http://lod.bco-dmo.org/id/dataset/662653
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-10-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2016-10-25
publication
2016-10-25
revision
BCO-DMO Linked Data URI
2016-10-25
creation
http://lod.bco-dmo.org/id/dataset/662653
Mary Ann Moran
University of Georgia
principalInvestigator
James M. Birch
Monterey Bay Aquarium Research Institute
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Moran, M., Birch, J. M. (2016) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/662653 [access date]
Microbial taxonomy and abundance from ESP, fall 2014 Dataset Description: Methods and Sampling: <p>Dilutions to the sample due to preservative, dyes and run volume:<br />
PFA = 0.95<br />
Hoechst = 0.98<br />
Run Volume = 0.10<br />
Correction Factor = 0.82</p>
<p>For methodology&nbsp;details, see:<br />
Varaljay, V., et al. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. The ISME Journal (2015), 1-10.&nbsp;doi:10.1038/ismej.2015.23</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1342694 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1342694
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
James M. Birch
Monterey Bay Aquarium Research Institute
7700 Sandholdt Rd.
Moss Landing
CA
95039
USA
jbirch@mbari.org
pointOfContact
asNeeded
Unknown
listmode_id
date
lat
lon
T
Num
syn_ml
peuk_ml
HiPE_phyto_mL
Hbact_mL
Syn_num
Peuk_num
HiPE_Phyto_num
HBact_num
Pro_Mean_FS
Pro_Mean_SS
Pro_Mean_Chl
Pro_Mean_DNA
Syn_Mean_FS
Syn_Mean_SS
Syn_Mean_Chl
Syn_Mean_DNA
Peuk_Mean_FS
Peuk_Mean_SS
Peuk_Mean_Chl
Peuk_Mean_DNA
HiPE_Phyto_Mean_FS
HiPE_Phyto_Mean_SS
HiPE_Phyto_Mean_Chl
HiPE_Phyto_Mean_DNA
HBact_Mean_FS
HBact_Mean_SS
HBact_Mean_DNA
Beckman Coulter Altra flow
theme
None, User defined
sample identification
date
latitude
longitude
time_elapsed
replicate
abundance
bacterial abundance
count
light backscattered
featureType
BCO-DMO Standard Parameters
Flow Cytometer
instrument
BCO-DMO Standard Instruments
Moran_Monterey_2014
service
Deployment Activity
Monterey Bay, CA
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(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.
Dimensions of Biodiversity
largerWorkCitation
program
Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
https://osprey.bco-dmo.org/project/541255
Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
<p>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.</p>
<p>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.</p>
<p>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.</p>
OceanSulfurFluxBact
largerWorkCitation
project
eng; USA
biota
oceans
Monterey Bay, CA
2016-10-25
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/663627.rdf
Name: listmode_id
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/663628.rdf
Name: date
Units: year-month=day
Description: <p>sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/663629.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663630.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663631.rdf
Name: T
Units: days
Description: <p>the sample day (0 is the first sample collection day, up to the 13th collection day</p>
http://lod.bco-dmo.org/id/dataset-parameter/663632.rdf
Name: Num
Units: unitless
Description: <p>replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/663633.rdf
Name: syn_ml
Units: cells/milliliter
Description: <p>Synechococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663634.rdf
Name: peuk_ml
Units: cells/milliliter
Description: <p>photosynthetic eukaryotes abundance (distinguished based on Chlorophyll and Scatter signatures)</p>
http://lod.bco-dmo.org/id/dataset-parameter/663635.rdf
Name: HiPE_phyto_mL
Units: cells/milliliter
Description: <p>abundance of cells with very high Phycoerythrin and very high Chlorophyll content</p>
http://lod.bco-dmo.org/id/dataset-parameter/663636.rdf
Name: Hbact_mL
Units: cells/milliliter
Description: <p>abundance of non-pigmented bacteria (distinguished based on DNA content (Hoechst stain) and scatter signatures)</p>
http://lod.bco-dmo.org/id/dataset-parameter/663637.rdf
Name: Syn_num
Units: cells
Description: <p>Synechococcus cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/663638.rdf
Name: Peuk_num
Units: cells
Description: <p>photosynthetic eukaryote cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/663639.rdf
Name: HiPE_Phyto_num
Units: cells
Description: <p>high Phycoerythrin and Chlorophyll content cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/663640.rdf
