http://lod.bco-dmo.org/id/dataset/787181
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
2020-01-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
FASTA file of sequences in Trichodesmium field metaproteomes mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018
2020-01-14
publication
2020-01-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-04-30
publication
https://doi.org/10.26008/1912/bco-dmo.787181.1
Mak A. Saito
Woods Hole Oceanographic Institution
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: Saito, M. A. (2020) FASTA file of sequences in Trichodesmium field metaproteomes mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018. Dataset version 2020-01-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.787181.1 [access date]
Dataset Description: FASTA file of sequences in Trichodesmium field metaproteomes analyzed by 2D LC-MS/MS mapped to a Trichodesmium metagenome (IMG ID 2821474806) plus cyanoGEBA species genomes (Shih et al, 2013). Samples were collected in North Atlantic surface waters, at station BATS (Bermuda Atlantic Time-series Study), and station ALOHA (A Long-Term Oligotrophic Habitat Assessment) between 2000 and 2018.
Related datasets:
Trichodesmium field metaproteomes - peptide spectral counts: https://www.bco-dmo.org/dataset/787168
Trichodesmium field metaproteomes - protein spectral counts: https://www.bco-dmo.org/dataset/787147
Trichodesmium sample provenance: https://www.bco-dmo.org/dataset/787093 - Sample provenance file, which includes sample locations, filter sizes Acquisition Description: <div>
<div><span style="font-size:13px">&nbsp;A 200um plankton net net was deployed to ~20m depth, then recovered to just below surface, repeating five times. Trichodesmium colonies were hand picked into 0.2um filtered surface seawater, rinsed twice in 0.2um filtered surface seawater, and decanted onto a 0.2-4um Supor filter (indicated in sample provenance table, see dataset https://www.bco-dmo.org/dataset/787093).&nbsp;</span><br />
&nbsp;</div>
<div><span style="font-size:13px">Proteins were extracted and trypsin digested in-gel following Saito et al., 2014 (Science). Peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion.</span></div>
</div>
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF3934
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3782 Award URL: https://www.moore.org/grant-detail?grantId=GBMF3782
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657766 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1657766
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850719 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1850719
completed
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
MS #51 266 Woods Hole Rd
Woods Hole
MA
02543-1541
USA
msaito@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Thermo Orbitrap Fusion mass spectrometer
theme
None, User defined
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
AT39-05
JC150
service
Deployment Activity
Tropical and subtropical Atlantic; 20 N - 8 S, 22 W - 67 W
North Atlantic Ocean
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.
Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean
https://www.bco-dmo.org/project/724451
Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean
<p>NSF abstract:</p>
<p>Marine cyanobacteria are able to use or "fix" atmospheric nitrogen gas, and so supply much of the essential nutrient nitrogen that supports open ocean food chains. Oceanographers have usually thought that the growth of these nitrogen-fixing cyanobacteria is limited at any particular time and place by the supply of either iron, or of phosphorus. Preliminary experiments have shown, though, that these nitrogen fixers instead grow best when both iron and phosphorus are scarce at the same time. In this project, the researchers will use cellular indicators that are specific for iron and phosphorus limitation to determine how important this type of "balanced limitation" of nitrogen-fixing cyanobacteria is in controlling the productivity of ocean food chains in the tropical Atlantic Ocean. Two graduate students will be trained at the University of Southern California (USC) and Woods Hole Oceanographic Institution, as well as a postdoctoral researcher at USC. Educational outreach efforts will take place at a Los Angeles inner city high school with a student body that is over 98% Hispanic and African-American, and with underrepresented undergraduates in the USC Global Environmental Microbiology course. In addition, two Research Experiences for Undergraduates students will be supervised for summer research projects to help them learn about science career options.</p>
<p>The researchers will investigate the biological and biogeochemical consequences of this unique balanced iron/phosphorus-limited phenotype, using both laboratory and fieldwork approaches. During the first year of this project, the nitrogen-fixing cyanobacteria will be cultured under iron and/or phosphorus limitation, followed by application of proteomics and transcriptomics to identify genes that are potential diagnostic biomarkers for iron/phosphorus balanced limitation. Preliminary work has already identified one promising candidate biomarker in one cyanobacterium, an EzrA protein domain that appears to be associated with the cell size decreases seen specifically under balanced limitation, and the researchers have identified numerous other potential candidates for similar biomarkers. During the second year, these new co-limitation biomarkers and others previously validated for iron limitation (IsiB) and phosphorus limitation (SphX) will be used to investigate balanced limitation during a research cruise transecting from relatively high-iron, low-phosphorus North Atlantic waters, to the relatively high-phosphorus, low-iron South Atlantic. This fieldwork component will survey nitrogen fixing cyanobacteria populations across this natural iron/phosphorus gradient for genetic, proteomic, and physiological indicators of balanced limitation, as well as testing their responses to iron and phosphorus manipulations in shipboard incubation experiments. The third year will be devoted to sample analysis, and publications exploring the responses of oceanic nitrogen fixers to simultaneous limitation by both iron and phosphorus.</p>
TriCoLim
largerWorkCitation
project
New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms
https://www.moore.org/grant-detail?grantId=GBMF3934
New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms
<p>In support of acquiring a high resolution mass spectrometer that incorporates the latest technologies for analyzing proteins and other organic materials.</p>
MM Proteins and Organics Tech
largerWorkCitation
project
