http://lod.bco-dmo.org/id/dataset/928033
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)
Results of diel cycle experiments including the full range of volatile organic compounds (VOCs) produced by the diatom P. tricornutum during laboratory experiments conducted in October of 2023
2024-05-21
publication
2024-05-21
revision
BCO-DMO Linked Data URI
2024-05-21
creation
http://lod.bco-dmo.org/id/dataset/928033
Kimberly Halsey
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. (2024) Results of diel cycle experiments including the full range of volatile organic compounds (VOCs) produced by the diatom P. tricornutum during laboratory experiments conducted in October of 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/928033 [access date]
Methods and Sampling: <p>Volatile organic compounds (VOCs) were collected from axenic <em>Phaeodactylum tricornutum</em>&nbsp;(urn:lsid:marinespecies.org:taxname:175584) every 2 hours across a diel cycle using proton transfer reaction time-of-flight mass spectrometry (PTR-TOF/MS; Ionicon, Austria) as previously described (Moore et al., 2020). Autoclaved f/2+Si media and HPLC-grade water were measured alongside the samples as blank (background) controls. 100 mL culture, media, or HPLC water was transferred to a dynamic stripping chamber (Halsey et al., 2017)<sup> </sup>and bubbled with breathing-grade air passed first through a hydrocarbon trap and then through a glass frit in the bottom of the chamber at 50 ml min<sup>-1</sup> for 5 min to strip VOCs from the sample.&nbsp;</p>
<p>The stripped gases were directed into the PTR-ToF/MS for measurement via soft ionization with H<sub>3</sub>O<sup>+</sup>. The mass spectrum (30-240 a.m.u.) was acquired at 5 s intervals.&nbsp;</p>
<p>PTR-TOF/MS data were analyzed using PTR viewer 3.4.3 (Ionicon Analytik).&nbsp;</p>
<div>Media recipe:<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</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
onGoing
Kimberly Halsey
Oregon State University
541-737-1831
226 Nash Hall Dept of Microbiology
Corvallis
OR
97333
US
halseyk@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Replicate_Name
Sample_Replicate
Sample_Name
Timepoint_hrs
Time
RelTime
Cycle
mz_plus_1
label
VOC
PTR-TOF 1000
theme
None, User defined
replicate
sample identification
time_elapsed
time of day
No BCO-DMO term
sample description
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
2023-10-01
2023-10-01
0
BCO-DMO catalogue of parameters from Results of diel cycle experiments including the full range of volatile organic compounds (VOCs) produced by the diatom P. tricornutum during laboratory experiments conducted in October of 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/998287.rdf
Name: Replicate_Name
Units: unitless
Description: <p>Replicate name. Identifies biological replicates and blanks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/998288.rdf
Name: Sample_Replicate
Units: unitless
Description: <p>Alternate replicate identifier for sample replicates (blanks not described).</p>
http://lod.bco-dmo.org/id/dataset-parameter/998289.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/998290.rdf
Name: Timepoint_hrs
Units: hours
Description: <p>hours elapsed since timepoint 0 when the experiment started.</p>
http://lod.bco-dmo.org/id/dataset-parameter/998291.rdf
Name: Time
Units: unitless
Description: <p>Time (format: %H:%m %p, e.g. 9:00 AM")"</p>
http://lod.bco-dmo.org/id/dataset-parameter/998292.rdf
Name: RelTime
Units: unitless
Description: <p>not documented. Assumed to be the relative time elapsed within a single cycle (sampling event).</p>
http://lod.bco-dmo.org/id/dataset-parameter/998293.rdf
Name: Cycle
Units: unitless
Description: <p>Cycle (each cycle is a 5 second interval) starting at 25. VOC measurements were collected over 5 sec with the first 2 min of data removed because of the instrument lag time.</p>
http://lod.bco-dmo.org/id/dataset-parameter/998294.rdf
Name: mz_plus_1
Units: unitless
Description: <p>Protonated mass-to-charge ratio (m/z) of detected volatile organic compounds (VOCs). m/z+1 values (detected mass + 1.008 (the mass of a proton)).</p>
http://lod.bco-dmo.org/id/dataset-parameter/998295.rdf
Name: label
Units: unitless
Description: <p>Label associated with the reported mz_plus_1 value. Examples: '(CH4O)H+_Peak0', 'hydrate cluster 1'</p>
http://lod.bco-dmo.org/id/dataset-parameter/998296.rdf
