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RRS James Clark Ross JR20030910 (AMT13, JR91)

Cruise summary report

Cruise Info. 
Ship name (ship code)RRS James Clark Ross (74JC)
Cruise identifierJR20030910 (AMT13, JR91)
Cruise period2003-09-10 — 2003-10-14
StatusCompleted
Port of departureImmingham, United Kingdom
Port of returnStanley, Falkland Islands (Malvinas)
PurposeResearch
ObjectivesAMT13 is the second in the new series of Atlantic Meridional Transect cruises, funded as a NERC consortium project, and is building on the successes and format developed by Plymouth Marine Laboratory in pioneering the first eleven of these types of cruises.
This cruise will transect through both the North and South Atlantic gyre systems and the NW African upwelling with the aim of understanding the physical and chemical structures that make up these ocean systems and how they interact with the atmosphere.
Chief scientistCarol Robinson (Plymouth Marine Laboratory)
ProjectAtlantic Meridional Transect (AMT), a NERC Consortium
Coordinating bodyPlymouth Marine Laboratory
Cruise reportRRS James Clark Ross JR20030910 (AMT13, JR91) cruise report jr91.pdf (5.20 MB)  RRS James Clark Ross JR20030910 (AMT13, JR91) cruise report jr_amt13.pdf (5.14 MB) 
Ocean/sea areas 
GeneralNorth Atlantic Ocean
South Atlantic Ocean
SpecificNorth and South Atlantic gyre systems and the NW African upwelling
Track chartsRRS James Clark Ross JR20030910 (AMT13, JR91) cruise track — jr91track.pdf (0.34 MB) 
Measurements 
Physical oceanography 
Surface measurements underway (T,S)Description: Seawater samples for salinity analysis on Guildline Autosal 8400B salinometer, for checking calibration and drift of conductivity sensor on underway thermosalinograph.
CTD stationsDescription: Seawater samples for salinity analysis on Guildline Autosal 8400B salinometer, for checking calibration and drift of conductivity sensors on both CTD systems.
Transparency (eg transmissometer)Quantity: number of profiles = 34
Description: Measurements of the 530nm volume scattering function at 100, 125 and 150 degrees.
Transparency (eg transmissometer)Quantity: number of profiles = 33
Description: Measurements of spectral attenuation and absorption at 412, 440, 488, 510, 532, 555, 650, 676 and 715nm. With concurrent CTD data for correction.
Transparency (eg transmissometer)Quantity: number of profiles = 20
Description: Measurement of UV downwelling irradiance from 280 to 550 nm at a resolution of 5nm.
Transparency (eg transmissometer)Quantity: number of profiles = 10
Description: Measurements of CDOM spectral absorption at 412, 440, 488, 510, 532, 555, 650 and 676.
Optics (eg underwater light levels)Quantity: number of profiles = 50
Description: Free fall profiler measurements of upwelling spectral radiance and downwelling spectral irradiance, tilt, roll and temperature to a depth of 50 m. Wavelengths (nominal) 412, 443, 490, 510, 555, 620, 665, 685 nm. With concurrent measurements of surface irradiance.
Chemical oceanography 
OxygenQuantity: number of stations = 74
Description: Gross production and dark community respiration measurements based on the analysis of dissolved oxygen in seawater taken from 5 depths at 23 stations and from the surface at 2 stations. Measurment of in-situ oxygen concentration for the calibration of the CTD oxygen sensor (49 stations).
OxygenQuantity: number of samples = 19
Description: Using incubation experiments and Winkler titrations to determine the amount of Oxygen consumed during Photo-degradation of CDOM
Carbon dioxideQuantity: number of samples = 50
Description: On-shore coulometric DIC measurements using the SOMMA system from surface samples taken from the ship's clean seawater line
Carbon dioxideQuantity: number of samples = 350
Description: On-shore coulometric DIC measurements using the SOMMA system from CTD samples
Carbon dioxideQuantity: activity duration in days = 31
Description: Measurements of atmospheric and equilibrated seawater CO2.
Other dissolved gasesQuantity: number of samples = 54
Description: Filtrates retained for daily (after 22/09/03) analysis of the trace gas dimethylsulphide (DMS), and the dissolved form of its precursor dimethylsulphoniopropionate (DMSPd) from non-toxic supply (at 1500 hrs)
Other dissolved gasesQuantity: number of samples = 108
Description: Filters analysed for the particulate form of dimethylsulphoniopropionate (DMSPp) from CTD 24 onwards
Other dissolved gasesQuantity: number of samples = 27
Description: Filters analysed daily (after 22/09/03) for the particulate form of dimethylsulphoniopropionate (DMSPp) from non-toxic supply (at 1500 hrs)
Other dissolved gasesQuantity: number of samples = 216
Description: Filtrates retained for analysis of the trace gas dimethylsulphide (DMS), and the dissolved form of its precursor dimethylsulphoniopropionate (DMSPd) from CTD 24 onwards
Other dissolved gasesQuantity: number of samples = 392
Description: Nitrous oxide and methane saturations using single phase equilibration gas chromatography. Taken at several depths from pre-dawn CTD.
PhosphateQuantity: number of profiles = 71
Description: Phosphate nutrient concentrations at up to 15 depths
NitrateQuantity: number of profiles = 71
Description: Nitrate nutrient concentrations at up to 15 depths
NitriteQuantity: number of profiles = 71
Description: Nitrite nutrient concentrations at up to 15 depths
AmmoniaQuantity: number of profiles = 71
Description: Ammonium nutrient concentrations at up to 15 depths
SilicateQuantity: number of profiles = 71
Description: Silicate nutrient concentrations at up to 15 depths
AlkalinityQuantity: number of samples = 350
Description: Potentiometric alkalinity determination with the VINDTA system from CTD samples
AlkalinityQuantity: number of samples = 50
Description: Potentiometric alkalinity determination with the VINDTA system from surface samples taken from the ship's clean seawater line
Trace elementsQuantity: number of samples = 25
Description: Dissolved iron samples collected with "bucket" sampler
RadioactivityQuantity: number of samples = 798
Description: Primary production measurements based on radio-isotope (14C) phytoplankton labelling experiments (dawn to dusk) using on-deck incubators. Includes size-fractionation at two depths.
RadioactivityQuantity: number of samples = 216
Description: Primary production measurements based on radio-isotope (14C) phytoplankton labelling experiments: Photosynthesis vs Irradiance (PvE) incubations.
IsotopesQuantity: number of samples = 396
Description: Size-fractionated new and regenerated production at 6 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) determined by 15N stable isotope labelling of phytoplankton growth in on-deck incubators using 15-NO3, 15-NH4 and 15-urea. NH4 excretion rates also measured by isotopic dilution.
IsotopesDescription: Water column 234 Thorium measurements from the CTD and zooplankton nets to calculate export production and downward POC flux.
IsotopesQuantity: number of samples = 1500
Description: Nitrification/ammonium regeneration/N-assimilation estimates at the chlorophyll maximum and 55% surface PAR measuring 15-N enrichment and dilution in the dissolved and particulate phases
IsotopesQuantity: number of samples = 97
Description: 20 litre samples from seven depths filtered onto 142 mm polycarbonate filters for particulate and dissolved thorium analysis. Filters are folded in reproducible manner and counted on board on a beta counter.
IsotopesQuantity: number of hauls = 13
Description: Samples collected from 100 m net haul (>50 um <200 um). Sample split: 1/8 of sample filtered onto GFF filter for POC/PON analysis, 6/8 of sample filtered onto 0.4 um polycarbonate filter for thorium analysis.
IsotopesQuantity: number of samples = 155
Description: 18O/16O and 15N/14N isotopic ratios of nitrous oxide using isotopic ratio mass spectrometry (IRMS). Taken at several depths from pre-dawn CTD.
IsotopesQuantity: number of samples = 340
Description: Delta15N isotope gaseous enrichment of water samples. These were filtered and the filters retained for Mass Spec analysis at a later time.
Other chemical oceanographic measurementsQuantity: number of samples = 91
Description: 4 litres sampled from corresponding stations and depths as those for thorium analysis and filtered onto GFF filters, stored frozen for future analysis of particulate organic carbon (POC) and particulate organic nitrogen (PON)
Other chemical oceanographic measurementsQuantity: number of samples = 199
Description: Samples for analysis of absorption of UV and Visible wavelengths of light to determine CDOM content of seawater using a UV/Visible Spectrometer and waveguide.
Other chemical oceanographic measurementsQuantity: number of samples = 26
Description: Sea water samples for semi-volatile organic analysis
Other chemical oceanographic measurementsQuantity: number of samples = 340
Description: Nitrogenase activity measurements by means of acetylene reduction to ethylene, using G.C. methods
Contamination 
Suspended matterQuantity: number of hauls = 13
Description: Samples collected from 100 m net haul (>50 um <200 um). Sample split: 1/8 of sample filtered onto GFF filter for POC/PON analysis, 6/8 of sample filtered onto 0.4 um polycarbonate filter for thorium analysis.
Suspended matterQuantity: number of samples = 91
Description: 4 litres sampled from corresponding stations and depths as those for thorium analysis and filtered onto GFF filters, stored frozen for future analysis of particulate organic carbon (POC) and particulate organic nitrogen (PON)
Biology and fisheries 
Primary productivityQuantity: number of samples = 396
Description: Size-fractionated new and regenerated production at 6 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) determined by 15N stable isotope labelling of phytoplankton growth in on-deck incubators using 15-NO3, 15-NH4 and 15-urea. NH4 excretion rates also measured by isotopic dilution.
Primary productivityQuantity: number of samples = 216
Description: Primary production measurements based on radio-isotope (14C) phytoplankton labelling experiments: Photosynthesis vs Irradiance (PvE) incubations.
Primary productivityQuantity: number of samples = 798
Description: Primary production measurements based on radio-isotope (14C) phytoplankton labelling experiments (dawn to dusk) using on-deck incubators. Includes size-fractionation at two depths.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of profiles = 70
Description: Measurements of fluorescence of Phycocyanin and Phycoerythrin.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of profiles = 43
Description: Measurements from Chelsea Instruments FRRF fluorometer from both morning and dawn casts.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 84
Description: Particle Absorbance samples at 3 euphotic light depths from the 11am optics cast. Samples stored frozen at -80.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 105
Description: Particle Absorbance samples at 3 depths from the 11am optics cast. Samples stored frozen at -80.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 295
Description: Duplicate HPLC samples at 5 or 6 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) from the 4am, single samples from the 11am optics cast. Samples stored frozen at -80.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 400
Description: Size-fractionated (0.2, 2, 5 and 10 um) chlorophyll-a samples at 5 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) from both the 3am and 11am CTD casts. Pigment extracted in 90% acetone.
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of samples = 295
Description: Chlorophyll-a samples at 5 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) from both the 3am and 11am CTD casts. Pigment extracted in 90% acetone.
Particulate organic matter (inc POC, PON)Quantity: number of samples = 295
Description: POC/N samples at 5 or 6 euphotic light depths (97%, 55%, 33%, 14%, 1% and 0.1%) from both the 4am and 11am optics cast. Samples stored at -20 deg C.
Dissolved organic matter (inc DOC)Quantity: number of samples = 250
Description: Duplicate DOC/N/P samples from all predawn CTD casts, preserved with phosphoric acid or frozen.
PhytoplanktonQuantity: number of stations = 6
Description: 6-litre seawater samples from chlorophyll maximum for feeding zooplankton during 24-hour grazing experiments.
PhytoplanktonQuantity: number of samples = 313
Description: Samples collected via CTD at 11 depths from 23 stations were fixed in Lugol's iodine and formalin for phytoplankton and mirozooplankton sizing and counting.
PhytoplanktonQuantity: number of profiles = 52
Description: Pico and nanophytoplankton abundance estimates from analyses of live samples from the CTD casts by flow cytometry from all available depths
PhytoplanktonQuantity: number of profiles = 1300
Description: DNA samples for later use in quantitative PCR protocol for Prochlorococcus spp. Clades
PhytoplanktonQuantity: number of samples = 250
Description: Water samples preserved in Lugol's solution and buffered formalin for the later enumeration of phytoplankton by microscopy.
PhytoplanktonQuantity: number of stations = 12
Description: 20-litre seawater samples chlorophyll from maximum for feeding zooplankton during 24-hour grazing experiments.
PhytoplanktonQuantity: number of samples = 308
Description: Samples collected via CTD at 10 depths from 28 stations were fixed in Lugol's iodine for microzooplankton sizing and counting
PhytoplanktonQuantity: number of stations = 20
Description: 50-litre seawater samples from surface or chlorophyll maximum (alternate days) for grazing experiments using dilution method technique.
PhytoplanktonQuantity: number of samples = 800
Description: Samples from the CTD casts from all available depths for analyses of pico- and nano-phytoplankton abundance and composition using flow cytometry. Samples stored frozen at -80deg C.
PhytoplanktonQuantity: number of experiments = 180
Description: Cultured samples of a heterotrophic dinoflagellate, exposed to 3 different regimes of UV exposure along the AMT and population numbers counted in a flow cytometer
ZooplanktonQuantity: number of samples = 150
Description: Epifluorescence staining of filters from filtration of seawater samples collected via CTD at 6 light depths from 25 stations for heterotrophic flagellate microscopic slide preparation
ZooplanktonQuantity: number of hauls = 6
Description: Zooplankton for the feeding experiment collected from 100 to 0 m vertical plankton tows made with a 50 um mesh net at 9 stations
ZooplanktonQuantity: number of stations = 6
Description: 6-litre seawater samples from chlorophyll maximum for feeding zooplankton during 24-hour grazing experiments.
ZooplanktonQuantity: number of hauls = 58
Description: Vertical 200 and 50 um "bongo" net hauls from 200 and 50 m depths collected at 23 stations. 50 um samples fixed in Lugol's iodine and formalin for later microscopic assessment. 200 um samples were fixed in formalin for later zooplankton sizing and counting.
