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RRS James Cook JC097
Cruise summary report
Cruise Info. | |
Ship name (ship code) | RRS James Cook (740H) |
Cruise identifier | JC097 |
Cruise period | 2013-12-28 — 2014-02-10 |
Status | Completed |
Port of departure | Balboa, Panama |
Port of return | Manzanillo, Mexico |
Purpose | Research |
Objectives | This 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 scientist | Mark Trimmer (Queen Mary University of London School of Biological and Chemical Sciences) |
Cruise report | (1.65 MB) |
Ocean/sea areas | |
General | North East Pacific Ocean (limit 180W) |
Specific | Eastern Tropical North Pacific (ETNP); off the west coast of Guatemala |
Track charts | (0.17 MB) |
Measurements | |
Physical oceanography | |
Surface measurements underway (T,S) | Quantity: number of track lines = 1 Description: Underway measurements from the non-toxic supply |
CTD stations | Quantity: 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 stations | Quantity: number of experiments = 126 Description: 1 L of water filtered for nucleic acid extraction and community analysis (organic 15N2 experiment) |
CTD stations | Quantity: number of samples = 7 Description: Collection of seawater samples from selected depths to check for methane production using IRMS (cryofocusing) |
CTD stations | Quantity: 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 stations | Quantity: number of experiments = 72 Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment) |
CTD stations | Quantity: 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 stations | Quantity: number of profiles = 11 Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode |
CTD stations | Quantity: number of profiles = 11 Description: CTD vertical profiles of pH in the water column, measured with pH-meter |
CTD stations | Quantity: number of profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC |
CTD stations | Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar |
CTD stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 stations | Quantity: 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 |
Chemical oceanography | |
Oxygen | Quantity: 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 |
Oxygen | Quantity: 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 |
Oxygen | Quantity: number of track lines = 1 Description: Seasoar deployed for continuous oxygen measurements. |
Carbon dioxide | Quantity: number of profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC |
Carbon dioxide | Quantity: 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 |
Other dissolved gases | Quantity: number of profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC |
Phosphate | Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar |
Nitrate | Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar |
Nitrite | Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar |
Ammonia | Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar |
pH | Quantity: number of profiles = 11 Description: CTD vertical profiles of pH in the water column, measured with pH-meter |
Radioactivity | Quantity: 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 |
Radioactivity | Quantity: 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 |
Isotopes | Quantity: 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 |
Isotopes | Quantity: 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 . |
Isotopes | Quantity: 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. |
Isotopes | Quantity: 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. |
Isotopes | Quantity: 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 |
Isotopes | Quantity: 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- |
Isotopes | Quantity: 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 |
Isotopes | Quantity: 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 |
Isotopes | Quantity: 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 |
Isotopes | Quantity: 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 |
Other chemical oceanographic measurements | Quantity: 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 measurements | Quantity: 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. |
Other chemical oceanographic measurements | Quantity: number of samples = 7 Description: Collection of seawater samples from selected depths to check for methane production using IRMS (cryofocusing) |
Other chemical oceanographic measurements | Quantity: number of profiles = 11 Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode |
Biology and fisheries | |
Primary productivity | Quantity: 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 = 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. |
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. |
Phytoplankton | Quantity: number of samples = 52 Description: SAPs deployment; filters transferred to the lab for bacterioplankton and phytoplankton analysis |
Phytoplankton | Quantity: number of samples = 61 Description: Collection of water samples and determination of the abundance of microplankton using a FloCam |
Zooplankton | Quantity: number of samples = 61 Description: Collection of water samples and determination of the abundance of microplankton using a FloCam |
Pelagic bacteria/micro-organisms | Quantity: number of samples = 52 Description: SAPs deployment; filters transferred to the lab for bacterioplankton and phytoplankton analysis |
Pelagic bacteria/micro-organisms | Quantity: 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-organisms | Quantity: number of samples = 61 Description: Collection of water samples and determination of the abundance of microplankton using a FloCam |
Pelagic bacteria/micro-organisms | Quantity: number of samples = 6 Description: Collection of sediment directly from the mega-corer cores; immediately freeze; transfer to the lab for bacterial community analysis |
Pelagic bacteria/micro-organisms | Quantity: number of experiments = 72 Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment) |
Pelagic bacteria/micro-organisms | Quantity: 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-organisms | Quantity: number of experiments = 126 Description: 1 L of water filtered for nucleic acid extraction and community analysis (organic 15N2 experiment) |
Meteorology | |
Routine standard measurements | Quantity: number of track lines = 1 Description: Ship-mounted meteorological sensors |
Geology and geophysics | |
Core - soft bottom | Quantity: 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 bottom | Quantity: 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 bottom | Quantity: 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. |
Core - soft bottom | Quantity: 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. |