Resources

RRS James Clark Ross JR18001 (AMT28)

Cruise summary report

Cruise Info. 
Ship name (ship code)RRS James Clark Ross (74JC)
Cruise identifierJR18001 (AMT28)
Cruise period2018-09-23 — 2018-10-29
StatusCompleted
Port of departureHarwich, United Kingdom
Port of returnStanley, Falkland Islands (Malvinas)
PurposeResearch
ObjectivesThe overall aim of the Atlantic Meridional Transect programme is: to quantify key biogeochemical and ecosystem processes and their inherent variability over extended time and spatial scales in the Atlantic Ocean. This is achieved by executing an annually repeated meridional transect through contrasting oceanic provinces, ranging from oligotrophic deserts, to highly productive shelf seas.

The specific objectives of AMT are:
- To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems;
- To quantify the effects of this variability on nutrient cycling, on biogenic export and on air-sea exchange of climate active gases;
- To construct multi-decadal, multidisciplinary ocean time-series which are integrated within a wider "Pole-to-pole" observatory concept;
- To provide essential sea-truth validation for current and next generation satellite missions;
- To provide essential data for global ecosystem model development and validation;
- To provide a valuable, highly sought after and unique training arena for the next generation of UK and International oceanographers.
Chief scientistGlen A Tarran (Plymouth Marine Laboratory)
ProjectAtlantic Meridional Transect (AMT)
Cruise reportRRS James Clark Ross JR18001 (AMT28) cruise report jr18001.pdf (8.14 MB) 
Ocean/sea areas 
GeneralNorth Atlantic Ocean
South Atlantic Ocean
Track chartsRRS James Clark Ross JR18001 (AMT28) cruise track — jr18001trk.pdf (0.49 MB) 
Measurements 
Physical oceanography 
Surface measurements underway (T,S)Quantity: activity duration in days = 36
Description: The ACO files from the ships underway system will be returned to BODC and processed to 60 second intervals. Data from the oceanlogger and the seatex-gga data loggers. Channels include Temp, salinity, conducitivy, transmittance, fluorescence, wind, coordinates, PAR, TIR.
Surface measurements underway (T,S)Quantity: activity duration in days = 30
Description: Magnetic Hull SST sensor at 4m depth ~ every 20 seconds.
Surface measurements underway (T,S)Quantity: activity duration in days = 30
Description: Continuous underway SST skin measurements from ISAR (Infrared SST Autonomous Radiometer).
CTD stationsQuantity: number of profiles = 63
Description: Processed CTD data using SeaBird data processing software, from all casts deployed. Data in ODV format and CNV format. Channels calibrated on board are salinity x 2 and oxygen.
CTD stationsQuantity: number of profiles = 16
Description: Samples collected from the pre-dawn CTD every other day from 6 depths. Samples filtered for particulate organic carbon, nitrogen (-20) and biogenic silica content (room temperature) for later analysis at UBO. From the 3 shallower depths. Samples incubated 24h with Si32 then filtered for silica production (room temperature) for later analysis at UBO.
Optics (eg underwater light levels)Quantity: activity duration in days = 30
Description: Optical measurements of the ship's seawater supply (beam attenuation, backscattering and absorption coefficients)
Optics (eg underwater light levels)Quantity: activity duration in days = 30
Description: Optical measurements of surface water (remote-sensing reflectance)
Instrumented wave measurementsQuantity: activity duration in days = 30
Description: Underway (approx. every 20 mins) Wave radar (Cband) measurements and camera footage with 40-80 images every 20 minutes.(alternative PI contact is Louis Marie (IFREMER))
Other physical oceanographic measurementsQuantity: number of samples = 168
Description: Salinity samples collected 4 times a day at approximately 8am, midday, 4pm and 8pm from the ships non-toxic underway supply. Salinity data to be used to calibrate the TSG salinity channel.
Other physical oceanographic measurementsQuantity: number of profiles = 63
Description: Salinity samples collected from 5 Niskin bottle depths each pre-dawn and noon CTD. Salinity sampes to be used for the calibration of the CTD salinity channels.
