BODC Cruise Metadata Report for RRS James Cook (740H) cruise JC097

Introduction

This report collates information from the BODC cruise inventory and oceanographic databases. It presents

Cruise Inventory Information
A summary of BODC data holdings for the cruise from the
- National Oceanographic Database
- Projects Database
References - including cruise tracks and cruise reports

Cruise Inventory Information

Long name	RRS James Cook (740H) cruise JC097
Short name	JC097
Objectives and Narrative	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.
Ship	RRS James Cook
Departure Port	Balboa, Panama
Departure Date	2013-12-28
Arrival Port	Manzanillo, Mexico
Arrival Date	2014-02-10
Principal Scientist(s)	Mark Trimmer (Queen Mary University of London School of Biological and Chemical Sciences)
Responsible Organisation	Queen Mary University of London School of Biological and Chemical Sciences
Associated Project(s)
IHB Sea Areas Visited	North East Pacific Ocean (limit 180W)
Marsden Squares Visited	46
Work Area Description	Eastern Tropical North Pacific (ETNP); off the west coast of Guatemala
Unable to lookup cruise bounds at this time
Work Area Bounding Polygon
Southern Limit	unknown
Northern Limit	unknown
Western Limit	unknown
Eastern Limit	unknown

Cruise Inventory Datasets

Physical oceanography
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 profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
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 = 11 Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode
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 experiments = 72 Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment)
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 = 126 Description: 1 L of water filtered for nucleic acid extraction and community analysis (organic 15N2 experiment)
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 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 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 = 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 = 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 = 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 = 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 = 7 Description: Collection of seawater samples from selected depths to check for methane production using IRMS (cryofocusing)
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 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 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
Surface measurements underway (T,S)	Quantity: number of track lines = 1 Description: Underway measurements from the non-toxic supply
Chemical oceanography
Ammonia	Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
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
Carbon dioxide	Quantity: number of profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
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
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 = 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 = 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 = 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 = 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 = 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 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 = 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 = 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 .
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
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 profiles = 11 Description: CTD vertical profiles of H2S in the water column, measured with a H2S unisense electrode
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 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 dissolved gases	Quantity: number of profiles = 20 Description: CTD vertical profiles of CO2, CH4, N2O in the water column, measured using GC
Oxygen	Quantity: number of track lines = 1 Description: Seasoar deployed for continuous oxygen measurements.
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
Phosphate	Quantity: number of profiles = 24 Description: CTD profiles - NO2, NO3, PO4, NH4+ in the water column, measured using Skalar
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
pH	Quantity: number of profiles = 11 Description: CTD vertical profiles of pH in the water column, measured with pH-meter
Biology and fisheries
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.
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.
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.
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)
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 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 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 = 72 Description: 1 L of water filtered for nucleic acid extraction and community analysis (15 N2O experiment)
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
Phytoplankton	Quantity: number of samples = 61 Description: Collection of water samples and determination of the abundance of microplankton using a FloCam
Phytoplankton	Quantity: number of samples = 52 Description: SAPs deployment; filters transferred to the lab for bacterioplankton and phytoplankton analysis
Phytoplankton pigs (eg chlorophyll, fluorescence)	Quantity: number of profiles = 6 Description: Filtered sea water for analysis of Chlorophyll, POC and lipids in the lab.
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
Zooplankton	Quantity: number of samples = 61 Description: Collection of water samples and determination of the abundance of microplankton using a FloCam
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 = 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 = 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 = 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.