Name: HBact_num
Units: cells
Description: <p>non-pigmented bacteria cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/663641.rdf
Name: Pro_Mean_FS
Units: unitless
Description: <p>Prochlorococcus mean forward scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663642.rdf
Name: Pro_Mean_SS
Units: unitless
Description: <p>Prochlorococcus mean side scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663643.rdf
Name: Pro_Mean_Chl
Units: unitless
Description: <p>Prochlorococcus chlorophyll mean content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663644.rdf
Name: Pro_Mean_DNA
Units: unitless
Description: <p>Prochlorococcus mean DNA content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663645.rdf
Name: Syn_Mean_FS
Units: unitless
Description: <p>Synechococcus mean forward scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663646.rdf
Name: Syn_Mean_SS
Units: unitless
Description: <p>Synechococcus mean side scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663647.rdf
Name: Syn_Mean_Chl
Units: unitless
Description: <p>Synechococcus chlorophyll mean content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663648.rdf
Name: Syn_Mean_DNA
Units: unitless
Description: <p>Synechococcus mean DNA content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663649.rdf
Name: Peuk_Mean_FS
Units: unitless
Description: <p>photosynthetic eukaryote mean forward scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663650.rdf
Name: Peuk_Mean_SS
Units: unitless
Description: <p>photosynthetic eukaryote mean side scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663651.rdf
Name: Peuk_Mean_Chl
Units: unitless
Description: <p>photosynthetic eukaryote chlorophyll mean content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663652.rdf
Name: Peuk_Mean_DNA
Units: unitless
Description: <p>photosynthetic eukaryote mean DNA content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663653.rdf
Name: HiPE_Phyto_Mean_FS
Units: unitless
Description: <p>high Phycoerythrin and Chlorophyll cell mean forward scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663654.rdf
Name: HiPE_Phyto_Mean_SS
Units: unitless
Description: <p>high Phycoerythrin and Chlorophyll cell mean side scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663655.rdf
Name: HiPE_Phyto_Mean_Chl
Units: unitless
Description: <p>high Phycoerythrin and Chlorophyll cell chlorophyll mean content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663656.rdf
Name: HiPE_Phyto_Mean_DNA
Units: unitless
Description: <p>high Phycoerythrin and Chlorophyll cell mean DNA content from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663657.rdf
Name: HBact_Mean_FS
Units: unitless
Description: <p>non-pigmented bacteria mean forward scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663658.rdf
Name: HBact_Mean_SS
Units: unitless
Description: <p>non-pigmented bacteria mean side scatter from flow cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/663659.rdf
Name: HBact_Mean_DNA
Units: unitless
Description: <p>non-pigmented bacteria mean DNA content from flow cytometer</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4470
https://datadocs.bco-dmo.org/file/oAAmoRxClNpzK6/cell_counts.csv
cell_counts.csv
Primary data file for dataset ID 662653
download
https://osprey.bco-dmo.org/dataset/662653/data/download
download
onLine
dataset
<p>Dilutions to the sample due to preservative, dyes and run volume:<br />
PFA = 0.95<br />
Hoechst = 0.98<br />
Run Volume = 0.10<br />
Correction Factor = 0.82</p>
<p>For methodology&nbsp;details, see:<br />
Varaljay, V., et al. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. The ISME Journal (2015), 1-10.&nbsp;doi:10.1038/ismej.2015.23</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- re-formatted date from m/d/yyyy to yyyy-mm-dd<br />
- added lat and lon of ESP mooring for mapping purposes</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Beckman Coulter Altra flow
Beckman Coulter Altra flow
PI Supplied Instrument Name: Beckman Coulter Altra flow PI Supplied Instrument Description:Simultaneously detects Hoechst stain (DNA), cell pigments, and forward and side (90 degrees) scatter. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Deployment: Moran_Monterey_2014
Moran_Monterey_2014
Univ_Georgia
laboratory
Moran_Monterey_2014
Mary Ann Moran
University of Georgia
Univ_Georgia
laboratory