Other physical oceanographic measurementsQuantity: number of observations = 62
Description: Water temperature measurements collected at a depth of 10cm at stations along the AMT cruise track using a small float and a surfboard fin that measures temperature
Chemical oceanography 
OxygenQuantity: number of profiles = 36
Description: Samples collected from 6 depths on pre-dawn CTD to 200m plus opportunistically to 1500m and analysed for dissolved oxygen using standard Winkler titration
PhosphateQuantity: number of profiles = 63
Description: 30mL samples collected at most depths from all 63 CTD casts for on board dissolved nutirent analysis of phosphate, nitrate, nitrite, and silicate. Total samples measured was 925.
NitrateQuantity: number of profiles = 63
Description: 30mL samples collected at most depths from all 63 CTD casts for on board dissolved nutirent analysis of phosphate, nitrate, nitrite, and silicate. Total samples measured was 925.
NitriteQuantity: number of profiles = 63
Description: 30mL samples collected at most depths from all 63 CTD casts for on board dissolved nutirent analysis of phosphate, nitrate, nitrite, and silicate. Total samples measured was 925.
SilicateQuantity: number of profiles = 63
Description: 30mL samples collected at most depths from all 63 CTD casts for on board dissolved nutirent analysis of phosphate, nitrate, nitrite, and silicate. Total samples measured was 925.
AlkalinityQuantity: number of profiles = 5
Description: In corespondence with SOCCOM float deployments, 500mL samples were taken from all depths with two random duplicate samples per station. Samples were poisoned for analysis at a later date on land. Total niskins sampled was 105 for the 5 stations.
pHQuantity: number of profiles = 60
Description: pH samples collected from 16 Niskin bottles depths from both the pre-dawn and noon CTD. pH data from spectrophotometria. Quantification of the carbonate system along the cruise.
pHQuantity: number of profiles = 5
Description: In corespondence with SOCCOM float deployments, 500mL samples were taken from all depths with two random duplicate samples per station. Samples were poisoned for analysis at a later date on land. Total niskins sampled was 105 for the 5 stations.
RadioactivityQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (120 µm net with cod end 63 µm) vertical haul from 200 m or 250 m to surface for Rhizaria isolation (Si32 incubations for silica production), biogenic silica content and POCPON of isolated Rhizaria, lugol samples for community composition and abundance by FlowCAM, ethanol samples (-20) for microsope sorting and DNA samples (-80).
RadioactivityQuantity: number of profiles = 16
Description: Samples collected from the pre-dawn CTD every other day from 6 depths. Samples filtered for particulate organic carbon, nitrogen (-20) and biogenic silica content (room temperature) for later analysis at UBO. From the 3 shallower depths. Samples incubated 24h with Si32 then filtered for silica production (room temperature) for later analysis at UBO.
Other chemical oceanographic measurementsQuantity: number of profiles = 5
Description: In corespondence with SOCCOM float deployments, 6 1L sample bottles were taken from both the chlorophyl max and surface niskins and filtered for POC/HPLC analysis at a later date on land. Total niskins sampled was 10 for teh 5 stations.
Other chemical oceanographic measurementsQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (120 µm net with cod end 63 µm) vertical haul from 200 m or 250 m to surface for Rhizaria isolation (Si32 incubations for silica production), biogenic silica content and POCPON of isolated Rhizaria, lugol samples for community composition and abundance by FlowCAM, ethanol samples (-20) for microsope sorting and DNA samples (-80).
Other chemical oceanographic measurementsQuantity: number of profiles = 16
Description: Samples collected from the pre-dawn CTD every other day from 6 depths. Samples filtered for particulate organic carbon, nitrogen (-20) and biogenic silica content (room temperature) for later analysis at UBO. From the 3 shallower depths. Samples incubated 24h with Si32 then filtered for silica production (room temperature) for later analysis at UBO.
Biology and fisheries 
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of profiles = 63
Description: Phytoplantkon pigment samples collected from each CTD cast at surface (5 m) and DCM for High Performance Chromatography Analysis (HPLC). Two samples per depth were collected. Samples were filtered, flash frozen in liquid nitrogen and stored in the -80°C freezer.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 62
Description: Phytoplankton pigment samples collected twice a day from the ship's underway system for High Performance Chromatography Analysis (HPLC). One sample was always taken during the noon CTD cast, while the other was collected at night (~2000). Samples were filtered, flash frozen in liquid nitrogen and stored in the -80°C freezer.
Particulate organic matter (inc POC, PON)Quantity: number of stations = 777
Description: Particulate organic matter samples collected from the underway seawater system. To be analyzed for particulate organic phosphorus, nitrogen, and carbon as well as chemical oxygen demand. The volume collect was biomass-dependent and varied between 3-8 L.
Particulate organic matter (inc POC, PON)Quantity: number of hauls = 29
Description: Daily predawn WP2 bongo (120 µm net with cod end 63 µm) vertical haul from 200 m or 250 m to surface for Rhizaria isolation (Si32 incubations for silica production), biogenic silica content and POCPON of isolated Rhizaria, lugol samples for community composition and abundance by FlowCAM, ethanol samples (-20) for microsope sorting and DNA samples (-80).
Particulate organic matter (inc POC, PON)Quantity: number of profiles = 16
Description: Samples collected from the pre-dawn CTD every other day from 6 depths. Samples filtered for particulate organic carbon, nitrogen (-20) and biogenic silica content (room temperature) for later analysis at UBO. From the 3 shallower depths. Samples incubated 24h with Si32 then filtered for silica production (room temperature) for later analysis at UBO.
Particulate organic matter (inc POC, PON)Quantity: number of samples = 29
Description: POM samples collected at pre-dawn for the analysis of POC/PON concentrations and the stable isotope signatures (13C and 15N) in seston.
Dissolved organic matter (inc DOC)Quantity: number of profiles = 26
Description: DOM samples collected from the pre-dawn CTD cast for 3 depths (surface, 33% light penetration and DCM) for determination of Dissolved Organic Matter at the home lab. Samples were filtered, acidified to pH=2 and passed over solid phase extraction columns. Column elutes stored frozen.
Dissolved organic matter (inc DOC)Quantity: number of profiles = 25
Description: Samples collected from the pre-dawn CTD at 4 depths corresponding to surface (5 m), DCM, DCM + 10 m, 200 m. Samples filtered and water frozen (-20 C) for later DOC/N/P analysis at UEA.
Dissolved organic matter (inc DOC)Quantity: number of profiles = 2
Description: DOM samples collected from deep CTD casts at 5, 50, 150, 250, 500, 1000, 2000, 3000 and 4000 m for large volume determination of Dissolved Organic Matter at the home lab. Samples were filtered, acidified to pH=2 and passed over solid phase extraction columns. Column elutes stored frozen.
Biochemical measurements (eg lipids, amino acids)Quantity: number of profiles = 25
Description: Bacterial production and respiration samples collected from the pre-dawn CTD cast for 3 depths (surface, 33% light penetration and DCM). Samples were supplied with radiolabeled Leucine to be collected as material on filters and as labeled CO2, subsequently counted on onboard scintillation counter and subjected to regression analysis. Samples saved for possible reanalysis on more sensitive equipment at NOCS.
Biochemical measurements (eg lipids, amino acids)Quantity: number of profiles = 25
Description: Samples collected from the pre-dawn CTD from 2 depths corresponding to the surface (5 m) and DCM for RNA. Samples filtered and filters frozen (-80 C) for later analysis at UEA.
PhytoplanktonQuantity: number of profiles = 25
Description: Samples for phytoplankton collected from the CTD at 2 depths corresponding to surface (5 m) and DCM and fixed immediately in Lugol's solution for analysis by PML.
PhytoplanktonQuantity: number of profiles = 63
Description: Quantification of pico- and nanophytoplankton abundance from all depths between the surface and 200m from CTD casts by flow cytometry
PhytoplanktonQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (200 µm) vertical haul from 200 m or 250 m to surface for mesoplankton community composition and abundance by microscopy/FlowCAM
PhytoplanktonQuantity: number of profiles = 25
Description: Samples for phytoplankton collected from the CTD at 2 depths corresponding to surface (5 m) and DCM. Samples concentrated and fixed in Lugol's solution for analysis by PML.
PhytoplanktonQuantity: number of profiles = 60
Description: Potencial role of Saharan dust as a fertilizer for marine phytoplankton. Water samples collected from 2 depths above DCM and 2 depths below in Niskin bottles from both CTD (pre-dawn and noon).
PhytoplanktonQuantity: number of profiles = 60
Description: Samples for phytoplankton collected from each CTD at 2 depths corresponding to surface (5 m) and DCM and fixed immediately in acidic Lugol's solution for later analysis by the University of Lisbon.
PhytoplanktonQuantity: number of profiles = 16
Description: Samples collected from the pre-dawn CTD every other day from 6 depths. Samples filtered for particulate organic carbon, nitrogen (-20) and biogenic silica content (room temperature) for later analysis at UBO. From the 3 shallower depths. Samples incubated 24h with Si32 then filtered for silica production (room temperature) for later analysis at UBO.
ZooplanktonQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (120 µm net with cod end 63 µm) vertical haul from 200 m or 250 m to surface for Rhizaria isolation (Si32 incubations for silica production), biogenic silica content and POCPON of isolated Rhizaria, lugol samples for community composition and abundance by FlowCAM, ethanol samples (-20) for microsope sorting and DNA samples (-80).
ZooplanktonQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (100 µm) vertical haul from 200 m or 250 m to surface for mesozooplankton (100-500, 500-2000, >2000 um size classes) metabolism and isotopic signatures (15N and 13C)
ZooplanktonQuantity: number of hauls = 29
Description: Daily predawn WP2 bongo (200 µm) vertical haul from 200 m or 250 m to surface for mesoplankton community composition and abundance by microscopy/FlowCAM
Pelagic bacteria/micro-organismsQuantity: number of profiles = 63
Description: Quantification of heterotrophic bacteria abundance from all depths between the surface and 200m from CTD casts by flow cytometry
Pelagic bacteria/micro-organismsQuantity: number of profiles = 31
Description: Samples collected at 6 depths (surface, 33% light, 14% light, DCM, DCM+10 m, 200 m) from the pre-dawn CTD for chlorophyll-a determination
Pelagic bacteria/micro-organismsQuantity: number of profiles = 31
Description: Quantification of microbial community respiration at 6 depths (surface, 33% light, 14% light, DCM, DCM+10 m, 200 m) from the pre-dawn CTD by analyzing the Electron Transport System activity.
Pelagic bacteria/micro-organismsQuantity: number of profiles = 22
Description: Molecular samples collected from the pre-dawn CTD cast for 3 depths (surface, 33% light penetration and DCM) for analysis of microbiota. Samples were non-fixed and fixed with 1% paraformaldehyde and stored at -80°C after flash freezing with LN, for later analysis at NOCS.
Pelagic bacteria/micro-organismsQuantity: number of profiles = 28
Description: Counts samples collected from the pre-dawn CTD cast for 3 depths corresponding to surface (5 m), 33% light penetration and DCM for flowcytometric determination of microbiota. Samples were fixed with 0.5% glutaraldehyde and 1% paraformaldehyde and stored at -80°C after flash freezing with LN, for later analysis at NOCS.
Other biological/fisheries measurementQuantity: number of samples = 126
Description: DNA samples from 5 m and 50 m at all stations along the AMT cruise track to be used for amplicon sequencing and metagenomic analyses
Other biological/fisheries measurementQuantity: number of profiles = 62
Description: Samples collected from both the pre-dawn and noon CTDs from two depths, the surface and the DCM for DNA analysis once returned to PML.
