http://lod.bco-dmo.org/id/dataset/962727
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
2025-05-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cell concentrations associated with genomics sampling to characterize bacterial responses to parasite-host metabolites from bottle incubation experiments in June of 2024
2025-05-29
publication
2025-05-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-17
publication
https://doi.org/10.26008/1912/bco-dmo.962727.1
Sean Anderson
University of New Hampshire
principalInvestigator
Elizabeth Harvey
University of New Hampshire
principalInvestigator
Kelsey Poulson-Ellestad
Roosevelt University
principalInvestigator
Philip Place
University of New Hampshire
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: Anderson, S., Place, P., Gray, L., Poulson-Ellestad, K., Harvey, E. (2025) Cell concentrations associated with genomics sampling to characterize bacterial responses to parasite-host metabolites from bottle incubation experiments in June of 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.962727.1 [access date]
Methods and Sampling: <p>Location description:<br />
Collected water and conducted bottle incubations off the UNH Coastal Marine Laboratory pier in June 2024.<br />
<br />
Cultures and incubation set-up:</p>
<p><em>Amoebophrya</em> sp. (RCC 4401) parasite spores were maintained by adding fresh host (<em>Scrippsiella acuminata,</em> strain <em>R</em>CC 1627)<!--EndFragment--> every 2-3 d at a ratio of 1:1 spore to host by volume. Parasite and host cultures were kept at 18 °C on a 12:12 hour light: dark cycle at 80-100 µmol photon m<sup>-2</sup> s<sup>-1</sup>. Prior to the incubation experiment, exudates from freshly lysed <em>S. acuminata</em> were collected by filtering parasite cultures through 0.2 µm filters (Long et al. 2021). As controls, exudates were also collected from healthy host cultures and f/2 media used for culturing. All exudates were stored at 4 °C for &lt;1 h before being combined with natural seawater for incubation experiments.</p>
<p>Surface seawater (20 L) was collected at high tide from the UNH Coastal Marine Laboratory (CML) pier that is located at the mouth of Portsmouth Harbor in New Castle, NH. Seawater was immediately brought back to the lab and filtered through a 1.2-µm mesh filter to isolate natural bacterial communities. Filtered seawater (500 mL) was combined with 1.5 L of either filtrate from infected, healthy host, or the f/2 culture media in triplicate 2-L polycarbonate bottles (Maas et al. 2020) to explore the bacterial response to sources of dissolved organic carbon (DOC). These treatments are represented as "Infected", "Host", or "Media" within the data file in the Treatment column. The baseline community is represented by "Natural" and reflects the bacterial community at the initial time of sampling (Time zero = T0). A total of 9 bottles were allowed to incubate at ambient sweater conditions for a total of 48 h in a crab trap fixed to the dock. Bottles were sampled at 6, 24, and 48 h for DNA/RNA filtration (~500 ml per bottle) and flow cytometry. Triplicate flow cytometry samples were also taken from the natural bacterial community at T0.</p>
<p>Flow cytometry:</p>
<p>Samples (1.8 mL) from each bottle and time point were fixed with 1% glutaraldehyde, stored at 4 °C, and run on a Guava easyCyte HT (Millipore) flow cytometer within 4 months of collection to estimate bulk bacterial abundances. To prepare for the run, 198 µl per sample was loaded onto a 96-well plate, stained with 100x SYBR Green (Thermo Fisher), and set in the dark at room temperature for 30 min (Nunn et al. 2024). Samples were run on the flow cytometer at low flow rate (0.24 µl s<sup>-1</sup>) for 3 min per well. Bulk heterotrophic bacteria populations were distinguished from pre-defined gates based on plots of forward scatter, which provides an indication of cell size, and green fluorescence (512 nm). In this case, green fluorescence at an emission wavelength of 512 nm reflects the binding of double-stranded DNA &nbsp;to the SYBR Green dye that emits fluorescence upon excitation.&nbsp;<br />
<br />
<br />
Organism information:<br />
<br />
TaxonomicName,&nbsp;Life Science Identifier (LSID), strain_identifier, organism_type<br />
Scrippsiella acuminata, urn:lsid:marinespecies.org:taxname:1321853, RCC 1627, host<br />
Amoebophrya sp., urn:lsid:marinespecies.org:taxname:109448,&nbsp;RCC 4401, parasite</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589
completed
Sean Anderson
University of New Hampshire
sra74866@uga.edu
pointOfContact
Elizabeth Harvey
University of New Hampshire
NH
USA
elizabeth.harvey@unh.edu
pointOfContact
Kelsey Poulson-Ellestad
Roosevelt University
kpoulsonellestad@roosevelt.edu
pointOfContact
Philip Place
University of New Hampshire
philip.place@unh.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_name
Treatment
Time
Replicate
Date
Cell_concentration_hbact
Guava easyCyte HT flow cytometer (Millipore)
theme
None, User defined
sample identification
treatment
time_elapsed
replicate
date
cell_concentration
featureType
BCO-DMO Standard Parameters
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.
