Dataset: ESP 2014 Cell Counts

Name: Taxonomy and abundance of microbial cells (phytoplankon and heterotrophic bacteria) during a deployment of the Environmental Sample Processor (ESP) in Fall, 2014 in Monterey Bay, CA
Published: 2016-10-25
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:36.835 E:-121.901 S:36.835 W:-121.901

Project:

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

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

Mary Ann Moran (University of Georgia, UGA)

Co-Principal Investigator:

James M. Birch (Monterey Bay Aquarium Research Institute, MBARI)

Contact:

Brent Nowinski (University of Georgia, UGA)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2016-10-25

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/662653/data

Taxonomy and abundance of microbial cells (phytoplankon and heterotrophic bacteria) during a deployment of the Environmental Sample Processor (ESP) in Fall, 2014 in Monterey Bay, CA

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Acquisition Description

Dilutions to the sample due to preservative, dyes and run volume:
PFA = 0.95
Hoechst = 0.98
Run Volume = 0.10
Correction Factor = 0.82

For methodology details, see:
Varaljay, V., et al. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. The ISME Journal (2015), 1-10. doi:10.1038/ismej.2015.23

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
- re-formatted date from m/d/yyyy to yyyy-mm-dd
- added lat and lon of ESP mooring for mapping purposes

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1342694

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Moran_Monterey_2014		2014-09-08	Univ_Georgia	Mary Ann Moran (Principal Investigator)	data info

Instruments

Flow Cytometer

(more info)

Short Name: Flow Cytometer

Community Standard Description

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)

PI supplied instrument name: Beckman Coulter Altra flow

Dataset-specific description

Simultaneously detects Hoechst stain (DNA), cell pigments, and forward and side (90 degrees) scatter.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
listmode_id	sample identification	unitless	sample
date	sampling date	year-month=day	date
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
T	the sample day (0 is the first sample collection day, up to the 13th collection day	days	time_elapsed
Num	replicate	unitless	replicate
syn_ml	Synechococcus abundance	cells/milliliter	abundance
peuk_ml	photosynthetic eukaryotes abundance (distinguished based on Chlorophyll and Scatter signatures)	cells/milliliter	abundance
HiPE_phyto_mL	abundance of cells with very high Phycoerythrin and very high Chlorophyll content	cells/milliliter	abundance
Hbact_mL	abundance of non-pigmented bacteria (distinguished based on DNA content (Hoechst stain) and scatter signatures)	cells/milliliter	bact_abund
Syn_num	Synechococcus cell count	cells	count
Peuk_num	photosynthetic eukaryote cell count	cells	count
HiPE_Phyto_num	high Phycoerythrin and Chlorophyll content cell count	cells	count
HBact_num	non-pigmented bacteria cell count	cells	count
Pro_Mean_FS	Prochlorococcus mean forward scatter from flow cytometer	unitless	light_bs
Pro_Mean_SS	Prochlorococcus mean side scatter from flow cytometer	unitless	light_bs
Pro_Mean_Chl	Prochlorococcus chlorophyll mean content from flow cytometer	unitless	light_bs
Pro_Mean_DNA	Prochlorococcus mean DNA content from flow cytometer	unitless	light_bs
Syn_Mean_FS	Synechococcus mean forward scatter from flow cytometer	unitless	light_bs
Syn_Mean_SS	Synechococcus mean side scatter from flow cytometer	unitless	light_bs
Syn_Mean_Chl	Synechococcus chlorophyll mean content from flow cytometer	unitless	light_bs
Syn_Mean_DNA	Synechococcus mean DNA content from flow cytometer	unitless	light_bs
Peuk_Mean_FS	photosynthetic eukaryote mean forward scatter from flow cytometer	unitless	light_bs
Peuk_Mean_SS	photosynthetic eukaryote mean side scatter from flow cytometer	unitless	light_bs
Peuk_Mean_Chl	photosynthetic eukaryote chlorophyll mean content from flow cytometer	unitless	light_bs
Peuk_Mean_DNA	photosynthetic eukaryote mean DNA content from flow cytometer	unitless	light_bs
HiPE_Phyto_Mean_FS	high Phycoerythrin and Chlorophyll cell mean forward scatter from flow cytometer	unitless	light_bs
HiPE_Phyto_Mean_SS	high Phycoerythrin and Chlorophyll cell mean side scatter from flow cytometer	unitless	light_bs
HiPE_Phyto_Mean_Chl	high Phycoerythrin and Chlorophyll cell chlorophyll mean content from flow cytometer	unitless	light_bs
HiPE_Phyto_Mean_DNA	high Phycoerythrin and Chlorophyll cell mean DNA content from flow cytometer	unitless	light_bs
HBact_Mean_FS	non-pigmented bacteria mean forward scatter from flow cytometer	unitless	light_bs
HBact_Mean_SS	non-pigmented bacteria mean side scatter from flow cytometer	unitless	light_bs
HBact_Mean_DNA	non-pigmented bacteria mean DNA content from flow cytometer	unitless	light_bs

Database

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Dataset: ESP 2014 Cell Counts