of nutrients carbon and water between the NW European continental shelf and the open North Atlantic Ocean yet it remains comparatively under sampled Within the context of the NERC DEFRA co funded Shelf Sea Biogeochemistry programme which aims to improve our understanding of the role of shelf seas in the global carbon cycle this cruise undertook a regional scale survey to determine the distribution and concentrations of dissolved inorganic carbon inorganic nutrients trace metals and other ancillary data on the Malin and Hebridean
68. Organic nutrients and stable isotopes Nealy Carr and Carl Springys Aims during DYO17 The aims of the organic nutrient biogeochemistry team were to a identify gradients in organic nutrients across the shelf edge of the Malin and Western Irish Shelf and b collect seawater samples to determine the stable nitrogen and oxygen isotope composition of nitrate S15N and 018O nitrate in deep waters Sampling A series of sampling regimes were followed a four cross shelf transects consisting of 5 7 stations Transect A C E and F and b sampling surface water from the uncontaminated seawater supply Table 7 Analytical methods Dissolved organic nutrients Seawater was collected in 1L pre cleaned 1076 HCI HDPE bottles and filtered through a pre combusted glass fibre filter nominal pore size 0 7 using a pre cleaned glass filtration rig Filtered seawater samples were collected into acid washed HDPE bottles and frozen immediately at 20 C The concentration of dissolved organic carbon and dissolved organic nitrogen will be determined by high temperature catalytic oxidation and dissolved organic phosphorous using UV digestion Chromophoric Fluorescent dissolved organic matter CDOM FDOM Seawater from up to 11 depths was filtered from the same sample in the same manner as above for dissolved organic nutrients The filtrate was then filtered through Durapore membrane filters 0 22 jm collected in pre cleaned 125 mL HDPE bottles
69. Sea y processing y processing END BOTTOM TRACK START WATER TRACK Routine dai y processing Restarted to try to solve data screening problem END WATER TRACK START BOTTOM TRACK Serial cable failure on files 9 and 10 CHANGE CALIBRATION TRANSDUCER ROTATION SET TO 45 DEGREES IN VmDas File 12 has Routine dai 75kHz note Routine dai Routine dai Routine dai Routine dai Routine dai Routine dai Routine dai new calibration applied y processing d as short range and flaky not entirely sure about 150 either Monitor y processing y processing y processing y processing y processing y processing y processing Note penetration was particularly poor this morning restarting vndas seemed to improve slightly Routine dai Routine dai y processing y processing Table 5 List of OS150 raw data files collected during DY017 Processed data It was initially hoped that it would be possible to generate one large file from the post processing for each ADCP but as different ADCP alignments were used in the early stages of the cruise the final processed file structure is as follows OS075 DY01700x 000000 23 abs series 5 24 75 kHz 18 43 15 42 21 10 14 09 30 05 11 14 Majority of cruise First few days are poor quality due to beam 4 failure OS150 DY01700x 000000 11 abs series 4 11 150 kHz 11 03 22 10 14 to 18 39 23 10 14 Steam across Malin Shelf towards Minch The misalignment
70. Shelves Of the seven planned transects six were completed with the seventh abandoned due to poor weather but a rich dataset of key biogeochemical parameters has been collected which will enable work on the stoichiometry of dissolved nutrients and exchange with the open ocean to be undertaken KEYWORDS ISSUING ORGANISATION National Oceanography Centre University of Southampton Waterfront Campus European Way Southampton SO14 3ZH UK Tel 44 0 23 80596116 Email nol noc soton ac uk A pdf of this report is available for download at http eprints soton ac uk Page intentionally left blank CONTENTS ACKNOWLEDGMENTS teet te eese hr ue tu ena ee ehe en ae Le ea na ena e eh aar Re ern 8 SCIENTIPIC PERSONNED 53 3 rd eii tent Ee iR e dde eal ede detur ecekadus 9 SHIPS PERSONNE O 5 5 eie deer art b ae hri ade ied enia eh RET ERR Rae 10 LIST OF FIGURES S 11 LISTOF TABLES duds decedere de relie cu ie arn ed ducetiates 12 ABSTRAGCT geld e dfe aie n ep he a dasa havea GR Fe EPA ER 13 T INIRODUGITION tt rte ter nee ee eter eae d etd atero de d P Een 13 2 CRUISE NARRATIVE etienne erste eti denen nennt n rhe e o a Ea ge 16 PSO EN Ditis e E 16 Master s Diary Summary od rte ferre ide ona da ee gea 23 3 TECHNICAL SUPPORT 26 CTD Opert tiOnis oi ode ertet der tpe np DER DR e VU eae Vlde tbe ee Fa 26 RRS Disco
71. Star CST Photon quanta received light Seawater Particulate density Transmissometer Table 2 Surface water sampling instrument suite on RRS Discovery TSG flow is approx 1 6 litres per minute whilst fluorometer and transmissometer flow is approx 20 l min Flow to instruments is degassed using a debubbler outlet with 10 l min inflow waste flow is usually around 8 10 l min adjusted to maintain balance but at a low rate to keep the TSG flow rate to around 1 6 l min DartCom HRPT L Band Polar Orbiter Satellite Imaging System The DartCom system comprises a 1 2m Parabolic Dish enclosed in a Radome It receives signals from satellites that take images of cloud coverage These images can be used to see the type of atmospheric and weather conditions nearby Specifications band polar orbiter pdf Location dyft data disc cruise reports instrument data sheets dartcom Data Displays Software for displaying useful science related information is provided around the ship SSDS Ship Scientific Display Screens These touchscreens located around the ship display a range of data from scientific and non scientific systems Gyro information GPS information from CNAV sensor information from SurfMet Depth from EA640 and winch information Waypoints to stations can also be entered on the ETA tab and propagated around the network to the other screens OLEX 3D Seafloor Mapping and Visualisation Software OLEX is a 3 D seafloor map visual
72. adjustment in this file is 45 to account for the misalignment in ADCP setup 85 OS150 DY01700x 000000 23 abs series 12 23 150 kHz 18 43 23 10 14 to 09 30 05 11 14 Remainder of cruise to southern Irish Sea The misalignment adjustment in this file is 0 to account for the misalignment in ADCP setup Dissolved oxygen measurements Victoria Hemsley Cruise objectives The objectives of the dissolved oxygen analyses were to provide calibration data for the oxygen sensors mounted on the CTD frames used during cruise DYO17 For this Winkler titrations were performed on water samples collected from the Niskin bottles mounted on the CTD frame Methods Dissolved oxygen samples were taken from the stainless steel and titanium CTD casts and were the first samples to be drawn from the Niskin bottles Up to twelve oxygen samples were collected in duplicate from stainless steel CTD casts but a maximum of five duplicate samples were collected from the titanium CTD casts due to water constraints The depths sampled were decided by examination of the oxygen trace during the downcast and samples were generally collected from regions without rapid changes in dissolved oxygen concentration samples were drawn through short pieces of silicon tubing into clear precalibrated narrow necked borosilicate flasks The temperature of each water sample was measured using an electronic thermometer probe and used to calculate any temperature dependant changes
73. alysis Filtration was completed in approximately three hours Samples collected A total of 100 samples were collected from 21 stations as detailed in Table 17 Sample analysis Samples will be analysed for both labile and refractory particulate Fe Mn Al Co Zn Cd Ba Ni Cu Ti and potentially other trace elements using ICP MS at the University of Plymouth For labile particulate trace elements the filter is subjected to a weak acid leach 2596 acetic acid at pH 2 with a mild reducing agent 0 02 M hydroxylamine hydrochloride and a heating step 20 min 90 95 This approach is fully detailed in Berger et al 2008 After the labile fraction has been determined the refractory trace elements will be determined following the method of Ohnemus and Lam Deep Sea Research in press Briefly the filters will be digested following a three step heating dry down process firstly H SO and H O are used to digest the filter followed by HNO and HF and finally HNO and H O to digest the particulate material The final solution is dried down and the residue brought back into solution with 2 HNO for analysis by ICP MS The samples are then spiked with an internal reference material such as In for drift correction Station Samples collected from Station Samples collected from separate depths separate depths Al 2 El 4 A2 2 E3 5 A4 5 4 6 5 7 5 9 3 F3 6 Cl 3 F4 5 C3 4 F5 3 C4 5 G4 3 C5 5 G5 5 C7 6 G6 8 D4 4 Ta
74. and lability of DOM across the shelf region Particulate Organic Matter POC PON and POP Up to 3 L of seawater from between 4 to 11 depths were filtered through pre combusted acid rinsed 10 fibre filter nominal pore size 0 7 using a pre cleaned triple port filtration rig The filter was collected onto muffled foil in a pre cleaned petri dish and immediately frozen at 20 and PON will be determined using standard methodology on a CHN analyser POP will be measured following combustion and acid hydrolysis lipid and pigment biomarkers and amino acids will be used to determine particle sources and degradation state Latitude Longitude Water Depth CTD Station N W approx m Date Sampled Number Al 058 36 130 005 48 138 118 23 10 2014 003 A2 058 48 026 006 11 617 121 23 10 2014 005 A3 058 57 58 006 30 00 107 24 10 2014 006 A4 059 11 770 006 56 960 234 24 10 2014 008 A5 059 23 827 007 19 454 1000 24 10 2014 010 Bl 058 26 796 007 11 617 90 27 10 2014 012 Cl 058 01 360 007 42 940 90 27 10 2014 014 C2 058 4 820 008 0 710 126 27 10 2014 015 C3 058 8 951 008 25 061 144 27 10 2014 017 C4 058 13 406 008 19 912 201 27 10 2014 019 C5 058 17 330 009 14 880 406 28 10 2014 020 C6 058 21 826 009 39 760 1323 28 10 2014 021 C7 058 26 006 010 04 237 1880 28 10 2014 023 El 056 2 529 008
75. and sampling Summary of sampling for particulate trace metal sampling 12 42 43 49 84 85 91 95 95 95 105 107 110 112 113 114 ABSTRACT The continental shelf region immediately west of the UK and North of Ireland is thought to be key region for the exchange of nutrients carbon and water between the NW European continental shelf and the open North Atlantic Ocean yet it remains comparatively under sampled Within the context of the NERC DEFRA co funded Shelf Sea Biogeochemistry programme which aims to improve our understanding of the role of shelf seas in the global carbon cycle this cruise undertook a regional scale survey to determine the distribution and concentrations of dissolved inorganic carbon inorganic nutrients trace metals and other ancillary data on the Malin and Hebridean Shelves Of the seven planned transects six were completed with the seventh abandoned due to poor weather but a rich dataset of key biogeochemical parameters has been collected which will enable work on the stoichiometry of dissolved nutrients and exchange with the open ocean to be undertaken 1 INTRODUCTION RRS Discovery cruise DYO17 was a UK National Capability funded cruise requested to support the scientific objectives of the NERC DEFRA co funded Shelf Sea Biogeochemistry SSB research programme http www uk ssb org The aim of the SSB programme is to reduce the uncertainty in our understanding of carbon and nutrient cycli
76. and stored in the dark at 4 C until analysis Samples were analysed on board within 5 days of collection using a Shimadzu spectrophotometer UV 1650 PC and Horiba scanning spectrofluorometer Fluoromax 4 90 Emission excitation matrices and spectral absorbance indices will be employed to determine the likely source of organic matter on the Malin Shelf and Western Irish Sea shelf Stable nitrogen and oxygen isotope composition of nitrate Seawater from up to 11 depths was filtered from the same sample in the same manner as above for dissolved organic nutrients The filtrate was collected in pre cleaned 10 HCI 60 mL HDPE bottles and immediately frozen at 20 C The stable nitrogen and oxygen isotope composition of nitrate N and 6 O of nitrate respectively will be analysed according to methods described and updated by Mcllvin and Casciotti 2011 using a Gas Bench attached to a Thermo Finnigan isotope ratio mass spectrometer This stable isotope approach will provide insight into the source and cycling of nitrate at the shelf edge Amino Acids Seawater from up to 11 depths was filtered from the same sample in the same manner as above for dissolved organic nutrients The filtrate was collected in pre cleaned 10 HCl and combusted 22 mL glass vials capped and immediately frozen at 20 C Isomeric ratios of amino acids present will be determined using high performance liquid chromatography and will provide insight into the degradation state
77. angle misalignment_xb and the scaling factor amplitude xb are set to and 1 respectively x n for narrowband mode x b for broadband mode For the second run when values for misalignment xb and amplitude xb have been calculated they should be set to the median mean mode or whichever value works best i e gives the smallest angle and amplitude after the second run To keep a record of the settings used to process a set of ADCP data the settings and the text displayed on screen during the processing are written to a diary called adcp proc log runX txt X will be 1 for the first run when misalignment_xb and amplitude xb are equal to O and 1 resp and 2 for the second run misalignment xb and amplitude xb unequal 0 and 1 resp After this introductory part the processing starts Arrays are declared for later use when calling some of the subroutines and the file containing calibration point data is deleted if it exists in the processed data directory Then the loop through all file sequences specified above starts First the filename is set Its general structure is CRUISE xxx yyyyyy At this point xxx is set to the file sequence number that is the current in the loop and yyyyyy is 000000 After the initialisations the run through the subroutines begins This includes all routines described in 4 4 2 to 4 4 11 Once all files have been passed through these routines and the loop is finished the functions described in 4 4 12 to 4 4 16 a
78. ansponders Kongsberg Simrad Simrad now part of Kongsberg is the supplier of the heavy artillery of echosounders EM122 Deep Water Multibeam Echosounder This echosounder is rated to 11 000m but probably up to 8 000m for good quality data The EM122 it is viewed and operated via SIS Seafloor Information Service Specifications Em122_product_description pdf 38 Location data disc cruise reports instrument data sheets EM710 Shallow Water Multibeam Echosounder This echosounder is rated to 2 000m but in reality you might consider switching to the EM122 between 600 1500 metres Within this range the EM710 gives a broader swathe with less detail so which one you use depends on what data you need to generate Specifications Em710_product_specification pdf Location dy _data_disc cruise_reports instrument_data_sheets SBP120 Sub Bottom Profiler The SBP120 is an extension to the EM122 Deep Water Echosounding Profiler the receiver part Specifications Sbp120_product_specification_Ir pdf Location dy _data_disc cruise_reports instrument_data_sheets EA640 Single beam Echosounder The EA640 is a special version of the EA600 commissioned for the RRS Discovery pretty much identical to the EA600 and can operate at either 12kHz or 10kHz as required The performance of each varies with output power e g kW or 2kW and pulse lengths They both have a wide bandwidth that overlaps and can be run at the same time
79. arge are set to NaN The same is done for the unfiltered heading change NOTE for mfilter m and the therein used Matlab function filtfilt m the data needs to have a minimum length of 3 times the filter order This means that files with less than 5 minutes of data will crash Velocities are set to NaN if the change in ship speed exceeds ship velocity change A last control is done on absolute horizontal velocities in a reference layer The eastward and northward velocities in the ninth depth bin are chosen and the ship velocity is added to obtain absolute velocities Then velocities of ping ensembles between which the change of either of these reference velocities is larger than 2m s are set to NaN The structure with the modified velocity array is returned to the main routine Hugh Venables modified the call to the quality control routine such that in the first run a quicker less thorough quality check is done using the routine qual control quick m to allow faster processing for quick data checks During the second run the above quality control is done calib points In this routine calibration points are extracted using 2 minute averages of ADCP data and various criteria these points have to fulfill It is called with the arguments OS75 sgl ping cal file which prdid fix ref uplim and ref lowlim cal file specifies where the data for calibration extracted here will be written to which prdid fix does the same as in ship vel m
