http://lod.bco-dmo.org/id/dataset/652438
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
2016-07-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Fluorescent in situ hybridization data from B/O Hermano Gines cruises for the CARIACO Basin Time Series Station from May to November 2014 (CariacoMetaOmics project)
2016-07-22
publication
2016-07-22
revision
BCO-DMO Linked Data URI
2016-07-22
creation
http://lod.bco-dmo.org/id/dataset/652438
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Gordon T. Taylor
Stony Brook University - SoMAS
principalInvestigator
Dr Craig Taylor
Woods Hole Oceanographic Institution
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: Taylor, G. T., Edgcomb, V. P., Taylor, C. (2016) Fluorescent in situ hybridization data from B/O Hermano Gines cruises for the CARIACO Basin Time Series Station from May to November 2014 (CariacoMetaOmics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version Final) Version Date 2016-07-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/652438 [access date]
Fluorescent in situ hybridization data from the CAR212 and CAR216 cruises. Dataset Description: <p>Fluorescent in situ hybridization (FISH) data enumerated from microscopic samples on 2 legs of each of the CAR212 and CAR216 cruises.</p> Methods and Sampling: <p>All samples were collected via Niskin bottles.</p>
<p>Seawater samples were fixed with 2% borate-buffered formaldehyde, frozen overnight, then filtered the next day onto 0.2-um polycarbonate membrane filters. Filters were refrozen at -20 degrees celsius until hybridization. All FISH hybridization procedures were performed according to Pernthaler et al. (2001) with fluorescent probes labeled with CY3 or fluorescein. Filters were counterstained with DAPI and probe-positive cells were enumerated as a percentage of the total community (DAPI-positive). FISH probes were:</p>
<p><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/CariacoMetaOmics/FISH_table.png" style="height:105px; width:739px" /></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335436 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1335436
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1336082 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1336082
onGoing
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
508-289-3734
Department of Geology and Geophysics 220 McLean Lab, MS #8
Woods Hole
MA
02543
USA
vedgcomb@whoi.edu
pointOfContact
Gordon T. Taylor
Stony Brook University - SoMAS
631-632-8688
Stony Brook University School of Marine and Atmospheric Sciences
Stony Brook
NY
11794-5000
USA
gordon.taylor@stonybrook.edu
pointOfContact
Dr Craig Taylor
Woods Hole Oceanographic Institution
508-289-2354
Mail Stop #52 Stanley W. Watson Laboratory for Biogeochemistry
Woods Hole
MA
02543
USA
ctaylor@whoi.edu
pointOfContact
asNeeded
Dataset Version: Final
Unknown
cruise_id
date_start
depth
delta495
delta495_sd
gam42a
gam42a_sd
eps682
eps682_sd
alf968
alf968_sd
Niskin bottle
theme
None, User defined
Cruise identfier
date_start
depth
No BCO-DMO term
standard deviation
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
CAR212_2
CAR212_3
CAR216_2
CAR216_3
service
Deployment Activity
CARIACO Basin Time Series Station
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.
Genetic and Metabolic Signatures of Marine Microorganisms in Oxygen Depleted and Varying Geochemical Seascapes
https://osprey.bco-dmo.org/project/562425
Genetic and Metabolic Signatures of Marine Microorganisms in Oxygen Depleted and Varying Geochemical Seascapes
<p>Oxygen depleted water columns (ODWCs) appear to be expanding in response to global climate change. This alters trophic structure, compresses habitat and modifies geochemical cycles of major elements. Oxygen depletion can vary in intensity and duration from seasonal hypoxia to permanent anoxia. The focus of this study is a classic example of the anoxic end-member, the Cariaco Basin. The overall goal is to examine how microbial functional potential (metagenomic), activity (metatranscriptomic), taxonomic diversity (based on SSU rRNA) and the ecological/geochemical consequences (in terms of measured rates of key processes) relate along vertical oxygen/geochemical gradients and between seasons in the Cariaco Basin. This will reveal relationships between expression of particular sets of genes, environmental differences in nutrients, energy substrates and oxidant availabilities.</p>
<p>
The objectives are to: (1) Integrate hydrographic, geochemical and microbial ecological data with metagenomic and metatranscriptomic profiles to understand regulatory and metabolic networks defining microbial community responses to environmental forcing during high and low productivity periods. This will help to understand the importance of processes, such as anaerobic oxidation of methane, utilization of redox-sensitive metals, the cryptic sulfur cycle in this ODWC, and the impacts of oxygen depletion on nitrogen transformations. (2) Determine the importance of associations between microbial eukaryotes (mEuks) and prokaryotes in this ODWC. (3) Identify "indicator" genes of known or unknown function that may be relevant to major elemental and trace gas cycling as targets for further biochemical characterization and molecular probe development, and quantify a key subset of these genes and transcripts across redox gradients using qPCR. (4) Provide a basis for developing monitoring tools using expressed genes indicative of important elemental transformations and fluxes for diagnosing the health status of natural and human engineered ecosystems. (5) Compare results with recent and ongoing studies of other ODWCs to discern shared and unique attributes of these systems.</p>
