http://lod.bco-dmo.org/id/dataset/953702
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
2025-02-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial abundance, bacterial organic carbon, and total organic carbon from remineralization bioassays conducted on R/V Robert Gordon Sproul cruises along the Southern California coast during July and August 2023
2025-02-18
publication
2025-02-18
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-23
publication
https://doi.org/10.26008/1912/bco-dmo.953702.1
Nicholas Baetge
Oregon State University
principalInvestigator
Craig A. Carlson
University of California-Santa Barbara
principalInvestigator
Jason Graff
Oregon State University
principalInvestigator
Allen J. Milligan
Oregon State University
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: Baetge, N., Graff, J., Milligan, A. J., Ver Wey, B., Hansen, P., Carlson, C. A., Opalk, K., Halewood, E. (2025) Bacterial abundance, bacterial organic carbon, and total organic carbon from remineralization bioassays conducted on R/V Robert Gordon Sproul cruises along the Southern California coast during July and August 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.953702.1 [access date]
DOM remineralization bioassays Dataset Description: Methods and Sampling: <p>All surface seawater was collected just prior to local sunrise from a SBE-911+ Conductivity-Temperature-Depth (CTD, Sea-Bird Scientific) Niskin bottle rosette cast and then transferred or directly filtered into acid-cleaned 20-liter (L) carboys with platinum-cured silicone tubing.</p>
<p>Bacterial growth and dissolved organic carbon (DOC) utilization were estimated in six microbial remineralization experiments following Baetge et al (2021), in which changes in bacterioplankton cell densities, bacterial organic carbon, and TOC were measured over five day incubations. For each experiment, 3-micrometer (µm) filtered surface seawater was directly and gently gravity-filtered through a mixed cellulose ester (MCE) membrane filter (EMD Millipore, 142-millimeters (mm)) in a polycarbonate filtration cartridge (Geotech Environmental Equipment, Inc.) with platinum-cured silicone tubing. The filtrate was then filtered through a 1.2- or a 0.2-µm MCE filter (EMD Millipore, 142 mm) to generate a bacterial inoculum or DOC media, respectively. Experiments were initiated when filtrates were mixed in a ratio of 1:4 bacterial inoculum to DOC media. Mixed seawater either remained unamended or was amended with ash leachate prior to being divided into a modified acid-washed 5 L polycarbonate bottle (Biotainer, Nalgene) (Baetge et al., 2021) and a set of 18 pre-combusted 40-milliliter (ml) EPA vials. Ash leachate DOC was added to experimental treatments at a final amendment concentration of ~4 µmol C/L Bottles and vials were incubated in the dark within ± 2 degrees Celsius (C) of in situ temperatures using wine coolers (YEG-2WS24-HD, YEEGO).</p>
<p>For each experiment, 2 ml samples for bacterial abundance were collected daily from all incubations. Triplicate 40 ml EPA vials were preserved daily as total organic carbon (TOC )samples after acidification to a pH of &lt; 3 with 4 N HCl. Bacterial organic carbon (BOC) samples were collected in triplicate 1 L polycarbonate bottles from the bacterial inoculum and as samples from the 5 L polycarbonate bottles on the second and fifth days of the experiment. Bacterioplankton abundance (cells/L) samples were fixed upon collection with paraformaldehyde to a final concentration of 1%, flash-frozen in liquid nitrogen, and stored at -20 degrees C. Sample volumes for BOC (micromoles C per liter (µmol C/L)) measurements were filtered through two stacked pre-combusted 0.3 µm GF/75 filters (25 mm, Advantec) in inline polypropylene cartridges (Cole-Parmer). At three experimental sites, DOC media (i.e., 0.2 µm filtrate) was also filtered to generate triplicate background correction samples to account for DOC filter adsorption (Graff et al., 2023). All filters were stored in pre-combusted 20 ml borosilicate glass vials (Wheaton) at -20 degrees C, and then later fumed for 24 hours with HCl and dried for 24 hours at 50 degrees C prior to analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2306993 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2306993
completed
Nicholas Baetge
Oregon State University
2820 SW Campus Way
Corvallis
OR
97331
USA
nicholasbaetge@gmail.com
pointOfContact
Craig A. Carlson
University of California-Santa Barbara
(805) 893-2541
University of California Department of Ecology, Evolution and Marine Biology
Santa Barbara
CA
93106-6150
USA
craig_carlson@ucsb.edu
pointOfContact
Jason Graff
Oregon State University
Cordley Hall 4517 2701 SW Campus Way
Corvallis
OR
97331
USA
graffja@oregonstate.edu
pointOfContact
Allen J. Milligan
Oregon State University
541-737-5276
Research Way Laboratory Building 4575 SW Research Way
Corvallis
OR
97333
USA
allen.milligan@science.oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
stn
lat
lon
dt
trt
bact_cells
sd_bact_cells
boc
mean_toc
sd_toc
CCE-440 Elemental Analyzer
Guava flow cytometer
Shimadzu TOC-V or TOC-L
theme
None, User defined
station
latitude
longitude
ISO_DateTime_UTC
treatment
abundance
organic carbon
featureType
BCO-DMO Standard Parameters
Elemental Analyzer
Flow Cytometer
Niskin bottle
Total Organic Carbon Analyzer
instrument
BCO-DMO Standard Instruments
SP2320
SP2319
service
Deployment Activity
Southern California coast
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.
