Dataset: IO Phytoplankton
Deployment: RR1604

Phytoplankton diversity along with carbon and nitrogen uptake rates along the GO-SHIP IO9 repeat hydrography section of the Indian Ocean

Principal Investigator:

Michael W. Lomas (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

Contact:

Steven E. Baer (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Regional variation of phytoplankton diversity and biogeochemical functioning in the subtropical Indian Ocean (IO Phytoplankton)

Current State:

Final no updates expected

Version:

22 February 2018

Deployment Synonyms:

GO-SHIP IO9

Version Date:

2018-02-22

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/723257/data

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Description

Phytoplankton diversity along with carbon and nitrogen uptake rates from cruise RR1604 along the GO-SHIP IO9 repeat hydrography section of the Indian Ocean.

Methods & Sampling

Dataset acquisition description

All nutrient and cell count methodology is described in the published work coming out of this data set (see below).

Samples were initially collected with a CTD/Niskin rosette, as supplied by the ship.

Urea and total dissolved phosphorus (for calculation of dissolved organic phosphorus) were determined on a Thermo Scientific Genesys 10UV spectrophotometer. See Lomas et al. (2010) for a description of the latter.

Cell counts for heterotrophic bacteria and nanoplankton (<20 um) cells were performed on a BD FACSJazz flow cytometer, using standard methods and 0.53 um bead stocks for reference material. Visualization of heterotrophic bacteria was performed with SYBR Green stain.

Biomass calculations were derived from flow cytometry data output, as per Casey et al. (2013).

Larger (>20 um) autotrophs were enumerated on a FlowCam (Fluid Imagining Technologies).

Biomass and isotopic enrichment, used to calculate specific and absolute uptake rates, were assessed on a Thermo Finnegan Delta V mass spectrometer, as operated by the Bigelow Analytical Services team.

Sample accuracy was assessed by using certified standards, for those measurements where standards are available. Certified standards were run with each analytical run and compared to long term control charts for respective analyses. For those analyses where there are no standards (e.g., flow cytometric cell counts) data were assessed for reasonableness based upon extensive experience of the PI’s.

Data Processing Description

Dataset Processing Description

Data processing was performed using mostly Microsoft Excel. Further statistical analyses and graphing were performed with SigmaPlot. All samples collected are included in the report. Any occurences of "nd" in the data mean those samples were not collected.

BCO-DMO Processing:
- modified parameter names to conform with BCO-DMO naming convetions (removed units, replaced spaces with underscores);
- replaced blank cells with "nd" ("no data").

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1559021	NSF Division of Ocean Sciences

Instruments

CTD - profiler

Supplied Name: CTD/Niskin rosette

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Flow Cytometer

Supplied Name: BD FACSJazz flow cytometer

Supplied Description:

Cell counts for heterotrophic bacteria smaller (<20 um) phytoplankton cells were performed on a BD FACSJazz flow cytometer, using standard methods and 0.53 um bead stocks for reference material.

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Mass Spectrometer

Supplied Name: Thermo Finnegan Delta V mass spectrometer

Supplied Description:

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Niskin bottle

Supplied Name: CTD/Niskin rosette

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Spectrophotometer

Supplied Name: Thermo Scientific Genesys 10UV spectrophotometer

Supplied Description:

Urea and total dissolved phosphorus (for calculation of dissolved organic phosphorus) were determined on a Thermo Scientific Genesys 10UV spectrophotometer.

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
station	Station number	unitless	station
latitude	Station latitude; positive values = North	decimal degrees	lat
longitude	Station longitude; positive values = East	decimal degrees	lon
depth	Sample depth	meters (m)	depth
urea	Urea concentration. BD = below detection (the detection limit for the urea method is 0.01 umol L-1).	micromoles per liter (umol L-1)	Urea
DOP	Dissolved organic phosphorus concentration	micromoles per liter (umol L-1)	DOP
chlorophyll_a	Chlorophyll a	milligrams per cubic meter (mg m-3)	chl_a
LNA_bacteria	Count of low-nucleic acid heterotrophic bacteria	cells per milliliter (cells ml-1)	bact_abund
HNA_bacteria	Count of high-nucleic acid heterotrophic bacteria	cells per milliliter (cells ml-1)	bact_abund
prochlorococcus	Count of Prochlorococcus cells	cells per milliliter (cells ml-1)	coccus_p
synechococcus	Count of Synechococcus cells	cells per milliliter (cells ml-1)	coccus_s
picoeukaryotes	Count of picoeukaryote (<3 um) cells	cells per milliliter (cells ml-1)	pico_euks
nanoeukaryotes	Count of nanoeukaryote (3-20 um) cells	cells per milliliter (cells ml-1)	phyto_e_n
bacteria_biomass	Biomass of all bacteria	micrograms carbon per liter (ug C L-1)	biomass_C
prochlorococcus_biomass	Carbon content of Prochlorococcus cells	micrograms carbon per liter (ug C L-1)	biomass_C
synechococcus_biomass	Carbon content of Synechococcus cells	micrograms carbon per liter (ug C L-1)	biomass_C
small_eukaryote_biomass	Carbon content of picoeukaryote and nanoeukaryote cells	micrograms carbon per liter (ug C L-1)	biomass_C
diatom_biomass	Carbon content of diatoms	micrograms carbon per liter (ug C L-1)	biomass_C
dinoflagellate_biomass	Carbon content of dinoflagellates	micrograms carbon per liter (ug C L-1)	biomass_C
ciliate_biomass	Carbon content of ciliates	micrograms carbon per liter (ug C L-1)	biomass_C
other_large_phyto_biomass	Carbon content of >20 um phytoplankton not included in other categories	micrograms carbon per liter (ug C L-1)	biomass_C
NO3_V	Nitrate specific uptake	per hour (h-1)	no_bcodmo_term
NO3_V_std_dev	Standard deviation of NO3_V	per hour (h-1)	no_bcodmo_term
NO3_rho	Nitrate absolute uptake	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
NO3_rho_std_dev	standard deviation of NO3_rho	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
NH4_V	Ammonium specific uptake	per hour (h-1)	no_bcodmo_term
NH4_V_std_dev	Standard deviation of NH4_V	per hour (h-1)	no_bcodmo_term
NH4_rho	Ammonium absolute uptake	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
NH4_rho_std_dev	Standard deviation of NH4_rho	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
urea_V	Urea specific uptake	per hour (h-1)	pUrea
urea_V_std_dev	Standard deviation of urea V	per hour (h-1)	pUrea
urea_rho	Urea absolute uptake	nanomoles per liter per hour (nmol N L-1 h-1)	pUrea
urea_rho_std_dev	Standard deviation of urea rho	nanomoles per liter per hour (nmol N L-1 h-1)	pUrea
C_V	Bicarbonate specific uptake	per hour (h-1)	no_bcodmo_term
C_V_std_dev	Standard deviation of Bicarbonate specific uptake	per hour (h-1)	no_bcodmo_term
C_rho	Bicarbonate absolute uptake	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
C_rho_std_dev	Standard deviation of C rho	nanomoles per liter per hour (nmol N L-1 h-1)	no_bcodmo_term

Database

Contribute Data

Dataset: IO Phytoplankton
Deployment: RR1604

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: IO PhytoplanktonDeployment: RR1604

Dataset acquisition description

Dataset Processing Description

Dataset: IO Phytoplankton
Deployment: RR1604