Marine Microbial Investigator Award: Investigator Mak Saito
https://www.bco-dmo.org/project/786672
Marine Microbial Investigator Award: Investigator Mak Saito
<p>In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.</p>
MM Saito
largerWorkCitation
project
Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions
https://www.bco-dmo.org/project/786679
Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions
<p>NSF abstract:<br />
The oceans absorb much of the heat generated by human activities, and this warming of the surface ocean has consequences for important groups of marine organisms. Marine cyanobacteria are one such key group of organisms, since they supply much of the essential carbon and nitrogen that supports nearly all the rest of the marine food web. Currently, the growth of cyanobacteria is mostly constrained by scarce supplies of the micronutrient element iron, but they are also very sensitive to the ongoing increases in seawater temperature. Preliminary results suggest that warming could partly mitigate the negative effects of iron limitation on marine cyanobacteria. This project examines in depth how these interactions between warming and iron limitation will affect the future ocean carbon and nitrogen cycles, using laboratory culture experiments showing how cyanobacteria respond to simultaneously changing temperature and iron supplies. Both short-term response studies and long-term evolutionary experiments testing for adaptation use a comprehensive set of molecular biology tools targeting genes to proteins. The final goal is to apply the results of these experiments to improve quantitative models predicting how the ocean's carbon and nitrogen cycles, biological productivity, and living resources will respond to a warming future climate. Two graduate students, a postdoc and 3-4 underrepresented undergraduate researchers are supported, and the investigators also mentor summer science interns from largely Hispanic local high schools.</p>
<p>The physiology, biochemistry and biogeography of nitrogen-fixing cyanobacteria and unicellular picocyanobacteria are strongly influenced by temperature, subjecting them to intense selective pressure as the modern ocean steadily warms up. These groups have likewise been rigorously selected under chronic iron (Fe) scarcity, and the availability of this crucial micronutrient is also changing with a shifting climate. This project examines short-term acclimation and long-term evolutionary responses of Fe-stressed marine cyanobacteria to a warmer environment. Preliminary data show that Iron Use Efficiencies (IUE, mols N fixed.hr-1 mol cellular Fe-1) of Fe-limited Trichodesmium increase 4 to 5-fold with a 5oC temperature increase, allowing the cells to much more efficiently leverage scarce available Fe supplies to grow and fix nitrogen. This means that warming can to a large degree mitigate the negative effects of Fe limitation on Trichodesmium, resulting in a modelled 22% increase in global nitrogen fixation by 2100 in a warmer climate. This project aims to uncover the cellular biochemical mechanisms involved in this Fe-limitation/thermal IUE effect in a four-year experimental evolution study of the diazotrophs Trichodesmium and Crocosphaera and the picocyanobacteria Synechococcus and Prochlorococcus, under a multi-variate selection matrix of temperature and Fe availability. The objectives are to 1) Assess the long-term adaptive responses of fitness, IUE and physiology to Fe limitation and warming interactions in these four major cyanobacterial groups; 2) Determine the molecular and biochemical mechanisms behind the surprising Fe/warming interactive effect on IUE using genomics, transcriptomics and quantitative proteomics coupled with 'metalloproteomics' determinations of Fe content in critical proteins; 3) Compare and contrast acclimation and adaptation responses to Fe limitation and warming in key cyanobacteria taxa, and 4) Integrate results using a published biogeochemical modeling approach to assess global consequences for marine productivity and nitrogen fixation. This project offers a mechanistic and predictive understanding of adaptation to Fe and warming co-stressors in a rapidly changing future ocean environment for some of the most important photoautotrophic functional groups in the ocean.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Cyanobacteria Warming Responses
largerWorkCitation
project
eng; USA
oceans
Tropical and subtropical Atlantic; 20 N - 8 S, 22 W - 67 W; North Atlantic Ocean
-158
-21.59
0.17
23.22
2000-07-27
2018-03-18
Tropical Atlantic
0
BCO-DMO catalogue of parameters from FASTA file of sequences in Trichodesmium field metaproteomes mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018
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
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
1063860
https://datadocs.bco-dmo.org/data/302/TriCoLim/787181/1/data/trimmed_fasta_trichoWT.fasta
download
https://www.bco-dmo.org/dataset/787181/data/download
download
onLine
dataset
<div>
<div><span style="font-size:13px">&nbsp;A 200um plankton net net was deployed to ~20m depth, then recovered to just below surface, repeating five times. Trichodesmium colonies were hand picked into 0.2um filtered surface seawater, rinsed twice in 0.2um filtered surface seawater, and decanted onto a 0.2-4um Supor filter (indicated in sample provenance table, see dataset https://www.bco-dmo.org/dataset/787093).&nbsp;</span><br />
&nbsp;</div>
<div><span style="font-size:13px">Proteins were extracted and trypsin digested in-gel following Saito et al., 2014 (Science). Peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion.</span></div>
</div>
Specified by the Principal Investigator(s)
<p>Thermo proteome discoverer 2.2 was used to search the data with the SEQUEST algorithm. Statistical validation was performed in Scaffold (Proteome Software) at the 1% protein and peptide false discovery rate (FDR) levels.t</p>
<p>A publicly available <em>Trichodesium</em>&nbsp;metagenome was used in this search (IMG ID 2821474806) as well as the contents of the CyanoGEBA project (Shih et al, 2013). This fasta file contains the sequences that were identified in the metaproteome analysis.</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
Thermo Orbitrap Fusion mass spectrometer
Thermo Orbitrap Fusion mass spectrometer
PI Supplied Instrument Name: Thermo Orbitrap Fusion mass spectrometer Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Cruise: AT39-05
AT39-05
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT39-05
David A. Hutchins
University of Southern California
Cruise: JC150
JC150
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
JC150
Claire Mahaffey
University of Liverpool
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel