Cruise inventory
RRS James Cook JC039 (AMT19, JC040)
Cruise summary report
| Cruise Info. | |
| Cruise period | 2009-10-13 — 2009-11-28 |
| Status | Completed |
| Port of departure | Falmouth, United Kingdom |
| Port of return | Punta Arenas, Chile |
| Purpose | Research |
| Objectives | AMT19 (JC039) is the second cruise of the third phase of the Atlantic Meridional Transect (AMT) programme. The programme is hosted by Plymouth Marine Laboratory in collaboration with the National Oceanography Centre, Southampton and provides an exceptional opportunity for nationally and internationally driven collaborative research and provides a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, AMT informs on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.
The aims of the AMT programme are to quantify the nature and causes of ecological and biogeochemical variability in the planktonic ecosystems of the Atlantic Ocean, and to assess the effects of this variability on biological carbon cycling and air-sea exchange of radiatively active gases and aerosols. Between 1995 and 2005 marine and atmospheric data were collected twice a year along a 13,500 km transect in the Atlantic Ocean. The cruise track enabled biogeochemical measurements to be made within the poorly studied North and South Atlantic oligotrophic gyres as well as within equatorial and coastal upwelling regions. The range of ecosystems sampled has facilitated the calibration and validation of newly developed techniques, provided a testbed for comparative ecology and enabled the development of atmospheric and oceanographic models. The unique AMT dataset continues to be deposited and made available to the wider community through the British Oceanographic Data Centre. The programme has provided a platform for national and international collaboration (~80 scientists from 11 countries), and has contributed to the training of >70 PhD students and staff. AMT has produced >170 peer reviewed publications. Cruise JC040 was part of JC039 (28/11/2009 - 01/12/2009) and involved the deployment SHRIMP (Seafloor High Resolution IMaging Platform) with 3 hours of bottom time at two sites (0.5knot towing speed). Stills and video were analysed to estimate diversity and relative abundance of megafauna. |
| Chief scientist | Andy Rees (Plymouth Marine Laboratory) |
| Project | Atlantic Meridional Transect (AMT) |
| Coordinating body | NERC |
| Cruise report |  (2.88 MB) |
| Ocean/sea areas | |
| Specific | Atlantic Ocean |
| Track charts | (0.19 MB) |
| Measurements | |
| Physical oceanography | |
| Surface measurements underway (T,S) | Quantity: number of stations = 31 Description: Water samples collected for iron and cobalt analysis, spectrophotometric seawater ph, nitrogen fixation using 15N isotope and co2 perturbation experiments. |
| Surface measurements underway (T,S) | Quantity: number of stations = 70 Description: Biological uptake of methanol, acetone and acetaldehyde made from CTDs at pre-dawn and solar noon stations. Vertical profiles analysed at 5 depths (surface ? 200m) from most pre-dawn casts, surface only measurements from solar noon cast. Analysis by onboard Liquid Scintillation Counting. Samples for DNA/RNA extractions (for identification of Methylotrophic bacteria) were also taken from approximately 4 depths from the pre dawn CTD and from surface only during the solar noon CTD. Samples collected in Sterivex filters. |
| Surface measurements underway (T,S) | Quantity: activity duration in days = 45 Description: Operated an along-track flow-through system from ship?s non-toxic seawater supply to characterize bio-optical properties of the water (backscattering, fluorescense) (~24 h/day). Also operated Micro-SAS system on the ship?s meteorological platform to measure upwelling radiance, downwelling radiance and total downwelling irradiance (~10h/day). |
| CTD stations | Quantity: number of stations = 31 Description: Water samples collected for iron and cobalt analysis, spectrophotometric seawater ph, nitrogen fixation using 15N isotope and co2 perturbation experiments. |
| Transparency (eg transmissometer) | Quantity: number of deployments = 78 Description: In-water optics rig: i) Fast Repetition Rate Fluorometer (phytoplankton physiology); ii) Satlantic UV sensor (downwelling spectral UV light at 305, 320, 340 and 380 nm); iii) Wetlabs ac-9 (attenuation and absorption at 9 wavelengths: 412, 440, 488, 510, 532, 555, 650, 676, 715 nm); iv) SeaBird SBE19+ CTD (temperature and salinity with depth for correction of the ac9); v) ancillary PAR measurements (determination of light levels in water column); vi) Hobilabs hydroscat 6 (bb6: backscatter at 6 wavelengths: 442, 488, 550, 620, 671, 852) |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 45 Description: Operated an along-track flow-through system from ship?s non-toxic seawater supply to characterize bio-optical properties of the water (backscattering, fluorescense) (~24 h/day). Also operated Micro-SAS system on the ship?s meteorological platform