http://lod.bco-dmo.org/id/dataset/735669
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
2018-05-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2.
2025-02-25
publication
2025-02-25
revision
BCO-DMO Linked Data URI
2025-02-25
creation
http://lod.bco-dmo.org/id/dataset/735669
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
James Jeffrey Morris
University of Alabama at Birmingham
principalInvestigator
Gwenn Hennon
Lamont-Doherty Earth Observatory
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: Hennon, G. (2025) Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1.1) Version Date 2025-02-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/735669 [access date]
Clones of Prochlorococcus MIT9312 and link to BioProject Dataset Description: <p>This dataset includes a link&nbsp;to Alteromonas/Prochlorococcus clone NCBI BioProject "Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2", and a listing of the associated FASTQ files.<br />
<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">PRJNA377729</a><a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">:&nbsp;</a><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729</a></p>
<p>These data were published in:&nbsp;<br />
Hennon et al. “The impact of elevated CO2 on Prochlorococcus and microbial interactions with 'helper' bacterium Alteromonas” (2018) ISME.&nbsp;Supplemental Table 4</p> Methods and Sampling: <p>Six clones of high light II Prochlorococcus VOL4, a streptomycin-resistant derivative of strain MIT9312 were isolated by dilution to extinction in Pro99 media pretreated with the helper bacterium Alteromonas sp. strain EZ55.&nbsp; Prochlorococcus clones were made axenic by addition of streptomycin. For co-culture experiments, Alteromonas bacteria were introduced to Prochlorococcus cultures prior to growth experiments. Alteromonas was diluted onto YTSS agar plates and each Prochlorococcus culture was inoculated with a single separate colony. Alteromonas stock cultures were grown in YTSS liquid medium and cryopreserved in 20% glycerol at -80 C.</p>
<p>Each of the six Alteromonas clones from co-culture experiments was grown axenically in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.</p>
<p>RNA extractions were performed with the RNeasy Mini Kit.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1314336 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1314336
completed
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
James Jeffrey Morris
University of Alabama at Birmingham
205-934-9498
1300 University Blvd CH253
Birmingham
AL
35294
USA
evolve@uab.edu
pointOfContact
Gwenn Hennon
Lamont-Doherty Earth Observatory
907-474-6735
College of Fisheries and Ocean Sciences Irving II Rm 331
Fairbanks
AK
99775
USA
gmhennon@alaska.edu
pointOfContact
asNeeded
Dataset Version: 1.1
Unknown
bioproject_accession
bioproject_link_url
bioproject_link_text
bioproject_link
biosample_accession
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filename2
Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA)
theme
None, User defined
accession number
external_link
sample identification
No BCO-DMO term
instrument
instrument model
sampling_method
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Dyhrman_2013
service
Deployment Activity
Dyhrman lab, LDEO
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.
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)
Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)
Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants
Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)
Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)
Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)
SEES-OA
largerWorkCitation
program
Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
https://osprey.bco-dmo.org/project/2276
Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
<p>Note: This project is also affiliated with the <a href="http://beacon-center.org/" target="_blank">NSF BEACON Center for the Study of Evolution in Action</a>.</p>
<p><em>Project Description from NSF Award:</em><br />
Human activities are driving up atmospheric carbon dioxide concentrations at an unprecedented rate, perturbing the ocean's carbonate buffering system, lowering oceanic pH, and changing the concentration and composition of dissolved inorganic carbon. Recent studies have shown that this ocean acidification has many short-term effects on phytoplankton, including changes in carbon fixation among others. These physiological changes could have profound effects on phytoplankton metabolism and community structure, with concomitant effects on Earth's carbon cycle and, hence, global climate. However, extrapolation of present understanding to the field are complicated by the possibility that natural populations might evolve in response to their changing environments, leading to different outcomes than those predicted from short-term studies. Indeed, evolution experiments demonstrate that microbes are often able to rapidly adapt to changes in the environment, and that beneficial mutations are capable of sweeping large populations on time scales relevant to predictions of environmental dynamics in the coming decades. This project addresses two major areas of uncertainty for phytoplankton populations with the following questions:<br />
1) What adaptive mutations to elevated CO2 are easily accessible to extant species, how often do they arise, and how large are their effects on fitness?<br />
2) How will physical and ecological interactions affect the expansion of those mutations into standing populations?</p>
<p>This study will address these questions by coupling experimental evolution with computational modeling of ocean biogeochemical cycles. First, cultured unicellular phytoplankton, representative of major functional groups (e.g. cyanobacteria, diatoms, coccolithophores), will be evolved under simulated year 2100 CO2 concentrations. From these experiments, estimates will be made of a) the rate of beneficial mutations, b) the magnitude of fitness gains conferred by these mutations, and c) secondary phenotypes (i.e., trade-offs) associated with these mutations, assayed using both physiological and genetic approaches. Second, an existing numerical model of the global ocean system will be modified to a) simulate the effects of changing atmospheric CO2 concentrations on ocean chemistry, and b) allow the introduction of CO2-specific adaptive mutants into the extant populations of virtual phytoplankton. The model will be used to explore the ecological and biogeochemical impacts of beneficial mutations in realistic environmental situations (e.g. resource availability, predation, etc.). Initially, the model will be applied to idealized sensitivity studies; then, as experimental results become available, the implications of the specific beneficial mutations observed in our experiments will be explored.</p>
<p>This interdisciplinary study will provide novel, transformative understanding of the extent to which evolutionary processes influence phytoplankton diversity, physiological ecology, and carbon cycling in the near-future ocean. One of many important outcomes will be the development and testing of nearly-neutral genetic markers useful for competition studies in major phytoplankton functional groups, which has applications well beyond the current proposal.</p>
P-ExpEv
largerWorkCitation
project
eng; USA
biota
oceans
Dyhrman lab, LDEO
2025-02-25
Experiment housed in laboratories at Michigan State University
0
BCO-DMO catalogue of parameters from Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2.