Name: VOC
Units: parts per billion by volume (ppbv)
Description: <p>Volatile organic compounds (VOC) concentration</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
https://osprey.bco-dmo.org/dataset/928033/data/download
download
onLine
dataset
<p>Volatile organic compounds (VOCs) were collected from axenic <em>Phaeodactylum tricornutum</em>&nbsp;(urn:lsid:marinespecies.org:taxname:175584) every 2 hours across a diel cycle using proton transfer reaction time-of-flight mass spectrometry (PTR-TOF/MS; Ionicon, Austria) as previously described (Moore et al., 2020). Autoclaved f/2+Si media and HPLC-grade water were measured alongside the samples as blank (background) controls. 100 mL culture, media, or HPLC water was transferred to a dynamic stripping chamber (Halsey et al., 2017)<sup> </sup>and bubbled with breathing-grade air passed first through a hydrocarbon trap and then through a glass frit in the bottom of the chamber at 50 ml min<sup>-1</sup> for 5 min to strip VOCs from the sample.&nbsp;</p>
<p>The stripped gases were directed into the PTR-ToF/MS for measurement via soft ionization with H<sub>3</sub>O<sup>+</sup>. The mass spectrum (30-240 a.m.u.) was acquired at 5 s intervals.&nbsp;</p>
<p>PTR-TOF/MS data were analyzed using PTR viewer 3.4.3 (Ionicon Analytik).&nbsp;</p>
<div>Media recipe:<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</div>
Specified by the Principal Investigator(s)
<p>A three-point calibration was performed on each .h5 file using a search range of 0.2 m/z. Within the three-point calibration mode, each mass spectrum was calibrated against three internal standards known to be present within the spectrum, namely 29.998 (NO+), 203.943, and 330.848 (1,3-diiodobenzene).</p>
<p>The first 30 s of acquired data were removed from the analysis because of the instrument lag time between the chamber headspace and detector.&nbsp;PTR-TOF/MS data were analyzed using PTR viewer 3.4.3 (Ionicon Analytik).&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
- Sheets extracted from the originally provided Excel File (see supplemental files).The first sheet contained metadata tables that were extracted to supplemental files cell_densities.csv and sample_info.csv. Additional metadata comments in sheet 1 outside of these tables were added to metadata fields directly. sheets2..n containing a table per replicate were extracted to csv files, one per table.
- originally provided excel file renamed from "Copy of 02022024_NSF combined diel cycle data.xlsx" to "diel-cycle-data_by_replicate-wideform.xlsx" and attached as a supplemental file to the dataset.
- Loaded 8 CSV replicate tables (4 "Blank" files and 4 "PT_BR" files).
- Unpivoted all columns matching pattern `(m[^ ]+) (.*)` across all 8 resources, extracting the m/z value (e.g., m21.022) into field `mz_plus_1`, the label portion (e.g., H3O 18+) into field `label`, and the numeric concentration values into field `VOC`
- Concatenated all 8 tables into a single resource named `928033_v1_p_tricornutum_diel_cycle_exp`, mapping `Sample_name` to `Sample_Name`, adding source filename as new column `Replicate_Name`
- Applied find/replace on `label` to strip surrounding parentheses from values (e.g., `(H3O 18+)` → `H3O 18+`)
- Removed ` (Conc)` suffix from `label` field values. This is captured in the column description metadata.
- Cleaned `Replicate_Name` values by removing the `diel-cycle-data_` prefix and `.csv` suffix
- Reordered fields to: `Replicate_Name`, `Sample_Replicate`, `Sample_Name`, `Timepoint_hrs`, `Time`, `RelTime`, `Cycle`, `mz_plus_1`, `label`, `VOC`
- Stripped leading `m` from `mz_plus_1` values (e.g., `m21.022` → `21.022`)
- Set field types: `Cycle` as integer, `RelTime` and `VOC` as number, `Time` as time with format `%H:%M %p`, `Timepoint_hrs` as integer, `mz_plus_1` as number, and string types for `Replicate_Name`, `Sample_Name`, `Sample_Replicate`, `label`
- Column Replicate_Name is the original name provided as the sheet name in the original excel file.
- Output written to `928033_v1_p_tricornutum_diel_cycle_exp.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
PTR-TOF 1000
PTR-TOF 1000
PI Supplied Instrument Name: PTR-TOF 1000 PI Supplied Instrument Description:PTR-TOF 1000. Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF/MS; Ionicon, Austria). 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/