http://lod.bco-dmo.org/id/dataset/636859
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
2016-01-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments
2016-01-28
publication
2016-01-28
revision
BCO-DMO Linked Data URI
2016-01-28
creation
http://lod.bco-dmo.org/id/dataset/636859
Annette R. Rowe
University of Southern California
principalInvestigator
Dr Kenneth H. Nealson
University of Southern California
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: Rowe, A. R., Nealson, K. H. (2016) 16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 28 Jan 2016) Version Date 2016-01-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636859 [access date]
16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments. Dataset Description: <p>16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments.</p>
<p><strong>Related Publications:</strong><br />
Rowe, A.R. et al. 2015. Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism.&nbsp;Frontiers in Microbiology (5). doi:<a href="http://dx.doi.org/10.3389/fmicb.2014.00784" target="_blank">10.3389/fmicb.2014.00784&nbsp;</a></p> Methods and Sampling: <p>The microbes isolated during this work were originally enriched from Catalina Harbor sediments from electrodes poised at reducing or electron donating redox potentials. Isolates are obtained from these enrichements based on the oxidation of elemental sulfur, elemental iron, or amorphous FeS. Approximately 30 isolates from 8 phylotypes were obtained. Ribosomal 16S sequences were obtained for all isolates using direct 16S rRNA amplification from pure culture DNA extracts. The universal bacterial primers 27F (5'-AGAGTTTGAT CCTGGCTCAG) and 1492R (5'-GGTTACCTTGTTACGACTT) were used. Approximately 20–40 ng of PCR product from each isolate were purified with a DNA Clean Concentrator Kit (ZymoResearch, Irvine, CA), and Sanger sequencing was per- formed viaGenewiz (La Jolla,CA) or BeckmanCoulter Genomics (Danvers, MA).</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
Annette R. Rowe
University of Southern California
513-556-9715
731F Rieveschl Hall 312 College Drive
Cincinnati
OH
45221
USA
annette.rowe@uc.edu
pointOfContact
Dr Kenneth H. Nealson
University of Southern California
213-821-2271
560 SHS, 825 Bloom Walk University of Southern California
Los Angeles
CA
90089
USA
knealson@usc.edu
pointOfContact
asNeeded
Dataset Version: 28 Jan 2016
Unknown
accession_num
species
lat
lon
method
accession_link
theme
None, User defined
accession number
species scientific name (binomial)
latitude
longitude
brief description
featureType
BCO-DMO Standard Parameters
CH_Sediment_Rowe
service
Deployment Activity
Catalina Harbor, Two Harbors, Catalina 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.
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
Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transports
https://osprey.bco-dmo.org/project/636843
Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transports
<p>Description from <a href="http://www.darkenergybiosphere.org/education/postdocsFunded.html" target="_blank">C-DEBI</a>:<br />
One of the major questions in subsurface biology is understanding how microrganisms in the subsurface are “making a living”. However, there is a dearth of knowledge concerning the physiology of major microbial groups that likely dominate the subsurface, including the lithotrophic or “rock-eating” microbes. This, in turn, makes one of the major research goals of C-DEBI, identifying and assessing activity in the deep subsurface biosphere, extremely difficult for these processes (i.e. not identified via “meta-omic” based studies) and in many cases these metabolisms are probably overlooked. Through my C-DEBI fellowship I was able to develop techniques for electrochemical cultivation of lithotrophic microbes to help facilitate identification and further study of microbial groups with these abilities. As part of this work I targeted cultivation of several groups of facultative lithotrophs that are phylogenetically related to organisms that are genetically tractable, and I’m currently in the process of building draft genomes for these microbes. It is my goal to use these microbes as model systems for understanding and biochemically characterizing the physiology of lithotrophs that will lead to better genetic markers to identify these physiologies in the environment. The work done through this fellowship has currently resulted in one publication in “Frontiers in Microbiology” on the electrochemical cultivation and isolation of facultative lithotrophs and tracking the physiology of cathode oxidizing microbes is the publication that will be submitted this summer. One of the most exciting results from this work is that the majority of microbes isolated from the one marine sediment tested, appear to have different redox potential where they catalyze the oxidation of a cathode suggesting a variety of different protein pathways used. This highlights both the unknown nature of these processes and the diversity of potential lithotrophic metabolic pathways.</p>
<p>This project was funded by a C-DEBI Postdoctoral Fellowship.</p>
PassElectronsThruMarSed
largerWorkCitation
project
eng; USA
biota
oceans
Catalina Harbor, Two Harbors, Catalina CA
2016-01-28
0
BCO-DMO catalogue of parameters from 16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments
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/636868.rdf
Name: accession_num
Units: dimensionless
Description: <p>NCBI accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636869.rdf
Name: species
Units: dimensionless
Description: <p>Species name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636870.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude. Positive values = North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636871.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude. Negative values = West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636872.rdf
Name: method
Units: dimensionless
Description: <p>Description of sequencing method.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636873.rdf
Name: accession_link
Units: dimensionless
Description: <p>Hyperlink to NCBI.</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
1579
https://datadocs.bco-dmo.org/file/3YY3qo1fXywVQR/COLI_16S_rRNA.csv
COLI_16S_rRNA.csv
Primary data file for dataset ID 636859
download
https://osprey.bco-dmo.org/dataset/636859/data/download
download
onLine
dataset
<p>The microbes isolated during this work were originally enriched from Catalina Harbor sediments from electrodes poised at reducing or electron donating redox potentials. Isolates are obtained from these enrichements based on the oxidation of elemental sulfur, elemental iron, or amorphous FeS. Approximately 30 isolates from 8 phylotypes were obtained. Ribosomal 16S sequences were obtained for all isolates using direct 16S rRNA amplification from pure culture DNA extracts. The universal bacterial primers 27F (5'-AGAGTTTGAT CCTGGCTCAG) and 1492R (5'-GGTTACCTTGTTACGACTT) were used. Approximately 20–40 ng of PCR product from each isolate were purified with a DNA Clean Concentrator Kit (ZymoResearch, Irvine, CA), and Sanger sequencing was per- formed viaGenewiz (La Jolla,CA) or BeckmanCoulter Genomics (Danvers, MA).</p>
Specified by the Principal Investigator(s)
<p>These nearly full length sequences were quality checked and assembled using Geneious 7.1© (Biomatters, New Zealand). Alignment of sequences against the Silva database was performed using the SINA aligner (v 1.2.11) (Pruesse et al., 2012; Quast et al., 2013). Nearest cultured representative microbes were also obtained through the Silva database (Quast et al., 2013). Maximum-likelihood estimation trees were constructed from alignments of sequences and nearest neighbors using RaxML (v.8) (Stamatakis, 2014) to assign taxonomy. A identity of 97% was used to designate a specific genera for a given sequence. All full length sequences have been deposited to Genbank (accession numbers KM088025-KM0 88033).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- separated location into lat and lon columns;<br />
- converted degrees and decimal minutes to decimal degrees;<br />
- replaced commas with semi-colons;<br />
- replaces spaces with underscores;<br />
- modified parameter names to conform with BCO-DMO naming conventions.</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
Deployment: CH_Sediment_Rowe
CH_Sediment_Rowe
Catalina Harbor
shoreside
CH_Sediment_Rowe
Annette R. Rowe
University of Southern California
Catalina Harbor
shoreside