Postdoctoral Fellowship: OCE-PRF: Smoke on the water: the impacts of wildfire ash deposition on surface ocean biology
https://osprey.bco-dmo.org/project/936868
Postdoctoral Fellowship: OCE-PRF: Smoke on the water: the impacts of wildfire ash deposition on surface ocean biology
<p><em>NSF Award Abstract:</em><br />
Climate-driven warming is projected to increase the frequency, intensity, and size of wildfires that can have severe environmental, human, and economic impacts, particularly along the U.S. West Coast. These wildfires result in dramatic CO2 emissions and deposition of ash carrying nutrients, organic matter, and trace metals onto the coastal and open ocean. Deposition of wildfire ash on the ocean can alter the carbon and energy flow through marine food webs by fertilizing microbial production or inhibiting microbial growth due to heavy metal toxicity. How the character of both the ash (e.g., chemical quality, fertilizing v. toxic) and the starting microbial community composition (e.g., diversity, size distribution) influences the microbial response to ash-derived material is unknown. This project will address this knowledge gap by investigating the physiological responses of marine plankton off the U.S West Coast to different types of ash generated from local wildfires and plant biomass. This work will advance interdisciplinary science, bridging biological oceanography with terrestrial ecology and biogeochemistry, by generating foundational knowledge of wildfire impacts on surface ocean biology and carbon and energy transfer from land to ocean. Results from this project will enable improved forecasts of changes in marine ecosystems in response to wildfires, which is information pertinent to communities and industries that depend on ocean ecosystem resources, including fisheries. The work will also inform national efforts to mitigate and adapt to the impacts of climate change by addressing whether wildfire-stimulated fertilization and carbon fixation in the ocean can offset CO2 emissions from wildfires. This project will broaden participation and education in ocean science by providing immersive research experiences for multiple undergraduate students and opportunities for them to disseminate their work through scientific conferences and publications. Additionally, a day-long content unit related to the project will be developed and implemented in Oregon State University’s annual week-long Microbiology Summer Camp, which provides local high school students with a hands-on learning experience in microbiology.</p>
<p>Specifically, this project consists of mechanistic studies designed to quantitatively describe the physiological responses (e.g., growth, productivity, cellular stoichiometry) of phytoplankton and bacterioplankton to a variety of ash types. The quantity and proportion of nutrients, organic matter, and trace metals leached from ash into seawater likely depends on the quality of the ash, which is influenced by vegetation type and the temperature at which the ash was produced. This study will assess how microbial production and growth are fertilized or inhibited by the composition of ash and will consist of two primary elements. In the first element, ash will be collected from the field and generated in the lab from plant biomass. The ash will then be leached in seawater and chemically characterized for inorganic and organic matter content. In the second element, seawater incubation experiments will be conducted to quantify physiological and diversity-based responses of naturally occurring phytoplankton and bacterial communities to different ash types. Data generated from this project will contribute to improved predictive models of wildfire-driven material transfer from the terrestrial system to the ocean and its impact on carbon and energy flow in marine food webs.</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>
Smoke on the water
largerWorkCitation
project
eng; USA
oceans
Southern California coast
-120.7948
-118.402
33.54503
34.37358
2023-08-02
2023-08-22
Pacific Ocean
0
BCO-DMO catalogue of parameters from Bacterial abundance, bacterial organic carbon, and total organic carbon from remineralization bioassays conducted on R/V Robert Gordon Sproul cruises along the Southern California coast during July and August 2023
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/953722.rdf
Name: stn
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/953723.rdf
Name: lat
Units: degrees North
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/953724.rdf
Name: lon
Units: degrees East
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/953725.rdf
Name: dt
Units: unitless
Description: <p>datetime (UTC) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/953726.rdf
Name: trt
Units: unitless
Description: <p>treatment type: control or amendment with (1) Thomas Fire ash leachate, (2) low temperature (<500 degrees C) ash leachate, or (3) high temperature (>500 degrees C) ash leachate</p>
http://lod.bco-dmo.org/id/dataset-parameter/953727.rdf
Name: bact_cells
Units: cells per milliliter
Description: <p>mean bacterial abundance between replicate samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/953728.rdf
Name: sd_bact_cells
Units: cells per milliliter
Description: <p>standard deviation of the mean bacterial abundance between replicate samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/953729.rdf
Name: boc
Units: micromoles C per liter (umol C/L)
Description: <p>bacterial organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/953730.rdf
Name: mean_toc
Units: micromoles C per liter (umol C/L)
