http://lod.bco-dmo.org/id/dataset/925841
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
2024-04-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Data and code from an examination of growth rates of cyanobacteria co-cultured with a heterotrophic bacterium, Alteromonas, under either present-day or predicted future pCO2 conditions
2025-03-26
publication
2025-03-26
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-05-06
publication
https://doi.org/10.26008/1912/bco-dmo.925841.1
James Jeffrey Morris
University of Alabama at Birmingham
principalInvestigator
Elizabeth Entwistle
University of Alabama at Birmingham
principalInvestigator
Zhiying Lu
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., Entwistle, E., Lu, Z. (2025) Data and code from an examination of growth rates of cyanobacteria co-cultured with a heterotrophic bacterium, Alteromonas, under either present-day or predicted future pCO2 conditions. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2025-03-26 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.925841.2 [access date]
The Long Term Phytoplankton Evolution Experiment: Culture Analysis Dataset Description: Methods and Sampling: <p>Detailed methods can be found in the manuscript "Marine phytoplankton and heterotrophic bacteria rapidly adapt to future pCO2 conditions in experimental co-cultures". A summary of major methods are provided here.</p>
<p>The phytoplankton used in this study as well as the media in which they were grown are <em>Prochlorococcus</em> MIT9312 (PEv medium), <em>Synechococcus</em> CC9311 (SEv medium), <em>Synechocystis</em> PCC6803 (SEv medium), <em>Thalassiosira oceanica</em> CCMP1005 (FEv medium), and <em>Emiliania huxleyi</em> CCMP371 (FEv medium). All media types were derived from media commonly used to cultivate each organism detailed in "Algal Culturing Techniques" edited by Andersen. Prior to use in experiments, phytoplankton cultures were rendered clonal and axenic, then mixed with pure cultures of the heterotrophic bacterium A<em>lteromonas</em> EZ55, obtained by streaking for isolation on YTSS agar.</p>
<p>Cultures were experimentally evolved for approximately 500 generations at 22 degrees Celisius (°C) under approximately 75 micromoles photons per square meter per second (µmol photons m-2 s-1) in acid-washed conical-bottom glass tubes with airtight caps where the carbonate system was manipulated by the addition of acid or base to achieve present-day (400 parts per million (ppm)) or year 2100 (800 ppm) pCO2 conditions. Phytoplankton growth was measured every 48 hours using a Guava HT1 flow cytometer equipped with a 488 nanometer (nm) laser. When phytoplankton cell densities crossed a cutoff value, cultures were diluted 26-fold into fresh media, representing log₂26 or 4.7 generations per transfer. Samples from each lineage were cryopreserved every 25 generations and again at the end of the experiment.</p>
<p>At the end of the evolution period, we subcultured clonal evolved <em>Alteromonas</em> strains by spread-plating evolved cultures on YTSS agar and selecting single, isolated colonies for growth in YTSS broth. <em>Prochlorococcus</em> was rendered axenic by the addition of 100 micrograms per milliliter (µg mL-1) streptomycin. All growth experiments were initiated by mixing axenic <em>Prochlorococcus</em> with a specific <em>Alteromonas</em> clone (or else remaining axenic) and acclimating the co-culture for 3 transfer cycles (approximately 14 generations) at the target pCO2 concentration. Growth was then monitored by flow cytometry as described above for at least 3 subsequent transfers under constant conditions.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1316101 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1316101
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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851085 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851085
completed
James Jeffrey Morris
University of Alabama at Birmingham
205-934-9498
1300 University Blvd CH253
Birmingham
AL
35294
USA
evolve@uab.edu
pointOfContact
Elizabeth Entwistle
University of Alabama at Birmingham
eentwis@umich.edu
pointOfContact
Zhiying Lu
University of Alabama at Birmingham
1-252-773-2353
Campbell Hall, Office 474 1300 University Blvd
Birmingham
AL
35233
USA
luzy@uab.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Percival algal growth chamber
Guava HT1 flow cytometer with 488nm laser
theme
None, User defined
Algal Growth Chamber
Flow Cytometer
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
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
https://osprey.bco-dmo.org/project/752763
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
<p><em>NSF Award Abstract:</em><br />
Carbon dioxide released from fossil fuels is causing the ocean to become more acidic. Much attention has been given to how this will affect shelled animals like corals, but acidification also affects the algae that form the base of the ocean food chain. It is possible that future algal communities will look very different than they do today, with potentially negative consequences for fisheries, recreation, and climate. Alternatively, it is possible that these algae will be able to adapt rapidly enough to avoid the worst of it. This study looks at algae adapting to acidification in real time in the lab, focusing on "marketplace" interactions between the algae and the bacteria they live alongside. The researchers also go to sea to learn whether adaptations from the lab experiments are beneficial under real-world conditions. Ultimately, this project is helping scientists better understand how the ocean's most important and most overlooked organisms will respond to the changes humans are causing in their habitat. The researchers also use their scientific work to create fun educational opportunities from grade school to college, including agar art classes where students learn about microbial ecology by "painting" with freshly-isolated ocean bacteria.</p>
<p>The effect of ocean acidification on calcifying organisms has been well-studied, but less is known about how changing pH will affect phytoplankton. Previous work showed that the mutualistic interaction between the globally abundant cyanobacterium Prochlorococcus and its "helper" bacterium Alteromonas broke down under projected future CO2 conditions, leading to a strong decrease in the fitness of Prochlorococcus. It is possible that such interspecies interactions between microbes are important for many ecological processes, but a lack of understanding of how these interactions evolve makes it difficult to predict how important they are. This project is using laboratory evolution experiments to discover how evolution shapes the interactions between bacteria and algae like Prochlorococcus, and how these co-evolutionary dynamics might influence the biogeochemical processes that shape Earth's climate. Four research cruises to the Bermuda Atlantic Time Series are also planned to study how natural algal/bacterial communities respond to acidification, and whether evolved microbes from laboratory experiments have a competitive advantage in complex, natural communities exposed to elevated CO2. The ultimate goal of this project is to gain a mechanistic understanding of microbial interactions that can be used to inform models of Earth's oceans and biological feedbacks on global climate.</p>
LTPE
largerWorkCitation
project
eng; USA
oceans
2013-08-01
2024-01-31
From projects that focused on the following 2 locations: 1. Experiment housed in laboratories at Michigan State University 2. Lab work: Birmingham, Alabama and New York, New York. Field Work: Bermuda Atlantic Time Series.
0
BCO-DMO catalogue of parameters from Data and code from an examination of growth rates of cyanobacteria co-cultured with a heterotrophic bacterium, Alteromonas, under either present-day or predicted future pCO2 conditions
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
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https://doi.org/10.26008/1912/bco-dmo.925841.1
download
onLine
dataset
<p>Detailed methods can be found in the manuscript "Marine phytoplankton and heterotrophic bacteria rapidly adapt to future pCO2 conditions in experimental co-cultures". A summary of major methods are provided here.</p>
<p>The phytoplankton used in this study as well as the media in which they were grown are <em>Prochlorococcus</em> MIT9312 (PEv medium), <em>Synechococcus</em> CC9311 (SEv medium), <em>Synechocystis</em> PCC6803 (SEv medium), <em>Thalassiosira oceanica</em> CCMP1005 (FEv medium), and <em>Emiliania huxleyi</em> CCMP371 (FEv medium). All media types were derived from media commonly used to cultivate each organism detailed in "Algal Culturing Techniques" edited by Andersen. Prior to use in experiments, phytoplankton cultures were rendered clonal and axenic, then mixed with pure cultures of the heterotrophic bacterium A<em>lteromonas</em> EZ55, obtained by streaking for isolation on YTSS agar.</p>
<p>Cultures were experimentally evolved for approximately 500 generations at 22 degrees Celisius (°C) under approximately 75 micromoles photons per square meter per second (µmol photons m-2 s-1) in acid-washed conical-bottom glass tubes with airtight caps where the carbonate system was manipulated by the addition of acid or base to achieve present-day (400 parts per million (ppm)) or year 2100 (800 ppm) pCO2 conditions. Phytoplankton growth was measured every 48 hours using a Guava HT1 flow cytometer equipped with a 488 nanometer (nm) laser. When phytoplankton cell densities crossed a cutoff value, cultures were diluted 26-fold into fresh media, representing log₂26 or 4.7 generations per transfer. Samples from each lineage were cryopreserved every 25 generations and again at the end of the experiment.</p>
<p>At the end of the evolution period, we subcultured clonal evolved <em>Alteromonas</em> strains by spread-plating evolved cultures on YTSS agar and selecting single, isolated colonies for growth in YTSS broth. <em>Prochlorococcus</em> was rendered axenic by the addition of 100 micrograms per milliliter (µg mL-1) streptomycin. All growth experiments were initiated by mixing axenic <em>Prochlorococcus</em> with a specific <em>Alteromonas</em> clone (or else remaining axenic) and acclimating the co-culture for 3 transfer cycles (approximately 14 generations) at the target pCO2 concentration. Growth was then monitored by flow cytometry as described above for at least 3 subsequent transfers under constant conditions.</p>
Specified by the Principal Investigator(s)
<p>The impact of experimental treatments on growth parameters was statistically analyzed using linear models in R with post-hoc statistical testing using extended marginal means with the <em>emmeans</em> package. Malthusian and exponential growth rates were calculated as described in our previous work (Hennon et al. 2017, ISME Journal). Because these experiments involved thousands of measurements collected over several years, a variety of clearly erroneous data points were recorded that led to several outlier growth rates that had a disproportionate impact on model output; rather than attempt to manually curate all growth rates, we simply removed either the most extreme 5% high and low Malthusian growth rates or eliminated exponential growth rates with r2 values lower than 0.95 for each strain in each experiment before conducting statistical tests.</p>
Specified by the Principal Investigator(s)
Version History:
Version 1 date: 2024-04-24
Version 2 date: 2025-03-26.
Version 2 includes revisions to files, addition of new files, and updated file descriptions.
Specified by BCO-DMO Data Managers
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 chamber
Percival algal growth chamber
PI Supplied Instrument Name: Percival algal growth chamber 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.
Guava HT1 flow cytometer with 488nm laser
Guava HT1 flow cytometer with 488nm laser
PI Supplied Instrument Name: Guava HT1 flow cytometer with 488nm laser 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/