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/735685.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession number; a collection of biological data related to a single initiative</p>
http://lod.bco-dmo.org/id/dataset-parameter/954717.rdf
Name: bioproject_link_url
Units: unitless
Description: <p>Link to NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/954718.rdf
Name: bioproject_link_text
Units: unitless
Description: <p>NCBI Accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/735686.rdf
Name: bioproject_link
Units: unitless
Description: <p>url for collection of biological data related to a single initiative</p>
http://lod.bco-dmo.org/id/dataset-parameter/735687.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/735688.rdf
Name: library_ID
Units: unitless
Description: <p>short unique identifier for the sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/735689.rdf
Name: title
Units: unitless
Description: <p>BioSample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/735720.rdf
Name: library_strategy
Units: unitless
Description: <p>type of sequencer used</p>
http://lod.bco-dmo.org/id/dataset-parameter/735721.rdf
Name: library_source
Units: unitless
Description: <p>sequencing location</p>
http://lod.bco-dmo.org/id/dataset-parameter/735722.rdf
Name: library_selection
Units: unitless
Description: <p>library preparation kit used</p>
http://lod.bco-dmo.org/id/dataset-parameter/735690.rdf
Name: library_layout
Units: unitless
Description: <p>Paired-end or Single</p>
http://lod.bco-dmo.org/id/dataset-parameter/735691.rdf
Name: platform
Units: unitless
Description: <p>type of DNA sequencing instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/735692.rdf
Name: instrument_model
Units: unitless
Description: <p>model of DNA sequencer</p>
http://lod.bco-dmo.org/id/dataset-parameter/735693.rdf
Name: design_description
Units: unitless
Description: <p>description of the methods used to create the sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/735694.rdf
Name: filetype
Units: unitless
Description: <p>type of file: FASTQ</p>
http://lod.bco-dmo.org/id/dataset-parameter/735695.rdf
Name: filename
Units: unitless
Description: <p>FASTQ file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/735696.rdf
Name: filename2
Units: unitless
Description: <p>additional FASTQ filename</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
4945
https://datadocs.bco-dmo.org/file/7DBM45OcER9l21/Alteromonas_accessions.csv
Alteromonas_accessions.csv
download
https://osprey.bco-dmo.org/dataset/735669/data/download
download
onLine
dataset
<p>Six clones of high light II Prochlorococcus VOL4, a streptomycin-resistant derivative of strain MIT9312 were isolated by dilution to extinction in Pro99 media pretreated with the helper bacterium Alteromonas sp. strain EZ55.&nbsp; Prochlorococcus clones were made axenic by addition of streptomycin. For co-culture experiments, Alteromonas bacteria were introduced to Prochlorococcus cultures prior to growth experiments. Alteromonas was diluted onto YTSS agar plates and each Prochlorococcus culture was inoculated with a single separate colony. Alteromonas stock cultures were grown in YTSS liquid medium and cryopreserved in 20% glycerol at -80 C.</p>
<p>Each of the six Alteromonas clones from co-culture experiments was grown axenically in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.</p>
<p>RNA extractions were performed with the RNeasy Mini Kit.</p>
Specified by the Principal Investigator(s)
<p>Sequence reads were de-multiplexed and trimmed to remove sequencing barcodes. Trimmed reads were aligned to the draft EZ55 genome (Genbank accession SRX022631)) using bowtie2 with sensitive end-to-end mode. Reads aligning to the EZ55 draft genome were counted with HT-seq count.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added links to NCBI BioProject page</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 Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA)
Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA)
PI Supplied Instrument Name: Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA) PI Supplied Instrument Description:Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY). 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: Dyhrman_2013
Dyhrman_2013
LDEO
laboratory
Dyhrman_2013
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
LDEO
laboratory