http://lod.bco-dmo.org/id/dataset/716766
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
2017-10-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cariaco metagenomes/metatranscriptomes for samples collected at the CARIACO Basin Time Series Station 10.5˚N, 64.7˚W on CAR212_2 and CAR_216_2
2017-10-12
publication
2017-10-12
revision
BCO-DMO Linked Data URI
2017-10-12
creation
http://lod.bco-dmo.org/id/dataset/716766
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Gordon T. Taylor
Stony Brook University
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: Edgcomb, V. P., Taylor, G. T. (2017) Cariaco metagenomes/metatranscriptomes for samples collected at the CARIACO Basin Time Series Station 10.5˚N, 64.7˚W on CAR212_2 and CAR_216_2. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-10-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/716766 [access date]
Description metadata and links for metagenome and metatranscriptome data Dataset Description: <p>Description metadata and links for metagenome and metatranscriptome data.</p>
<p>Location:&nbsp;CARIACO Basin Time Series Station 10.5˚N, 64.7˚W.</p> Methods and Sampling: <p>DNA for metagenomes:</p>
<p>Samples for DNA were collected at 10-12 depths from standard rosette-mounted Niskin bottles. Niskin bottles were slightly pressurized with N<sub>2</sub> or argon gas from the top vent to prevent O<sub>2</sub> contamination during sample transfer. Eight or 12L samples were filtered directly from Niskin bottles sequentially through a 2.7µm hydrophilic glass fiber filter (EMD Millipore) and then 0.2µm in-line Millipore® Sterivex™ filter units (EMD Millipore) for the particle-associated and free-living fractions, respectively. Filters were immediately treated with lysis buffer (50mM Tris-HCL, 40mM EDTA, 0.73M sucrose) and stored frozen. DNA samples were extracted according to Frias-Lopez et al. (2008) and Ganesh et al. (2014). DNA was purified with the Genomic DNA Clean and Concentrator -25 kit (Zymo Research), eluted into 10mM Tris for qPCR samples or into TE buffer for sequencing samples, and stored at -80˚C for downstream analyses.</p>
<p>RNA for transcriptomes:</p>
<p>For RNA samples ~2L water was filtered and preserved in situ in RNALaterfrom each depth using a custom instrument MS-SID (C. Taylor/V. Edgcomb, WHOI). RNA was isolated using the MirVana MiRNA Isolation kit, and cDNA prepared and libraries constructed with the ScriptSeq RNA Seq library preparation kit.</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
631-632-8688
Stony Brook University School of Marine and Atmospheric Sciences
Stony Brook
NY
11794-5000
USA
gordon.taylor@stonybrook.edu
pointOfContact
asNeeded
Unknown
Library_kind
geo_loc_name
collection_date
Depth_m
Size_Fraction
Replicate
Sequencing_Center
Genome_Size_assembled
Gene_Count_assembled
Release_date
OID_number
OID_link
theme
None, User defined
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Sea-Bird SBE 25 Sealogger CTD
instrument
BCO-DMO Standard Instruments
CAR212_2
CAR216_2
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
biota
oceans
CARIACO Basin Time Series Station
2017-10-12
Southern Caribbean Sea - 10" 30' N, 64" 40' W (CARIACO Ocean Time Series Station)
0
BCO-DMO catalogue of parameters from Cariaco metagenomes/metatranscriptomes for samples collected at the CARIACO Basin Time Series Station 10.5˚N, 64.7˚W on CAR212_2 and CAR_216_2
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/722809.rdf
Name: Library_kind
Units: no units
Description: <p>Library kind</p>
http://lod.bco-dmo.org/id/dataset-parameter/722810.rdf
Name: geo_loc_name
Units: no units
Description: <p>Location name</p>
http://lod.bco-dmo.org/id/dataset-parameter/722811.rdf
Name: collection_date
Units: no units
Description: <p>collection data</p>
http://lod.bco-dmo.org/id/dataset-parameter/722812.rdf
Name: Depth_m
Units: meters
Description: <p>Depth_m</p>
http://lod.bco-dmo.org/id/dataset-parameter/722813.rdf
Name: Size_Fraction
Units: um
Description: <p>Size_Fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/722814.rdf
Name: Replicate
Units: no units
Description: <p>Replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722815.rdf