80. ary Conductivity Sensor SBE 4C 4C 2231 F1 All stainless casts Digiquartz Pressure sensor Paroscientific 100898 F2 All stainless casts Secondary Temperature Sensor SBE 3P 3P 5495 Ti F3 All stainless casts Secondary Conductivity Sensor SBE 4C 4C 3874 Ti F4 stainless casts Primary Pump SBEST 5T 3085 n a stainless casts Secondary Pump SBE 5T 5T 3086 n a stainless casts 24 way Carousel SBE 32 32 19817 0243 n a stainless casts Dissolved Oxygen Sensor SBE 43 43 1624 VO stainless casts Biospherical QCP stainless casts Irradiance Sensor DWIRR Cosine PAR 70510 V2 Biospherical QCP stainless casts Irradiance Sensor UWIRR Cosine PAR 70520 V3 Altimeter Benthos 916T 59493 V4 stainless casts Light Scattering Sensor WETLabs BBRTD BBRTD 1055 V5 stainless casts CTG Alphatracka stainless casts Transmissometer MKII 161048 V6 CTG Aquatracka stainless casts Fluorometer MKIII 88 2615 124 V7 Stainless casts 001 20L Water Samplers OTE 1 24 n a 036 Stainless casts 037 10L Water Samplers OTE 1D 24D n a 056 34 Titanium Frame Sensor Information Manufacturer Serial Casts Used Number Instrument Sensor Model Channel 11P 34173 Primary CTD deck unit SBE 11plus 0676 n a casts 09P 77801 All titanium casts CTD Underwater Unit SBE 9plus 1182 Ti n a SBE CTD All titanium casts Titanium 24 way frame NOCS TITAI n a Primary Temperature Sensor SBE 3P 3P 5700 1 FO
81. as then connected on each pair in sequence to a CTD test cable to the CTD NB Because of the inherently large internal resistance of this seacable the termination must be completed with only two cores and the remaining two cores must be dead ended The SBE 9 was successfully operated on deck collecting data firing bottles etc for at least 15 minutes on each pair with no modulo or other electronic errors Appendix B Configuration files Titanium CTD frame Date 10 20 2014 Instrument configuration file C Program Files Sea Bird Seasave V7 D YO17 DY017_tita NMEA xmlcon Configuration report for SBE 911plus 917plus CTD Frequency channels suppressed 0 Computer interface RS 232C Voltage words suppressed 0 29 Deck unit SBE1 plus Firmware Version gt 5 0 Scans to average 11 NMEA position data added Yes NMEA depth data added No NMEA time added Yes NMEA device connected to PC Surface PAR voltage added No Scan time added Yes 1 Frequency 0 Temperature Serial number 03P 5700 Calibrated on 11 April 2014 G 4 34159706e 003 H 6 28508868e 004 I 1 87468534e 005 J 1 17132278e 006 FO 1000 000 Slope 1 00000000 Offset 0 0000 2 Frequency 1 Conductivity Serial number 04C 4138 Calibrated on 27 February 2014 G 9 83474601 000 1 45187267 000 1 86002512e 003 J 221735389e 004 CTcor 3 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 3
82. ast side of the Isle of Lewis Conditions were calm and sunny but ultimately misleading because by midday a noticeable increase in wind speed to F7 and above had occurred Conditions continued to deteriorate throughout the afternoon and weather forecasts indicated GF10 winds and a 210 m swell offshore in our work area Sunday Oct 26 Day 299 We awoke to steady Force 7 winds though we were well protected from the worst of the swell by virtue of our sheltering in Broad Bay Winds did not decrease until late in the afternoon preventing our departure We eventually departed Broad Bay at 41940 and cautiously headed north to test the conditions Although a little lumpy the sea conditions were passable and we proceeded back to the survey area As a result of the loss of time the scientific party decided to drop Transect B and instead focus on the more southerly Transects during the remaining time The one exception was to be station Monday Oct 27 Day 300 We arrived at station B1 at 0230 58 26 79N 7 11 620W and proceeded to deploy both the titanium CTD011 and stainless steel CTD s CTD012 followed by the plankton net NET002 All deployments went smoothly helped by light winds and little swell and we left the station at 0430 We arrived at station C1 58 1 36N 7 42 94W at 0855 and proceeded to deploy the titanium CTD CTD013 the stainless steel CTD CTD014 and the plankton net NET003 We departed for station C2 at 1110
83. ation 17 40 02 11 2014 18 47 Stn F1 SS CTD and Plankton Net 18 47 02 11 2014 23 45 Relocate for next station 23 45 03 11 2014 00 22 Stn GI Tit CTD and Plankton Net 03 11 2014 00 22 03 11 2014 02 12 Relocate for next station 02 12 03 11 2014 02 44 Stn G2 SS CTD 02 44 03 11 2014 04 39 Relocate for next station 04 39 03 11 2014 05 44 Stn G3 SS CTD 05 44 03 11 2014 07 24 Relocate for next station 07 24 03 11 2014 07 55 Stn G4 Tit CTD 07 55 03 11 2014 09 35 Relocate for next station 09 35 03 11 2014 13 10 Stn G5 Tit CTD Plankton Net Near surfce sampling 13 10 03 11 2014 14 45 Relocate for next station 14 45 03 11 2014 21 13 Stn G6 SS and Tit CTD Plankton Net Near Surface Sampling 21 13 05 11 2014 16 00 Passage to Falmouth Pilots 05 11 2014 16 00 05 11 2014 17 12 Pilotage to berth County Wharf 3 TECHNICAL SUPPORT CTD Operations Jeff Benson with additional Deep Tow comments from A Davies James Burris and Julie Wood 1 Two CTD systems were prepared The first water sampling arrangement was a 24 way titanium frame system s n SBE CTD TITA1 and the initial sensor configuration was as follows Sea Bird 9plus underwater unit s n 09P 71442 1142 Sea Bird 3P temperature sensor s n 03P 5700 Frequency primary Sea Bird 4C conductivity sensor s n 04C 4138 Frequency 1 primary Digiquartz temperature compensated pressure sensor s n 124216 Frequency 2 Sea Bird 3P temperature sensor s n 03P 5785 Frequency 3 s
84. ble 17 Summary of sampling for particulate trace metal sampling 114 5 DISCUSSION We were able to achieve the majority of the pre cruise scientific objectives sampling both on the shelf and in deeper waters and completed 6 of the planned 7 transects Given the time of year and the exposure of the western shelf to the open North Atlantic Ocean this should be construed as a very successful outcome Nevertheless time constraints and weather forced the difficult decision to drop the most westerly station at the end of each transect and transect B was almost lost in its entirety With good spatial coverage of the region the preliminary results are highly encouraging and have already revealed some surprises In particular the intensity of the slope current which was far stronger than reported by the 2013 FASTNEt cruise Sam Jones pers comm suggests an important seasonal component and work to understand the significance of this for open ocean exchange is at an incipient stage The various research activities conducted on board ship will in time likely prove equally surprising and initial indications are that the distributions of iron trace metals and dissolved inorganic carbon in conjunction with inorganic nutrient fields will be important for understanding the stoichiometry of dissolved nutrients on and off the shelf as well as potentially resolving pathways of exchange with the open ocean 115 References Berger C J M S M Li
85. by adding the ship velocity to the horizontal velocities percent good from the fourth beam a value for bottom range for each ping ensemble with the condition that it is between 50 and 1200 m depth and using the median of the four beams the difference between the headings from the ENX and from the N2R file set to NaN if the ENX heading does not change for two successive ping ensembles pitch and roll set to NaN if data is missing i e gt 998 the PC clock offset the echo intensity as mean over all beams The navigation data is set to NaN for ping ensembles where there is no velocity data in any of the beams and any of the depth bins For the averaging the heading is broken up into components cos and sin and reconverted to angles in degrees afterwards Of the extracted variables the ones included in the averaging are absolute velocity all three directions reference velocity heading difference in ENX and N3R heading PC clock offset echo intensity percent good and bottom range Additionally ship velocity and navigation data time longitude latitude are averaged For pitch and roll the standard deviation is calculated The data from ping ensembles that were remainders after the averaging is written to d missed and returned to the main routine The averaged absolute velocity is converted back to velocity relative to the ship by subtracting the averaged ship velocity The reference layer velocity is then recalculated from
86. by which the ADCP is misaligned in addition to the physical misalignment set in the command files Quick n dirty How to get processed ADCP data data in data processed routines 0575_ICR_D376 functions Create a file structure as shown above The master function OS75_DY017 m lives in matlab_routines all others go in the subfolder functions Depending on your version of Matlab you may need the signal processing and stats toolboxes There are a few things that have to be set for each cruise in file OS75_DY017 m These are 1 Add the correct path to the functions subfolder line 54 2 Point Matlab variable RAWPATH to data in and PATH to data_processed Remember the forward slash character Lines 62 70 3 The expected VMDAS output filename Line 73 Note that both the length and the position of file numbers has to be correct or the program will not get very far If file length numbering is different there s also a bit of tinkering to be done at line 287 hint the program counts backwards from the end of the filename 3 The cruise name variable cruise The name is used when reading in raw data and saving processed data and appears in the plots Line 74 4 The file sequences variable files This determines which of the file sequences are to be processed Files can be a single number or a vecto
87. chard found it to be clogged up and cleaned it out All enquiries about this system should be directed to Dr Vas Kitidis vak 2 pml ac uk 48 4 SCIENTIFIC INVESTIGATIONS Lowered CTD data processing and calibration Stuart Painter A total of 56 CTD casts were completed during DY017 Table 3 These comprised both stainless steel 34 casts and titanium 22 casts CTD rosette frames Both CTD systems worked reliably throughout the cruise with only minimal problems reported Deployment of the stainless steel system was initially conducted with 20 L Niskin bottles up to CTD036 using the Deep Tow winch and cable but following isolation of this winch for safety reasons the remaining casts from CTD037 onwards were conducted with 10 L bottles using the trace metal free winch system Only provisional examination of the data was undertaken at sea The final data processing and calibration was undertaken immediately after the cruise and details are included here for the formal record CTD Survey Date DOY Time Lat N Lon W Cast types No Line TiT titanium Station No StS steel CTD001 Test 22 10 2014 295 19 15 56 5758 6 4813 TiT CTD002 AI 23 10 2014 296 10 25 58 6021 5 8023 TiT CTD003 Al 23 10 2014 296 11 04 58 6022 5 8023 StS CTD004 A2 23 10 2014 296 17 20 58 8004 6 1936 TiT CTD005 A2 23 10 2014 296 18 12 58 8004 6 1936 StS CTD006 A3 24 10 20
88. consistently at 953 955 m it became apparent that the release was entangled Although not clear precisely what went wrong in all likelihood one of the ropes attaching the release to the lander base failed to disengage cleanly from the acoustic release A diagnostic test at 1608 indicated that 19 the release was in a vertical position indicative of it being above the ADCP instrument Sadly there was nothing more we could do A short 3 point survey was undertaken to correctly position the mooring on the seabed after which the trace metal tow fish FISH002 was redeployed at 57 06 6N 9 20 4W We transited back to station D3 57 37 287N 8 54 044W to complete the inner half of Transect D and arrived on station at 2115 where we deployed the stainless steel CTD CTD027 Upon successful recovery of the CTD package we steamed on to station D2 57 37 295n 8 29 992w deploying the steel CTD CTD028 at 2345 Thursday Oct 30 Day 303 Conditions today were grey overcast and frequently wet but sufficiently calm to allow us to work We reached station D1 57 36 958N 8 11 140W at 0140 and deployed the steel CTD CTD029 which was safely inboard by 0218 The plankton net NET008 was then deployed before we moved on to Transect E We arrived at station E1 at 0800 56 52 526N 8 10 984W and deployed the titanium CTD CTD030 the steel CTD CTD031 and the plankton net NET009 As it was a little early to deploy the air sea buoy we cancelled
89. continue the science using the metal free winch system Following this unwelcome turn of events we proceeded north to the position of the ADCP lander to undertake a secondary check on the acoustic releases Friday Oct 31 Day 304 On arrival at 0109 the acoustic releases were reranged This secondary check was to confirm whether the entangled release had broken free over night and whether there had been any 20 change to the orientation of the horizontal releases to be used for recovery Early on Thursday evening at 1710 a fishing trawler Jean Claude Coulon 2 had been spotted fishing extremely close to the lander position and was obviously following a bathymetric contour so this opportunity to recheck that the lander was still in place allayed fears that the entangled buoyancy had made this deployment short lived As evidenced by the choice of lander design an anti trawl design it is likely however that fishing in this region may well encounter the buoyancy at some stage in future We arrived at station E5 at 0400 but the wind had increased to F7 and all work was suspended In the end we chose to move on to station E6 arriving at 0700 56 52 210N 10 5 613W where we deployed the steel CTD CTD037 At this station a winch test of the deep tow system was also undertaken in an effort to replicate the problems seen last night Winch test complete we then proceeded back to station E5 arriving at 1330 where we deployed the steel CTD CTD038
90. corder Files to Host gt TS TS 14 10 20 17 46 32 Time Set yr mon day hour min sec gt PSO Instrument S N 20467 Frequency 76800 HZ Configuration 4 BEAM JANUS Match Layer 10 Beam Angle 20 DEGREES Beam Pattern CONVEX Orientation DOWN Sensor s HEADING TILT 1 TILT 2 DEPTH TEMPERATURE PRESSURE Pressure Sens Coefficients c3 1 773849E 10 c2 1 369659E 06 cl 1 395053E 00 Offset 1 095539E 02 Temp Sens Offset 0 03 degrees C CPU Firmware 50 40 0 Boot Code Ver Required 1 16 Actual 1 16 DEMOD 1 Ver ad48 Type 1f DEMOD 2 Ver ad48 Type 1f PWRTIMG Ver 8543 Type 6 Board Serial Number Data 48 00 00 07 68 CA 30 09 REC727 1004 06A 25 00 00 07 28 4B 4E 09 HPA727 3009 00B 3C 00 00 07 68 C9 DE 09 CPU727 2011 00E AB 00 00 07 68 41 09 DSP727 2001 06H 8B 00 00 07 68 DC 8F 09 TUN727 1005 06A 5D 00 00 07 68 DF FF 09 HPI727 3007 00A gt PRE DEPLOYMENT TESTS CPU TESTS RS PASS RAM ide PASS 101 RECORDER TESTS PC Card 0 DETECTED Card PASS PASS DOS PASS Sector Test short PASS PC Card 1 NOT DETECTED DSP TESTS Timing PASS Demod PASS Demod PASS FIFOS 5 Ie PASS SYSTEM
91. d on each station No depths sampled Transect A 56 Transect B 6 Transect C 99 Transect D 65 Transect E 93 Transect F 83 Transect G 74 Total 476 Sample analysis commenced immediately after collection and analysis of profiles was in all cases completed within 24 hours after sampling most often within 12 hours analyses were performed on two VINDTA 3C Versatile INstrument for the Determination of Total Alkalinity designed and built by Dr L Mintrop Marine Analytics and Data Kiel Germany These instruments were slightly modified the peristaltic sample pump was replaced with an overpressure system 0 5 bar overpressure and a 1 m long though coiled 1 8 stainless steel counter flow heat exchanger that was placed between the sampling line and the water bath circulation circuit This setup allows for the rapid convenient and bubble free loading of the pipettes with sample of 25 x 0 1 irrespective of the samples initial temperature There were also underway samples collected from the ship s seawater system often once a day but more often during transit to and from the study region These samples were poisoned with 50 ul 50 mercuric chloride solution About half of these samples were analyzed onboard while the rest will be analyzed back at NOC Salinity samples were collected together with the DIC TA samples until the 4 of Nov to calibrate the thermosalinograph The analysis and correction of the raw data is in progr
92. depths were not sampled Deployment and use of the clean tow fish went well however its positioning on the starboard side of the ship needs to be re assessed for future cruises During this cruise the fish rode very 108 close to the ship and during the bad weather was observed to knock the side of the ship I think this is in part due to the ships wake pulling the fish in towards the ship With regards to the new clean sampling laboratory overall the new facility has worked well and the close vicinity of the laboratory to the rosette system has aided efficient deployment and recovery of the clean OTE bottles The general set up in the laboratory is very good and being positioned within the ship as opposed to a container on the aft deck has allowed work to continue even in bad weather However there have been some noticeable issues that have been raised during the course of the cruise One problem relates to a lack windows in either of the two outside doors that are used to enter the outer changing area of the clean sampling laboratory To maintain a clean environment in the inner laboratory these outer doors should not be opened at the same time as the inner door This has resulted in shouting between the inner and outer doors to ensure that one is closed before the other is opened With regards to actual sampling the clamps that are needed to keep the bottles closed while under pressure for sampling are difficult to attach This is due to t
93. e id with the positions identifiers of the data fields in the binary data files The next step is the first call to the subroutine read buf also within read_os m read_buf This is the part where the binary data is read During the first call with only one argument the configuration of the OS75 ADCP is extracted from the fixed leader data and stored in the structure config If one of the checks on number of bytes header or data source ID or checksum fails an error message will be returned to read_os m Otherwise information about ADCP hardware and setup that remains the same for all pings is read After that and during the second call with two arguments the variable bottom track attitude and navigation data is extracted After the first call to read_buf the configuration data is used to set up the variables and the reading loop During the second call the data requested by using the various switches is stored Before returning to the main routine variables are adjusted for negative numbers or NaNs All raw data read in is stored in the structure OS75_raw and returned to the main function and written to the file CRUISE_xxx_yyyyyy_raw mat remove zero ensembles m The structure OS75 raw is handed over to remove zero ensembles m A search for all ensembles whose ensemble number 12 OS75 raw ens num is not zero is done and only those are kept and handed back to the main routine as OS75 sgl ping remove bad navigation Depending on which
94. e averaged is given by superaverage As the ping ensembles in a file of a file sequence are not necessarily divisible into the specified time intervals without remainder the structure d missed is used to carry on the surplus ensembles and add them to the ping ensembles of the next file in the same file sequence If there are ping ensembles left at the end of a file sequence they will not be included in the averaging First a check is done whether any ping ensembles from the previous file were carried forward If that is the case and the bin depth is the same in both files they are added to the current file in the loop A depth range for the reference layer velocity is set as is the maximum number of depth bins Pings are averaged in intervals determined by superaverage and using the time stamps in OS75 sgl ping nav txyX where X is either 1 or 2 depending on which prdid fix 76 Throughout the routine there are various occasions where usually three dimensional arrays are split up into several 2d arrays This is done using the reshape command and the size of the velocity fields To avoid problems when the original velocity field is 2d instead of 3d a check is introduced and the variable containing the size of the field is adjusted Several variables are extracted and derived the reference layer velocity zonal and meridional as mean of the horizontal velocities in the depth range specified by ref uplim and ref lowlim absolute velocities
95. e remaining PRDID lines and stored If heading is missing 999 pitch and roll are set to 999 as well From PADCP lines the ping ensemble number and the PC time of the ping ensembles converted to decimal Julian days are extracted After all files are read the ping ensemble number is checked and corrected for duplicates which can appear due to the splitting of the files after the maximum number of lines is read The data is stored in the structure att which is written to CRUISE xxx 000000 att mat Pitch roll and heading are plotted and the figures saved to adcp_prh eps Figures need to be improved After that return to include att disc2 m The file CRUISE xxx 000000 att mat with the att structure is loaded in If the structure contains data the following is done For further processing the ping ensemble number has to be increasing When the ADCP times out while waiting for a response and resets the ensemble number goes back to 1 Here the ensemble numbers are modified so that they increase throughout the file for and throughout the files of a file ensemble in OS75 sgl ping ens num There is already attitude data in the structure 0575 sgl ping which comes from the ENX file To extract pitch roll heading and PC clock offset which are relevant for the current ENX file a vector is created for each variable of the length max highest ensemble number in att highest ensemble number from the ENX attitude data and filled with NaNs Th
96. e samples see section on Particulate Trace Metals a Sartobran 300 Sartorius filter capsule 0 2 was used to collect filtered seawater samples into clean LDPE sample bottles Bottles and caps were rinsed 3 times with the filtered sample before being filled All samples including underway samples were acidified to 0 024 M UpA HCI Romil and stored double bagged for shore based analysis Samples collected Samples for total dissolvable and dissolved iron were collected at 21 stations as detailed in Table 14 a total of 530 samples were collected for analysis Station Samples collected from Station Samples collected from separate depths separate depths Dissolvable 4 Dissolved Dissolvable 4 Dissolved Al 6 6 El 949 A2 6 6 11 11 4 12 12 4 17 17 5 19 19 5 22 22 545 F3 6 6 6 6 4 11 11 C3 949 F5 23 23 C4 12 12 G4 6 6 C5 15 15 G5 13 13 C7 24 24 G6 23 23 D4 10 10 Table 14 Summary of sampling for total dissolvable and dissolved iron measurements Sample analysis Samples for dissolved iron will be analysed at the University of Plymouth after 2 months acidification whereas samples for total dissolvable iron will be left for at least 6 months prior to analyses Flow Injection with chemiluminescence detection FI CL Obata et al 1993 de Jong 1998 Klunder et al 2011 will be used for all sample analyses using Toyopearl AF 650 M resi
97. e was raised and lowered through the top 10 m of the ocean by winch attached to a floating buoy that was loosely tethered to the ship Tubing is also connected to this cage through which water is pumped back to the ship at 4 L min for analysis for the partial pressure of CO Figure 12 The Near Surface Ocean Profiler On board ship the water is passed through a membrane equilibrator where it was rapidly equilibrated with a counter air flow at 100 ml min The air flow was then dried using a nafion dryer and passed into a Licor 7000 for analysis for CO content The Licor measured a number of variables including the CO partial pressure and CO concentration pressure temperature and water vapour content A number of sensors were also connected including a flow meter and separate pressure and temperature sensors 3 Standards were also run just after the morning calibration and after the deployment was complete the times that these standards were run was noted in the lab book A temperature calibration was run near the end of the cruise at 3 different temperatures to determine temperature variation between the PT1000 sensors and the two CTD s Issues 104 There were a number of technical issues relating to the NSOP deployments These were mainly electrical and saw the winch stop working halfway through the first deployment and operate without user input midway through the cruise It is suspected this is due to damage to the antenna of
98. econdary Sea Bird 4C conductivity sensor s n 04C 4143 Frequency 4 secondary Sea Bird 5T submersible pump s n 05T 3088 primary Sea Bird 5T submersible pump s n 05T 3090 secondary Sea Bird 32 Carousel 24 position pylon s n 32 60380 0805 Sea Bird 11plus deck unit s n 11P 34173 0676 main Sea Bird 11plus deck unit s n 11P 24680 0589 back up logging 2 The auxiliary input initial sensor configuration was as follows Sea Bird 43 dissolved oxygen sensor s n 43 2055 VO WETLabs light scattering sensor s n BBRTD 758R V4 Benthos PSA 916T altimeter s n 62679 V5 Chelsea Aquatracka MKIII fluorometer s n 088244 V6 Chelsea Alphatracka MKII transmissometer s n 161049 V7 26 3 Sea Bird 9plus configuration file DYO17 NMEA xmlcon was used for the initial titanium frame CTD casts 4 The second water sampling arrangement was the Zubkov 24 way stainless steel frame system s n 75313 and the initial sensor configuration was as follows Sea Bird 9plus underwater unit s n 09P 46253 0869 Sea Bird 3P temperature sensor s n 03P 4782 Frequency primary Sea Bird 4C conductivity sensor s n 04C 2231 Frequency 1 primary Digiquartz temperature compensated pressure sensor s n 100898 Frequency 2 Sea Bird 3P temperature sensor s n 03P 5495 Frequency 3 secondary Sea Bird 4C conductivity sensor s n 04C 3874 Frequency 4 secondary Sea Bird 5T submersible pump s n 05T 3085 primary Sea Bird 5T submersible pum
99. ed all science and whilst most people on board were able to get some water from the titanium cast nothing more could be done at this station and we reluctantly steamed on to station C6 arriving at 0430 where we waited whilst a retermination and load test was undertaken Tuesday Oct 28 Day 301 A sunny morning punctuated with cloud greeted us which was a nice opener for the day ahead Conditions were calm and were predicted to remain so for the next few days at least By 0900 the retermination of the deep tow cable was complete but during the load test of the cable further problems were encountered with the winch which included slippage of the cable under tension This necessitated further downtime to investigate and resolve Fortunately by 1400 a deployment was deemed possible and we cautiously deployed the steel CTD CTD021 at station C6 The deployment was without issue and we departed for station C7 at 1600 We reached station C7 58 26 01NM 10 4 6W at 1810 and had the titantum CTD in the water at 1847 for cast CTD022 This was followed by a steel cast CTD023 at 2121 and NETO0S Due to the loss of time caused by the retermination of the deep tow cable and the need to reach the ADCP mooring location during a period of good weather we broke the survey at this point and headed to station D5 Wednesday Oct 29 Day 302 We arrived at station D5 57 37 56N 9 42 44W at 0500 and deployed the steel CTD CTD024 and the plankton net
100. elf Edge Study blue hexagon FastNet green circle and the approximate working area of the Outer Hebrides process cruise The green line represents the 200 m bathymetric contour Chart showing Outer Hebrides work area with DYO17 cruise track red line position of completed CTD stations green dots benthic ADCP lander location blue dot and the UK Irish maritime limits blue line The thick black line represents the 200 m bathymetric contour RRS Discovery instrumentation suite Summary of CTD salinity calibrations Panels a and c show temporal salinity residuals for the stainless and titanium CTD systems respectively whilst panels b and d show the vertical pressure residuals Panels E and F show final residuals after calibration Vertical blue lines in panel f indicate 0 002 offset range Summary of CTD oxygen calibrations Panels a and c show temporal oxygen residuals for the stainless and titanium CTD systems respectively whilst panels b and d show the vertical pressure residuals Panels E and F show final residuals after calibration Vertical blue lines in panel f indicate 2 umol L offset range Schematic of the master processing script for DYO17 OS75_DY017 m Sodium thiosulphate standardization results Depth distributions of TON phosphate and silicate umol L for Transect E AL 500 with concrete base ready for deployment ADCP heads protected by white dome Internal view of Trawl Resistant Bottom
101. en the attitude information from att is written into the vector and on the data points corresponding to the ensemble numbers from the ENX file are stored If att is empty heading pitch roll and PC clock offset are set to NaN The extracted attitude data is written to OS75 sgl ping att The attitude data relevant to the current ENX file is also saved in the new structure att in CRUISE xxx yyyyyyd att mat The modified OS75 sgl ping is returned to the main routine 73 subst bad The arguments OS75 sgl ping att and sea file are handed over In sea file the number of accepted and rejected due to bad Seatex data data points will be stored A search on OS75 sgl ping att data is done for ensembles where heading 0 heading 999 pitch and roll 0 the second differential of heading 0 The total number of those ensembles is printed on screen and saved as bad in CRUISE bad heading mat OS75 sgl ping contains two headings 0575 sgl ping heading which comes from the ENX file and 0575 sgl ping att heading from the N2R file Both are from the same instrument Seapath Seatex but maybe slightly different due to a very small time difference in when they are recorded Therefore the velocities in OS75 sgl ping rotated by the difference To get bottom track velocities in the correct orientation OS75 sgl ping bt vel is multiplied by 1 OS75 sgl ping with the modified values is returned to the main routine
102. en as a persistent absence of velocity returns occasional gaps are normal and are averaged out The software can perform 3 beam solutions but parts of the QC in the Matlab routines had to be suppressed as they check for a threshold percentage good in all beams After email discussion with NOC the deck unit handling the OS75 feed was swapped with a spare which rectified the problem Detailed description in the Ship Technician s report Range and noise issues 63 Throughout the cruise the range of both instruments fluctuated and was generally poorer than expected as was the amount of noise in the return signal This seemed to be unrelated to the weather or movement of the vessel and should investigated by a skilled operator Presumably the cause could be one of the following poor choice of setting in some obscure part of the ADCP setup instrument problems or acoustic features inherent to the new Discovery Though it pains me to write this when the return signal became particularly poor sometimes closing and re opening the VMDAS software solved the problem Bottom tracking Bottom tracking is an option which can be enabled on the VMDAS setup and provides data on the ship s heading in shallow waters from the ADCP pings reaching the sea floor Water tracking is performed in the Matlab post processing steps and uses relatively stable water from a specified depth as a velocity reference frame The original intention was to switch bottom
103. er of ensembles arrays first row time in decimal Julian days second row longitude third row latitude txy1 is data from the first PRDID fix after the previous ADCP ping txy2 is from the last PRDID fix before the actual ADCP ping config structure containing the setup information about the OS75 and VmDas depth 1 x number of bins array The array contains the depth of the bins in the configuration used for the actual file sequence error if reading of data fails an error message will be stored here otherwise it should be empty There is one such file for each ENX file in a file sequence CRUISE xxx 000000 att mat In this file the structure att contains the attitude information from all N2R files of a file sequence read during read nmea att disc2 m This includes the following 1 x number of ensembles arrays heading pitch roll 79 pc time time from the ADCP PC clock e pc time offset offset of the ADCP PC clock from UTC in seconds ens num the ping ensemble number Per file sequence one file CRUISE xxx 000000 att mat is produced CRUISE xxx yyyyyyd att mat For each file in a file sequence attitude data is extracted and saved in CRUISE xxx yyyyyyd att mat It contains a structure att which consists of the following arrays of size 1 x number of ensembles per ENX file att heading att pitch att roll heading pitch and roll from the N2R files for the ping ensembles in the corresp
104. erated by running the script msam 02 m This script calculates a series of residual values between bottle samples and CTD sensor measurements to aid the calibration process The standard version of this script generates 1 bottle salinity CTD salinity Channel 1 2 bottle salinity CTD salinity Channel 2 3 bottle oxygen CTD oxygen in addition following the derivation of bottle conductivity were calculated 4 bottle conductivity CTD conductivity Channel 1 5 bottle conductivity CTD conductivity Channel 2 55 6 bottle conductivity CTD conductivity Channel 1 7 bottle conductivity CTD conductivity Channel 2 8 bottle salinity CTD salinity Channel 1 9 bottle salinity CTD salinity Channel 2 10 CTD temp channel 1 CTD temp Channel 2 input sam DYO17 Output sam DYO017 NNN resid nc Residual files were then grouped by CTD type stainless steel or titanium frame and appended together using mapend m to create two master files The master files were examined in a series of plots mplotxy to identify outlier values in the residual variables particularly No 6 and 7 above which were removed from sequential versions of the master files using either mdatpik or mplxyed Stainless steel CTD calibration The calibration of the two Seabird conductivity channels to the salinometry results revealed a good agreement in both cases Plots of conductivity difference against sta
105. eries number is incremented each time VMDAS is stopped and restarted the number of sub files per series is therefore variable DYO017 operated both on and off the shelf but bottom tracking was switched on for the majority of the cruise Alignment and amplitude corrections were calculated for the whole cruise period and were as follows OS150 files 3 11 misalignment xb 45 3847 amplitude xb 1 0020 OS150 files 12 23 misalignment xb 0 3847 amplitude xb 1 0020 OS75 files 5 24 misalignment_xb 20 8262 amplitude_xb 1 007092 File sequences during DYOI7 OS75 Raw Data Files 83 Date c cc R2 R2 R2 YY DW 2 21 2 2 81 ka ky ku ky SSI 5 9 e e e Table 4 Time Filename 2014 18 57 05075 DYO 2014 19 52 05075 DYO 2014 19 55 05075 DYO 2014 1542 05075 DYO 2014 1542 05075 DYO 2014 11 02 05075 DYO 2014 11 02 05075 DYO 2014 20 25 08075 DYO 2014 20 28 09075 DYO 2014 08 39 09075 DYO 2014 08 39 09075 DYO 2014 1 18 05075 DYO 2014 1 18 05075 DYO 2014 3 04 05075 DYO 2014 3 04 08075 DYO 2014 4 43 08075 DYO 2014 4 43 08075 2014 8 43 05075 DYO 2014 8 44 05075 DYO 2014 08 54 08075 DYO 2014 08 54 08075 DYO 2014 0 12 05075 DYO
106. ess Final results will be available within one month Dissolved inorganic carbon DIC Dissolved inorganic carbon DIC was determined by coulometric titration An automated extraction line takes a 20 mL subsample which is subsequently purged of CO in a stripping chamber containing 1 mL of 8 5 phosphoric acid H3PO A stream of nitrogen carries the CO gas into a coulometric titration cell via a condenser to strip the gas flow of any water 89 The CO reacts with the cathode solution in the cell to form hydroxyethylcarbamic acid which is then titrated with hydroxide ions OH generated by the coulometer The current of the coulometer is then integrated over the duration of the titration to obtain the total amount of carbon titrated The power to the two coulometers were stabilized with a UPS Total Alkalinity TA Determinations of total alkalinity TA were performed by acid titration that combines aspects from both the commonly used closed cell method and the open cell method following the VINDTAs standard settings A single 20 L batch of acid of 0 1M and salinity 35 was prepared to be used by both VINDTAs Potential drift in acid strength due to HCl gas loss to acid vessel headspace is not accounted for Certified reference material CRM Batch 140 obtained from Dr Andrew Dickson at Scripps Institute of Oceanography San Diego California was used for calibration purposes and quality control for both DIC and TA
107. for next station Stn D3 SS CTD Relocate for next station Stn D2 SS CTD Relocate for next station Stn D1 SS CTD and Plankton Net Relocate for next station Stn E1 SS and MF CTD Plankton Net Relocate for next station Stn E2 SS CTD and near surface sampling buoy Relocate for next station Stn E3 SS and MF CTD Plankton Net Relocate for next station Stn E4 MF and SS CTD During operation of deep tow unexplained change over to core winch Deep Tow wire use suspended Reposition to check lander position and status of flotation package Checking position of lander Relocate for next station At Stn E5 Swell conditions prevent deployments Relocate for next station Stn E6 Waiting on reduction in swell heave Stn E6 SS CTD on MFCTD wire Tests of deep tow wire using dummy weights Unable to replicate fault all further CTD deployments on MFCTD wire Relocate for next station Stn E5 SS and MFCTD both on MFCTD wire Near surface sampling using crane and deck winch Plankton net Relocate for next station Stn F7 SS CTD Relocate for next station Stn F6 Waiting on weather and reduction in swell heave Stn F6 SS CTD and Plankton Net Relocate for next station Stn F5 SS and MF CTD Relocate for next station Stn F4 SS and MF CTD Plankton Net Relocate for next station Stn F3 SS and Tit CTD Relocate for next station Stn F2 Near Surface sampling using crane and deck winch SS CTD Relocate for next st
108. he Propellers The software used is Ranger 2 Inputs Vertical Reference Units VRUs Gyro Compass DGPS Surface Positioning GPS Time Synchronisation Transponders 1km depth Wide band Sub Mini WSM and 3km depth DP Transponder Outputs it logs data itself into a file that can be taken away can also output a data string to TechSAS in this case you only get the position of one beacon at a time in the water you can put this info into the Level C system and plot some data from it it outputs to the OLEX 3D seafloor mapping software that provides a visual display It can also output DP telegram format data Specification Operator Manual pdf Location dyf data disc cruise reports instrument data sheets USBL Pole Teledyne RDI Ocean Surveyor Acoustic Doppler Current Profilers The ADCP transducers are located in the hull in blisters in a forward aft configuration approximately 6m below the water line There are two systems that operate at two frequencies 75 kHz and 150kHz Both the heads have a rotation relative to the ship s centre line of 45 The software used for configuring and datalogging with the ADCP is called VmDAS Vessel Mounted Data AcquisitionSystem VmDAS gets data from the ship s attitude sensor and uses that to convert ship velocities into earth co ordinates VmDAS can be configured either by loading or editing a command file or by changing settings on the interface Users should be aware that it s possib
109. he positioning of the gas lines the wall brackets that the drainage trays are attached to and the closeness of the bottles This results in clamping and therefore sampling taking longer While this did not prevent any stations from being sampled it did increase the amount of time taken to have the OTE bottles sampled and ready for the next station this became very challenging when the station spacing was very close 1 5 h apart Sampling for suspended particulate material SPM has been a particular challenge this is in part due to the drainage trays not being low enough and also the bottles clamps being too close together Though alterations can and will be made to the filtration apparatus for future cruises it would still not be possible to collect SPM from all the OTE bottles as has been done on past UK GEOTRACES cruises The positioning of the drainage trays also hinders the collection of filtered samples using the cartridge filter Finally it is not possible to empty the OTE bottles into the drainage trays without seawater ending up on the floor as the bottles are not centred over the trays The poor drainage in the laboratory floor there is only one drain hole along the middle of the side wall means that salt water often ends up behind the fridge and freezer until the ships role allows for cleaning this up Total dissolvable and dissolved iron Antony Birchill Objectives Iron Fe is an essential nutrient for primary productivity
110. his file CRUISE 000 000000 zz ave ping mat zz highest file ensemble number included in the processing The structure OS75 ave ping contains data after averaging over a chosen time interval xyz number of velocity profiles after averaging vel number of bins x x xyz array of average velocity zonal meridional and vertical amp pg number of bins x xyz arrays echo intensity and percent good 81 ship velocity 2 x xyz array of zonal and meridional ship velocity if bottom track velocity is available then the ship velocity equals the bottom track velocity heading 1 x xyz array nav structure containing txy1 3 x xyz array of time decimal Julian days longitude and latitude att structure containing heading difference 1 x xyz array of the difference between heading from ENX and N2R hopefully equal to zero pitch roll pc time 1 x xyz arrays ref structure with velocity 2 x xyz array average over the reference layer and bins vector containing the depth bins that lie within the reference layer bt structure containing range 1 x xyz array of bottom track range depth 1 x number of bins array bin depths of the setting of the last file sequence processed CRUISE 000 000000 zz abs mat zz highest file ensemble number included in the processing In this file both OS75 abs and OS75 ave ping are saved The latter contains the same fields as in CRUIS
111. ial organic carbon gains and losses in two filtration based techniques Marine Chemistry 105 208 228 Wakelin S L J T Holt J C Blackford J I Allen M Butenschon and Y Artioli 2012 Modeling the carbon fluxes of the northwest European continental shelf Validation and budgets Journal of Geophysical Research 117 C05020 doi 05010 01029 02011JC007402 118
112. ial calibration points have to fulfill are the change in ship heading is small the change in ship speed is small the ship speed is within the interval average ship speed standard deviation the ship heading is within the interval average ship heading standard deviation the bottom speed is larger than a specified minimum speed there are a minimum number of possible calibration points in a row that fulfill the criteria Relevant data at the calibration points are extracted and saved in the structure cal This includes bottom velocity speed heading and range ADCP velocities and heading ship speed and heading and the navigation data The scaling factor at the calibration points is calculated as is the misalignment angle To enable quality control of the intervals of calibration points interval row of successive calibration points and possible filtering by hand after the processing some statistics are done and included in the structure average and standard deviations of ship velocity and heading bottom velocity and heading scaling factor and misalignment angle and the number of 2 minute averages in the interval If the file does not exist yet it is created otherwise the data is added to the existing file average pings m The routine is called with the arguments OS75 sgl ping d missed OS75 ave ping superaverage ref uplim ref lowlim and which prdid fix The time in seconds over which the ping ensembles ar
113. ic sound waves via Air Wind speed and direction ultrasound transceivers Vaisala BaroCap PTBI00A Change in electrical resistance via Air Air pressure Barometric Pressure sensor a deflectable diaphragm strain gauge within a pressure transducer Kipp amp Zonen CM6B Electromagnetic radiation flux Sunlight Total Irradiance Pyranometer density by converting solar Solar energy radiation into heat and thence into a voltage Skye Instruments SKE510 Electromagnetic radiation flux Sunlight Total Irradiance Solar PAR Photosynthetic Active density by converting solar energy within a fixed range Radiation Pyranometer radiation into heat and thence of wavelengths for into a voltage passed through a photosynthesis bandpass filter Table 1 Meteorological instrument suite on RRS Discovery Surface Water Sampling Instruments SWS The Surface Water part of the SurfMet system collects seawater known as non toxic or underway water from the upper 5 3 metres of the ocean and passes it through a suite of instruments Table 2 42 The instrument called the Measures In to calculate SeaBird 45 Temperature and conductivity Seawater Salinity Thermosalinograph SeaBird 38 Change in resistance via a thermistor Seawater Temperature Digital Oceanographic Thermometer WetLabs WetStar WS3S Reflected light frequency difference Seawater Marine floral density Fluorometer between beams of light passed through water WetLabs Wet
114. irst depth bin length of transmit pulse distance between pulse repetitions Variable leader data variable leader ID ping ensemble number date and time speed of sound transducer depth heading pitch and roll salinity and temperature Variable data velocity correlation magnitude echo intensity and status data Bottom track BT BT ID BT number of pings correlation magnitude evaluation amplitude BT mode error velocity maximum BT range BT velocity BT correlation magnitude BT evaluation amplitude BT maximum depth receiver signal strength indicator gain level for shallow water most significant byte of the vertical range from the ADCP to the sea bottom Attitude fixed and variable attitude data Fixed attitude data includes the command settings and is the same for all pings Variable attitude data changes with every ping and consists of heading pitch and roll Navigation ENS ENX STA and LTA files only navigation ID UTC date and time PC clock offset latitude and longitude received after the previous ADCP ping UTC time of last fix last latitude and longitude received prior to the current ADCP ping average navigation speed true navigational ship track direction and magnetic navigation ship track direction speed made good direction made good flags ADCP ensemble number date and time pitch roll and heading number of samples average since the previous ADCP ping for speed true track magnetic track heading
115. isation software that has a shared seafloor data files and installed on a dedicated PC OLEX receives data from navigation depth multibeam and ship 43 positioning systems it can also position data from USBL Olex provides rapid visualisation of multibeam data as well as showing where in the world the ship is Specifications Olex engelsk pdf Location dyf data disc cruise reports instrument data sheets olex Manufacturer http www olex no index e html Computing and Instrumentation Jack McNeill Overview This is the first full science cruise for RRS Discovery The main activities are ADCP work including the first full configuration of the ADCPs deployment of CTDs and the deployment of a towfish and a lander Deployed Equipment This is the first full science cruise The equipment deployed was as follows e Networking Servers Computers Displays Printers Network Infrastructure A public network drive for scientists updated via Syncback e Datasystems IFREMer TechSAS logged data and converted it to NetCDF format NetCDF Format given in DY017_netcdf_description docx Logged Instruments given in DY017_ship_fitted_information_sheet_dy doc Data was also logged to NERC RVS Level C format also described in netcdf description docx NERC software Level C SurfMet Express CLAM 2014 SSDS3 Olex e Hydroacoustics Kongsberg echosounders EM122 EM710 EA640 Teledyne RDI ADCPs e Telecommunications GPS amp DGPS POS
116. ise files are overwritten Max Size 10 Mb rolls over to new sub file automatically Setting the file size to very large can cause it to crash NAV NMEA ship position sources NMEA1 Transform Heading tilt source PRDID NMEA2 Custom NMEA from CNRDINV mDas ADCP alignment correction Heading 45 Averaging First time interval 120 seconds Second time interval 600 seconds Data screening All unchecked Discussion of data acquisition during DY017 and more generally on board Discovery During the cruise the ADCP VMDAS system presented numerous challenges due variously to relatively untested systems equipment failure and incorrect setup Below is a brief discussion of the problems we encountered and mostly overcame in the hope that some might be avoided on future cruises Using and misusing VMDAS The RDI VMDAS software looks intimidating but is in fact quite easy to use It is recommended that future users download and at least skim read the user manual prior to embarkation A key feature of VMDAS is the ability to import command files for the ADCP and processing setup or to manually dictate settings using the configuration panels and tick boxes A potential stumbling block is that you can simultaneously have a command file loaded and alter the settings via tick boxes leading to a conflict The manual states that in this situation the command file is loaded first so is effectively overridden by the tick boxes The p
