http://lod.bco-dmo.org/id/dataset/748024
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
2018-10-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014
2018-09-05
publication
2018-09-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-20
publication
https://doi.org/10.26008/1912/bco-dmo.748024.1
Frederick Colwell
Oregon State University
principalInvestigator
Andrew Thurber
Oregon State 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: Colwell, F., Thurber, A. (2021) 16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-09-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.748024.1 [access date]
16S gene sequencing of microbial communities from South China Sea sediments Dataset Description: <p>Three locations in the SCS were cored during IODP Expedition 349 at sites U1431 (15° 22.5379’ N, 117° 00.0022’ E, 4240 meters below sea level (mbsl)), U1432 (18° 21.0831’ N, 116° 23.4504’ E, 3829 mbsl), and U1433 (12° 55.1380’ N, 115° 02.8345’ E, 4379 mbsl). Cores were split lengthwise onboard to reveal geological interfaces and the exposed sediment was aseptically scraped away prior to sampling. Samples were collected only from the center of the cores, avoiding the outside edges of the cores that may have contacted the core barrel. Samples were stored at -80°C until analysis. Down-core measurements of sediment methane concentrations, alkalinity, and pore water sulfate, ammonium, and phosphate were made onboard. Sediment ages were calculated based on paleomagnetic analysis and nanofossil characterization for each site.</p>
<p>All samples described in this study were collected using an advanced piston core, a tool that minimizes core disturbance. In order to check whether contamination occurred, and consistent with other deep microbiology coring studies, we compared microbial communities present in fluids that drained from the core barrel (possibly from seawater intrusion during core retrieval) to those present in the center of the cores, a so-called fluid community tracer (FCT) approach. Samples of the drilling fluid from core U1433 were collected immediately when cores were brought onto the deck and were frozen at -80°C until analysis. To compare microbial communities in the drilling fluids to those in the cores, DNA from 10 FCT samples (235-790 mbsf) and a whole-round sample (13.5 mbsf) was extracted using a FastDNA Spin Kit for Soil (MP Biomedical, OH, USA). Pyrosequencing of the archaeal 16S rRNA gene of the FCT samples and the whole-round sample was conducted with a Roche 454 GS FLX+ Titanium platform (Roche 454 Life Sciences, CT, USA) at the Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Primers used for amplification were Arch_344F (5′-ACGGGGCGCAGCAGGCGCGA-3′) and Arch_915R (5′-GTGCTCCCCCGCCAATTCCT-3′).</p>
<p>Additional award numbers:</p>
<p>Consortium for Ocean Leadership; award number: IUSSP410<br />
C-DEBI; subaward number: 59209190<br />
DCO/DLC; subaward number: 53587</p>
<p>Data are publicly accessible at NCBI under accession number PRJNA362622.</p> Methods and Sampling: <p>DNA was extracted from 0.25 g of wet sediment using a MoBio PowerSoil DNA Isolation Kit. Extracted DNA was amplified in technical triplicate 25 uL reactions using universal 16S rRNA gene primers 515-fwd and 806-rev with Illumina sequencing adapters and barcodes.&nbsp; Triplicate PCR products were pooled, visualized on an agarose gel, and cleaned using a MoBio UltraClean PCR Clean-Up Kit. PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing. Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing. A sediment-free extraction was amplified and sequenced alongside sediment samples.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Frederick Colwell
Oregon State University
541-737-5220
519 Weniger Hall, Oregon State University, Corvallis, OR 97331
rcolwell@coas.oregonstate.edu
pointOfContact
Andrew Thurber
Oregon State University
541-737-4500
athurber@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
collection_date
depth
lat
lon
sedimentology
elev
advanced piston core
Illumina MiSeq
Qubit fluorometer
theme
None, User defined
sample identification
date
depth core
latitude
longitude
sample description
depth
featureType
BCO-DMO Standard Parameters
Advanced Piston Corer
Automated DNA Sequencer
Fluorometer
instrument
BCO-DMO Standard Instruments
IODP-349
service
Deployment Activity
South China Sea
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones
https://osprey.bco-dmo.org/project/745593
Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones
<p>Project summary:</p>