Name: Sequencing_Center
Units: no units
Description: <p>Seqencing_Center</p>
http://lod.bco-dmo.org/id/dataset-parameter/722816.rdf
Name: Genome_Size_assembled
Units: no units
Description: <p>Genome size assembled</p>
http://lod.bco-dmo.org/id/dataset-parameter/722817.rdf
Name: Gene_Count_assembled
Units: no units
Description: <p>Genome count assembled</p>
http://lod.bco-dmo.org/id/dataset-parameter/722818.rdf
Name: Release_date
Units: no units
Description: <p>Release_date</p>
http://lod.bco-dmo.org/id/dataset-parameter/722819.rdf
Name: OID_number
Units: no units
Description: <p>OID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/722820.rdf
Name: OID_link
Units: no units
Description: <p>OID link</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
19367
https://datadocs.bco-dmo.org/file/l880lx0CXB6pPZ/Genomes_IMG_2017.csv
Genomes_IMG_2017.csv
Primary data file for dataset ID 716766
download
https://osprey.bco-dmo.org/dataset/716766/data/download
download
onLine
dataset
<p>DNA for metagenomes:</p>
<p>Samples for DNA were collected at 10-12 depths from standard rosette-mounted Niskin bottles. Niskin bottles were slightly pressurized with N<sub>2</sub> or argon gas from the top vent to prevent O<sub>2</sub> contamination during sample transfer. Eight or 12L samples were filtered directly from Niskin bottles sequentially through a 2.7µm hydrophilic glass fiber filter (EMD Millipore) and then 0.2µm in-line Millipore® Sterivex™ filter units (EMD Millipore) for the particle-associated and free-living fractions, respectively. Filters were immediately treated with lysis buffer (50mM Tris-HCL, 40mM EDTA, 0.73M sucrose) and stored frozen. DNA samples were extracted according to Frias-Lopez et al. (2008) and Ganesh et al. (2014). DNA was purified with the Genomic DNA Clean and Concentrator -25 kit (Zymo Research), eluted into 10mM Tris for qPCR samples or into TE buffer for sequencing samples, and stored at -80˚C for downstream analyses.</p>
<p>RNA for transcriptomes:</p>
<p>For RNA samples ~2L water was filtered and preserved in situ in RNALaterfrom each depth using a custom instrument MS-SID (C. Taylor/V. Edgcomb, WHOI). RNA was isolated using the MirVana MiRNA Isolation kit, and cDNA prepared and libraries constructed with the ScriptSeq RNA Seq library preparation kit.</p>
Specified by the Principal Investigator(s)
<p>Transcriptome library quality control was performed using Trimmomatic and assembled into contigs using Trinity 2.03.</p>
<p>Metagenome library quality control was performed using Trimmomatic and assembled using IDBA v. 1.11.</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
PI Supplied Instrument Name: Instrument Name: Sea-Bird SBE 25 Sealogger CTD Instrument Short Name:CTD SBE 25 Instrument Description: The Sea-Bird SBE 25 SEALOGGER CTD is battery powered and is typically used to record data in memory, eliminating the need for a large vessel, electrical sea cable, and on-board computer. All SBE 25s can also operate in real-time, transmitting data via an opto-isolated RS-232 serial port. Temperature and conductivity are measured by the SBE 3F Temperature sensor and SBE 4 Conductivity sensor (same as those used on the premium SBE 9plus CTD). The SBE 25 also includes the SBE 5P (plastic) or 5T (titanium) Submersible Pump and TC Duct. The pump-controlled, TC-ducted flow configuration significantly reduces salinity spiking caused by ship heave, and in calm waters allows slower descent rates for improved resolution of water column features. Pressure is measured by the modular SBE 29 Temperature Compensated Strain-Gauge Pressure sensor (available in eight depth ranges to suit the operating depth requirement). The SBE 25's modular design makes it easy to configure in the field for a wide range of auxiliary sensors, including optional dissolved oxygen (SBE 43), pH (SBE 18 or SBE 27), fluorescence, transmissivity, PAR, and optical backscatter sensors. More information from Sea-Bird Electronics: http:www.seabird.com. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0040/
Cruise: CAR212_2
CAR212_2
B/O Hermano Gines
vessel
Cruise: CAR216_2
CAR216_2
B/O Hermano Gines
vessel
B/O Hermano Gines
vessel