http://lod.bco-dmo.org/id/dataset/928039
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
2024-05-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial transcriptional response to picoeukaryote Micromonas commoda
2024-07-15
publication
2024-07-15
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-07-15
publication
https://doi.org/10.26008/1912/bco-dmo.928039.1
Mary Ann Moran
University of Georgia
principalInvestigator
Maria Hamilton
University of Georgia
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: Moran, M. A., Hamilton, M., Ferrer-González, F. X., Smith, C. (2024) Bacterial transcriptional response to picoeukaryote Micromonas commoda. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-15 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.928039.1 [access date]
picoeukaryote Micromonas commoda Dataset Description: <p>The data are linked to&nbsp;Hamilton et al., 2024 (see related publications).&nbsp;</p> Methods and Sampling: <p>Axenic cultures of <em>Micromonas commoda</em> RCC299 (National Center for Marine Algae, NMCA) were grown in 1 L of organic-carbon free defined medium L1-Si [31] as modified by NCMA (https://ncma.bigelow.org/) at a salinity of 35 in 1900 mL vented polystyrene tissue culture flasks. Flasks were maintained at 18 <sup>o</sup>C under 16 h light at 160 μmol photons m<sup>−2</sup>s<sup>−1</sup> and 8 h dark. Pre-cultures of <em>Micromonas </em>were sequentially upscaled (50 ml, 200 ml, 1 L) with transfers occurring during the exponential growth phase. After growing for 7 d (early stationary growth phase; ~2.7 × 10<sup>6</sup> cells ml−1), three marine bacteria pre-grown in YTSS medium (<em>Ruegeria pomeroyi</em> DSS-3, <em>Stenotrophomonas</em> sp. SKA14, and <em>Polaribacter dokdonensis</em> MED152 were washed 5 times in sterile L1 medium at 6000 RCF and inoculated into the axenic cultures at ~10<sup>6</sup> cells ml<sup>−1</sup>. Three or four replicate co-cultures were established for each bacterial strain and also for an axenic phytoplankton control. Three additional treatments were established with bacterial strains introduced individually into L1 medium with 400 μM C glucose as the sole carbon source (which supports all 3) at the same initial cell concentration as the co-cultures. As this treatment contained a single, known metabolite, it served as a control for co-culture&nbsp;transcriptome analysis. Bacterial contamination of the axenic phytoplankton cultures was ruled out based on lack of colony formation from culture aliquots spread onto YTSS plates and absence of bacterial-size particles in flow cytometry scattergrams.</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
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Maria Hamilton
University of Georgia
maria.hamilton@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Bottle_ID
Treatment
Time_h
Micromonas_cells_ml
Bacteria_cells_ml
NH4_uM
NO3_uM
PO4_uM
NCBI_Sample_ID
Accession
BioProject
Organism
Taxonomy_ID
Description
Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA)
DX500 Ion Chromatograph (Dionex Co.)
Model Spectronic 21D (Spectronic Instrumentation)
theme
None, User defined
bottle number
treatment
sample time
cell_concentration
Ammonium
Nitrate
reactive phosphorus (PO4)
sample identification
NCBI BioSample accession
NCBI BioProject accession
species scientific name (binomial)
taxon_code
sample description
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Ion Chromatograph
Spectrophotometer
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.
