Cruise inventory

RRS James Cook JC097

Cruise summary report

Cruise Info. 
Ship name (ship code)RRS James Cook (740H)
Cruise identifierJC097
Cruise period2013-12-28 — 2014-02-10
StatusCompleted
Port of departureBalboa, Panama
Port of returnManzanillo, Mexico
PurposeResearch
ObjectivesThis research cruise is the follow-up of a preceding one (D373) in the same area of the ocean. With these cruises we aim to study the N cycle in the oxygen minimum zone (OMZ) of Eastern Tropical North Pacific (ETNP). The overall aim of this project is to link N cycling to bacterial diversity and gene expression across a gradient of OMZ intensity in the Eastern Tropical North Pacific (ETNP). First we created high resolution vertical profiles based on the measured concentraions of gases (i.e. N2O, CO2, CH4) and nutrients (i.e. NO2-, NO3-, PO4-, NH4+) in the water column. Subsequently, we set up experiments to test if the ratio of N2 to N2O production is 'fixed' or 'flexible', screen for N2 production coupled to 15N organic-N, and fixation of 15N2. In parallel, we filtered seawater in order to collect bacterial cells for molecular analysis of the active communities involved in the metabolism of the aformentioned gases. In order to determine the extent of variation and potential within the water column, we performed experiments at 6 different sites, within and around the core of the OMZ. Sediment samples were also collected to check for N2 gas production via denitrification or anammox. Understanding the nitrogen metabolism will help us predict the conditions under which N2O (a greenhouse gas) accumulates and will further clarify the mechanisms of fine tuning of the nitrogen cycle in the global ocean.

Furthermore, we set up experiments for the measurement of anaerobic and aerobic methane oxidation following the addition of 13C-labelled CH4, as well as methane production in the water column and sediments. This will offer insights into carbon cycling in this area of the ocean, i.e. what are the sources and sinks of methane.
Chief scientistMark Trimmer (Queen Mary University of London School of Biological and Chemical Sciences)
Cruise reportRRS James Cook JC097 cruise report jc097.pdf — access key 'C' (1.65 MB) 
Ocean/sea areas 
GeneralNorth East Pacific Ocean (limit 180W)
SpecificEastern Tropical North Pacific (ETNP); off the west coast of Guatemala
Track chartsRRS James Cook JC097 cruise track — jc097trk.pdf (00 MB) 
Measurements 
Physical oceanography 
Surface measurements underway (T,S)Quantity: number of track lines = 1
Description: Underway measurements from the non-toxic supply
CTD stationsQuantity: number of samples = 6
Description: Addition of different stable isotopes ( 15NO3- /15NH4+/ 15NH4 + 14NO3- ) in sediment slurries and incubation on-board; transfer to the lab to measure N2 production (as a result anammox in the sediment) by IRMS
CTD stationsQuantity: number of samples = 21
Description: Addition of 3H-leucine in water samples under anoxic conditions; incubation on-board and fixation ; flow sorting of cells on board or transfer to the lab for analysis
CTD stationsQuantity: number of profiles = 20
Description: Seawater samples fixed and stained with DNA-specific dye and analysed by flow cytometry on-board; additional samples fixed, frozen and transferred for analysis ashore
CTD stationsQuantity: number of measurements = 1
Description: On-board measurement of biological respiration using a set of microrespiration chambers and oxygen micoelectrode for 35 seperate surface plankton samples
CTD stationsQuantity: number of profiles = 20
Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
CTD stationsQuantity: number of samples = 7
Description: Collection of seawater samples from selected depths to check for methane production using IRMS (cryofocusing)
CTD stationsQuantity: number of samples = 3
Description: Filtering water from the Niskins under anoxic conditions; transfer the filters in 12 ml exetainers with degassed water; transfer to the lab for measurement of CH4 production using GC
CTD stationsQuantity: number of profiles = 11
Description: CTD vertical profiles of pH in the water column, measured with pH-meter
CTD stationsQuantity: number of profiles = 11
Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode
CTD stationsQuantity: number of samples = 12
Description: Treatment with pre-mixed gases/15NO2- and 15NH4+ addition in seawater samples and incubation on-board; transfer to the lab to measure N2 and N2O production by IRMS
CTD stationsQuantity: number of samples = 5
Description: Addition of 13CH4 and 15NO2- to water samples, onboard incubation and transfer to the lab for IRMS analysis of the produced CO2 and N2 .
