http://lod.bco-dmo.org/id/dataset/709113
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
2017-07-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S tag data, metagenomic data, and a draft assembled genome of Altermonas macleodii derived from laboratory-maintained Trichodesmium erythraeum cultures
2018-03-09
publication
2018-03-09
revision
BCO-DMO Linked Data URI
2018-03-09
creation
http://lod.bco-dmo.org/id/dataset/709113
David A. Hutchins
University of Southern California
principalInvestigator
Eric A. Webb
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: Hutchins, D. A., Webb, E. A. (2018) 16S tag data, metagenomic data, and a draft assembled genome of Altermonas macleodii derived from laboratory-maintained Trichodesmium erythraeum cultures. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 09 March 2018) Version Date 2018-03-09 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/709113 [access date]
16S tag data, metagenomic data, and a draft assembled genome of Altermonas macleodii derived from laboratory-maintained Trichodesmium erythraeum cultures Dataset Description: <p>These data are all derived from laboratory-maintained Trichodesmium erythraeum cultures and contain 16S tag data, metagenomic data, and a draft assembled genome of Altermonas macleodii.</p>
<p>3 DNA sequence datasets have been uploaded to NCBI in their appropriate locations. The accession information is presented here:</p>
<p>FastQ files of 16S rRNA amplicon data have been uploaded to NCBI’s Sequence Read Archive (SRA) under accession number SRP078329.</p>
<p>FastQ files of 5 metagenomic sequence datasets have been deposited in NCBI’s SRA under SRP078343.</p>
<p>A FastA file of a draft genome has been uploaded to NCBI’s Whole Genome Shotgun (WGS) database under the accession MBSN00000000.</p>
<p>These datasets were released upon publication of the paper: <em>The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions</em>, by Lee et al. (doi:<a href="http://dx.doi.org/10.1038/ismej.2017.49" target="_blank">10.1038/ismej.2017.49</a>), published in April 2017. Detailed sample information is included in the supplemental spreadsheets to that publication, specifically tables S1 and S2.&nbsp;</p>
<p>These data were also utilized in the paper:<br />
Walworth, N. G., Lee, M. D., Suffridge, C., Qu, P., Fu, F., Saito, M. A., ... &amp; Hutchins, D. A. (2018). Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium.&nbsp;<em>Frontiers in Microbiology</em>,&nbsp;<em>9</em>, 189. doi:&nbsp;<a href="https://doi.org/10.3389/fmicb.2018.00189" target="_blank">10.3389/fmicb.2018.00189</a></p> Methods and Sampling: <p>For sampling and analytical methodology, refer to the paper:<br />
Lee, at al. (2017)&nbsp;The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions. The ISME Journal,11, 1813–1824; doi:<a href="http://dx.doi.org/10.1038/ismej.2017.49" target="_blank">10.1038/ismej.2017.49</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260233 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260233
completed
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Eric A. Webb
University of Southern California
213-740-7954
Department of Biological Sciences, Marine and Environmental Biology Section; Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway AHF 331
Los Angeles
CA
90089-0371
USA
eawebb@usc.edu
pointOfContact
asNeeded
Dataset Version: 09 March 2018
Unknown
accession_number
accession_link
description
BioProject_id
BioProject_link
theme
None, User defined
accession number
sample description
featureType
BCO-DMO Standard Parameters
lab_Webb_Hutchins_Fu
service
Deployment Activity
Southern California
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.
Adaptation of key N2-fixing cyanobacteria to changing CO2
https://osprey.bco-dmo.org/project/551230
Adaptation of key N2-fixing cyanobacteria to changing CO2
<p><em>Description from NSF award abstract:</em><br />
This study will employ a novel combination of experimental evolution techniques and state-of-the-art molecular methods to yield unique insights into adaptive changes in the keystone marine cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> in response to selection by high CO2. Several studies have suggested that N2-fixation rates of the biogeochemically-critical cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> may increase dramatically in the future high CO2 ocean, but these have all used the same limited set of cultured isolates and considered cells only briefly acclimated to elevated CO2. The investigator's new results, however, demonstrate that a broad diversity of high- and low-CO2 adapted ecotypes exists within each diazotroph genus. Furthermore, in a preliminary four year experimental evolution study with <em>Trichodesmium</em>, the PIs observed large adaptive responses following 500-700 generations of selection by high CO2- but in a completely unexpected way. All of the six replicate high CO2-adapted cell lines exhibited strong constitutive up-regulation of N2 fixation rates. These very elevated N2 fixation rates continued, even though the cultures have were switched back to low-CO2 conditions for many months. Expression of the nif operon and N assimilatory genes was also up-regulated in these cell lines, as is expression of many intergenic regions of the genome.</p>
<p><strong>The investigators hypothesize that constitutive up-regulation of cellular N2 fixation systems may be a common adaptive response of both <em>Trichodesmium</em> and <em>Crocosphaera</em> under extended selection by elevated CO2. This project will test this hypothesis in a four-year experimental evolution study to determine the adaptive responses of both high- and low-CO2 specialized ecotypes of these two diazotrophs to increased CO2.</strong></p>
<p>The investigators will grow representative high- and low-CO2 adapted ecotypes from each genus in well-replicated cell lines at 380 ppm and 750 ppm CO2 for up to 1000 generations. Periodically, they will perform "switch" experiments to measure N2 and CO2 fixation rates and growth rates of high CO2-selected cell lines grown briefly (one week) at low CO2, and vice versa. These switch experiments will allow screening for cell lines which exhibit adaptive changes in phenotypically-expressed rate parameters, such as those observed in the preliminary <em>Trichodesmium</em> study. Evolutionary mechanisms in the CO2-selected cell lines will be examined by comparison of changes in their genomes, transcriptomes, and proteomes over time relative to reference genomes, using frozen samples archived monthly during the preceding selection period. Examination of these molecular and biochemical changes will be coordinated with an in-depth array of physiological and biogeochemical analyses. This combined approach will allow an evaluation of potential adaptive mechanisms in diazotrophic cyanobacteria ranging from indel, duplication, single nucleotide polymorphism, and transposition mutations to altered putative non-coding RNA expression, protein expression, and post-translational protein modifications, and then allow the investigators to link these mechanisms directly with their potential impacts on ecosystem-level biogeochemical processes like N2 and CO2 fixation. Finally, the research team will determine how long term selection by high CO2 affects the iron and phosphorus requirements of <em>Trichodesmium </em>and <em>Crocosphaera</em>, since constitutive up-regulation of N2 fixation would also have major implications for limitation of diazotrophs by these two critical nutrients in the future high CO2 ocean.</p>
HiCO2_AdaptCyano
largerWorkCitation
project
eng; USA
biota
oceans
Southern California
2018-03-09
Culture study at the University of Southern California, Los Angeles
0
BCO-DMO catalogue of parameters from 16S tag data, metagenomic data, and a draft assembled genome of Altermonas macleodii derived from laboratory-maintained Trichodesmium erythraeum cultures
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/730122.rdf
Name: accession_number
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/730123.rdf
Name: accession_link
Units: unitless
Description: <p>Hyperlink to NCBI for the accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/730126.rdf
Name: description
Units: unitless
Description: <p>Description of the accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/730127.rdf
Name: BioProject_id
Units: untiless
Description: <p>NCBI BioProject ID number for the accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/730128.rdf
Name: BioProject_link
Units: unitless
Description: <p>Hyperlink to NCBI for the BioProject ID number</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
938
https://datadocs.bco-dmo.org/file/zqqADK8tw6ANPl/tricho_metagenomics.csv
tricho_metagenomics.csv
Primary data file for dataset ID 709113
download
https://osprey.bco-dmo.org/dataset/709113/data/download
download
onLine
dataset
<p>For sampling and analytical methodology, refer to the paper:<br />
Lee, at al. (2017)&nbsp;The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions. The ISME Journal,11, 1813–1824; doi:<a href="http://dx.doi.org/10.1038/ismej.2017.49" target="_blank">10.1038/ismej.2017.49</a></p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
-09 March 2018: added links to NCBI accession numbers.</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: lab_Webb_Hutchins_Fu
lab_Webb_Hutchins_Fu
Webb-Hutchins-Fu USC
laboratory
Webb-Hutchins-Fu USC
laboratory