Effects of Climate Change Variables on Microbial Autotroph-Heterotroph Carbon Flux
https://osprey.bco-dmo.org/project/787536
Effects of Climate Change Variables on Microbial Autotroph-Heterotroph Carbon Flux
<p><em>NSF Award Abstract:</em><br />
Phytoplankton in the surface ocean are responsible for roughly half of all photosynthesis on the planet. Much of the organic material created by these photosynthetic organisms is ultimately consumed by diverse marine bacteria with differing preferences for specific types of chemical compounds. This project investigates how climate change (temperature and CO2) might alter the types and amounts of organic compounds produced by different species of marine phytoplankton and the types and amounts of compounds transferred from phytoplankton to marine bacteria. Shifts in organic compounds transferred to bacteria could alter the distribution of bacterial species in the ocean, their growth rates and efficiencies, and flows of energy through the global ocean. This project helps scientists better understand the effects of climate change on marine ecosystems. Two graduate students and a postdoctoral researcher are supported by the project, receiving interdisciplinary training in biology, chemistry, and ocean sciences. Summer research internships in the PIs' laboratories are offered to AP Biology students enrolled at Cedar Shoals High School in Athens, GA, a school that serves a diverse social and economic community.</p>
<p>Much of the bacterial secondary production in the surface ocean is supported by rapid uptake of labile metabolites released from phytoplankton, either directly through excretion and diffusion or indirectly through lysis and predation. This project investigates the effects of two climate change variables (temperature and CO2) on the metabolite pools produced and released by three model phytoplankton species (a diatom, a coccolithophore, and a cyanobacterium) and assesses changes in the composition and fate of metabolites transferred to bacteria. Phytoplankton species are being grown axenically at two different temperatures and CO2 concentrations in a factorial design and endo- and exometabolite composition is determined using NMR. A suite of phytoplankton physiological characteristics is measured and evaluated in the context of metabolite composition. Experiments with heterotrophic bacteria (either model bacteria or natural bacterial communities) are being conducted to assess the effects of climate change variables on metabolite transfer from phytoplankton to marine bacteria. In the first experiment type, bacteria are co-cultured with the phytoplankton at different temperatures and CO2 concentrations, and changes in bacterial gene expression and metabolite concentrations are used to assess shifts in the composition of metabolites transferred. In the second type, bacteria are grown on phytoplankton metabolite pools produced at different temperatures and CO2 concentrations in high-throughput bioassays, and changes in bacterial traits (growth rate, carrying capacity, growth efficiency) resulting from the different climate scenarios are used to indicate changes in metabolite quality. Knowledge of how the heterotrophic processing of phytoplankton metabolites might shift in response to climate change allows better prediction of Earth's future carbon cycle.</p>
<p>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.</p>
CC_Auto_Hetero_Fluxes
largerWorkCitation
project
eng; USA
oceans
-83.3576
-83.3576
33.9519
33.9519
2021-01-01
2021-12-31
Laboratory in Athens, GA, USA, and waters around Sapelo Island, GA, USA
0
BCO-DMO catalogue of parameters from Bacterial transcriptional response to picoeukaryote Micromonas commoda
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/932194.rdf
Name: Bottle_ID
Units: unitless
Description: <p>Bottle ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/932195.rdf
Name: Treatment
Units: unitless
Description: <p>Lab treatment description: DSS-3, MED152, SKA14, axenic</p>
http://lod.bco-dmo.org/id/dataset-parameter/932196.rdf
Name: Time_h
Units: hour (h)
Description: <p>Time after start of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/932197.rdf
Name: Micromonas_cells_ml
Units: cells per milliliter (cell/ml)
Description: <p>Micormonas cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/932198.rdf
Name: Bacteria_cells_ml
Units: cells per milliliter (cell/ml)
Description: <p>Bacteria cell count</p>
http://lod.bco-dmo.org/id/dataset-parameter/932199.rdf
Name: NH4_uM
Units: micromolar (uM)
Description: <p>Ammonium (NH4+) concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/932200.rdf
Name: NO3_uM
Units: micromolar (uM)
Description: <p>Nitrate (NO3-) concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/932201.rdf
Name: PO4_uM
Units: micromolar (uM)
Description: <p>Phosphate (PO43-) concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/932202.rdf
Name: NCBI_Sample_ID
Units: unitless
Description: <p>Identifier of lab sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/932203.rdf
Name: Accession
Units: unitless
Description: <p>NCBI Biosample Accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/932204.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI Bioproject Accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/932205.rdf
Name: Organism
Units: unitless
Description: <p>Organism name</p>
http://lod.bco-dmo.org/id/dataset-parameter/932206.rdf
Name: Taxonomy_ID
Units: unitless
Description: <p>Taxonomy ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/932207.rdf
Name: Description
Units: unitless
Description: <p>Sample description</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
3717
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/79fdb2c2-c4ce-4535-8fb5-4c8bc9c5530e/content
download
https://doi.org/10.26008/1912/bco-dmo.928039.1
download
onLine
dataset
<p>Axenic cultures of <em>Micromonas commoda</em> RCC299 (National Center for Marine Algae, NMCA) were grown in 1 L of organic-carbon free defined medium L1-Si [31] as modified by NCMA (https://ncma.bigelow.org/) at a salinity of 35 in 1900 mL vented polystyrene tissue culture flasks. Flasks were maintained at 18 <sup>o</sup>C under 16 h light at 160 μmol photons m<sup>−2</sup>s<sup>−1</sup> and 8 h dark. Pre-cultures of <em>Micromonas </em>were sequentially upscaled (50 ml, 200 ml, 1 L) with transfers occurring during the exponential growth phase. After growing for 7 d (early stationary growth phase; ~2.7 × 10<sup>6</sup> cells ml−1), three marine bacteria pre-grown in YTSS medium (<em>Ruegeria pomeroyi</em> DSS-3, <em>Stenotrophomonas</em> sp. SKA14, and <em>Polaribacter dokdonensis</em> MED152 were washed 5 times in sterile L1 medium at 6000 RCF and inoculated into the axenic cultures at ~10<sup>6</sup> cells ml<sup>−1</sup>. Three or four replicate co-cultures were established for each bacterial strain and also for an axenic phytoplankton control. Three additional treatments were established with bacterial strains introduced individually into L1 medium with 400 μM C glucose as the sole carbon source (which supports all 3) at the same initial cell concentration as the co-cultures. As this treatment contained a single, known metabolite, it served as a control for co-culture&nbsp;transcriptome analysis. Bacterial contamination of the axenic phytoplankton cultures was ruled out based on lack of colony formation from culture aliquots spread onto YTSS plates and absence of bacterial-size particles in flow cytometry scattergrams.</p>
Specified by the Principal Investigator(s)
<p>Bacterial cell counts: Cell counts were periodically obtained by flow cytometry. Samples were fixed at a final concentration of 1% glutaraldehyde, incubated at 4°C for 20 min, and stored at −80°C. Just prior to analysis, an internal standard of 5 μm fluorescent particles (ACFP-50-5; Spherotech, Lake Forest, IL, USA) was added, followed by staining for 15 min with SYBR Green I (final concentration 0.75X; Life Technologies, Waltham, MA, USA). Samples were analyzed on an Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA) with a 405 nm laser using a 530/30 bandpass filter for SYBR Green.</p>
<p>Micromonas cell counts: Cell counts were periodically obtained by flow cytometry. Samples were fixed at a final concentration of 1% glutaraldehyde, incubated at 4°C for 20 min, and stored at −80°C. Just prior to analysis, an internal standard of 5 μm fluorescent particles (ACFP-50-5; Spherotech, Lake Forest, IL, USA) was added, followed by staining for 15 min with SYBR Green I (final concentration 0.75X; Life Technologies, Waltham, MA, USA). Samples were analyzed on an Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA) with a 405 nm laser using a 695/40 bandpass filter for chlorophyll a (phytoplankton).</p>
<p>Nutrient analysis: At the 8 h time point, 50 ml of each sample was used for nutrient analysis. Samples were filtered through 0.2 μm pore-size 47 mm Supor filters to remove cells. The filtrate was frozen and stored at -20°C. Nutrient analyses were performed by the University of Georgia Laboratory of Environmental Analysis. Concentrations of nitrate (NO3-), nitrite (NO2-), and phosphate (PO43-) were measured using ion chromatography on a DX500 Ion Chromatograph (Dionex Co.) with an initial cartridge treatment (OnGuard-Ag cartridge from Dionex) performed to remove chloride ions. Measurements for ammonium (NH4+) were done separately via the phenate method with spectrophotometric analysis on a Model Spectronic 21D (Spectronic Instrumentation).</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
Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA)
Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA)
PI Supplied Instrument Name: Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA) PI Supplied Instrument Description:Agilent Quanteon flow cytometer (Acea, Biosciences Inc, San Diego CA) with a 405 nm laser using a 530/30 bandpass filter for SYBR Green for bacterial cell counts. 405 nm laser using a 695/40 bandpass filter for chlorophyll a (phytoplankton) was used for micromonas cell counts. 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/
DX500 Ion Chromatograph (Dionex Co.)
DX500 Ion Chromatograph (Dionex Co.)
PI Supplied Instrument Name: DX500 Ion Chromatograph (Dionex Co.) PI Supplied Instrument Description:DX500 Ion Chromatograph (Dionex Co.) with an initial cartridge treatment (OnGuard-Ag cartridge from Dionex) performed to remove chloride ions. Instrument Name: Ion Chromatograph Instrument Short Name:Ion Chromatograph Instrument Description: Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
Model Spectronic 21D (Spectronic Instrumentation)
Model Spectronic 21D (Spectronic Instrumentation)
PI Supplied Instrument Name: Model Spectronic 21D (Spectronic Instrumentation) PI Supplied Instrument Description:Measurements for ammonium (NH4+) were done separately via the phenate method with spectrophotometric analysis on a Model Spectronic 21D (Spectronic Instrumentation). Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/