http://lod.bco-dmo.org/id/dataset/687822
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
2017-04-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project)
2017-04-11
publication
2017-04-11
revision
BCO-DMO Linked Data URI
2017-04-11
creation
http://lod.bco-dmo.org/id/dataset/687822
David L. Valentine
University of California-Santa Barbara
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: Valentine, D. L. (2017) Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-04-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/687822 [access date]
Protein sequences from diversity-generating retroelements in groundwater microorganisms Dataset Description: <p>This dataset includes links to diversity-generating retroelement sequences files in .fasta format. &nbsp;There are separate .fasta files for reverse transcriptase protein sequences and variable protein sequences. &nbsp;These sequences were derived from&nbsp;previously generated sequence accessions at the National Center for Biotechnology Information (NCBI). &nbsp;Original&nbsp;sampling took place near Rifle, Colorado between 2011 and 2012.</p>
<p>To access the .fasta files and the list of source sequences, click the "Get Data" button at the top of this page.</p>
<div>These data are published in the following journal article:<br />
Paul, B.G., Burstein, D., Castelle, C.J., Handa, S., Arambula, D., Czornyj, E., Thomas, B.C., Ghosh, P., Miller, J.F., Banfield, J.F. and Valentine, D.L. (2017) Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nature Microbiology, 2, p.17045. doi: <a href="http://doi.org/10.1038/nmicrobiol.2017.45" target="_blank">10.1038/nmicrobiol.2017.45</a></div> Methods and Sampling: <p>A bioinformatic analysis of metagenome-assembled genomes to identify retroelements was performed. This study used data from several previously described&nbsp;sampling efforts (Brown et al. 2015, Castelle et al. 2015, and Anantharaman et al. 2016). Original sampling was conducted within an unconfined aquifer at the&nbsp;Rifle Integrated Field Research Challenge (IFRC) site, which is adjacent to the&nbsp;Colorado River, near Rifle, Colorado, USA (39.5291, -107.7721). &nbsp;Samples were collected between&nbsp;August 25th to December 12th of 2011, and August 2nd to December 12th of 2012. Sequencing of these&nbsp;samples took place at the Joint Genome Institute&nbsp;using the&nbsp;Illumina HiSeq 2000 platform to generate 2 × 150 paired-end reads.</p>
<p>For more information&nbsp;about sampling methodology see Paul et al. 2017.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046144 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046144
completed
David L. Valentine
University of California-Santa Barbara
805-893-2973
Department of Earth Science 1006 Webb Hall
Santa Barbara
CA
93106
USA
valentine@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sequence_id
accession_id
accession_link
Illumina HiSeq 2000
theme
None, User defined
sequence
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Valentine_IFRC_site
service
Deployment Activity
near Rifle, Colorado
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
Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems
https://osprey.bco-dmo.org/project/2158
Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems
<p>Marine methanotrophic ecosystems are responsible for consuming around 75 Tg of methane annually, preventing this potent greenhouse gas from entering the atmosphere. These microbial ecosystems thus play a vital role in the global climate system. The nature of these communities depends on the presence or absence of oxygen: methanotrophy is a bacterial lifestyle in aerobic shallow sediments, but in deeper anaerobic sediments it is the exclusive province of archaea, in syntrophy with sulfate-reducing bacteria. It is known which phyla are most commonly found in methanotrophic environments. However, because of these environments' physical inaccessibility and because nearly all microbes from these systems have resisted cultivation, understanding of these communities lags far behind their importance. The cultivation-resistance of microbial hosts from these systems has additionally prevented the use of classical methods to study the viral community. Thus, to date science is largely unable to fill in the broad outlines of marine methanotrophic biodiversity, to fully describe the microbial communities or determine what shapes them.</p>