to measure upwelling radiance, downwelling radiance and total downwelling irradiance (~10h/day). |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 10 Description: Underway hyperspectral particulate beam attenuation and absorption collected using a WetLabs ACs meter |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 45 Description: Underway volume scattering function (0.01 to ~11 deg) collected using a Sequoia Scientific LISST-100X |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 45 Description: Underway optical backscattering at three wavelengths (470, 526, 656 nm) collected using a WetLabs ECO-BB3 meter Underway optical beam attenuation coefficient at two wavelengths (526, 650 nm) collected using two WetLabs Cstar meters |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 46 Description: Deck mounted (over the CTD winch cab) Satlantic HyperSAS sensor: Hyperspectral (300 ? 900 nm) water-leaving reflectance measurements at 6 minute intervals through daylight hours; measurements integrated over 30 s. These include water, sky and sun radiance measuring sensors (3). |
| Optics (eg underwater light levels) | Quantity: activity duration in days = 35 Description: Underway multispectral particulate beam attenuation and absorption collected using a WetLabs AC9 meter |
| Optics (eg underwater light levels) | Quantity: number of deployments = 78 Description: In-water optics rig: i) Fast Repetition Rate Fluorometer (phytoplankton physiology); ii) Satlantic UV sensor (downwelling spectral UV light at 305, 320, 340 and 380 nm); iii) Wetlabs ac-9 (attenuation and absorption at 9 wavelengths: 412, 440, 488, 510, 532, 555, 650, 676, 715 nm); iv) SeaBird SBE19+ CTD (temperature and salinity with depth for correction of the ac9); v) ancillary PAR measurements (determination of light levels in water column); vi) Hobilabs hydroscat 6 (bb6: backscatter at 6 wavelengths: 442, 488, 550, 620, 671, 852) |
| Chemical oceanography | |
| Oxygen | Quantity: number of stations = 15 Description: Vertical profiles in the N. and S. subtropical Atlantic thermocline (~150-500m, depth variable) for dissolved gases (Ar, N2, Kr, O2) to examine diapycnal mixing. Winkler dissolbed oxygen samples also taken. Sampled exclusively from the mid-day CTD. |
| Oxygen | Quantity: number of stations = 38 Description: Measurements for mixed layer dissolved gas (Ar, N2, Kr, O2) concentrations for insight into air-sea gas exchange processes and net productivity. One depth (roughly 10m) sampled per station; primarily but not exclusively pre-dawn stainless cast. Winkler dissolved oxygen and DIC-13 samples also taken. |
| Oxygen | Quantity: number of stations = 29 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. 6 depths sampled per station in the euphotic zone for production/respiration incubations. Calibration samples for the two CTD systems used during the cruise. A range of depths and concentrations taken from the Niskin bottles (143 & 159 samples for the stainless steel and titanium framed instruments respectively). |
| Carbon dioxide | Quantity: number of stations = 31 Description: Water samples collected for iron and cobalt analysis, spectrophotometric seawater ph, nitrogen fixation using 15N isotope and co2 perturbation experiments. |
| Carbon dioxide | Quantity: number of stations = 76 Description: Dissolved inorganic carbon for isotope measurements, 30ml filtered through 0.2um filter into HgCl2 prepoisoned vial. Particulate Organic Carbon for isotope measurements, surface and DCM, different size fractions: total, <53um, <3um onto precombusted 0.7um GF/F filter |
| Carbon dioxide | Quantity: activity duration in days = 49 Description: Atmospheric (marine air) and surface ocean (underway) pCO2 measurement using Dartcom-PML?s 'Live pCO2' autonomous instrument with LiCOR infrared gas analyzer |
| Other dissolved gases | Quantity: number of stations = 15 Description: Vertical profiles in the N. and S. subtropical Atlantic thermocline (~150-500m, depth variable) for dissolved gases (Ar, N2, Kr, O2) to examine diapycnal mixing. Winkler dissolbed oxygen samples also taken. Sampled exclusively from the mid-day CTD. |
| Other dissolved gases | Quantity: number of stations = 38 Description: Measurements for mixed layer dissolved gas (Ar, N2, Kr, O2) concentrations for insight into air-sea gas exchange processes and net productivity. One depth (roughly 10m) sampled per station; primarily but not exclusively pre-dawn stainless cast. Winkler dissolved oxygen and DIC-13 samples also taken. |
| Phosphate | Quantity: number of stations = 72 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for micro-molar nutrient analysis. Average 10 depths sampled per station. |
| Total - P | Quantity: number of stations = 33 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples trace element composition of phytoplankton as well as genetic composition. Average 4 depths sampled per station. Samples will be analysed after the cruise. |