<p>Intellectual Merit: Previous studies of ODWCs have underscored the need for more data on microbial community structure and functionality in ODWCs, particularly biochemical rate measurements and other data on community responses to changing conditions. Better predictive models of responses of marine microbial communities and biogeochemical processes to global climate change are essential for informing future policy and management decisions. Data from an anoxic end-member ODWC like Cariaco Basin are critically needed to compare with data from other recent and ongoing studies of seasonally-depleted coastal systems and permanently-depleted deep basin and western boundary oxygen minimum zones (OMZs) to construct more skillful models. This study will advance the understanding of impacts of expanding ODWCs around the world, moving beyond assessments based only on taxonomic diversity, to yield new insights into the ecology and physiology of major microbial groups in these environments and interactions among Bacteria, Archaea and microbial eukaryotes.</p>
<p>Broader Impacts: The PIs and their collaborators will train one Research Associate, one postdoctoral investigator, a graduate student, and numerous undergraduates from SBU. All personnel will be trained in various aspects of microbial ecology and oceanography, with an emphasis on both traditional (e.g., microscopy) and "cutting edge" (e.g. metagenomics/transcriptomics) techniques. The PIs will also involve the Zephyr Education Foundation's marine science literacy and education program, located in Woods Hole, MA. The PIs will work with this organization to educate inner city K-12 students using local boat field trips organized by Zephyr, and lectures, and classroom laboratory exercises designed by the PIs. Additionally, this project will have broad implications for understanding how ODWCs affect marine ecosystems, and may influence future management strategies and models describing the cycling of C and N between the ocean and atmosphere.</p>
CariacoMetaOmics
largerWorkCitation
project
eng; USA
oceans
CARIACO Basin Time Series Station
2016-07-22
Southern Caribbean Sea - 10" 30' N, 64" 40' W (CARIACO Ocean Time Series Station)
0
BCO-DMO catalogue of parameters from Fluorescent in situ hybridization data from B/O Hermano Gines cruises for the CARIACO Basin Time Series Station from May to November 2014 (CariacoMetaOmics 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
http://lod.bco-dmo.org/id/dataset-parameter/652450.rdf
Name: cruise_id
Units: unitless
Description: <p>cariaco cruise number and leg number</p>
http://lod.bco-dmo.org/id/dataset-parameter/652451.rdf
Name: date_start
Units: unitless
Description: <p>start date; mm/dd/yyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/652452.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/652453.rdf
Name: delta495
Units: dimensionless
Description: <p>percent Delta495 cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652454.rdf
Name: delta495_sd
Units: dimensionless
Description: <p>standard deviation of the percent Delta495 cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652455.rdf
Name: gam42a
Units: dimensionless
Description: <p>percent Gam42a cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652456.rdf
Name: gam42a_sd
Units: dimensionless
Description: <p>standard deviation of the percent Gam42a cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652457.rdf
Name: eps682
Units: dimensionless
Description: <p>percent Eps682 cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652458.rdf
Name: eps682_sd
Units: dimensionless
Description: <p>standard deviation of the percent Eps682 cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652459.rdf
Name: alf968
Units: dimensionless
Description: <p>percent Alf968 cells of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/652460.rdf
Name: alf968_sd
Units: dimensionless
Description: <p>standard deviation of the percent Alf968 cells of total</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
3895
https://datadocs.bco-dmo.org/file/M77XqOPIq7659V/Fluor_insitu_Hybrid.csv
Fluor_insitu_Hybrid.csv
Primary data file for dataset ID 652438
download
https://osprey.bco-dmo.org/dataset/652438/data/download
download
onLine
dataset
<p>All samples were collected via Niskin bottles.</p>
<p>Seawater samples were fixed with 2% borate-buffered formaldehyde, frozen overnight, then filtered the next day onto 0.2-um polycarbonate membrane filters. Filters were refrozen at -20 degrees celsius until hybridization. All FISH hybridization procedures were performed according to Pernthaler et al. (2001) with fluorescent probes labeled with CY3 or fluorescein. Filters were counterstained with DAPI and probe-positive cells were enumerated as a percentage of the total community (DAPI-positive). FISH probes were:</p>
<p><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/CariacoMetaOmics/FISH_table.png" style="height:105px; width:739px" /></p>
Specified by the Principal Investigator(s)
<p>All data were normalized to volume of seawater.</p>
<p><span style="font-size:11px">DMO Notes:</span></p>
<p><span style="font-size:11px">-transferred FISH data section into&nbsp;separate&nbsp;a data object.<br />
-reformatted the date to comply with BCO-DMO standards.<br />
-reformatted some column names to comply with BCO-DMO standards.</span></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
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:All samples were collected via Niskin bottles. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: CAR212_2
CAR212_2
B/O Hermano Gines
vessel
Cruise: CAR212_3
CAR212_3
B/O Hermano Gines
vessel
Cruise: CAR216_2
CAR216_2
B/O Hermano Gines
vessel
Cruise: CAR216_3
CAR216_3
B/O Hermano Gines
vessel
B/O Hermano Gines
vessel