<p>For subseafloor microorganisms, defined geological and chemical gradients affect population sizes and community structure. We examined how distinct sediment types influence microbial diversity and community composition and the factors that drive deep-subsurface microbial community structure (e.g., depth, interstitial water chemistry, sample location). During IODP Expedition 349 (South China Sea Tectonics), either coupled ash/clay or turbidite/clay boundaries were sampled, DNA extracted, and the 16S rRNA gene analyzed on an Illumina MiSeq platform. Microbial communities in sediments were distinct from communities in drilling fluid, indicating that drilling-based contamination was unlikely. Illumina sequencing of the 16S rRNA gene yielded 5,453 OTUs (97% identity) representing 44 bacterial phyla and 3 archaeal phyla. Members of the Atribacteria dominated all microbial communities among all sites. Sulfate-reducing bacteria were relatively rare within sulfate-replete sediments in all cores. Ordination of the microbial communities using weighted UniFrac distances revealed significant differences in communities both between sites and between the sulfate reduction zone and methanogenic zone at two of the sites. The number of observed taxa followed an exponential decline with sediment age only in the sulfate reduction zone. Species evenness increased linearly with sediment age regardless of geochemical zonation in the sediment column. Our investigation helps to characterize the factors that drive microbial community structure of the subseafloor and highlights the need to focus on habitat heterogeneity at a scale pertinent to bacteria and archaea in studies of microbial ecology.</p>
<p>This project is funded with:<br />
Center for Dark Energy Biosphere Investigations (C-DEBI); subaward number: 59209190<br />
Deep Carbon Observatory (DCO) /Deep Life Community (DLC); subaward number: 53587<br />
Consortium for Ocean Leadership; award number: IUSSP410</p>
<p> </p>
Edginess in the subsurface
largerWorkCitation
project
eng; USA
oceans
South China Sea
115.0472
117
12.919
18.3514
2014-01-30
2014-03-07
South China Sea
0
BCO-DMO catalogue of parameters from 16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014
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/748047.rdf
Name: Sample_Name
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/748048.rdf
Name: collection_date
Units: unitless
Description: <p>date the sediment was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/748049.rdf
Name: depth
Units: meters (m)
Description: <p>depth where samples were taken below sea floor.</p>
http://lod.bco-dmo.org/id/dataset-parameter/748050.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude in decimal degrees north</p>
http://lod.bco-dmo.org/id/dataset-parameter/748051.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude in decimal degrees east</p>
http://lod.bco-dmo.org/id/dataset-parameter/748052.rdf
Name: sedimentology
Units: unitless
Description: <p>description of sediment type</p>
http://lod.bco-dmo.org/id/dataset-parameter/748054.rdf
Name: elev
Units: meters (m)
Description: <p>water depth at the sampling site</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
4972
https://darchive.mblwhoilibrary.org/bitstream/1912/27142/1/dataset-748024_south-china-sea-16s__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.748024.1
download
onLine
dataset
<p>DNA was extracted from 0.25 g of wet sediment using a MoBio PowerSoil DNA Isolation Kit. Extracted DNA was amplified in technical triplicate 25 uL reactions using universal 16S rRNA gene primers 515-fwd and 806-rev with Illumina sequencing adapters and barcodes.&nbsp; Triplicate PCR products were pooled, visualized on an agarose gel, and cleaned using a MoBio UltraClean PCR Clean-Up Kit. PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing. Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing. A sediment-free extraction was amplified and sequenced alongside sediment samples.</p>
Specified by the Principal Investigator(s)
<p>Sequences were processed using mothur (v 1.38.0; (38)). Reads were clustered at 97% and classified against the SILVA database (v. 119). Singleton OTUs were removed prior to analysis. OTUs that were present in greater than 1% relative abundance in the negative (sediment-free) control and classified as common human or kit contaminants (39) were removed from the dataset. To confirm their identity, phylogenetic trees were generated for all OTUs classified as ANME and for the 8 most abundant OTUs classified to known sulfate-reducing bacteria lineages with Fasttree (v. 2.1.10; 40)) using the Jukes-Cantor model (Supp. Figs. 1 and 2).&nbsp;</p>
<p>BCO-DMO Processing Notes:</p>
<ul>
<li>translated the "collection_date" fromat from DD-Mon-YY (7-Mar-14) to YYYY-MM-DD (2014-03-14).</li>
<li>added conventional header with dataset name, PI name, version date</li>
<li>modified parameter names to conform with BCO-DMO naming conventions</li>
<li>removed hemisphere declarations in the latitude and longitude fields.&nbsp;</li>
</ul>
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
advanced piston core
advanced piston core
PI Supplied Instrument Name: advanced piston core PI Supplied Instrument Description:All samples described in this study were collected using an advanced piston core, a tool that minimizes core disturbance. Instrument Name: Advanced Piston Corer Instrument Short Name:APC Instrument Description: The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.
More information is available from IODP (PDF).
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Qubit fluorometer
Qubit fluorometer
PI Supplied Instrument Name: Qubit fluorometer PI Supplied Instrument Description: PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Cruise: IODP-349
IODP-349
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
IODP-349
Chun-Feng Li
Tongji University
http://publications.iodp.org/proceedings/349/349title.html
Report describing IODP-349
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel