http://lod.bco-dmo.org/id/dataset/871678
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
2022-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Mass-to-charge ratio +1 values in microbial cultures (Synechococcus WH8102) detected by proton transfer reaction time-of-flight mass spectrometer in 2021 and 2022
2022-03-18
publication
2022-03-18
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-02-09
publication
https://doi.org/10.26008/1912/bco-dmo.871678.1
Kimberly Halsey
Oregon State University
principalInvestigator
Stephen Giovannoni
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: Halsey, K., Giovannoni, S. (2024) Mass-to-charge ratio +1 values in microbial cultures (Synechococcus WH8102) detected by proton transfer reaction time-of-flight mass spectrometer in 2021 and 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-03-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.871678.1 [access date]
Dataset Description: <p>See the "Related Datasets" section for more data from this study with Phaeodactylum tricornutum and cocultures.&nbsp;&nbsp;<br />
<br />
PTR ToF-MS in the name of this dataset refers to proton-transfer reaction time-of-flight mass spectrometry (PTR-TOF/MS).</p> Methods and Sampling: <p><strong>Methodology:&nbsp;</strong></p>
<p>Volatile organic compounds (VOCs)&nbsp;were sampled and measured using dynamic stripping chambers coupled to a proton transfer reaction time-of-flight mass spectrometer (Moore et al. 2020). VOC concentrations (ppbv) are exported directly from the PTR-MS Viewer 3.2.1.2 software (Ionicon Analytik GmbH, Innsbruck, Austria) into .txt files. Air concentrations for each m/z (+1) detected are reported already corrected for mass calibration, transmission efficiencies, and primary ion signals. Data include experiment, culture conditions, and flow conditions. 2-point calibration mode, 0.3 m/z search range, cycle 1000, and using an average of 10 spectra.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong><br />
Samples are measured directly from cultures or media blanks. Culture conditions are given as the growth phase (exponential or stationary phase). Cell densities are provided. The protocol is well described in Moore et al. (2020).</p>
<div><strong>Media recipe:</strong><br />
<br />
Artificial seawater + 882 μM NO3 + 36.2 μM PO4 + 106 μM Si + 1x f/2 Trace metal mix + 1 x f/2 Vitamin mix<br />
&nbsp;</div>
<div><strong>Cell density when VOCs from Synechococcus WH8102 cultures were measured:</strong></div>
<div>Synechococcus_WH8102-A 3.60E+06</div>
<div>Synechococcus_WH8102-B 3.81E+06</div>
<div>Synechococcus_WH8102-C 1.59E+06</div>
<div>Synechococcus_WH8102-D 2.09E+06<br />
<br />
Taxon:&nbsp;<br />
Synechococcus,&nbsp; LSID urn:lsid:marinespecies.org:taxname:160572</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948163 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948163
completed
Kimberly Halsey
Oregon State University
541-737-1831
226 Nash Hall Dept of Microbiology
Corvallis
OR
97333
US
halseyk@oregonstate.edu
pointOfContact
Stephen Giovannoni
Oregon State University
541-737-1835
OSU/Department of Microbiology Nash Hall Rm 248
Corvallis
OR
97331
United States
stephen.giovannoni@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
Sample_Name_internal
Sample_Replicate
Sample_Tech
Time_seconds
mz_value
mz_signal
TOF-1000
theme
None, User defined
sample identification
replicate
time_elapsed
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
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.
Interactions between phytoplankton and bacterioplankton mediated by volatile organic compounds
https://osprey.bco-dmo.org/project/850075
Interactions between phytoplankton and bacterioplankton mediated by volatile organic compounds
<p>NSF Award Abstract:<br />
Communication amongst plants and animals often occurs through molecules that readily evaporate at normal temperatures, called volatile organic compounds (VOCs). Some VOCs that are produced in the ocean and then enter the atmosphere as gases have been seen to play an important role in climate. Since marine microbes both produce and consume these compounds they affect the concentration of VOCs in the surface ocean. The investigators found that as much as 20% of the carbon resulting from photosynthesis leaked out of microscopic plants in the form of VOCs. These molecules were then used by bacteria as a source of carbon and energy. This suggests that VOCs may play a more important role in the flow of carbon in the marine environment than previously thought. This project examines how microscopic plants and bacteria produce and consume different VOCs. It supports professional development training workshops for Oregon high school teachers from rural areas in OSU’s Science & Math Investigative Learning Experiences (SMILE) program. SMILE’s mission is to close the achievement gap for underserved students by increasing their STEM-content knowledge, preparing them to succeed in higher education, and inspiring them to pursue STEM careers. This project also contributes to three workshops per year, training teachers and engaging students with hands-on learning activities on the topic of Carbon Cycling by Marine Microorganisms such as “Clouds in a Bottle”. One graduate student, one post-doctoral scholar, and at least six undergraduate researchers are being trained by participating in research activities.</p>
<p>Field observations suggest that volatile organic compounds (VOCs) produced by phytoplankton are either rapidly consumed by bacterioplankton in the surface ocean or emitted into the atmosphere. VOCs are an understudied path for carbon transfer in microbial food webs throughout sunlit marine ecosystems because these compounds require specialized detection methods. Using a new system to study VOCs in suspensions of live plankton cells, 20% of photosynthetic carbon fixation was seen to be transferred as VOCs from a diatom to SAR11 bacterioplankton in co-cultures. Many of these transferred VOC compounds were not known to be growth substrates for bacterioplankton. Both the magnitude and complexity of the observed VOC transfer were surprising. This project extends these observations to a larger set of phytoplankton and bacterioplankton through controlled studies of cultures, co-cultures, and mesocosms. VOC are detected via proton transfer reaction time-of-flight mass spectrometry and isotopic labeling is used to measure the impact of VOC exchange on rates of photosynthesis and bacterial production. VOC production by phytoplankton is measured in response to nutrient-driven variation in growth rates, and over day-night cycles to discern the relationship of VOC production to photosynthetic metabolism and other cellular processes. These experiments enable a better understanding of field observations, in which bacterial consumption of VOCs can appear to significantly outpace production, while temporal variability in VOC production across daily to seasonal scales can cause VOCs to accumulate transiently to pM-nM concentrations in the surface ocean. This project contributes to close the significant gap in knowledge about the range and quantity of VOCs produced by phytoplankton, and about the roles played by these compounds in phytoplankton metabolism.</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>
Plankton Interactions and VOC
largerWorkCitation
project
eng; USA
oceans
2021-01-01
2022-01-01
0
BCO-DMO catalogue of parameters from Mass-to-charge ratio +1 values in microbial cultures (Synechococcus WH8102) detected by proton transfer reaction time-of-flight mass spectrometer in 2021 and 2022
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/871757.rdf
Name: Sample_Name
Units: unitless
Description: <p>Microbe in culture or coculture with Phaeodactylum tricornutum</p>
http://lod.bco-dmo.org/id/dataset-parameter/871758.rdf
Name: Sample_Name_internal
Units: unitless
Description: <p>Internal reference for culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/871759.rdf
Name: Sample_Replicate
Units: unitless
Description: <p>Biological replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/871760.rdf
Name: Sample_Tech
Units: unitless
Description: <p>Technical replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/871761.rdf
Name: Time_seconds
Units: seconds (s)
Description: <p>time of sampling period (seconds)</p>
http://lod.bco-dmo.org/id/dataset-parameter/871762.rdf
Name: mz_value
Units: unitless
Description: <p>Mass-to-charge (m/z) +1 value identified by PTR-MS. This is the atomic mass plus 1 for a chemical compound detected by the mass spectrometer.</p>
http://lod.bco-dmo.org/id/dataset-parameter/871763.rdf
Name: mz_signal
Units: parts per billion by volume (ppbv)
Description: <p>Mass-to-charge (m/z) signal</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
2982715
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2fd51e98-3f51-4825-acc2-b88be6984d02/content
download
https://doi.org/10.26008/1912/bco-dmo.871678.1
download
onLine
dataset
<p><strong>Methodology:&nbsp;</strong></p>
<p>Volatile organic compounds (VOCs)&nbsp;were sampled and measured using dynamic stripping chambers coupled to a proton transfer reaction time-of-flight mass spectrometer (Moore et al. 2020). VOC concentrations (ppbv) are exported directly from the PTR-MS Viewer 3.2.1.2 software (Ionicon Analytik GmbH, Innsbruck, Austria) into .txt files. Air concentrations for each m/z (+1) detected are reported already corrected for mass calibration, transmission efficiencies, and primary ion signals. Data include experiment, culture conditions, and flow conditions. 2-point calibration mode, 0.3 m/z search range, cycle 1000, and using an average of 10 spectra.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong><br />
Samples are measured directly from cultures or media blanks. Culture conditions are given as the growth phase (exponential or stationary phase). Cell densities are provided. The protocol is well described in Moore et al. (2020).</p>
<div><strong>Media recipe:</strong><br />
<br />
Artificial seawater + 882 μM NO3 + 36.2 μM PO4 + 106 μM Si + 1x f/2 Trace metal mix + 1 x f/2 Vitamin mix<br />
&nbsp;</div>
<div><strong>Cell density when VOCs from Synechococcus WH8102 cultures were measured:</strong></div>
<div>Synechococcus_WH8102-A 3.60E+06</div>
<div>Synechococcus_WH8102-B 3.81E+06</div>
<div>Synechococcus_WH8102-C 1.59E+06</div>
<div>Synechococcus_WH8102-D 2.09E+06<br />
<br />
Taxon:&nbsp;<br />
Synechococcus,&nbsp; LSID urn:lsid:marinespecies.org:taxname:160572</div>
Specified by the Principal Investigator(s)
<p>VOC concentrations (ppbv) are exported directly from the PTR-MS Viewer 3.4.4 software (Ionicon Analytik GmbH, Innsbruck, Austria) into .txt files. Air concentrations for each m/z (+1) detected are reported already corrected for mass calibration, transmission efficiencies, and primary ion signals.</p>
Specified by the Principal Investigator(s)
BCO-DMO Data Manager Processing Notes:
* Data from source file "Synechococcus WH8102 data repositoryv2.xlsx", sheets "Syn_WH8102_data" and "Media_Blank_data", were imported into the BCO-DMO data system and combined into one data table.
* Information from sheet "Sample Information" added to metadata text on this page, and a supplemental data table titled "Sample Information: Synechococcus WH8102" added to the Supplemental File section of this page.
* Values "NA" in the source file were classified as missing data identifiers.
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions
* Data table unpivoted. Format of the data table converted from wide form where there were data columns for each mz_value containing mz_signals. Converted to long format data table where there is a column "mz_value" and a column "mz_signal."
* Data table sorted by {Sample_Name}{Sample_Replicate}{Sample_Tech}{mz_value}{Time_seconds}
* Missing data values (Blank/Null) values in this dataset are displayed according to the format of data you access. For example, in csv files it will be blank values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as "nd" meaning "no data." See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions
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
TOF-1000
TOF-1000
PI Supplied Instrument Name: TOF-1000 PI Supplied Instrument Description:Proton transfer reaction time of flight mass spectrometer. Ionicon Analytik, Innsbruck, Austria. TOF-1000. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/