117. ise we also deployed the plankton net NET017 and air sea buoy BUOY007 for good measure All activities were completed and inboard by 2100 and this marked the end of science for this cruise We departed the survey area at 2110 and begun our steam back to Falmouth Tuesday Nov 4 Day 308 Fine weather conditions greeted us today ideal for a smooth transit back to land and for lab break down Good views of Ireland were encountered as we entered the North Channel Wednesday Nov 5 Day 309 Transit and lab break down We docked in Falmouth at 1900 22 Thursday Nov 6 Day 310 We demobilised the RRS Discovery throughout the morning packing equipment onto lorries for return to NOC and other home institutions The scientific party disembarked from late morning onwards Identified problems Given well publicised problems with and anguish over the operation of winches on RRS Discovery there is no point reiterating those issues here as remedial work is already planned for after DYO17 The use of the deep tow winch put in place to allow DYO17 to get to sea generally worked for the majority of the cruise allowing much of the planned science to be undertaken However following an incident on Oct 30 this winch was quarantined reducing scientific activities to use of a single winch system the metal free winch and also requiring a reduction in bottle volume from 20L to 10L bottles on the steel frame This did impact the science
118. its planned deployment at this station and moved it to the next We arrived at station E2 56 56 22N 8 30 012W at 1055 and deployed the steel CTD CTD032 which was back on deck by 1132 We then deployed the air sea buoy BUOY003 the deployment of which took longer than planned due to technical problems By 1330 work was completed and the buoy brought back inboard Station E3 was moved prior to our arrival to a position closer to the shelf break 56 52 19N 9 03 516W On arrival at 1600 we deployed the titanium CTD CTD033 steel CTD CTD034 and plankton net NET010 With all work completed by 1800 we proceeded to station E4 On arrival at station E4 56 52 186N 9 17 917W we deployed the titanium CTD CTD035 and steel CTD CTD036 systems During deployment of the steel CTD on the deep tow winch however numerous errors were encountered and a major problem emerged in the winch room The nature of the problem operation of multiple winch drums simultaneously was entirely new to the ships company and halted the deployment A temporary resolution was found which allowed continuation of the deployment but after recovery of the package at 2330 all further use of the deep tow cable was suspended Further guidance from Rolls Royce Norway was immediately sought and until such guidance is received the deep two cable will remain non operational In response to this we have downsized from 20L Niskin bottles to 10L bottles on the steel frame and will
119. l moved off the drop zone by several hundred meters Parachute failure At 1602 the parachute was released and release confirmations received but it failed to surface maintaining a steady slant range of 935m Multiple release attempts were made returning slight variations in range but due to the swell and position keeping it was not possible to say whether the height the parachute had changed At 1608 a diagnostic test was made that confirmed the release was vertical and the battery voltage was 8 9V 98 Figure 11 AL 500 showing three legged bridle and part of buoyancy parachute top It was thought the most likely reason the parachute did not detach successfully was one or more of the eyes of the three legged bridle suspending the TRBM becoming trapped after the acoustic release was activated Figure 11 Trilateration Confirmation of the TRBM s location was carried out by trilateration Position 1 57 09818 N 9 32464 W slant range 1227m Position 2 57 09843 N 9 35067 W slant range 1184m Position 3 57 11046 N 9 34013 W slant range 1110m The position of RTADCPI was fixed at 57 10302 N 9 33799 W which is 147m NNW of the drop position Two days later at 0125 on 31 10 2014 communication was again made with the parachute acoustic release s n 1916 from position 57 10239 N 9 32892 W and slant range 938m The release was confirmed as still in place and in the vertical orientation Range and diagnostic commands were made to the
120. le to simultaneously load and use a command file and adjust settings using the interface which can lead to command conflicts in which case the interface overrides the command file Data is logged to local hard disc and then create a back up on the server Set up file is editable when starting the VmDAS software 40 Specification OS TM Aprl14 pdf Location please ask the SST for assistance 75KHz Vessel Mounted ADCP VMADCP Inputs GPS Gyrocompass iXSea PhINS so it can calculate accurate speed and direction of currents Range 520 650m Long range Low quality 310 430m Short range High quality 150 kHz Vessel Mounted ADCP VMADCP Inputs the same as for the 75kHz Range 325 350m or 375 400m Long Range Low Quality 200 250m or 220 275m Short Range High Quality Sound Velocity Sensors Discovery has a hull mounted AML SmartSV Probe and a portable Valeport Midas SV Profiler The Valeport uses DataLogExpress datalogger software and have a maximum depth of 5000m The Kongsberg SIS software has a new application called MDM for bringing the saved profiles in Specifications valeport datalogexpress pdf valeport midas svp profiler hardware manual pdf Location data disc cruise reports instrument data sheets Meteorological RRS Discovery has the same meteorological instruments and sensors as the RRS James Cook OceanWaves WaMoS Wave Radar WaMosS is an X Band nautical RADAR with a range of 100m to 4km
121. les see section on Particulate Trace Metals a Sartobran 300 Sartorius filter capsule 0 2 was used to collect filtered seawater samples into clean LDPE sample bottles Bottles and caps were rinsed 3 times with the filtered sample before being filled samples including those from the underway system were acidified to 0 016 M UpA HCI Romil and stored double bagged for shore based analysis Samples collected Samples for total dissolvable and dissolved trace metals were collected at 21 stations as detailed in Table 15 a total of 530 samples were collected for analysis Sample analysis Samples will be analysed for a range of trace metals e g Ag Al Mn Cd Zn Cu by inductively coupled mass spectrometry ICP MS at GEOMAR Milne et al 2010 For AI analysis flow injection with fluorescence detection Resing and Measures 1994 will be used following the modified method of Brown and Bruland 2008 Dissolved samples will be analysed after 2 months acidification whereas dissolvable samples will be left for at least 6 months before analysis 111 Station Samples collected from Station Samples collected from separate depths separate depths Dissolvable 4 Dissolved Dissolvable 4 Dissolved AI 6 6 El 9 9 2 6 6 11 11 4 12 12 4 17 17 5 19 19 5 22 22 5 5 6 6 CI 6 6 F4 11 411 C3 9 9 5 23 23 4 12 4 12 G4 6 6 5 15 15 G5 13 13 C7 24 24 G6 23 4 23 D4 10 10
122. linity offsets derived from calibrated conductivities are shown in Figure 4 It should be noted that the final salinity offsets obtained for the titanium CTD appear poorer than those obtained from the stainless steel CTD which most likely reflects the reduced number of bottle salinity samples collected from the titanium CTD The linear regression between Seabird 43 oxygen concentrations in mmol l and bottle titrations produced a regression equation of y 1 1535 CTDoxy 14 647 where y corrected oxygen concentration umol l The typical range of residual oxygen values i e corrected Seabird oxygen concentration bottle titration estimate was 5 umol l Figure 5 Relative to the stainless CTD the calibration for the titanium system appears poorer with a number of calibrated data points outside the 2 umol l range Figure 5 Despite the greatly reduced number of bottle titrations collected from the titanium CTD the mean residual 0 0029 umol l and standard deviation 57 2 087 umol l were comparable to the results obtained from the stainless CTD system suggesting comparable accuracies have been obtained from both systems dbi Stainless Steel 28 0 008 0 006 0 004 0 002 I Raw data Calibrated 0 002 0 004 0 006 0 008 0 01 Pressure db Bottle CTD salinity offset o i i 2500 i i 0 1000 2000 3000 4000 5000 6000 0 0
123. mDas Data Options ENS binary ADCP data after screening for RSSI and correlation either by VmDas adjusted by user and navigation data from NMS file ENX binary ADCP single ping data and navigation data after having been bin mapped transformed to Earth coordinates and screened for error velocity vertical velocity and false targets 64 NIR ASCII text raw NMEA data see section 3 ASCII text raw NMEA data see section 3 NMS binary navigation data after screening and pre averaging VMO ASCII text option setting used for collection the data LOG ASCII text all logging output and error messages More options are available and information about the data files and their format is available in the various OS user guides Here a short overview about the structure of the binary data files is given The structure varies slightly depending on whether only narrowband OR broadband mode are turned on or both are on Header header ID data source ID number of data types i e fixed leader variable leader etc and their offsets Fixed leader data fixed leader ID ADCP hardware configuration number of beams cells and pings per ensemble depth cell length blank after transmit signal processing mode narrow or broadband output controls amount of time between ping groups coordinate transform parameters heading alignment heading bias sensor source sensors available distance to middle of f
124. ming them to be completed Therefore until you are happy with the outputs it is best to regularly delete the contents of the data processed folder or at least move them elsewhere Brief description of Matlab processing steps 68 1 RDI binary file with extension ENX single ping ADCP ship referenced data from VMDAS and extension N2R ascii NMEA output from PosMV saved by VMDAS read into MATLAB environment NB The N2R file consists of ADCP single ping time stamps PADCP string and PosMV pitch roll and heading information SPRDID string 2 Ensembles with no ADCP data removed 3 Ensembles with bad or missing PosMV GPS heading data identified and adjusted GYRO heading substituted 4 Attitude information time merged with single ping data 5 Heading data used to rotate single ping ADCP velocities from vessel centreline reference to True North reference 6 Transducer mis alignment error corrected for derived from the mis alignment determination 7 Ship velocity derived from PosMV positional information 8 Further data screening performed Max heading change between pings 10 degrees per ping Max ship velocity change between pings gt 2ms pingrate Error velocity greater than twice Stdev of error velocities of single ping profile 9 All data averaged into 120 second super ensembles user selectable 10 Determine absolute water velocities from either bottom track derived ship velocity or PosMV GPS derived ship
125. mpler no 10 had small leak through upper left lanyard guide also after cast 022 Water sampler no 12 had small leak through upper left lanyard guide after cast 035 All samplers now repaired Stainless Steel CTD Re terminated wire because of crushed section as cable came out of over boarding sheave Approximately 50m removed Autosal A Guildline 8400B s n 71126 was installed in the Salinometer Room as the main instrument for salinity analysis second Guildline 8400B s n 71185 was installed in the Salinometer Room as a spare instrument The Autosal set point was 24C and samples were processed according to WOCE cruise guidelines The salinometer was standardized at the beginning of the first set of samples and checked with an additional standard analysed prior to setting the RS Once standardized the Autosal was not adjusted for the duration of sampling unless the set point was changed Additional standards were analysed every 24 samples to monitor amp record drift These were labeled sequentially and decreasing beginning with number 999 Standard deviation set to 0 00001 Deep tow RG 58 BNC cable to Lemo connectors installed in Main Lab at the High Voltage terminal to connect to SBE 11P deck unit Slip ring tray removed and inspected terminal torque proper strain relief condition of interface wires correct labeling etc The interior of the drum was then observed during CTD haul and veer at varying speeds from 5m min up to
126. n for pre concentration 110 Total dissolvable and dissolved trace metals Dagmara Rusiecka Objectives Iron is well established as a limiting element for phytoplankton growth however the role and cycling of other trace elements are less understood and there is a lack of data on the concentration and distribution of these elements in the global ocean While elements such as cadmium zinc and cobalt have a biological role reflected in their nutrient like profiles other trace elements can be used as tracers of inputs to the ocean e g aluminium Al is an indicator of aerosol deposition Tria et al 2007 and manganese Mn can indicate sedimentary or hydrothermal inputs Johnson et al 1992 Middag et al 2011 As with Fe there is a paucity of data concerning the input and cycling of trace metals from shelf regions The questions surrounding the magnitude and export of Fe from the shelf to the open ocean also apply to a suite of trace metals We aim to investigate and quantify the supply and transport of selected trace metals from the shelf off the North West of Scotland Sampling protocol Following recovery of the Ti rosette the OTE bottles were transferred into a clean sampling laboratory where they were immediately sampled for oxygen nutrients salinity and total dissolvable trace metals before being pressurised to approximately 7 psi with 0 2 filtered air using an oil free compressor After the collection of particulate samp
127. n was 0 00447 Final salinity offsets derived from calibrated conductivities are shown in Figure 4 The linear regression between Seabird 43 oxygen concentrations in mmol l and manual titrations produced a regression equation of y 1 1428 CTDoxy 12 638 where y corrected oxygen concentration umol l The typical range of residual oxygen values i e corrected Seabird oxygen concentration bottle titration estimate was 4 umol l but the majority of observations were better than 2 umol l Figure 5 The mean residual was 0 0051 umol l with a large standard deviation of 2 31 umol l due to the spread within the data Titanium CTD calibration Following the same approach as for the stainless steel CTD Coefficient A was determined to be 1 000141 and coefficient B was determined to be 1 000114 Corrected Seabird conductivities were again calculated through the application of coefficient A to primary conductivity and coefficient B to the secondary conductivity channel derived variables were then recalculated Residual conductivity differences calculated as bottle conductivity corrected Seabird conductivity were generally better than 0 004 mS cm for both channels but some scatter was present within the data On conductivity channel 1 the mean residual was calculated as 0 0003 mS cm and the standard deviation was 0 0044 On conductivity channel 2 the mean residual was 0 0011 mS cm and the standard deviation was 0 0031 Final sa
128. nch nc mwin 04 m Pastes winch data from fir file into the sam file input fir DYO17 winch nc Output sam DY017 NNN nc At this point all data were examined and edited for spikes using mctd rawedit m This is a graphical interface which allows you to remove spikes in temperature conductivity and oxygen editing is performed on the raw data files DYO17 NNN raw nc but a backup is made first ctd DYO17 raw original nc and the edited file saved as ctd DYO17 NNN raw corrected nc input ctd DYO17 Output ctd DYO17 raw original nc ctd DYO17 raw corrected nc Once edits are complete it is necessary to re run some of the early stages to correct derived variables accordingly This is done by running the batch script Smallscript m This batch script reruns mctd 02b mctd_03 04 mfir 03 and mfir 04 Bottle sample data A separate ascii file is first created for each CTD cast and for each bottle sample data type i e salinity oxygen nutrients CO chlorophyll etc The format of the ascii file is dependent upon the data type for example the salinity file format looks like the standard output file from the salinometer i e a file with the same number of header lines but containing less data whilst the nutrient file consists of several columns of data one for each nutrient and the a data quality flag It is best to find and modify existing template file