CTD stationsQuantity: number of experiments = 72
Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment)
CTD stationsQuantity: number of samples = 30
Description: Organic N stable isotopes addition in seawater samples and incubation on-board; transfer to the lab to measure N2 production by IRMS
CTD stationsQuantity: number of experiments = 126
Description: 1 L of water filtered for nucleic acid extraction and community analysis (organic 15N2 experiment)
CTD stationsQuantity: number of samples = 18
Description: 15NO2- stable isotope addition in seawater samples and incubation at different temperatures; transfer to the lab to measure N2 production (as a result of water column denitrification) by IRMS
CTD stationsQuantity: number of samples = 9
Description: Addition of 13CH4 gas to water samples and incubation on board, transfer to the lab to measure 13CO2 production with IRMS
CTD stationsQuantity: number of samples = 6
Description: Addition of 15N2 to 1 L and 30ml of water; incubation at different temperatures and filtering on-board; transfer of the filters in the lab to determine nitrogen fixation by IRMS
CTD stationsQuantity: number of samples = 13
Description: Addition of 15NO2- in seawater samples and fixation at various time points to account depending on the O2 consumption (until water became anoxic); transfer to the lab to measure N2 production (by IRMS) as a function of O2 consumption
CTD stationsQuantity: number of samples = 3
Description: Collection of 10 ml of water and addition of three different concentrations of 15NH4+. Transfer to lab to measure conversion of 15NH4+ to 15NO3- (nitrification in the water column) and measure N2 production by IRMS after conversion from 15NO3-
CTD stationsQuantity: number of profiles = 24
Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
Chemical oceanography 
OxygenQuantity: number of track lines = 1
Description: Seasoar deployed for continuous oxygen measurements.
OxygenQuantity: number of measurements = 1
Description: On-board measurement of biological respiration using a set of microrespiration chambers and oxygen micoelectrode for 35 seperate surface plankton samples
OxygenQuantity: number of samples = 13
Description: Addition of 15NO2- in seawater samples and fixation at various time points to account depending on the O2 consumption (until water became anoxic); transfer to the lab to measure N2 production (by IRMS) as a function of O2 consumption
Carbon dioxideQuantity: number of samples = 9
Description: Addition of 13CH4 gas to water samples and incubation on board, transfer to the lab to measure 13CO2 production with IRMS
Carbon dioxideQuantity: number of profiles = 20
Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
Other dissolved gasesQuantity: number of profiles = 20
Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
PhosphateQuantity: number of profiles = 24
Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
NitrateQuantity: number of profiles = 24
Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
NitriteQuantity: number of profiles = 24
Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
AmmoniaQuantity: number of profiles = 24
Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
pHQuantity: number of profiles = 11
Description: CTD vertical profiles of pH in the water column, measured with pH-meter
RadioactivityQuantity: number of samples = 11
Description: Addition of sodium 14C-bicarbonate tracer to plankton net concentrates; on-board incubation and cell fixation; filtration and count of carbon fixation rates by scintillation counting
RadioactivityQuantity: number of samples = 21
Description: Addition of 3H-leucine in water samples under anoxic conditions; incubation on-board and fixation ; flow sorting of cells on board or transfer to the lab for analysis
IsotopesQuantity: number of samples = 12
Description: Treatment with pre-mixed gases/15NO2- and 15NH4+ addition in seawater samples and incubation on-board; transfer to the lab to measure N2 and N2O production by IRMS
IsotopesQuantity: number of samples = 6
Description: Addition of 15N2 to 1 L and 30ml of water; incubation at different temperatures and filtering on-board; transfer of the filters in the lab to determine nitrogen fixation by IRMS
IsotopesQuantity: number of samples = 5
Description: Addition of 13CH4 and 15NO2- to water samples, onboard incubation and transfer to the lab for IRMS analysis of the produced CO2 and N2 .
IsotopesQuantity: number of samples = 9
Description: Addition of 13CH4 gas to water samples and incubation on board, transfer to the lab to measure 13CO2 production with IRMS
IsotopesQuantity: number of samples = 18
Description: 15NO2- stable isotope addition in seawater samples and incubation at different temperatures; transfer to the lab to measure N2 production (as a result of water column denitrification) by IRMS
IsotopesQuantity: number of samples = 13
Description: Addition of 15NO2- in seawater samples and fixation at various time points to account depending on the O2 consumption (until water became anoxic); transfer to the lab to measure N2 production (by IRMS) as a function of O2 consumption
IsotopesQuantity: number of samples = 6
Description: Addition of different stable isotopes ( 15NO3- /15NH4+/ 15NH4 + 14NO3- ) in sediment slurries and incubation on-board; transfer to the lab to measure N2 production (as a result anammox in the sediment) by IRMS
IsotopesQuantity: number of samples = 22
Description: Addition of 15NO3- to intact sediment samples (cores); measurement of oxygen and on-board incubation; fixation and transfer to the lab to measure N2 production, using IRMS.