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
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.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
Characterizing plankton parasite-host metabolites and the response of heterotrophic bacteria
https://osprey.bco-dmo.org/project/953588
Characterizing plankton parasite-host metabolites and the response of heterotrophic bacteria
<p>Nearly half of annual primary production in the ocean is released by phytoplankton as labile metabolites, making up a large portion of dissolved organic carbon (DOC) that can fuel microbial food webs and mediate cell signaling and species interactions. Phytoplankton mortality is a major source of labile DOC, and yet, the contribution of different sources of mortality to carbon cycling remains unclear. This is especially true for parasitism. In recent genomics surveys, parasitic protists have been found to be widespread in the ocean and well-connected to potential phytoplankton hosts via network analysis. The family Amoebophryaceae (Syndiniales) are one of the ubiquitous and phylogenetically diverse groups of protist parasites, known to infect a range of hosts and drive shifts in microbial diversity and bloom phenology. Though not well quantified, these parasites are thought to have a similar impact on carbon cycling as viruses, with rapid host infection (2-3 d) and a rerouting of particulate carbon to labile DOC. In this project, we performed culture-based experiments and used untargeted metabolomics to profile labile DOC released over an infection cycle. Phytoplankton cultures included two strains of <em>Amoebophrya</em> sp. that infect the same dinoflagellate host (<em>Scrippsiella acuminata</em>), allowing us to explore new insights into strain-level infection dynamics. Separate incubation experiments were also conducted to expose parasite-derived filtrate (collected fresh from cultures after host lysis) to natural bacterial communities. Samples were collected for metabarcoding and metatranscriptomics at discrete time points to characterize changes in bacterial community assembly and gene expression in the presence of labile DOC. This work aims to provide new perspectives on plankton parasitism and its role in biogeochemical cycling, which can inform future research directions in microbial parasite-host systems and lead to more accurate food web and ecosystem models in a changing ocean environment.</p>
Plankton parasite-host metabolites
largerWorkCitation
project
eng; USA
oceans
-70.712
-70.712
43.072
43.072
2024-06-04
2024-10-04
0
BCO-DMO catalogue of parameters from Cell concentrations associated with genomics sampling to characterize bacterial responses to parasite-host metabolites from bottle incubation experiments in June of 2024
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/962795.rdf
Name: Sample_name
Units: unitless
Description: <p>Unique name specifying treatment, incubation time, and replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/962796.rdf
Name: Treatment
Units: unitless
Description: <p>Infected, healthy host, or f/2 filtrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/962797.rdf
Name: Time
Units: hours
Description: <p>Hours of incubation post filtrate added</p>
http://lod.bco-dmo.org/id/dataset-parameter/962798.rdf
Name: Replicate
Units: unitless
Description: <p>Treatment bottle replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/962799.rdf
Name: Date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/962800.rdf
Name: Cell_concentration_hbact
Units: Cells per ml (cells mL-1)
Description: <p>Concentration of bulk heterotrophic bacteria</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
1313
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/718ab719-0d7d-4154-b2a7-f82c98007b9a/content
download
https://doi.org/10.26008/1912/bco-dmo.962727.1
download
onLine
dataset
<p>Location description:<br />
Collected water and conducted bottle incubations off the UNH Coastal Marine Laboratory pier in June 2024.<br />
<br />
Cultures and incubation set-up:</p>