129. ng within shelf seas and to improve our understanding of the role of shelf seas in global biogeochemical cycles As part of the SSB programme a large NW European shelf wide sampling programme has been instigated in partnership between several of the UK s leading marine research centres and national agencies responsible for both the UK s e g CEFAS Marine Scotland etc and Irish Marine Institute statutory monitoring requirements Despite this huge collaborative effort initial planning for this programme suggested that the region west of the UK consisting of the Malin and Hebridean continental shelves would be comparatively under sampled compared to the English Channel Celtic Sea North Sea and waters west of Ireland Cruise DYO17 was specifically requested to fill this data gap The western shelf has been the focus of several NERC funded research programmes including the Shelf Edge Study conducted in the mid 1990 s Souza et al 2001 the Extended Ellett Line hydrographic section run annually since 1975 Holliday and Cunningham 2013 and most recently the FASTNEt programme in 2013 Figure 1 It remains however a comparatively less well sampled region than other areas of the NW European Shelf Despite this the area is recognised as being important for exchange with the open ocean and numerical models indicate that the majority of shelf edge exchange likely takes place in this region Holt et al 2009 Huthnance ef al 2009 Wakelin et al 2012
130. ntial Table 10 Description of underway sample labelling for sample UW1N 95 Niskin bottle Station 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 A1 A2 XX A3 A4 AS B1 mK XXX C1 C2 C3 C4 XX 5 C6 C7 D1 D2 4 D4 PS 4 D5 E1 E2 E3 4 ES E6 F1 F2 4 P lt F5 F6 G1 G2 PS G3 X G4 G5 PS X X X G6 X X X X X Table 11 Summary table of sampling for particulate material 96 ADCP lander John Beaton Mooring description One mooring was deployed during the cruise On 29 10 2014 an acoustic current meter was deployed in support of the UK OSNAP project by John Beaton for Stuart Cunningham of SAMS The deployment was named RTADCPI Figure 9 AL 500 with concrete base ready for deployment ADCP heads protected by white dome The plan was to deploy the 75KHz ADCP in a low profile seabed mount at latitude 57 1 N and depth 750m at an expected longitude of approxima
131. of the actual sampled depth Strong winds were also likely to affect the phytoplankton structure in surface layers No clear chlorophyll maxima were apparent in the fluorescence CTD profiles as the upper ocan was well mixed Spikes in fluorescence were present at some sites but could easily have been noise rather than true fluorescence peaks Fluorescence profiles indicated a well mixed surface layer of phytoplankton with a rapid decline of fluorescence commonly at the mixed layer depth 107 between 60 and 100 m Some shallower stations were entirely mixed throughout the water column Issues with the winch system onboard caused further delays in sampling and a switch from using 20 L bottles to 10 L bottles after the 28 October Measurements of ammonium were originally planned for the cruise but were cancelled due to technical issues with the fluorometer Trace Metal Sampling Angela Milne Antony Birchill and Dagmara Rusiecka Samples were collected for trace metal analysis in both the dissolved and particulate fractions using the dedicated trace metal 10 L OTE bottles mounted on a Ti frame rosette system Additional sample logs for all Ti CTD casts and fish sampling are available from the authors The trace metal samples collected will be analysed at different institutes for differing parameters Total dissolvable and dissolved Iron Antony Birchill at the University of Plymouth Total dissolvable and dissolved Trace Metals excl
132. olycarbonate filters however it was decided that due to allocated processing time it was more effective to change to 0 8ym polycarbonate filters Labelling of samples samples were labelled to a uniform system Table 8 Each type of analysis as described above was given a unique code that is displayed in Table 1 below This code was then used alongside the station number and niskin bottle number to provide a unique code for each sample undertaken The code NA12 is described below in its unique parts in Table 9 as an example As well as this unique code the last three numbers of the JDay on which the sample was processed was logged along with the time of the CTD deployment and the volume of water that was filtered Sample Code Analysis type N POC PON P POP S BSi C POC Table 8 Labelling code given to each type of analysis N Al 2 Analysis type Station number Niskin bottle number Table 9 Description of CTD sample labelling for sample NA12 For underway samples a similar labelling technique was applied for each analysis type an example underway code UWIN is described below in Table 10 as an example The numbering of underway samples was sequential and was logged alongside the time that the sample was collected and the JDay so that a specific coordinate could be produced from the ships logs UW 1 Underway pample Analysis sample seque
133. on This was also done using potassium iodate The reagents were added to a sample 86 of milli Q water in reverse order as with the thiosulphate standardisation method and then 1 ml of 5 N iodate was added This was titrated to completion and this process repeated 5 times The blank was calculated as the average of all five blanks or remaining samples once outliers were excluded This mean value was then also used in the calculation of the final dissolved oxygen concentrations Change in Thiosulphate Standard Titration Volume o 1 2 3 4 Calibration Number Figure 7 Sodium thiosulphate standardization results Sampling A summary of all sampling during DY017 is presented in Table 6 CTD cast Number of Niskin bottle sampled depths sampled 1 0 2 2 3 6 3 10 1 3 5 7 9 15 17 19 21 23 4 3 1 4 6 5 8 2 4 6 8 10 12 14 16 6 8 1 3 7 9 13 15 21 23 7 4 1 5 10 12 8 12 1 3 5 7 9 11 13 15 17 19 21 23 9 5 4 25 17 21 24 10 11 1 3 5 7 9 10 11 15 17 19 22 11 3 1 4 6 12 7 1 3 7 10 14 18 20 13 3 1 3 6 14 8 1 3 7 9 13 15 20 23 87 15 11 2 3 5 7 9 11 13 15 17 20 21 16 0 17 12 1 3 5 7 9 11 13 15 17 19 21 23 18 0 19 7 4 7 9 11 13 15 19 20 0 21 12 1 3 5 6 7 11 12 13 16 17
134. onding ENX file heading orig heading from the ENX file ens num the ping ensemble number lat latitude of the ping ensemble The difference between att heading and heading orig should be small and therefore negligible CRUISE xxx yyyyyy sgl ping mat Again one file with single ping data is produced for each ENX file In the structure OS75 sgl ping after several steps of quality control filtering and correcting for misalignment and scaling after final processing data from the four beams bottom track data navigation data configuration data and information about the processing environment are stored all variables that exist in OS75 raw in the file CRUISE xxx yyyyyy raw mat are included additional variables filename CRUISE xxx 000000 path rawpath paths to the directories where the processed data is written to path and where the raw data files are stored rawpath att structure containing heading pitch roll and PC clock offset heading orig number of ping ensembles x 1 array heading from the ENX file ship velocity 2 x number of ping ensembles array containing the eastward first row and the northward second row ship velocity 80 CRUISE cal points mat In this file all information at bottom track calibration points needed for the calculation of misalignment angle and scaling factor are stored This includes bt structure with bottom track data arrays vel 2 x number
135. onductivities Convert from binary to ascii format 51 At this stage the CTD data is transferred to mstar mstar processing To begin a set of ascii template files were created containing a full list of all variables and their units required in the final CTD and bottle data files These template files are used to generate blank mstar NetCDF files and it is important that the names of variables and their units are consistently adhered to across different file types These template files were created based on previous cruises and initially included sam DY017 varlist csv A list of variables coincident with sampling stops on the up cast e g temp salinity nitrate alkalinity etc ctd dy017 renamelist csv A list of variables in ctd profile data streams dcs DYO17 varlist csv A list of variables related to sampling times positions etc After creation of the template files the following processing routines were run ctd all part1 m A batch script which calls a variety of mstar routines including msam O01 m which creates an empty sample file of name sam DYO17 NNN nc based on the template file sam DYO017 varlist csv input sam DYO17 varlist csv Output sam_DYO17_NNN nc 01 m reads 24Hz SeaBird data in ascii format into netcdfd format Input 24Hz SeaBird data Output DYOI7 NNN mctd 02a m renames some variables in the raw input file input DYOI7 Output ctd DYOI7
136. or Ocean Circulation pp38 Holliday N P and S A Cunningham 2013 The Extended Ellett Line Discoveries from 65 years of marine observations west of the UK Oceanography 26 2 156 163 Holt J S Wakelin and J Huthnance 2009 Down welling circulation of the northwest European continental shelf driving mechanism for the continental shelf carbon pump Geophysical Research Letters 36 1 14602 doi 14610 11029 12009GL038997 Hurst M P and K W Bruland 2007 An investigation into the exchange of iron and zinc between soluble colloidal and particulate size fractions in shelf waters using low abundance isotopes as tracers in shipboard incubation experiments Marine Chemistry 103 211 226 Hutchins D A and K W Bruland 1998 Iron limited diatom growth and Si N uptake ratios in a coastal upwelling regime Nature 393 6685 561 564 Huthnance J M J T Holt and S L Wakelin 2009 Deep ocean exchange with west European shelf seas Ocean Science 5 621 634 Johnson K S W M Berelson K H Coale T L Coley V A Elrod W R Fairey H D Iams T E Kilgore and J L Nowicki 1992 Manganese flux from continental margin sediments in a transect through the oxygen minimum Science 257 1242 1245 Kiriakoulakis K E Fisher A Freiwald M White and G A Wolff 2007 Organic matter quality supply to deep water coral mound systems of the NW European Continental Margin International Journal of Earth Sciences 96
137. ow you want it set up Command files were generated from DY017 and will be saved with the final data suite Be aware that these will load settings made by relatively inexperienced VMDAS operators and should be checked and amended sooner rather than later OS150 ADCP misalignment The majority of the ship velocity is automatically removed by VMDAS in the raw processing stages though truly raw velocities are also output For this it needs information on the rotation of the ADCPs relative to the ship s hull specified in the VMDAS setup On arrival on Discovery it was found that the OS150 ADCP was still configured with factory settings and had probably not been used in anger The ADCP settings were mostly copied from the OS75 machine but the ADCP alignment in the hull was set at 0 initially rather than 45 as with the OS75 post processing the data it was discovered that the correct misalignment was in fact 45 as well The Matlab routines are able to correct for this but after email discussion with Brian King NOC we decided to correct it to avoid any unknown errors creeping in The output files of the OS150 are therefore divided into those requiring a 45 correction at the beginning of the cruise and those requiring a 0 5 correction for the rest of the cruise OS75 beam failure Early in the cruise it was discovered that the fourth beam of the OS75 was not working With the VMDAS display set to real time this was se
138. p s n 05T 3086 secondary Sea Bird 32 Carousel 24 position pylon s n 32 19817 0243 Sea Bird 11plus deck unit s n 11P 34173 0676 main Sea Bird 11plus deck unit s n 11P 24680 0589 back up logging 5 The auxiliary input initial sensor configuration was as follows Sea Bird 43 dissolved oxygen sensor s n 43 1624 VO Biospherical QCP Cosine PAR irradiance sensor DWIRR s n 70510 V2 Biospherical QCP Cosine PAR irradiance sensor UWIRR s n 70520 V3 Benthos PSAA 916T altimeter s n 59493 V4 WETLabs light scattering sensor s n BBRTD 1055 V5 Chelsea Alphatracka MKII transmissometer s n 161048 V6 Chelsea Aquatracka MKIII fluorometer s n 88 2615 124 V7 6 Sea Bird 9plus configuration file DYO17 stainless NMEA xmlcon was used for all stainless steel frame CTD casts Total number of casts 22 titanium frame 34 S S frame Casts deeper than 2000m 0 titanium frame 1 S S frame Deepest casts 1862m titanium frame 2066m S S frame 27 Appendix A Technical detail report Titanium CTD Water sampler no 8 had small leak through mounting block replaced with no 25 prior to cast 002 Water sampler no 13 had small leak through upper left lanyard guide replaced with no 26 prior to cast 011 Water sampler no 9 had broken centre mounting block replaced with no 8 prior to cast 018 Water samplers no s 2 15 26 amp 11 had broken centre mounting blocks occurred upon hard landing on deck after cast 022 Water sa
139. perational with a 3 beam solution for the first week This was rectified by replacement of the ADCP deck unit and the instrument worked reliably thereafter however recognition and resolution of this problem was slow and as a result we have lost data from the first 2 transects of the cruise Master s Diary Summary Start End Date Time Date Time Activity 16 10 2014 09 00 19 10 2014 17 00 Mobilisation for DYO17 incl bunkering and storing 19 10 2014 17 00 20 10 2014 07 30 Waiting to sail 20 10 2014 07 30 20 10 2014 10 12 Pilotage and Stand by to Needles Fairway Buoy 23 22 10 2014 23 10 2014 24 10 2014 25 10 2014 26 10 2014 27 10 2014 28 10 2014 29 10 2014 10 12 18 35 20 43 10 12 14 52 17 10 19 30 21 20 08 20 10 43 13 06 16 00 18 30 23 21 08 48 19 30 02 35 05 15 09 05 11 03 12 18 14 38 16 43 19 07 21 00 23 32 01 20 03 15 04 52 14 00 16 00 18 20 00 02 05 08 07 25 08 34 11 38 22 10 2014 22 10 2014 23 10 2014 23 10 2014 23 10 2014 23 10 2014 23 10 2014 24 10 2014 24 10 2014 24 10 2014 24 10 2014 24 10 2014 24 10 2014 25 10 2014 26 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 27 10 2014 28 10 2014 28 10 2014 28 10 2014 28 10 2014 28 10 2014 28 10 2014 29 10 2014 29 10 2014 29 10 2014 29 10 2014 29 10 2014 29 10 2014 18 35 20 43 10 12 14 52
140. ppiatt M G Lawrence K W and Bruland 2008 Application of a chemical leach technique for estimating labile particulate aluminum iron and manganese in the Columbia River plume and coastal waters off Oregon and Washington Journal of Geophysical Research Oceans 113 COOBO1 doi 10 1029 2007JC004703 Brown M T and K W Bruland 2008 An improved flow injection analysis method for the determination of dissolved aluminum in seawater Limnology and Oceanography Methods 6 87 95 Bruland K W and M C Lohan 2004 Controls on trace metals in seawater In the Oceans and Marine Geochemistry Vol 6 Treatise on Geochemistry eds H D Holland and K K Turekian Elsevier London pp 23 49 Bucciarelli E S Blain and P Treguer 2001 Iron and manganese in the wake of the Kerguelen Islands Southern Ocean Marine Chemistry 73 21 36 Croot P L and M Johansson 2000 Determination of iron speciation by cathodic stripping voltammetry in seawater using the competing ligand 2 2 thiazolylazo pcresol Electroanalysis 12 565 576 Culberson C H and S Huang S 1987 Automated Amperometric oxygen titration Deep Sea Res A 34 5 6 875 880 Dauwe B and J J Middelburg 1998 Amino acids and hexosamines as indicators of organic matter degradation state in North Sea sediments Limnology and Oceanography 43 5 782 798 de Baar H J W A G J Buma R F Nolting Cadee G Jacques and P J Treguer 1990 On i
141. pted from JC88 amp JR239 cruise reports For those hoping to access processed VMADCP data you are most likely to require file type CRUISE 000 000000 zz abs mat detailed in section 4 5 8 Dates and times covered by files are given in section 5 1 For cruises on Discovery in the near future it is recommended that you read section 1 1 which outlines the specific issues we encountered some of which probably easily rectified by a skilled operator A quick start guide to setting up the Matlab software on another machine is included in section 4 3 OS75 and OS150 configuration RRS Discovery is fitted with RD Instruments 75kHz and 150 kHz Ocean Surveyor ADCPs The instruments are mounted in the ship s hull in a forward aft configuration approximately 6 m below the waterline Their nominal rotation relative to the centreline of the ship is 45 but fine tuning of this value is performed by the water track or bottom track calculations in the Matlab routines The exact determination of this rotation offset is crucial to removing ship velocity from the data Positional and attitude information is provided via a PosMV multi receiver GPS attitude sensor Ship s heading information from the vessel s Gyro though streamed to and saved by the logging PC was not used in the processing steps described here The RDI proprietary software VMDAS was used to configure the ADCP and perform velocity mapping to the reference frame of the vessel