IsotopesQuantity: number of samples = 3
Description: Collection of 10 ml of water and addition of three different concentrations of 15NH4+. Transfer to lab to measure conversion of 15NH4+ to 15NO3- (nitrification in the water column) and measure N2 production by IRMS after conversion from 15NO3-
IsotopesQuantity: number of samples = 6
Description: Addition of 15NO3- to sediment samples (slurries); incubation at different temperatures; transfer to the lab to measure N2 production (via denitrification), using IRMS.
Other chemical oceanographic measurementsQuantity: number of profiles = 11
Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode
Other chemical oceanographic measurementsQuantity: number of samples = 3
Description: Filtering water from the Niskins under anoxic conditions; transfer the filters in 12 ml exetainers with degassed water; transfer to the lab for measurement of CH4 production using GC
Other chemical oceanographic measurementsQuantity: number of samples = 7
Description: Collection of seawater samples from selected depths to check for methane production using IRMS (cryofocusing)
Other chemical oceanographic measurementsQuantity: number of samples = 5
Description: Sediment collection from mega-corer into exetainers with water from the top of the core; dagassing with Helium; incubation and measurement on GC for CH4 production.
Biology and fisheries 
Primary productivityQuantity: number of samples = 11
Description: Addition of sodium 14C-bicarbonate tracer to plankton net concentrates; on-board incubation and cell fixation; filtration and count of carbon fixation rates by scintillation counting
Phytoplankton pigs (eg chlorophyll, fluorescence)Quantity: number of profiles = 6
Description: Filtered sea water for analysis of Chlorophyll, POC and lipids in the lab.
Particulate organic matter (inc POC, PON)Quantity: number of profiles = 12
Description: 6 day profiles and 6 midnight profiles of snow-catcher fractions. Collected particles, analysed under microscope and flow cam onboard. Filtered for POC/N/P and lipids for analysis at the lab.
Particulate organic matter (inc POC, PON)Quantity: number of profiles = 6
Description: Filtered sea water for analysis of Chlorophyll, POC and lipids in the lab.
Biochemical measurements (eg lipids, amino acids)Quantity: number of profiles = 6
Description: Filtered sea water for analysis of Chlorophyll, POC and lipids in the lab.
Biochemical measurements (eg lipids, amino acids)Quantity: number of profiles = 12
Description: 6 day profiles and 6 midnight profiles of snow-catcher fractions. Collected particles, analysed under microscope and flow cam onboard. Filtered for POC/N/P and lipids for analysis at the lab.
PhytoplanktonQuantity: number of samples = 61
Description: Collection of water samples and determination of the abundance of microplankton using a FloCam
PhytoplanktonQuantity: number of samples = 52
Description: SAPs deployment; filters transferred to the lab for bacterioplankton and phytoplankton analysis
ZooplanktonQuantity: number of samples = 61
Description: Collection of water samples and determination of the abundance of microplankton using a FloCam
Pelagic bacteria/micro-organismsQuantity: number of samples = 61
Description: Collection of water samples and determination of the abundance of microplankton using a FloCam
Pelagic bacteria/micro-organismsQuantity: number of profiles = 20
Description: Seawater samples fixed and stained with DNA-specific dye and analysed by flow cytometry on-board; additional samples fixed, frozen and transferred for analysis ashore
Pelagic bacteria/micro-organismsQuantity: number of experiments = 126
Description: 1 L of water filtered for nucleic acid extraction and community analysis (organic 15N2 experiment)
Pelagic bacteria/micro-organismsQuantity: number of experiments = 72
Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment)
Pelagic bacteria/micro-organismsQuantity: number of samples = 30
Description: Organic N stable isotopes addition in seawater samples and incubation on-board; transfer to the lab to measure N2 production by IRMS
Pelagic bacteria/micro-organismsQuantity: number of samples = 52
Description: SAPs deployment; filters transferred to the lab for bacterioplankton and phytoplankton analysis
Pelagic bacteria/micro-organismsQuantity: number of samples = 6
Description: Collection of sediment directly from the mega-corer cores; immediately freeze; transfer to the lab for bacterial community analysis
Meteorology 
Routine standard measurementsQuantity: number of track lines = 1
Description: Ship-mounted meteorological sensors
Geology and geophysics 
Core - soft bottomQuantity: number of samples = 5
Description: Sediment collection from mega-corer into exetainers with water from the top of the core; dagassing with Helium; incubation and measurement on GC for CH4 production.
Core - soft bottomQuantity: number of samples = 6
Description: Collection of sediment directly from the mega-corer cores; immediately freeze; transfer to the lab for bacterial community analysis
Core - soft bottomQuantity: number of samples = 22
Description: Addition of 15NO3- to intact sediment samples (cores); measurement of oxygen and on-board incubation; fixation and transfer to the lab to measure N2 production, using IRMS.
Core - soft bottomQuantity: number of samples = 6
Description: Addition of 15NO3- to sediment samples (slurries); incubation at different temperatures; transfer to the lab to measure N2 production (via denitrification), using IRMS.