<p>This project seeks to define the importance of viruses in structuring functional, genetic, and taxonomic diversity in methanotrophic marine ecosystems. The underlying assertion is that viruses structure the diversity of archaeal and bacterial communities in these ecosystems by causing both mortality and horizontal gene transfer. To establish viral contributions to biodiversity of aerobic and anaerobic marine methanotrophic ecosystems, this project combines biogeochemical, genomic, and metagenomic approaches, in both field and laboratory settings.</p>
<p>The project first seeks to assess viral activity in situ by extending established stable isotope probing techniques to quantify rates of viral production at sea floor methane seeps. The same techniques will be used to track the flow of carbon from methane to microbes to viruses and to isolate genetic material from just those organisms that actively cycle methane-derived carbon, enabling the production of microbial and viral metagenomes that are anchored in ecosystem function. Comparisons among these metagenomes will reveal any functional sequences in transit between organisms, providing the basis for an evaluation of the relationships between functional and genetic diversity. At the same time, single-cell whole-genome amplification will pinpoint individual cells for comparison with the microbial and viral assemblages, permitting assessment of the relationships between taxonomic and genetic diversity. Last, the comparison of genomic and metagenomic data both within and across distinctive marine methanotrophic ecosystems will enable analysis of the relationship between functional and taxonomic diversity.</p>
Viruses in Methanotrophic Marine Ecosystems
largerWorkCitation
project
eng; USA
oceans
near Rifle, Colorado
-107.7721
-107.7721
39.5291
39.5291
2017-04-11
0
BCO-DMO catalogue of parameters from Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems 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/692452.rdf
Name: sequence_id
Units: unitless
Description:
http://lod.bco-dmo.org/id/dataset-parameter/692453.rdf
Name: accession_id
Units: unitless
Description:
http://lod.bco-dmo.org/id/dataset-parameter/692454.rdf
Name: accession_link
Units: unitless
Description:
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
265728
https://datadocs.bco-dmo.org/file/oAWJwXguPrQqnG/DGR_RT_aa_Sequences.fasta
DGR_RT_aa_Sequences.fasta
Reverse transcriptase protein sequences from diversity-generating retroelements identified in groundwater metagenomes
download
60806
https://datadocs.bco-dmo.org/file/p9WVxLmIO8ZKq6/DGR_VP_aa_Sequences.fasta
DGR_VP_aa_Sequences.fasta
Variable protein sequences from diversity-generating retroelements identified in groundwater metagenomes
download
60555
https://datadocs.bco-dmo.org/file/vm6JErYi72lgRY/sequence_sources.csv
sequence_sources.csv
# List of previously generated sequence accessions used for the groundwater microorganism retroelement protein sequence dataset
# PI: David Valentine
# N.B. This list of accessions has various authors, see accession links for full metadata at NCBI
download
https://osprey.bco-dmo.org/dataset/687822/data/download
download
onLine
dataset
<p>A bioinformatic analysis of metagenome-assembled genomes to identify retroelements was performed. This study used data from several previously described&nbsp;sampling efforts (Brown et al. 2015, Castelle et al. 2015, and Anantharaman et al. 2016). Original sampling was conducted within an unconfined aquifer at the&nbsp;Rifle Integrated Field Research Challenge (IFRC) site, which is adjacent to the&nbsp;Colorado River, near Rifle, Colorado, USA (39.5291, -107.7721). &nbsp;Samples were collected between&nbsp;August 25th to December 12th of 2011, and August 2nd to December 12th of 2012. Sequencing of these&nbsp;samples took place at the Joint Genome Institute&nbsp;using the&nbsp;Illumina HiSeq 2000 platform to generate 2 × 150 paired-end reads.</p>
<p>For more information&nbsp;about sampling methodology see Paul et al. 2017.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>These sequences were processed using Python v2.7.12, and Geneious v8.1.4.</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
Illumina HiSeq 2000
Illumina HiSeq 2000
PI Supplied Instrument Name: Illumina HiSeq 2000 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.
Deployment: Valentine_IFRC_site
Valentine_IFRC_site
Colorado_River
shoreside
Valentine_IFRC_site
David L. Valentine
University of California-Santa Barbara
Colorado_River
shoreside