142. r containing the numbers of several file sequences A new file sequence is begun each time you switch the VMDAS on off Line 105 5 The averaging interval variable superaverage superaverage sets the interval over which ping ensembles will be averaged Unit is seconds Leave as is if unsure Line 117 6 The year variable YYYY 67 7 switch for which lat lon fix to be used see below 5 4 variable which prdid fix Options are a 1 to use the fix directly after the previous ADCP ping or b any other number to use the fix directly before the current ADCP ping Set it to 1 presently and has negligible impact on the resultant data 8 The upper and lower limit of the reference layer variables ref uplim and ref lowlim Those are needed for calculation of a reference velocity which is used when doing calibration by water tracking Unit is meters Useful if a particular layer of water is known to be particularly good bad as a reference level due to tides etc Leave as is if unsure 9 The misalignment angle and the scaling factor variables misalignment_nb misalignment_bb and amplitude_nb amplitude bb When running OS75_DY017 m the first time set the misalignment to 0 and amplitude to 1 Currently Line 183 While the nb and bb suffixes refer to the narrowband and broadband setting in VMDAS regardless of which setting you use keep the nb and bb settings the same as each other
143. race elements between the dissolved and particulate phases required for their realistic incorporation into biogeochemical ocean models is to measure the standing stock of the particulate fraction To address this particulate material will be filtered on selected water samples collected using the trace metal rosette Sampling protocol OTE bottles were transferred from the Ti rosette into a clean sampling laboratory where they were immediately sampled for oxygen nutrients salinity and total dissolvable elements The OTE bottles to be sampled for particulate material were inverted three times to gently mix the seawater and re suspend particulates before being pressurised to approximately 7 psi with 0 2 filtered air using an oil free compressor Clean filter holders Swinnex Millipore containing acid washed 25 mm 0 2 polyethersulfone filters PES Supor Pall Gellman were attached to the taps of the OTE bottles and up to a maximum of 7 L of seawater from 113 selected depths was then passed over the filters Following filtration the filter holders were removed and placed in a laminar flow bench Using an all polypropylene syringe attached to the top of the filter holder residual seawater was forced through the filter using air from within the flow hood The filter holders were gently opened and the PES filter folded in half using plastic tweezers the filters were then placed in acid clean 2 mL LDPE vial and frozen at 20 C until an
144. re called After that all data is processed and saved in the specified directory The last thing in the main function is a plot of velocities cross sections of the zonal and meridional velocities against time are produced and the plots are saved in adcp_vel_contours ps 70 Master 575 JCR m um structure O 75 raw raw dota from binary dota fie OS75 raw in CRUISE soo rawar save plot of pitch aed heading in adep_prh ps save structure att navigation daca in CRUISE oo 000000 art mat save relevant att daea for fle in loop in CRUISE xxx edditions in OS75 sg ping navigation dete from NIR files save O575_s f_ping CRUISE yyyyyy sg mas es poire bum jeo en save newlrotized structure cal in CRUISE new structure edd te structure OS75 ave ping 3 doe CRUISE cal file reat exiit no yes 4 tave modified structure cal ie CRUISE save plot of esisslignment angle and scaling factor in cab cale os save O575_ave_pong CRUISE 000 000000 zz ave pigmat new structure OS75 obs save 0675 abs and modified OS75 ave ping in 000 000000 zz save contour plot of velocities i adep wel coreours ps fun Dad time with sdjuited sissignment angie and scaling factor Be yequence wher 2nd rua suse naierclinn dab sequence number The Eng Figure 6 Schematic of
145. referable option is always to load a reliable command file from a previous cruise VMDAS can read command files from other ships but be aware that some settings are ship specific 62 We were thrown by the fact that on loading a command file the tick boxes are not automatically updated to reflect the settings therein We took this as meaning that the command file was not being read whereas actually the tick boxes simply override the command file On arrival on the ship we therefore recommend loading a command file from previous cruise on the same vessel one which generated good VMADCP data and starting with most boxes in the configuration menu unchecked Specify only what is necessary for your requirements bin size bottom tracking etc and if necessary test the effect of other settings through trial and error outside the scientific portion of the cruise processing the output daily to monitor changes Command files to immortalise your settings can be generated through Options Save as Two types of command file have been generated by previous cruises one is four A4 pages long and lists all ADCP and VMDAS settings The other is much shorter and commented The difference between the two and their intended functions is slightly unclear Suspect the commented command files text format are supplied by RDI to get the user started in various modes whereas the long version ini is the user generated settings output which specify exactly h
146. rocess cruise The green line represents the 200 m bathymetric contour 14 60 N Cruise Track CTD station ADCP mooring UK Irish maritime limit 59 N 58 N Latitude N 57 N 56 N 55 N 12 W 10 W 8 W 6 W 49W Longitude Figure 2 Chart showing Outer Hebrides work area with DYOI17 cruise track red line position of completed CTD stations green dots benthic ADCP lander location blue dot and the UK Irish maritime limits blue line The thick black line represents the 200 bathymetric contour 15 2 CRUISE NARRATIVE PSO s Diary Monday Oct 20 Day 293 We departed the NOC berth in Southampton at 0730 prepared for a 3 day transit to the work area west of the Hebrides and having been forewarned that the imminent arrival of ex hurricane Gonzalo was likely to make conditions a little bumpy for the first few days Weather conditions on departure were good with light winds and sunny periods and good progress was made down the Channel Weather conditions deteriorated from early afternoon onwards with strengthening winds and a building swell throughout the evening Tuesday Oct 21 Day 294 We turned the corner around Land s End at lam and true to predictions the sea conditions became noticeably worse leading to a rather unsettled night for most onboard We awoke to Gale Force GF 10 winds but only a moderate swell yet Discovery proved to be a stable platform in bad weather
147. ron limitation of the Southern Ocean experimental observation in the Weddell and Scotia Seas Marine Ecology Progress Series 65 2 105 122 De Baar HJ W J T M de Jong 2001 Distributions Sources and Sinks of Iron in Seawater Chapter 5 in Turner D and Hunter K A eds Biogeochemistry of Iron in Seawater IUPAC Book Series on Analytical and Physical Chemistry of Environmental Systems Volume 7 pp 123 254 De Jong J T M J Den Das U Bathmann M H C Stoll G Kattner R F Nolting and H J W De Baar 1998 Dissolved iron at subnanomolar levels in the Southern Ocean as determined by ship board analysis Analytica Chimica Acta 377 113 124 Dickson A G C L Sabine and J R Christian Eds 2007 Guide to best practices for ocean measurements PICES Special Publication 3 191 pp Duce R A and N W Tindale 1991 Atmospheric transport of iron and its deposition in the ocean Limnology and Oceanography 36 1715 1726 Elrod V A M Berelson Coale and K S Johnson 2004 The flux of iron from continental shelf sediments A missing source for global budgets Geophysical Research Letters 31 L12307 doi 10 1029 2004GL020216 116 Grasshoff K M Ehrhardt and Kremling Eds 1999 Methods of Seawater Analysis 3 edition Wiley VCH Verlag GmbH Weinheim 600 pp Holley S E and D J Hydes 1994 Procedures for the determination of dissolved oxygen in seawater James Rennell Centre f
148. s before starting and rigidly ensuring that all formats are strictly adhered to Once the various ascii files were created the following scripts were used to read the data into mstar netcdf and to subsequently merge the data with the sam file Salinity msal 01 m convert the ascii file into NetCDF This routine will ask you for the salinometer bath temperature and whether you want to apply a conductivity ratio offset The Offset was set to zero throughout Tweak script for changes to variable names before use 54 input ascii csv file e g sal DYOI7 NNN csv Output sal DYO17 NNN nc msal 02 m paste the bottle salinity data into the sample file input sal dy0I7 Output sam DYO17 Nutrients mnut 01 m Read in the csv ascii file and convert to NetCDF Tweak script for changes to variable names before use input ascii csv file e g nut DYOI7 NNN csv Output nut DYOI7 NNN nc mnut 02 m paste the bottle nutrient data into the sample file input nut dy017 Output sam DYO17 Oxygen moxy_01 m Read in the csv ascii file and convert to NetCDF Tweak script for changes to variable names before use input ascii csv file e g oxy DYOI7 NNN csv Output DYOI7 NNN nc moxy 02 m paste the bottle oxygen data into the sample file input 4 017 NNN Output sam DYOI7 NNN nc Conductivity and Oxygen calibration A set of residual values were gen
149. s routine was added by Hugh Venables during JR218 to filter out spikes in the GPS data It is called with the arguments 0575 sgl ping and which prdid fix and returns the modified structure 0575 sgl ping qual con rol m Several criteria are used in this routine for further quality control Therefore the arguments OS75 sgl ping beam heading change and ship velocity change are included in the call beam is the number of beams of the ADCP instrument heading change is the maximum change in heading allowed at any one time step and ship velocity change is the maximum change in ship velocity allowed at any one time step Large changes lead to less reliable ADCP data 74 The first step of quality control uses the error velocity provided through the fourth beam vel 4 A variable err vel is set to 2 times standard deviation of the error velocity and the velocities of all ping ensembles where the absolute value of this velocity exceeds err vel are set to NaN Then if beam 0 a check using percent good is performed velocities of ping ensembles with percentage of good four beam solutions equal to zero are set to NaN The two following steps look at the heading changes First a smoothed version of the heading change diff heading created using a Hamming window based second order filter is checked for values exceeding heading change and the velocities of affected ping ensembles i e the two ensembles in between which the change is l
150. sect G We reached station G1 55 22 236N 08 05 864W and deployed the stainless steel CTD CTD050 just before midnight This was followed with another plankton net haul NET015 and we were soon on our way to station G2 Monday Nov 3 Day 307 Station G2 was reached at 0200 where we deployed the steel CTD CTD051 completing the deployment by 0240 At Station G3 we undertook a stainless steel CTD cast CTD052 and the package was inboard by 0524 having taken only 20 minutes due to the shallow depth of the station 100 m Weather conditions were ideal for rapid progress with light winds and little swell and we reached station G4 at 0700 and deployed the titanium CTD CTD053 which was also to be used to collect water for other participants due to our desire to maximise time on the last day of science This was inboard by 0747 We have made good time overnight and throughout the morning and reached the shelf break station G5 at 0940 We deployed the titanium CTD CTD054 the plankton net NET016 and the air sea buoy BUOY006 instrument package via the aft davit Due to excellent progress overnight we reached the last objective for this cruise station G6 at 1415 and deployed the titanium CTD CTD055 for the last time at 1457 This was safely inboard by 1636 and after a short delay to remove bottles and switch CTD systems the steel CTD CTD056 was deployed at 1733 and recovered by 1921 To complete scientific activities for this cru
151. served Preliminary Data 92 Data were processed during the cruise and the final quality of these data will take place back at the NOC over the coming months particularly concerning the TON data from Transect A CTDs The quality control process is not expected to significantly change the data from all other transects Below in Figure 8 are the distributions of TON phosphate and silicate from all Stainless Steel CTDs in transect E 0 ae F 500 1547 1000 10 1500 5 2000 10 9 5 9 8 5 8 Longitude VV 1 2 500 1 1000 08 3 1500 0 6 5 o 2000 em 10 9 5 9 8 5 8 Longitude WV J 14 500 12 107 1000 8 D 6 O 1500 4 i5 2000 10 9 5 9 8 5 8 Longitude V Figure 8 Depth distributions of TON phosphate and silicate umol L for Transect E 93 POC PON POP BSi and PIC underway and CTD sampling Stephanie Allen and Lucie Munns CTD Sampling For each stainless steel CTD cast and where necessary from some titanium CTD casts 2 4 litres water from each of 6 8 depths generally with higher resolution in the surface mixed layer was drawn into 10 L black carboys In most cases 1 L was filtered for POC PON 1 L for POP and 0 5 for Biogenic Silica and PIC When water volumes were restricted a reduced volume of 0 75 L were filtered for POC PON and POP Underway sampling Occasionally samples were taken from the ships underway supply in
152. t 2300 This was safely back on deck by 0116 and the titanium CTD was subsequently deployed CTD043 With all work finished by 0400 we proceeded onwards to station F4 Sunday Nov 2 Day 306 On arrival at station F4 the wind had increased in intensity and it looked like a deployment of either CTD system was going to be delayed Fortunately the decision was taken to try and we deployed the steel CTD CTD044 under less than ideal conditions at 0627 The package was safely back on deck by 0653 and we proceeded to deploy the titanium CTD CTD045 and plankton net NET013 All work was finished by 0830 and we proceeded to the next station We arrived at station at 0945 and deployed the steel CTD046 and titanium CTD CTD047 All instrument packages were inboard by 1130 and we proceeded onwards 21 Wind speeds continued to blow a constant F5 and on arrival at station F2 the air sea buoy was not deployed as planned Instead we deployed the instrument package via the aft starboard davit as had been perfected earlier at station E5 BUOY005 This deployment was complete by 1450 and was followed by the deployment of the stainless steel CTD CTD048 This was complete by 15 56 Station F1 56 07 177N 08 06 149W was reached at 1730 and we immediately deployed the stainless steel CTD system CTD049 and followed this with another plankton net haul NET014 With this complete we departed the end of Transect and headed south to Tran
153. tely 9 33 W The deployment consisted of a Teledyne RD Instruments 75KHz ADCP in a DeepWater Buoyancy AL 500 Trawl Resistant Bottom Mount TRBM with a non recoverable concrete base Figure 9 The AL 500 was fitted with a pair of Ixsea AR861 acoustic releases to provide redundancy in the event of individual failure Figure 10 Recovery aids fitted were a Novatech Iridium beacon and a Novatech strobe both pressure activated on surfacing 97 Figure 10 Internal view of Trawl Resistant Bottom Mount showing twin acoustic releases recovery aids and ADCP battery case Deployment method Deployment was by freefall from the surface with a detachable buoyancy parachute consisting of three 17 Benthos glass spheres on 4 chain above an Ixsea acoustic release that could be released once the frame was confirmed on the seabed Pre deployment tests included a pressure and function test of all three acoustic releases by attaching to a CTD frame and lowering to 1000m then firing at 800m The entire package was lifted with the port hand crane and swung out over the stern inside the extended stern gantry With the entire package under the surface of the water a Seacatch quick release was used to release it from the crane at 1531 57 10179 N 9 33682 W The TRBM and parachute were tracked using an Ixsea TT801 deck unit at a descent rate of about 50m min and was on the bottom at 1546 with a slant range of 789m Before release was attempted the vesse
154. the line to look for looks like this SPRDID 000 76 002 03 259 94 7E This contains the pitch roll and heading values and a couple of digits which might be a checksum from VMDAS and are not needed Processing in Matlab The Matlab routines For the post processing of the VmDas data we used a set of Matlab routines They were first obtained from IfM Kiel by Mark Inall and adapted for use on the RRS James Clark Ross by Deb Shoosmith During JR165 Mark Brandon and Angelika Renner cleaned up large parts of the routines and added comments throughout Since JR165 some further debugging and refinement have been done by numerous operators The structure general processing and in and output formats remain the same The following description of the routines and the output data files are adapted from the JR235 cruise report Remarks and Glossary Whenever it says run a routine program function it means type in the function name in the Matlab command window and hit enter A few terms should be clear file sequence all files for which in the filename CRUISE xxx yyyyyy END the number at position xxx is the same These files have been recorded without stopping the ADCP in between and the same setting was used amplitude scaling factor A Throughout the routines the factor by which the ADCP data has to be scaled for calibration is called either amplitude scaling factor or 66 misalignment angle phi synonyms for the angle
155. the master processing script for DYO17 OS75_DY017 m read os m In this routine the raw binary data from VmDas are read In case of DY017 we used the ENX files which contain ADCP single ping and navigation data The ADCP single 71 ping data has already been bin mapped transformed to Earth coordinates and screened for error velocity vertical velocity and false targets see VmDas User s Guide read os m is called with the file name variable and optional arguments The latter define which part of the raw data is read ends ens list list of ensemble numbers yearbase start year second set read narrow band mode data when both broad and narrow band are collected vel read velocity cor read correlation magnitude amp read echo intensity pg read percent good ts read pitch roll and heading bt read bottom track data nav read navigation data all includes vel cor amp ts bt and pg More than one argument can be passed on to read_os m Arguments can also be numbers After the switches are set the subroutine os_id which is within read_os m is called with the argument id_arg The value of id_arg depends on the offset of the positions of the data If both narrowband and broadband data are collected in broadband mode this also decides which data are read If id_arg 1 the narrowband data is extracted os_id returns the structur
156. the receiver This meant that after the first 3 deployments continued deployment of the NSOP was not possible and the decision was made to deploy the cage separately from a crane arm and to pay out a measured length of line manually This resulted in a reduced vertical resolution but did allow deployments when the swell would have been too high for the NSOP Weather conditions prevented deployments on several days Measurements and deployment dates The measurements for this cruise consist of the CTD Licor PT1000 pressure sensor flow rate sensor data for the 3 NSOP deployments the 2327 and the 30 October and the 4 standalone cage deployments on the 2 3 and two on the 4 November Table 12 The pCO system was also setup to sample under way data for 1 day on the 1 November to make a direct comparison with the ships underway system Deployment Date Deployment method 1 23 10 2014 NSOP 2 27 10 2014 NSOP 3 30 10 2014 NSOP 4 2 11 2014 Davit Crane 5 3 11 2014 Davit Crane 6 4 11 2014 Davit Crane 7 4 11 2014 Davit Crane Table 12 Summary of deployments Phytoplankton community structure Beatrix Siemering Introduction All samples were taken by Beatrix Siemering a second year PhD student based at SAMS the Scottish Marine Institute Samples were taken as part of her PhD project Advective transport of harmful phytoplankton The project focuses on transport of Karenia Dinophysis and
157. through a 47 mm glass fibre filter and frozen at 20C for subsequent analysis back at SAMS Frozen samples will be treated with acetone sonicated and measured for chlorophyll fluorescence using a trilogy fluorometer CARD fish Three 125 ml replicates were taken from the underway at each station Samples were filtered through a polycarbonate filter cushioned with a glass fibre filter inside a vacuum filter holder and a syringe Each polycarbonate filter was incubated in 5 ml saline ethanol in a 6 well plate for an hour Saline Ethanol fixative was prepared freshly for each station from 12 5 ml ethanol 1 ml MilliQ water and 1 5 ml SET buffer SET buffer contains 3 75M NaCl 25 mM EDTA and 0 5M Tris After 1 hour saline ethanol was pipetted off and passed back through the filter Filters were frozen at 20C and taken back to SAMS for further analyses by Ruth Patterson 106 Sampling Station CTD No Cruise Sampled Niskin Nethaul Cruise Approx Underway Event Depth m Bottle No Event depth sampled No No m Al CTD003 4 10 30 50 14 18 22 NETO001 5 0 50 Y A3 CTD007 9 10 30 40 12 15 24 Y A4 CTDO008 11 10 30 50 18 20 23 Y A5 CTD010 13 10 30 50 22 23 24 Y X Y B1 CTD012 15 10 30 50 11 16 19 NET002 16 0 50 Y CI CTDO014 18 30 50 70 3 9 15 19 0 70 Y C4 CTD019 25 15 50 100 13 17 21
158. tion number i e time revealed no drift with time indicating that both sensors were stable SeaBird claim that the correct in situ calibration for their conductivity sensors is a linear function of conductivity with no offset Plots of conductivity difference against conductivity added support to this and therefore the calibration coefficients A and B were calculated as conductivity A primary conductivity conductivity B secondary conductivity where A Y Cond Cond Cond Cond 2 T Cond Cond i and 2 Cond2 Cond2 Cond2 Cond 2 _ X Cona2 Cond2 and cond2 is the sample bottle conductivity determined with the secondary temperature variable Coefficient A was determined to be 1 000002 and coefficient was determined to be 0 999946 Corrected Seabird conductivities were calculated through the application of coefficient A to primary conductivity and coefficient B to the secondary conductivity channel derived variables were then recalculated 56 Residual conductivity differences calculated as bottle conductivity corrected Seabird conductivity were typically better than 20 003 mS cm for both channels but some scatter was present within the data On conductivity channel 1 the mean residual was calculated as 0 00019 mS cm and the standard deviation was 0 00444 On conductivity channel 2 the mean residual was 0 00007 mS cm and the standard deviatio
159. uding iron Dagmara Rusiecka at NOCS and GEOMAR Ligands Dagmara Rusiecka at NOCS and GEOMAR Suspended Particulate Material SPM Angela Milne and Antony Birchill at the University of Plymouth A total of 265 depths over 21 stations were sampled this amounted to 530 samples 265 total dissolvable and 265 dissolved each for Iron and Trace Metal analysis Selected depths at all stations were sampled for Suspended Particulate Material resulting in 100 samples In addition unfiltered samples were collected for macronutrients from all OTE bottles and at selected depths for oxygen and salinity At three stations C5 G4 and G5 unfiltered samples were also collected for DOC DIC macronutrient Particulates and Chlorophyll Underway surface samples were collected by pumping surface seawater into a trace metal clean sampling laboratory using a Teflon diaphragm pump Almatec A 15 Germany connected by an acid washed braided PVC tubing to a towed fish positioned at approximately 2 3m depth alongside the ship Seawater samples were filtered in line using a 0 2 um Sartonbran P membrane filter capsule Sartorius Surface seawater samples were collected at and in between stations when possible a total of 50 surface samples were collected Bottle misfires and comments on sampling Over the 21 stations sampled for trace metals there were 3 stations where a total of 4 OTE bottles did not fire at Stations B1 D4 and G6 and therefore these
160. uise Hydroacoustics Generally worked OK 46 Kongsberg EA640 10kHz run 12kHz run for a while but not needed so turned off Kongsberg EM710 Not requested but some data logged May be a transposition error in the all files Used until on station north of Lewis on Friday the 24th then switched to the EM122 as it seemed the EM710 needed some faultfinding Kongsberg EM122 Not requested but some data logged Used after the EM710 had a hiccup Kongsberg SBP120 Not requested but some data logged Kongsberg EK60 Not requested not switched on no data logged Sound Velocity Profiles Not used just a manual setting of 1500m s Teledyne RDI ADCP I set anew command file for both ADCPs at the start of the cruise and got a copy of the latest manual as the previous one was from 2012 This was a main focus of the cruise and Stuart Painter and Sam Jones spent a fair bit of time adjusting the settings and also setting a new configuration file for the 75kHz which had never been set 75kHz 47 Fault noticed where beam 4 was faulty The system was tested and the deck unit replaced on the 29th of October at approximately 11 20am and the system worked fine after that 150kHz Worked fine throughout the cruise Sonardyne USBL Not requested no data logged Third Party Instrumentation DartCom Live PCO2 Used and looked after by PML PhD student Richard Sims on this cruise A flow meter failed but Ri
161. ut still have the prefix OS75 The same Matlab scripts are used for both and I have not yet managed to iron 78 out all of these instances It s only a naming convention and the files concerned are not otherwise affected The structure OS75 raw in this file contains the raw unedited data from the ENX file as read in in include att disc2 m and read nmea att disc2 m The structure consists of vel cor amp pg arrays of size number of bins x number of beams x number of ensembles velocity correlation magnitude echo intensity and percent good for the four beams heading pitch roll as 1 x number of ensembles array temperature soundspeed 1 x number of ensembles array The temperature here is the temperature of the water at the transducer head It is either set manually or measured The soundspeed is calculated or set manually dday ens pings 1 x number of ensembles Jarray dday is decimal day ens num the ensemble number of the pings and num ping the number of pings in each ensemble bt structure containing the bottom track data vel range cor amp rssi arrays of size 4 x number of ensembles bottom track velocity range correlation magnitude echo intensity and receiver signal strength indicator for the four beams n v structure containing navigation data sec pc minus utc number of ensembles x 1 array containing the PC clock offset in seconds txyl txy2 3 x numb
162. velocity dependent on depth Detailed description of the processing functions The master function OS75 DY017 m The main function for the processing is OS75_DY0O17 m In there the environment and variables are set and the subfunctions are called Figure 6 gives an overview of the processing routines their order and the output In the first part the work environment is defined the paths to the processing routines are added to the Matlab search path the directory with the raw data and the directory for the processed data are declared the file and cruise names are defined and the vector containing the numbers of the file sequences that are to be processed is created Several choices can be made for the processing the variable superaverage is used to define the interval over which pings will be averaged in time unit is seconds which PASHR string sets i e the first PASHR fix after the previous PADCP string or the last one before the current PADCP string The values for ref uplim and ref lowlim give the upper and lower limits of the reference layer of which a velocity is 69 calculated and used as reference velocity This is of importance mostly for water track calibration in cases where no bottom track data is available or the bottom track calibration is not satisfactory Then during the first run through OS75 DY017 m where no data are processed yet and no calibration data are available the correction values for the misalignment
163. very Instrumentation 1 en nnns 36 Computing and Instrumentation ee eee ceeccesecesceceseeeseecaeecaeesaaeeeaeeseaeseaeeseeeseneeeeeeeees 44 4 SCIENTIFIC INVESTIGATIONS eee en eene nee eene nnne nre nere 49 Lowered CTD data processing and e 49 Vessel mounted ADCP VMADCP processing using an RDI OS75 RDI OS150 and POSMV positioning reae e e n a o a na 60 Dissolved oxygen measurements nere 86 Dissolved Inorganic Carbon Total Alkalinity 89 Organic nutrients and stable isotopes eene emere 90 Inorganic Nutrient Analysis adiit ariii nennen nennen 92 POC PON POP BSi and PIC underway and CTD 94 ADCP Tan Cte aki Saee ttu ce dts du td bote rre T OE ERES 97 Near Surface Ocean Profiler Measurement eese eene 104 Phytoplankton community structure essseeeeeeeeeeeeeeen eene nenne 105 Trace MetalSainpling ar eod edat eer fev eet dee A CHR stares 108 Total dissolvable and dissolved iron eem 109 Total dissolvable and dissolved trace metals em 111 ta iuto stets 112 Particulate trace metals eia dben ceu ve n ko toco ERR anb ca d CRDI IRAE 113 Ds DISCUSSION
164. were undertaken with 1034 samples analysed in total 681 from the Stainless Steel CTD 303 from the Titanium CTD and 50 from the Tow Fish An artificial seawater matrix ASW of 40g litre sodium chloride was used as the inter sample wash and standard matrix A single set of mixed standards were made up by diluting 5mM solutions made from weighed dried salts in 1 litre The accuracy of the analyser was tested by running certified reference material CRM of nutrients on each run Data processing was undertaken using Skalar proprietary software The wash time and sample time were 90 seconds the lines were washed daily with Milli Q and 1096 Decon Performance of the analyser During the first sample run CTDs 2 5 the cadmium column used in the TON line showed significant degradation and dust entered into the detector during the analysis of CTD 3 such that the TON data for CTDs 3 5 was erroneous These samples were refrigerated until the following day where they were re run after the cadmium column was replaced However post processing of runs 2 and 3 3 10 showed large standard deviations between replicate samples for the TON line but not for phosphate or silicate Further investigation of the source of the variability revealed that the neoprene gloves used during the collection and handling of samples were the source of the contamination For the remainder of the cruise vinyl gloves were used and no further contamination was ob
165. y morning as we finished our transit of the Irish Sea Once out of the North Channel however both the wind speed and sea swell increased with gusts of GF 9 experienced around midday A preliminary plan to test the acoustic releases for the UK OSNAP benthic ADCP lander at the shelf edge was abandoned due to unfavourable conditions and instead we continued our northwards passage to station A1 Hopes of deploying the ADCP lander on our northward passage were further dashed after receiving news that the Naval Test Firing Zone situated west of the Hebrides was in use at the time of our northward passage As fate would have it the proposed position of the lander is squarely in the middle of the firing range It now looks like the next opportunity to test the acoustic releases will be at the end of transect A 16 Ongoing problems with the Surfmet system mean that no data has yet been collected with the underway instrumentation Despite close scrutiny fault finding has yet to reveal a definitive cause for the lack of data Suspicion is now on the instrument themselves rather than a communication problem At 1840 we stopped in the lee of Coll 56 58N 6 48W to deploy the titanium CTD system CTD001 to collect seawater to condition the bottles with prior to deploying the bottles again at station Al The CTD was back on deck at 1936 The trace metal tow fish was prepared and deployed and we left at 2045 to continue northwards to station A1 Thursday Oct 23

RRS Discovery Cruise DY017, 20 Oct

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