Other biological/fisheries measurementQuantity: number of profiles = 25
Description: Samples collected from 6 depths on the pre-dawn CTD for determination of plankton community respiration derived from dissolved oxygen consumption
Other biological/fisheries measurementQuantity: number of profiles = 25
Description: Samples collected from 6 depths on the pre-dawn CTD for determination of plankton community respiration derived from INT reduction
Meteorology 
Upper air observationsQuantity: number of observations = 9
Description: Sky Infrared Brightness temperature measurements (9.5 to 11 um), full sky coverage. All sky camera 1 s time lapse during Sky BT measurements.
Routine standard measurementsQuantity: number of deployments = 28
Description: Radiosonde deployments measuring air temperature, humidity, wind speed and wind direction (alternative PI cnotacts are Gavin Tilstone (PML) or Steve Cowell (BAS))
Routine standard measurementsQuantity: activity duration in days = 30
Description: Underway continuous 3-axis wind speed and direction. Humidity and temperature sensors.
Atmospheric chemistryQuantity: number of observations = 27
Description: Aerosol samples were collected every 24-48 hours using an Andersen high-volume dust collector. Resulting filters were stored in the -20°C freezer and will be initially analysed for its content in trace elements by the UEA, before being analysed for its dust particle-size and bulk-composition at NIOZ.
Other meteorological measurementsQuantity: activity duration in days = 36
Description: The ACO files from the ships underway system will be returned to BODC and processed to 60 second intervals. Data from the oceanlogger and the seatex-gga data loggers. Channels include Temp, salinity, conducitivy, transmittance, fluorescence, wind, coordinates, PAR, TIR.
Moorings, landers, buoys 
Physical oceanography 
Neutrally buoyant floats24° 54' 22" S  25° 54' 10" W — Univ. Washington Argo Float 12776 Deployment
Neutrally buoyant floats34° 34' 52" S  36° 5' 29" W — UK Met Office Argo Float 8064 Deployment
Neutrally buoyant floats37° 0' 43" S  38° 50' 5" W — UK Met Office Argo Float 8065 Deployment
Neutrally buoyant floats27° 12' 1" S  28° 15' 0" W — SOCCOM Float 12696 Deployment
Neutrally buoyant floats15° 24' 27" S  25° 0' 0" W — Univ. Washington Argo Float 12691 Deployment
Neutrally buoyant floats15° 24' 28" S  25° 0' 0" W — UK Met Office Argo Float 7001 Deployment
Neutrally buoyant floats20° 22' 45" S  25° 3' 35" W — Univ. Washington Argo Float 12632 Deployment
Neutrally buoyant floats26° 37' 40" S  27° 39' 18" W — UK Met Office Argo Float 7001 Deployment
Neutrally buoyant floats27° 12' 3" S  28° 14' 59" W — SOCCOM Float 12883 Deployment
Neutrally buoyant floats32° 22' 37" S  33° 40' 30" W — SOCCOM Float 12881 Deployment
Neutrally buoyant floats34° 34' 59" S  36° 5' 30" W — SOCCOM Float 12700 Deployment
Neutrally buoyant floats39° 12' 36" S  41° 28' 30" W — SOCCOM Float 12747 Deployment
Neutrally buoyant floats41° 22' 10" S  44° 0' 45" W — SOCCOM Float 12778 Deployment
Biology and fisheries 
Sediment traps18° 32' 42" S  25° 4' 47" W — Sediment trap and current meter mooring recovery
Sediment traps18° 32' 42" S  25° 4' 48" W — Sediment trap and current meter mooring deployment.
Data held at BODC Get data
Discrete samples 
63  CTD frame plus rosette sampler
63  Drifting Buoy
2  Instrument mooring
14  Metocean Argos Drifting Buoy
30  Optical instruments
28  Radiosonde
168  Sample taken from ship's non-toxic supply
29  Twin WP-2 net mounted on a frame