Description: <p>total organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/953731.rdf
Name: sd_toc
Units: micromoles C per liter (umol C/L)
Description: <p>standard deviation of the mean total organic carbon between replicate samples</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
-1
download
https://doi.org/10.26008/1912/bco-dmo.953702.1
download
onLine
dataset
<p>All surface seawater was collected just prior to local sunrise from a SBE-911+ Conductivity-Temperature-Depth (CTD, Sea-Bird Scientific) Niskin bottle rosette cast and then transferred or directly filtered into acid-cleaned 20-liter (L) carboys with platinum-cured silicone tubing.</p>
<p>Bacterial growth and dissolved organic carbon (DOC) utilization were estimated in six microbial remineralization experiments following Baetge et al (2021), in which changes in bacterioplankton cell densities, bacterial organic carbon, and TOC were measured over five day incubations. For each experiment, 3-micrometer (µm) filtered surface seawater was directly and gently gravity-filtered through a mixed cellulose ester (MCE) membrane filter (EMD Millipore, 142-millimeters (mm)) in a polycarbonate filtration cartridge (Geotech Environmental Equipment, Inc.) with platinum-cured silicone tubing. The filtrate was then filtered through a 1.2- or a 0.2-µm MCE filter (EMD Millipore, 142 mm) to generate a bacterial inoculum or DOC media, respectively. Experiments were initiated when filtrates were mixed in a ratio of 1:4 bacterial inoculum to DOC media. Mixed seawater either remained unamended or was amended with ash leachate prior to being divided into a modified acid-washed 5 L polycarbonate bottle (Biotainer, Nalgene) (Baetge et al., 2021) and a set of 18 pre-combusted 40-milliliter (ml) EPA vials. Ash leachate DOC was added to experimental treatments at a final amendment concentration of ~4 µmol C/L Bottles and vials were incubated in the dark within ± 2 degrees Celsius (C) of in situ temperatures using wine coolers (YEG-2WS24-HD, YEEGO).</p>
<p>For each experiment, 2 ml samples for bacterial abundance were collected daily from all incubations. Triplicate 40 ml EPA vials were preserved daily as total organic carbon (TOC )samples after acidification to a pH of &lt; 3 with 4 N HCl. Bacterial organic carbon (BOC) samples were collected in triplicate 1 L polycarbonate bottles from the bacterial inoculum and as samples from the 5 L polycarbonate bottles on the second and fifth days of the experiment. Bacterioplankton abundance (cells/L) samples were fixed upon collection with paraformaldehyde to a final concentration of 1%, flash-frozen in liquid nitrogen, and stored at -20 degrees C. Sample volumes for BOC (micromoles C per liter (µmol C/L)) measurements were filtered through two stacked pre-combusted 0.3 µm GF/75 filters (25 mm, Advantec) in inline polypropylene cartridges (Cole-Parmer). At three experimental sites, DOC media (i.e., 0.2 µm filtrate) was also filtered to generate triplicate background correction samples to account for DOC filter adsorption (Graff et al., 2023). All filters were stored in pre-combusted 20 ml borosilicate glass vials (Wheaton) at -20 degrees C, and then later fumed for 24 hours with HCl and dried for 24 hours at 50 degrees C prior to analysis.</p>
Specified by the Principal Investigator(s)
- Imported original file "BACTERIA_DOM.csv" into the BCO-DMO system.
- Flagged "NA" as a missing data value; missing data are empty/blank in the final CSV file.
- PI applied rounding to numeric values and provided a new file.
- Saved final data file as "953702_v1_dom_remineralization_bioassays.csv".
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
CCE-440 Elemental Analyzer
CCE-440 Elemental Analyzer
PI Supplied Instrument Name: CCE-440 Elemental Analyzer PI Supplied Instrument Description:BOC samples were analyzed on a CCE-440 Elemental Analyzer (Exeter Analytics) calibrated with acetanilide standards. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Guava flow cytometer
Guava flow cytometer
PI Supplied Instrument Name: Guava flow cytometer PI Supplied Instrument Description:Bacterial cells were stained with SYBR Green I (ThermoFisher) and enumerated on a Guava flow cytometer (Millipore) (Gasol et al., 2016). 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/
PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Shimadzu TOC-V or TOC-L
Shimadzu TOC-V or TOC-L
PI Supplied Instrument Name: Shimadzu TOC-V or TOC-L PI Supplied Instrument Description:Samples for TOC concentration measurements were acidified to a pH of < 3 with 60 µl 4 N HCl and quantified on a Shimadzu TOC-V or TOC-L using the high-temperature combustion method (Halewood et al., 2022). Precision for DOC analysis was ~1 µmol C L-1 and data quality was assessed by measuring Santa Barbara Channel surface and deep water samples that were calibrated against DOC consensus reference material provided by Hansell (2005). Instrument Name: Total Organic Carbon Analyzer Instrument Short Name:TOC analyzer Instrument Description: A unit that accurately determines the carbon concentrations of organic compounds typically by detecting and measuring its combustion product (CO2). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/bs116.pdf Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Cruise: SP2320
SP2320
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP2320
Allen J. Milligan
Oregon State University
Cruise: SP2319
SP2319
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP2319
Allen J. Milligan
Oregon State University
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel