http://lod.bco-dmo.org/id/dataset/839925
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
2021-02-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Data on laboratory cultures and statistical analysis code associated with the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology
2021-02-05
publication
2021-02-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-09
publication
https://doi.org/10.26008/1912/bco-dmo.839925.1
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: Morris, J. J. (2021) Data on laboratory cultures and statistical analysis code associated with the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-02-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.839925.1 [access date]
Syn-Pro Co-cultures Dataset Description: <p>The data and code in this package allow one to re-run all the analyses performed in the paper "Co-culture with Synechococcus facilitates Prochlorococcus growth under ocean acidification conditions", published in Environmental Microbiology (doi:<a href="http://dx.doi.org/10.1111/1462-2920.15277" target="_blank">10.1111/1462-2920.15277</a>). Each file is provided separately and all files are packaged into the file Syn-Pro_Co-cultures.zip.&nbsp;</p>
<p>To re-run the analyses, place all the files in one directory, set that directory to the working directory in R, and copy-and-paste the entire contents of the file KnightDataAnalysis.txt into the R window and hit "enter". You may need to install the plyr, lme4, and emmeans packages beforehand. A description of each file is in the ReadMe.txt file.&nbsp;</p> Methods and Sampling: <p>All data from this study are based on growth rate measurements from laboratory cultures of cyanobacteria acclimated to either 400 ppm or 800 ppm pCO2. Full details are included in Knight &amp; Morris (2020). Brief summaries of the two experiments and their analyses are reported below.</p>
<p><strong>1. Survey of <em>Prochlorococcus</em> and <em>Synechococcus</em> culture responses to year 2100 pCO2.</strong> We tested the growth rate response of several different strains of each genus, representing the most globally abundant ecotype varieties, to 800 ppm pCO2, similar to what is expected to exist by the end of the century. Cultures were acclimated for 3 cycles of semi-continuous culture at the target pCO2, and then growth curves were collected by flow cytometry for 3 further transfer cycles. Cultures were diluted into fresh media while still in exponential growth phase. Both exponential growth rates (slope of cell density vs. time during logarithmic growth) and Malthusian growth rates (based only on starting and ending cell densities, and the elapsed time of the culture) were calculated. Growth rate responses were expressed as the ratio of growth rate at 800 ppm over 400 ppm, and were compared to values reported previously in the literature for other marine cyanobacteria.</p>
<p><strong>2. Head-to-head <em>Prochlorococcus</em> vs. <em>Synechococcus</em> experiments.</strong> We chose one strain of each genus from Experiment 1 to compete in co-culture with each other. Strains were chosen to have opposite growth rate responses, such that <em>Prochlorococcus </em>was predicted to be outcompeted at 800 ppm pCO2. Growth of each competitor was measured by flow cytometry, where the two genera have easily distinguishable fluorescence signatures. Relative fitness of <em>Prochlorococcus</em> was expressed as the difference in growth rate between <em>Prochlorococcus</em> and <em>Synechococcus</em>. Linear models were used to analyze the effects of cell density and relative frequency on competition outcomes.</p>
<p>Media preparation: All experiments were conducted in media with an artificial seawater base. Carbonate parameters were carefully measured using titration to determine alkalinity and either potentiometric or colorimetric assays to determine pH. pCO2 was manipulated by addition of calibrated doses of HCl or NaOH, along with NaHCO3 to preserve alkalinity if necessary, in hermetically sealed test tubes with approximately no headspace. Culture growth was assessed every two days by removing a 100 uL aliquot for flow cytometric analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1540158 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1540158
completed
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
Percival algal growth chambers
Luminex Guava HT-1 flow cytometer
custom-calibrated pH probe
BioTek Synergy H1 spectrophotometer plate reader
Mettler-Toledo titrator
theme
None, User defined
Algal Growth Chamber
Flow Cytometer
pH Sensor
plate reader
Titrator
instrument
BCO-DMO Standard Instruments
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
oceans
2021-02-05
Experiment housed in laboratories at Michigan State University
0
BCO-DMO catalogue of parameters from Data on laboratory cultures and statistical analysis code associated with the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology
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
24845
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/1/Together.csv
download
43203
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/2/Syn-Pro_Co-cultures.zip
download
4355
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/3/ReadMe.txt
download
55795
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/4/KnightDataAnalysis.txt
download
2888
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/5/GRR.csv
download
28704
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/6/GrowthRates.csv
download
24509
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/7/CompDataProcessed.outlierremoved.csv
download
11771
https://darchive.mblwhoilibrary.org/bitstream/1912/26657/8/CompDataProcessed.csv
download
https://doi.org/10.26008/1912/bco-dmo.839925.1
download
onLine
dataset
<p>All data from this study are based on growth rate measurements from laboratory cultures of cyanobacteria acclimated to either 400 ppm or 800 ppm pCO2. Full details are included in Knight &amp; Morris (2020). Brief summaries of the two experiments and their analyses are reported below.</p>
<p><strong>1. Survey of <em>Prochlorococcus</em> and <em>Synechococcus</em> culture responses to year 2100 pCO2.</strong> We tested the growth rate response of several different strains of each genus, representing the most globally abundant ecotype varieties, to 800 ppm pCO2, similar to what is expected to exist by the end of the century. Cultures were acclimated for 3 cycles of semi-continuous culture at the target pCO2, and then growth curves were collected by flow cytometry for 3 further transfer cycles. Cultures were diluted into fresh media while still in exponential growth phase. Both exponential growth rates (slope of cell density vs. time during logarithmic growth) and Malthusian growth rates (based only on starting and ending cell densities, and the elapsed time of the culture) were calculated. Growth rate responses were expressed as the ratio of growth rate at 800 ppm over 400 ppm, and were compared to values reported previously in the literature for other marine cyanobacteria.</p>
<p><strong>2. Head-to-head <em>Prochlorococcus</em> vs. <em>Synechococcus</em> experiments.</strong> We chose one strain of each genus from Experiment 1 to compete in co-culture with each other. Strains were chosen to have opposite growth rate responses, such that <em>Prochlorococcus </em>was predicted to be outcompeted at 800 ppm pCO2. Growth of each competitor was measured by flow cytometry, where the two genera have easily distinguishable fluorescence signatures. Relative fitness of <em>Prochlorococcus</em> was expressed as the difference in growth rate between <em>Prochlorococcus</em> and <em>Synechococcus</em>. Linear models were used to analyze the effects of cell density and relative frequency on competition outcomes.</p>
<p>Media preparation: All experiments were conducted in media with an artificial seawater base. Carbonate parameters were carefully measured using titration to determine alkalinity and either potentiometric or colorimetric assays to determine pH. pCO2 was manipulated by addition of calibrated doses of HCl or NaOH, along with NaHCO3 to preserve alkalinity if necessary, in hermetically sealed test tubes with approximately no headspace. Culture growth was assessed every two days by removing a 100 uL aliquot for flow cytometric analysis.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong>All data were analyzed in R v 3.6.1. Linear models were used for most analyses, with post-hoc comparisons conducted using the emmeans package Full code necessary to re-run our analyses is contained in the file KnightDataAnalysis.txt included with this package.</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
Percival algal growth chambers
Percival algal growth chambers
PI Supplied Instrument Name: Percival algal growth chambers PI Supplied Instrument Description:Cultures were incubated in Percival algal growth chambers. Instrument Name: Algal Growth Chamber Instrument Short Name: Instrument Description: A chamber specifically designed for the growth of algae in flasks. The chamber typically provides controlled temperature, humidity, and light conditions.
Luminex Guava HT-1 flow cytometer
Luminex Guava HT-1 flow cytometer
PI Supplied Instrument Name: Luminex Guava HT-1 flow cytometer PI Supplied Instrument Description:Most data in this study were collected using a Luminex Guava HT-1 flow cytometer. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
custom-calibrated pH probe
custom-calibrated pH probe
PI Supplied Instrument Name: custom-calibrated pH probe PI Supplied Instrument Description:pH was measured using either a custom-calibrated pH probe or colorimetrically using m-cresol purple administered by sequential injection in a BioTek Synergy H1 spectrophotometer plate reader. Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
BioTek Synergy H1 spectrophotometer plate reader
BioTek Synergy H1 spectrophotometer plate reader
PI Supplied Instrument Name: BioTek Synergy H1 spectrophotometer plate reader PI Supplied Instrument Description:pH was measured using either a custom-calibrated pH probe or colorimetrically using m-cresol purple administered by sequential injection in a BioTek Synergy H1 spectrophotometer plate reader. Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
Mettler-Toledo titrator
Mettler-Toledo titrator
PI Supplied Instrument Name: Mettler-Toledo titrator PI Supplied Instrument Description:Alkalinity was measured using a Mettler-Toledo titrator. Instrument Name: Titrator Instrument Short Name:Titrator Instrument Description: Titrators are instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB12/