Cell abundance, nutrient and DMSP concentrations measured during a mesocosm study of the effect of phytoplankton composition on bacterial DMSP transformation (OceanSulfurFluxBact project)

Website: https://www.bco-dmo.org/dataset/662681
Data Type: experimental
Version:
Version Date: 2016-10-25

Project
» Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere (OceanSulfurFluxBact)

Program
» Dimensions of Biodiversity (Dimensions of Biodiversity)
ContributorsAffiliationRole
Moran, Mary AnnUniversity of Georgia (UGA)Principal Investigator
Birch, James M.Monterey Bay Aquarium Research Institute (MBARI)Co-Principal Investigator
Kiene, Ronald P.University of South Alabama (USA)Co-Principal Investigator
Landa, MarineUniversity of Georgia (UGA)Contact
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Coverage

Spatial Extent: Lat:36.835 Lon:-121.901

Methods & Sampling

Cell counts: Ruegeria pomeroyi, Thalassiosira pseudonana, and Alexandrium tamarense cells were measured using a flow cytometer.

DIN: Cadmium reduction method; Nitrate is measured by reducing it to nitrite in an alkaline-buffered solution passing through a column of copper-cadmium metal filings and then measuring nitrite by diazotizing with sulfanilamide and coupling with N-(1-naphthyl)-ethylenediamine dihydrochloride to form a pink colored azo dye which is measured colorimetrically. Instrument: Alpkem and Astoria-Pacific Autoanalyzers

DIP: Orthophosphate method; PO4 is measured colorimetrically as an antimony-phospho-molybdate complex (APHA 4500-P F) that is reduced to an intensely blue-colored complex by ascorbic acid. Instrument: Alpkem and Astoria-Pacific Autoanalyzers

DOC: Combustion method; Total dissolved carbon and dissolved inorganic carbon are determined by combustion of an unacidified and acidified 0.2 micron filtered subsamples. DOC concentration is calculated by subtracting the DIC concentration from the TDC concentration. Instrument: Shimadzu TOC-5000A Total Organic Carbon Analyzer

TOC: Combustion method; Total organic carbon is determined by combustion of an unacidified and unfiltered sample. Instrument: Shimadzu TOC-5000A Total Organic Carbon Analyzer

DMSP: See: Rellinger, A., et al. Occurrence and turnover of DMSP and DMS in deep waters of the Ross Sea, Antarctica. Deep-Sea Research I 56 (2009) 686–702. doi:10.1016/j.dsr.2008.12.010


Data Processing Description

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- replaced commas with underscores


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Data Files

File
switch.csv
(Comma Separated Values (.csv), 4.08 KB)
MD5:b14b9daa3d22d826e12a20df8e8d386d
Primary data file for dataset ID 662681

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Parameters

ParameterDescriptionUnits
timepointTime point unitless
cubitainerCubitainer identification: treatment and replicate number unitless
Ruegeria_pomeroyiNumber of bacterial cells per ml of culture; determined by flow cytometry cells/milliliter
Thalassiosira_pseudonanaNumber of diatom cells per ml of culture; determined by flow cytometry cells/milliliter
Alexandrium_tamarenseNumber of dinoflagellate cells per ml of culture; determined by flow cytometry cells/milliliter
DINConcentrations of dissolved inorganic nitrogen; infered from the measurements of nitrate and nitrite concentrations. micromoles/liter of culture
DIPConcentrations of dissolved inorganic phosphorus; infered from the measurements of phosphate concentrations. micromoles/liter of culture
DOCConcentrations of dissolved organic carbon micromoles/liter of culture
TOCConcentrations of total organic carbon micromoles/liter of culture
DMSP_totalTotal dimethylsufoniopropionate concentrations nanomoles/liter of culture
DMSP_dissDissolved dimethylsufoniopropionate concentrations nanomoles/liter of culture


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Instruments

Dataset-specific Instrument Name
Alpkem and Astoria-Pacific Autoanalyzers
Generic Instrument Name
Nutrient Autoanalyzer
Dataset-specific Description
To measure DIN and DIP
Generic Instrument Description
Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.

Dataset-specific Instrument Name
Shimadzu TOC-5000A Total Organic Carbon Analyzer
Generic Instrument Name
Total Organic Carbon Analyzer
Dataset-specific Description
To measure DOC and TOC
Generic Instrument Description
A unit that accurately determines the carbon concentrations of organic compounds typically by detecting and measuring its combustion product (CO2). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/bs116.pdf

Dataset-specific Instrument Name
flow cytometer
Generic Instrument Name
Flow Cytometer
Dataset-specific Description
To measure abundance of cells.
Generic Instrument 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)

Dataset-specific Instrument Name
Shimadzu GC-2014 gas chromatograph equipped with a Chromosil 330 column and a flame photometric detector for quantification
Generic Instrument Name
Gas Chromatograph
Dataset-specific Description
To measure DMSP concentrations
Generic Instrument Description
Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)


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Deployments

Moran_Monterey_2014

Website
Platform
Univ_Georgia
Start Date
2014-09-08
End Date
2014-09-08
Description
Microbial collections and environmental data collected by moored ESP and CTD.


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Project Information

Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere (OceanSulfurFluxBact)


Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.

The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.

This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.



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Program Information

Dimensions of Biodiversity (Dimensions of Biodiversity)


Coverage: global


(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF]

The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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