ZooplanktonQuantity: number of samples = 520
Description: Samples collected via CTD at surface depth from 28 stations which were recorded at T0, then incubated at T24, and T48 for 3 different regimes of UV exposure, and then fixed in Lugol's iodine for microzooplankton sizing and counting
ZooplanktonQuantity: number of hauls = 24
Description: Vertical 53 um triple net hauls from 200 m depth collected at 24 stations. 53 um samples fixed in formalin for later microscopic assessment and counting.
ZooplanktonQuantity: number of hauls = 12
Description: Zooplankton for the feeding experiment collected from 200 to 0 m vertical plankton tows made with a 53 um mesh net at 12 stations
ZooplanktonQuantity: number of hauls = 24
Description: Vertical 53 um triple net hauls from 200 m depth collected at 24 stations. 53 um samples frozen for later chlorophyll gut contents analysis.
ZooplanktonQuantity: number of stations = 12
Description: 20-litre seawater samples chlorophyll from maximum for feeding zooplankton during 24-hour grazing experiments.
ZooplanktonQuantity: number of stations = 20
Description: 50-litre seawater samples from surface or chlorophyll maximum (alternate days) for grazing experiments using dilution method technique.
Pelagic bacteria/micro-organismsQuantity: number of samples = 800
Description: Samples (+ 400 filters) from the CTD casts from all available depths for analyses of bacterial abundance and composition using flow cytometry and FISH. Samples stored frozen at -80deg C.
Pelagic bacteria/micro-organismsQuantity: number of profiles = 52
Description: Heterotrophic bacteria abundance estimates from analyses of fixed samples from the CTD casts by flow cytometry from all available depths
Meteorology 
Atmospheric chemistryQuantity: number of samples = 22
Description: Rain samples collected along track
Atmospheric chemistryQuantity: number of samples = 23
Description: Aerosol samples collected along track
Atmospheric chemistryQuantity: number of samples = 50
Description: Aerosol samples collected along track
Data held at BODC Get data
Discrete samples 
37  Atmospheric air sampling pumpMetal concentrations in the atmosphere
Inorganic phosphorus species concentrations in the atmosphere
Inorganic silicon species concentrations in the atmosphere
Concentration of nitrogen species in the atmosphere
Concentration of inorganic halogens in the atmosphere
Concentration of organic matter in the atmosphere
Concentrations of carboxylic acids and carboxylates in the atmosphere
Sulphur species concentrations in the atmosphere
78  CTD frame plus rosette samplerAmmonium and ammonia concentration parameters in water bodies
Phytoplankton taxonomic biomass in water bodies
Raw suspended particulate material concentration sensor output
Particulate total and organic carbon concentrations in the water column
Oxygen production and respiration in the water column
Particulate total and organic nitrogen concentrations in the water column
Visible waveband radiance and irradiance measurements in the water column
Transmittance and attenuance of the water column
Bacteria generic abundance in water bodies
Organosulphur and organoselenium species concentration parameters in water bodies
Microzooplankton taxonomy-related biomass expressed as carbon per unit volume of the water column
Density of the water column
Chlorophyll pigment concentrations in water bodies
Phytoplankton taxonomic abundance in water bodies
Primary production in the water column
Silicate concentration parameters in the water column
Microzooplankton non taxonomy-related biomass expressed as carbon per unit volume of the water column
Salinity of the water column
Temperature of the water column
Carotenoid and flavenoid pigment concentrations in water bodies
Raw light meter output
Nitrate concentration parameters in the water column
Plankton abundance per unit volume of the water column
Dissolved oxygen parameters in the water column
Plankton biomass expressed as carbon per unit volume of the water column
Concentration of alkanes in the water column
Microzooplankton taxonomic abundance in water bodies
Microzooplankton generic abundance in water bodies
Nitrite concentration parameters in the water column
Phosphate concentration parameters in the water column
Dissolved concentration parameters for other gases in the water column
38  Moving Vessel Profiler instrument
11  Rain water collectorPrecipitation chemistry
Metadata parameters
186  Sample taken from ship's non-toxic supplyOrganosulphur and organoselenium species concentration parameters in water bodies
Chlorophyll pigment concentrations in water bodies
Nitrate concentration parameters in the water column
Nitrite concentration parameters in the water column
2  Surface water sample collected by a bucket on a ropeBacteria generic abundance in water bodies
Organosulphur and organoselenium species concentration parameters in water bodies
Phytoplankton taxonomic abundance in water bodies
Nitrate concentration parameters in the water column
Plankton abundance per unit volume of the water column
Nitrite concentration parameters in the water column
48  Twin WP-2 net mounted on a frameZooplankton non taxonomy-related biomass expressed as nitrogen per unit volume of the water column
Zooplankton non taxonomy-related biomass expressed as carbon per unit volume of the water column
Metadata parameters
Zooplankton non taxonomy-related abundance per unit volume of the water column
24  WP-2 zooplankton netZooplankton taxonomy-related abundance per unit volume of the water column
Fish abundance in water bodies