| Nitrate | Quantity: number of stations = 72 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for micro-molar nutrient analysis. Average 10 depths sampled per station. |
| Nitrite | Quantity: number of stations = 72 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for micro-molar nutrient analysis. Average 10 depths sampled per station. |
| Nitrite | Quantity: number of stations = 33 Description: Solid phase extraction of the synthesized Sudan-1 dye from discrete water samples (at 14%sPAR, 1%sPAR and 1%-50m sPAR depths) for determination of ambient NO2- concentration and rate of NH4+ oxidation using isotope dilution technique-GC/MS in PML; Filtration of samples for PON prior to dye development. |
| Total - N | Quantity: number of stations = 33 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples trace element composition of phytoplankton as well as genetic composition. Average 4 depths sampled per station. Samples will be analysed after the cruise. |
| Ammonia | Quantity: number of stations = 72 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for micro-molar nutrient analysis. Average 10 depths sampled per station. |
| Silicate | Quantity: number of stations = 72 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for micro-molar nutrient analysis. Average 10 depths sampled per station. |
| Trace elements | Quantity: number of stations = 33 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples trace element composition of phytoplankton as well as genetic composition. Average 4 depths sampled per station. Samples will be analysed after the cruise. |
| Trace elements | Quantity: number of stations = 12 Description: Trace metal concentrations (for Alex Baker UEA, Norwich) and Iron organic speciation in dry and wet atmospheric inputs and in surface seawater |
| Trace elements | Quantity: number of stations = 31 Description: Water samples collected for iron and cobalt analysis, spectrophotometric seawater ph, nitrogen fixation using 15N isotope and co2 perturbation experiments. |
| Isotopes | Quantity: number of stations = 38 Description: Measurements for mixed layer dissolved gas (Ar, N2, Kr, O2) concentrations for insight into air-sea gas exchange processes and net productivity. One depth (roughly 10m) sampled per station; primarily but not exclusively pre-dawn stainless cast. Winkler dissolved oxygen and DIC-13 samples also taken. |
| Other chemical oceanographic measurements | Quantity: number of stations = 69 Description: Vertical profiles from CTD niskin bottles at 69 stations and 107 sites of surface samples taken from the ship?s non-toxic seawater supply. Discrete samples obtained for analysis of PIC, POC, Biogenic silica, and coccolith enumeration. |
| Contamination | |
| Other dissolved substances | Quantity: number of stations = 60 Description: Measurements for Oxygenated Volatile Organic Compounds (OVOCs) made from CTDs at pre-dawn and solar noon stations. Vertical profiles analysed at 5 depths (surface ? 200m) from most pre-dawn casts, surface only measurements from solar noon cast. Analysis by Membrane Inlet - Proton Transfer Reaction / Mass Spectrometry (PTR/MS) |
| Biology and fisheries | |
| Primary productivity | Quantity: number of measurements = 29 Description: Active chlorophyll fluorescence measurements: continuous measurements from UW (CTG FAST tracka FRRf) |
| Primary productivity | Quantity: number of stations = 38 Description: Vertical profile (6 depths) for size-fractionated phytoplankton production from titanium pre-dawn CTD casts |
| Primary productivity | Quantity: number of stations = 65 Description: Active chlorophyll fluorescence measurements: discrete acquires (Fast repetition rate) on a vertical profile from deep chlorophyll max (DCM) to surface from titanium CTD (6 depths) Sampling for RNA and DNA from UW non toxic and sampling for proteins from DCM and surface (Julie Laroche IFM Geomar, Kiel, Germany/ Bess Ward, Princeton,USA) |
| Primary productivity | Quantity: number of stations = 42 Description: Productivity measurements of bacterial and eukaryotic populations using radiotracers |
| Primary productivity | Quantity: number of stations = 31 Description: Water samples collected for iron and cobalt analysis, spectrophotometric seawater ph, nitrogen fixation using 15N isotope and co2 perturbation experiments. |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: activity duration in days = 45 Description: Operated an along-track flow-through system from ship?s non-toxic seawater supply to characterize bio-optical properties of the water (backscattering, fluorescense) (~24 h/day). Also operated Micro-SAS system on the ship?s meteorological platform to measure upwelling radiance, downwelling radiance and total downwelling irradiance (~10h/day). |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of stations = 74 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for abundance of phytoplankton pigments by High Performance Liquid Chromatography (HPLC). Average 6 depths sampled per station. Samples will be analysed after the