http://lod.bco-dmo.org/id/dataset/688162
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
2017-04-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project)
2017-04-24
publication
2017-04-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-28
publication
https://doi.org/10.26008/1912/bco-dmo.688162.1
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
James Jeffrey Morris
University of Alabama at Birmingham
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: Dyhrman, S. T., Morris, J. J. (2021) Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-04-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.688162.1 [access date]
Clones of Prochlorococcus MIT9312 and link to BioProject Dataset Description: <p>This dataset includes a link&nbsp;to Prochlorococcus clone NCBI BioProject and associated metadata.<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> 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 Prochlorococcus clones was grown in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.</p>
<p>The mRNA libraries were prepared for Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).</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
asNeeded
Dataset Version: 1
Unknown
sample
sample_title
NCBI_BioProject
BioProject_link
organism
strain
isolate
isolation_source
collection_date
geo_loc_name
sample_type
biomaterial_provider
collected_by
lat_lon
depth
env_biome
genotype
passage_history
samp_size
temp_C
light_level
light_dark_hr
CO2
Alkalinity
pH
DIC
co_cultured_with
Media
Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA)
theme
None, User defined
sample identification
sample description
accession number
external_link
taxon
No BCO-DMO term
date
site description
sample type
laboratory
latitude
depth
region
count
water temperature at measurement depth
PAR_photons
Partial pressure of CO2
total alkalinity (TA)
pH
dissolved inorganic Carbon
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
2015-12-01
2015-12-31
Experiment housed in laboratories at Michigan State University
0
BCO-DMO catalogue of parameters from Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv 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/692235.rdf
Name: sample
Units: unitless
Description: <p>sequencing facility sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/692236.rdf
Name: sample_title
Units: unitless
Description: <p>laboratory sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/692237.rdf
Name: NCBI_BioProject
Units: unitless
Description: <p>collection of biological data related to a single initiative</p>
http://lod.bco-dmo.org/id/dataset-parameter/692238.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/692239.rdf
Name: organism
Units: unitless
Description: <p>bacterium used in this study</p>
http://lod.bco-dmo.org/id/dataset-parameter/692240.rdf
Name: strain
Units: unitless
Description: <p>population of organism that descends from a single organism or pure culture isolate</p>
http://lod.bco-dmo.org/id/dataset-parameter/692241.rdf
Name: isolate
Units: unitless
Description: <p>specific individual from which this sample was obtained</p>
http://lod.bco-dmo.org/id/dataset-parameter/692242.rdf
Name: isolation_source
Units: unitless
Description: <p>physical/ environmental/ geographic source of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/692243.rdf
Name: collection_date
Units: date
Description: <p>date sample was obtained</p>
http://lod.bco-dmo.org/id/dataset-parameter/692244.rdf
Name: geo_loc_name
Units: unitless
Description: <p>geographical origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/692245.rdf
Name: sample_type
Units: unitless
Description: <p>sample type such as whole organism, mixed culture, cell culture, metagenomic assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/692246.rdf
Name: biomaterial_provider
Units: unitless
Description: <p>laboratory and principal investigator where sample came from</p>
http://lod.bco-dmo.org/id/dataset-parameter/692247.rdf
Name: collected_by
Units: unitless
Description: <p>laboratory and principal investigator where organism was isolated</p>
http://lod.bco-dmo.org/id/dataset-parameter/692248.rdf
Name: lat_lon
Units: decimal degrees
Description: <p>geographical coordinates of the location where the sample was collected; north and east are positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/692249.rdf
Name: depth
Units: meters
Description: <p>vertical distance below the surface where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/692250.rdf
Name: env_biome
Units: unitless
Description: <p>descriptor of the broad ecological context of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/692251.rdf
Name: genotype
Units: unitless
Description: <p>observed genotype</p>
http://lod.bco-dmo.org/id/dataset-parameter/692252.rdf
Name: passage_history
Units: generations
Description: <p>number of sample generations</p>
http://lod.bco-dmo.org/id/dataset-parameter/692253.rdf
Name: samp_size
Units: number of cells
Description: <p>amount of sample collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/692254.rdf
Name: temp_C
Units: degrees Celsius
Description: <p>temperature at which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/692255.rdf
Name: light_level
Units: micromol photons m-2 s-1
Description: <p>light level at which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/692256.rdf
Name: light_dark_hr
Units: hours:hours
Description: <p>number of hours of light:dark for a 24 hour period</p>
http://lod.bco-dmo.org/id/dataset-parameter/692257.rdf
Name: CO2
Units: ppm
Description: <p>carbon dioxide concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/692258.rdf
Name: Alkalinity
Units: umoles/kg
Description: <p>buffering capacity of water</p>
http://lod.bco-dmo.org/id/dataset-parameter/692259.rdf
Name: pH
Units: unitless
Description: <p>scale of acidity</p>
http://lod.bco-dmo.org/id/dataset-parameter/692260.rdf
Name: DIC
Units: umoles/kg
Description: <p>dissolved inorganic carbon concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/692261.rdf
Name: co_cultured_with
Units: unitless
Description: <p>additional organisms grown with the primary organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/692262.rdf
Name: Media
Units: unitless
Description: <p>type of water or broth organism was grown in</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
8441
https://darchive.mblwhoilibrary.org/bitstream/1912/27184/1/dataset-688162_proancestor__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.688162.1
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 Prochlorococcus clones was grown in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.</p>
<p>The mRNA libraries were prepared for Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).</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 both the MIT9312 gene models (accession: NC_007577.1) and the draft EZ55 genome (Genbank accession TBD) using bowtie2 with sensitive end-to-end mode. Reads aligning to coding sequences in the MIT9312 gene models were counted with samtools idxstats. 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<br />
- replaced blanks with nd (no data)</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