<p><em>Amoebophrya</em> sp. (RCC 4401) parasite spores were maintained by adding fresh host (<em>Scrippsiella acuminata,</em> strain <em>R</em>CC 1627)<!--EndFragment--> every 2-3 d at a ratio of 1:1 spore to host by volume. Parasite and host cultures were kept at 18 °C on a 12:12 hour light: dark cycle at 80-100 µmol photon m<sup>-2</sup> s<sup>-1</sup>. Prior to the incubation experiment, exudates from freshly lysed <em>S. acuminata</em> were collected by filtering parasite cultures through 0.2 µm filters (Long et al. 2021). As controls, exudates were also collected from healthy host cultures and f/2 media used for culturing. All exudates were stored at 4 °C for &lt;1 h before being combined with natural seawater for incubation experiments.</p>
<p>Surface seawater (20 L) was collected at high tide from the UNH Coastal Marine Laboratory (CML) pier that is located at the mouth of Portsmouth Harbor in New Castle, NH. Seawater was immediately brought back to the lab and filtered through a 1.2-µm mesh filter to isolate natural bacterial communities. Filtered seawater (500 mL) was combined with 1.5 L of either filtrate from infected, healthy host, or the f/2 culture media in triplicate 2-L polycarbonate bottles (Maas et al. 2020) to explore the bacterial response to sources of dissolved organic carbon (DOC). These treatments are represented as "Infected", "Host", or "Media" within the data file in the Treatment column. The baseline community is represented by "Natural" and reflects the bacterial community at the initial time of sampling (Time zero = T0). A total of 9 bottles were allowed to incubate at ambient sweater conditions for a total of 48 h in a crab trap fixed to the dock. Bottles were sampled at 6, 24, and 48 h for DNA/RNA filtration (~500 ml per bottle) and flow cytometry. Triplicate flow cytometry samples were also taken from the natural bacterial community at T0.</p>
<p>Flow cytometry:</p>
<p>Samples (1.8 mL) from each bottle and time point were fixed with 1% glutaraldehyde, stored at 4 °C, and run on a Guava easyCyte HT (Millipore) flow cytometer within 4 months of collection to estimate bulk bacterial abundances. To prepare for the run, 198 µl per sample was loaded onto a 96-well plate, stained with 100x SYBR Green (Thermo Fisher), and set in the dark at room temperature for 30 min (Nunn et al. 2024). Samples were run on the flow cytometer at low flow rate (0.24 µl s<sup>-1</sup>) for 3 min per well. Bulk heterotrophic bacteria populations were distinguished from pre-defined gates based on plots of forward scatter, which provides an indication of cell size, and green fluorescence (512 nm). In this case, green fluorescence at an emission wavelength of 512 nm reflects the binding of double-stranded DNA &nbsp;to the SYBR Green dye that emits fluorescence upon excitation.&nbsp;<br />
<br />
<br />
Organism information:<br />
<br />
TaxonomicName,&nbsp;Life Science Identifier (LSID), strain_identifier, organism_type<br />
Scrippsiella acuminata, urn:lsid:marinespecies.org:taxname:1321853, RCC 1627, host<br />
Amoebophrya sp., urn:lsid:marinespecies.org:taxname:109448,&nbsp;RCC 4401, parasite</p>
Specified by the Principal Investigator(s)
<p>Cell concentrations (cells mL<sup>-1</sup>) were estimated within the Guava InCyte software based on abundances measured per gate and the volume of sample analyzed.</p>
Specified by the Principal Investigator(s)
* Submitted data file "bacteria_counts.csv" renamed to "bacteria_counts.xlsx" so it could be imported into the BCO-DMO data system for this dataset. File was in xlsx format not plain text.
* Sheet 1 within file "bacteria_counts.xlsx" was imported into the BCO-DMO data system for this dataset. Values "nd" imported as missing data values. Table will appear as Data File: 962727_v1_bacterial_fcm_data.csv (along with other download format options).
Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Taxonomic identifiers added from name matches at the World Register of Marine Species (WoRMS), they exactly matched known names there as of 2025-05-29.
* References added for the RCC strains cited in metadata.
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
Guava easyCyte HT flow cytometer (Millipore)
Guava easyCyte HT flow cytometer (Millipore)
PI Supplied Instrument Name: Guava easyCyte HT flow cytometer (Millipore) PI Supplied Instrument Description:Guava easyCyte HT flow cytometer (Millipore) to measure cell counts of bulk heterotrophic bacteria. 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/