cruise. |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of stations = 110 Description: Water collected on Whatman GF/F filters for HPLC phytoplankton pigment analysis |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of stations = 65 Description: Active chlorophyll fluorescence measurements: discrete acquires (Fast repetition rate) on a vertical profile from deep chlorophyll max (DCM) to surface from titanium CTD (6 depths) Sampling for RNA and DNA from UW non toxic and sampling for proteins from DCM and surface (Julie Laroche IFM Geomar, Kiel, Germany/ Bess Ward, Princeton,USA) |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of deployments = 78 Description: In-water optics rig: i) Fast Repetition Rate Fluorometer (phytoplankton physiology); ii) Satlantic UV sensor (downwelling spectral UV light at 305, 320, 340 and 380 nm); iii) Wetlabs ac-9 (attenuation and absorption at 9 wavelengths: 412, 440, 488, 510, 532, 555, 650, 676, 715 nm); iv) SeaBird SBE19+ CTD (temperature and salinity with depth for correction of the ac9); v) ancillary PAR measurements (determination of light levels in water column); vi) Hobilabs hydroscat 6 (bb6: backscatter at 6 wavelengths: 442, 488, 550, 620, 671, 852) |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of samples = 163 Description: Fluorometric determination of surface chlorophyll a to calibrate against TSG fluormeter |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: number of measurements = 29 Description: Active chlorophyll fluorescence measurements: continuous measurements from UW (CTG FAST tracka FRRf) |
| Phytoplankton pigs (eg chlorophyll, fluorescence) | Quantity: activity duration in days = 45 Description: Underway fast repetition rate fluorescence data collected using a custom made instrument |
| Particulate organic matter (inc POC, PON) | Quantity: number of stations = 69 Description: Vertical profiles from CTD niskin bottles at 69 stations and 107 sites of surface samples taken from the ship?s non-toxic seawater supply. Discrete samples obtained for analysis of PIC, POC, Biogenic silica, and coccolith enumeration. |
| Particulate organic matter (inc POC, PON) | Quantity: number of stations = 75 Description: Water collected on precombusted Whatman GF/F filters for particulate organic carbon and nitrogen analysis |
| Particulate organic matter (inc POC, PON) | Quantity: number of stations = 33 Description: Solid phase extraction of the synthesized Sudan-1 dye from discrete water samples (at 14%sPAR, 1%sPAR and 1%-50m sPAR depths) for determination of ambient NO2- concentration and rate of NH4+ oxidation using isotope dilution technique-GC/MS in PML; Filtration of samples for PON prior to dye development. |
| Particulate organic matter (inc POC, PON) | Quantity: number of stations = 76 Description: Dissolved inorganic carbon for isotope measurements, 30ml filtered through 0.2um filter into HgCl2 prepoisoned vial. Particulate Organic Carbon for isotope measurements, surface and DCM, different size fractions: total, <53um, <3um onto precombusted 0.7um GF/F filter |
| Biochemical measurements (eg lipids, amino acids) | Quantity: number of stations = 15 Description: Fluorescence In-situ hybridisation (FISH) for coccolithophore. 2L from surface and DCM fixed with PFA filtered onto 0.2um Anodisc filters |
| Biochemical measurements (eg lipids, amino acids) | Quantity: number of stations = 45 Description: DNA from CTD, surface and DCM, for coccolithophore environmental analysis. Predawn station, prefiltered through 53um mesh |
| Phytoplankton | Quantity: number of stations = 35 Description: Filters for light microscope and SEM analysis of coccolithophore biogeochemistry, transect plus vertical measurements. 2nd predawn CTD, 6 depths (surface to 2 x below DCM). 2L through 1um filters for each preparation |
| Phytoplankton | Quantity: number of stations = 42 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for abundance and phytoplankton genetic composition. Average 6 depths sampled per station. Samples will be analysed after the cruise. |
| Phytoplankton | Quantity: number of stations = 69 Description: Vertical profiles from CTD niskin bottles at 69 stations and 107 sites of surface samples taken from the ship?s non-toxic seawater supply. Discrete samples obtained for analysis of PIC, POC, Biogenic silica, and coccolith enumeration. |
| Phytoplankton | Quantity: number of stations = 9 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for phytoplankton transcriptomics and genomics. Average 2 depths sampled per station. Samples will be analysed after the cruise. |
| Phytoplankton | Quantity: number of stations = 76 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples for abundance of phytoplankton smaller than 20 micrometres analysed by flow cytometry. Average 10 depths sampled per station. |
| Phytoplankton | Quantity: number of stations = 33 Description: Vertical profiles from CTD Niskin bottles at stations along the cruise track. Discrete samples trace element composition of phytoplankton as well as genetic composition. Average 4 depths sampled per station. Samples will be analysed after the cruise. |
| Phytoplankton | Quantity: number of stations = 58 Description: Water samples run through a FACScan flow cytometer |
| Phytoplankton | Quantity: number of stations = 19 Description: Trichodesmium sp. collection - net cast 5 m |
| Zooplankton | Quantity: number of hauls = 41 Description: Double (Bongo) WP2 Net casts 0-180m integrated. 1 net through OPC to waste; 1 net split: half in 4% buffered formalin for PML analysis; half in 4% buffered formalin to Dr Antje Voelker, Portugal. Southern hemisphere: no split - all of 2nd net to PML. |
| Zooplankton | Quantity: activity duration in days = 40 Description: Near-continuous (except for station stops) OPC size distributed biomass from surface zooplankton (non-toxic supply through OPC). |
| Zooplankton | Quantity: number of hauls = 36 Description: Single 60cm diameter net frame with 50um mesh net & cod end. Sample preserved in Ethanol for Dr. Claudia Castellani, SAHFOS |
| Pelagic bacteria/micro-organisms | Quantity: number of stations = 42 Description: Productivity measurements of bacterial and eukaryotic populations using radiotracers |
| Pelagic bacteria/micro-organisms | Quantity: number of stations = 76 Description: Enumeration of bacterial cells using FACSort flow cytometer |
| Other biological/fisheries measurement | Quantity: number of stations = 2 Description: Video and photographic stills were collected using SHRIMP (Seafloor High Resolution IMaging Platform) with 3 hours of bottom time at each site (0.5knot towing speed). Stills and video will be analysed to estimate diversity and relative abundance of megafauna at the two stations. |
| Other biological/fisheries measurement | Quantity: number of stations = 43 Description: bioaerosols sampling in atmospheric inputs (dry and wet) and surface seawater sampling for detection of bioaerosols |
| Meteorology | |
| Incident radiation | Quantity: activity duration in days = 46 Description: Deck mounted (over the CTD winch cab) Satlantic HyperSAS sensor: Hyperspectral (300 ? 900 nm) water-leaving reflectance measurements at 6 minute intervals through daylight hours; measurements integrated over 30 s. These include water, sky and sun radiance measuring sensors (3). |
| Incident radiation | Quantity: activity duration in days = 47 Description: Deck mounted Trios UV sensor: i) Hyperspectral (2.5 nm resolution: 200 ? 500 nm wavelength) UV at 5 minute intervals through daylight hours; ii) decomposed hyperspectral into broadband UV-A and UV-B DATA NOT USABLE BECAUSE OF OIL INGRESS |
| Incident radiation | Quantity: activity duration in days = 45 Description: Operated an along-track flow-through system from ship?s non-toxic seawater supply to characterize bio-optical properties of the water (backscattering, fluorescense) (~24 h/day). Also operated Micro-SAS system on the ship?s meteorological platform to measure upwelling radiance, downwelling radiance and total downwelling irradiance (~10h/day). |
| Other meteorological measurements | Quantity: activity duration in days = 45 Description: Microtops sunphotometer measurements: i) Aerosol optical thickness at 340, 440, 675 and 870 nm; ii) water vapour content (cm) |
| Other meteorological measurements | Quantity: activity duration in days = 24 Description: Atmospheric measurement of Oxygenated Volatile Organic Compounds (OVOCs) by Proton Transfer Reaction / Mass Spectrometry (PTR/MS). |
| Other meteorological measurements | Quantity: number of stations = 35 Description: Dry aerosol sampling on filters for major ions and for physical speciation (for Alex Baker, UEA, Norwich). Rainwater sampling for chemical composition (Anions, Cations and DOC) for Karine DesBoeufs, LISA, Paris, France. |
| Data held at BODC | |
| Discrete samples | |
| 120 CTD frame plus rosette sampler | Primary production in the water column Phytoplankton taxonomic abundance in water bodies Phosphate concentration parameters in the water column Density of the water column Visible waveband radiance and irradiance measurements in the water column Electrical conductivity of the water column Transmittance and attenuance of the water column Plankton abundance per unit volume of the water column Silicate concentration parameters in the water column Dissolved oxygen parameters in the water column Nitrate concentration parameters in the water column Raw oxygen sensor output Temperature of the water column Carotenoid pigment concentrations in the water column Salinity of the water column Dissolved metal concentrations in the water column Nitrite concentration parameters in the water column Chlorophyll pigment concentrations in the water column Oxygen production and respiration in the water column |
| 254 Sample taken from ship's non-toxic supply | Phaeopigment concentrations in the water column Carotenoid pigment concentrations in the water column Salinity of the water column Chlorophyll pigment concentrations in the water column |
