http://lod.bco-dmo.org/id/dataset/788911
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
2020-01-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial cell abundance,carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise on RV/Atlantis cruise AT37-12, May 2017
2020-01-30
publication
2020-01-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-02
publication
https://doi.org/10.26008/1912/bco-dmo.788911.1
Stefan M. Sievert
Woods Hole Oceanographic Institution
principalInvestigator
Jeremy Rich
University of Maine
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: Sievert, S., Rich, J. (2020) Microbial cell abundance,carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise on RV/Atlantis cruise AT37-12, May 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-01-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.788911.1 [access date]
Carbon fixation rates Crab Spa Dataset Description: <p>This dataset includes microbial cell abundance, carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa site, East Pacific Rise in the Eastern Tropical North Pacific (ETNP) on RV/Atlantis cruise AT37-12, May 2017.&nbsp;Crab Spa is&nbsp;at 9.8398N, 104.2913W, and depth 2503 meters.</p> Methods and Sampling: <p>During Alvin Dive 4905, May 8, 2017, 5 major samples were collected at the diffuse-flow vent Crab Spa. The fluid from these samplers was used in an on-deck Vent-SID incubation. The purpose of the incubation was to simulate a sea-floor incubation of the Vent-SID. Upon arrival of majors on the ship, we transferred fluid from the majors into N2 flushed 1L Restek bags. The bags were stored at 4˚C and taken out as needed for setting up a new Vent-SID incubation. In total,&nbsp;six incubations were conducted, all at 25(+/-2)˚C.</p>
<p><strong>Microbial cell counts</strong>: Samples for cell numbers were fixed with formaldehyde (1% final concentration) and then counted on the board the ship after staining with acridine orange by fluorescence microscopy as described in McNichol et al. (2016).</p>
<p><strong>Carbon fixation rates</strong>: 13C-labeled bicarbonate was added to the incubation chambers to assess chemoautotrophic production.&nbsp;At the beginning and the end of the incubation, fluids were filtered onto pre combusted GFF filters, which were frozen until analysis back in the shore lab. Gas chromatography combustion (Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel) coupled to an isotope ratio mass spectrometer (GC-IRMS) (Finnigan-MAT Conflo-II interface attached to a DeltaPlus Isotope Ratio Mass Spectrometer) was used to measure the incorporation of 13C-labelled bicarbonate into biomass during the incubations to determine chemoautotrophic production.</p>
<p><strong>Nitrate concentrations</strong>:&nbsp;&nbsp;Vent fluid from the Crab Spa site was incubated on the deck of the ship in the Vent-SID reaction chamber, in the dark at a temperature of 25(+/- 2)°C. Incubations consisted of a vent fluid with added NO3- (10 µmol/L), NO2- (1 µmol/L) and H13CO3- (0.7 mmol/L) and time-point samples were taken for nitrate+nitrite measurements at 0, 3, and 6 hours. Six incubations were conducted that varied in combinations of 15NO3-/14NO3 or 15NO2-/14NO2-, keeping the total concentration of added NO3- and NO2- constant across incubations.&nbsp;</p>
<p>Nitrate concentrations were measured in time-point samples utilizing the vanadium(III) reduction of nitrate and nitrite method described by Braman and Hendrix, 1989. Samples were injected into a heated Vanadium acid solution whereby NO3- and NO2- were reduced to NOx gases. The NOx then passed into a Teledyne T200 NOx analyzer where a photodetector measured the light produced from the chemiluminescent reaction of NOx and instrument generated ozone.</p>
<p>After initial collection, vent fluid samples were stored in 15 mL conical tubes at -20C until analyzed on the Teledyne NOx analyzer. Once thawed, samples were injected using Hamilton 1700 series gastight syringes and Nitrate concentrations were calculated alongside standards generated from a Ricca Nitrate Nitrogen Standard (CAT#5459-16, 1000 ppm N, 4427 ppm NO3). The series of standards ranged from 1 uM to 50 uM and were made up by diluting the Ricca standard in Milli-Q water.</p>
<p>Peak Simple Version 4.49 was used to generate chromatographs from the photodetector and raw data was further processed in Microsoft Excel.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559198 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559198
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559042 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559042
completed
Stefan M. Sievert
Woods Hole Oceanographic Institution
508 289 2305
Biology Department Watson Bldg. MS #52
Woods Hole
MA
02543
USA
ssievert@whoi.edu
pointOfContact
Jeremy Rich
University of Maine
207-563-8302
Darling Marine Center 193 Clarks Cove Rd
Walpole
ME
04573
jeremy.rich@maine.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
incubation
time_elapsed
cell_abund
carbon_fix
NOX
DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface
•Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel
Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System
Vent-SID
theme
None, User defined
sample identification
time_elapsed
cell_concentration
No BCO-DMO term
nitrate plus nitrite
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
Fluorescence Microscope
Elemental Analyzer
Elemental Analyzer
Shipboard Incubator
instrument
BCO-DMO Standard Instruments
AT37-12
service
Deployment Activity
East Pacific Rise vent area
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.
Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate
https://www.bco-dmo.org/project/685773
Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate
<p><em>NSF award abstract:</em></p>
<p>Deep-sea hydrothermal vents, first discovered in 1977, are exemplary ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Chemosynthetic microorganisms use the energy generated by oxidizing reduced inorganic chemicals contained in the vent fluids, like hydrogen sulfide or hydrogen gas, to convert carbon dioxide (CO2) into cell material. By doing so, they effectively transfer the energy from a geothermal source to higher trophic levels, in the process supporting the unique and fascinating ecosystems that are characterized by high productivity - oases in the otherwise barren deep ocean landscape. While the general view of the functioning of these ecosystems is established, there are still major gaps in our understanding of the microbiology and biogeochemistry of these systems. Particularly lacking are studies measuring rates of microbial activity in situ, which is ultimately needed to understand production of these ecosystems and to assess their impact on global biogeochemical cycles. This project makes use of the Vent-Submersible Incubation Device (Vent-SID), a robotic micro-laboratory that was recently developed and tested in the field. This instrument makes it possible for the first time to determine rates of carbon fixation at both in situ pressures and temperatures, revolutionizing the way we conduct microbial biogeochemical investigations at deep-sea hydrothermal vents. This is an interdisciplinary and collaborative effort between two US and foreign institutions, creating unique opportunities for networking and to foster international collaborations. This will also benefit two graduate students working in the project, who will get exposed to a wide range of instrumentation and scientific fields, facilitating their interdisciplinary education. In collaboration with Dr. Nitzan Resnick, academic dean of The Sage School, an elementary school outreach program will be developed and a long-term partnership with the school established. Further, a cruise blog site to disseminate the research to schools and the broader public will be set up. The results will be the topic of media coverage as well as be integrated into coursework and webpages existing either in the PI's labs or at the institution.</p>
<p>This project is using a recently developed robotic micro-laboratory, the Vent-SID, to measure rates of chemoautotrophic production and to determine the relative importance of oxygen and nitrate in driving chemosynthesis at deep-sea hydrothermal vents at in situ pressures and temperatures and to tackle the following currently unresolved science objectives: 1) obtain in situ rates of chemoautotrophic carbon fixation, 2) obtain in situ nitrate reduction rate measurements, and 3) directly correlate the measurement of these processes with the expression of key genes involved in carbon and energy metabolism. Although recent data suggests that nitrate reduction either to N2 (denitrification) or to NH4+ (dissimilatory reduction of nitrate to ammonium) might be responsible for a significant fraction of chemoautotrophic production, NO3-reduction rates have never been measured in situ at hydrothermal vents. The researchers hypothesize that chemoautrophic growth is strongly coupled to nitrate respiration in vent microbial communities. During a cruise that will take place approximately 12 months into the project (~Feb 2017), the researchers will carry out a total of 4 deployments of the Vent-SID as well as ancillary sampling collection at the 9°46N to 9°53N segment of the East Pacific Rise. They will focus efforts on two diffuse-flow vent sites, "Crab Spa" and "Teddy Bear". "Crab Spa" is a diffuse flow vent site (T: 25°C) that has been used as a model system to gain insights into chemoautotrophic processes and has been frequently sampled over the last several years. This vent site has been very well characterized, both geochemically and microbiologically, providing excellent background data for the proposed process oriented studies. "Teddy Bear" is a diffuse-flow site that was discovered in Jan 2014, and it has a lower temperature (T: 12°C), making it a good comparative site. The researchers will perform a number of short duration time-course incubations to assess the role of different environmental parameters that have been identified as likely key variables (e.g., O2, temperature, NO3-), and to link these process rate measurements to the expression of functional genes using metatranscriptomic analyses. This study will be the first attempt to measure critical metabolic processes of hydrothermal vent microbial assemblages under critical in situ conditions and to assess the quantitative importance of electron donor and acceptor pathways in situ. In the future, it is envisioned that the Vent-SID will become a routine application by the oceanographic community for measuring time series rates of relevant metabolic processes at hydrothermal vents under in situ pressures and vent fluid temperatures.</p>
vent O2 NO3 roles
largerWorkCitation
project
eng; USA
biota
oceans
East Pacific Rise vent area
-104.2913
-104.2912
9.8387
9.8398
2017-05-08
2017-05-08
Deep-Sea hydrothermal vent field at 9 deg N on the East Pacific Rise
0
BCO-DMO catalogue of parameters from Microbial cell abundance,carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise on RV/Atlantis cruise AT37-12, May 2017
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/788946.rdf
Name: incubation
Units: unitless
Description: incubation run identifier
http://lod.bco-dmo.org/id/dataset-parameter/788947.rdf
Name: time_elapsed
Units: hours
Description: time since start of incubation
http://lod.bco-dmo.org/id/dataset-parameter/788948.rdf
Name: cell_abund
Units: cells/milliliter
Description: microbial cell abundance
http://lod.bco-dmo.org/id/dataset-parameter/788949.rdf
Name: carbon_fix
Units: microgram Carbon/liter/day
Description: carbon fixation rate
http://lod.bco-dmo.org/id/dataset-parameter/788950.rdf
Name: NOX
Units: micromol/liter
Description: Nitrate+nitrite concentration during incubations
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
402
https://darchive.mblwhoilibrary.org/bitstream/1912/25931/1/dataset-788911_incubations-cell-abundance-carbon-fixation-rates-nitrates__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.788911.1
download
onLine
dataset
<p>During Alvin Dive 4905, May 8, 2017, 5 major samples were collected at the diffuse-flow vent Crab Spa. The fluid from these samplers was used in an on-deck Vent-SID incubation. The purpose of the incubation was to simulate a sea-floor incubation of the Vent-SID. Upon arrival of majors on the ship, we transferred fluid from the majors into N2 flushed 1L Restek bags. The bags were stored at 4˚C and taken out as needed for setting up a new Vent-SID incubation. In total,&nbsp;six incubations were conducted, all at 25(+/-2)˚C.</p>
<p><strong>Microbial cell counts</strong>: Samples for cell numbers were fixed with formaldehyde (1% final concentration) and then counted on the board the ship after staining with acridine orange by fluorescence microscopy as described in McNichol et al. (2016).</p>
<p><strong>Carbon fixation rates</strong>: 13C-labeled bicarbonate was added to the incubation chambers to assess chemoautotrophic production.&nbsp;At the beginning and the end of the incubation, fluids were filtered onto pre combusted GFF filters, which were frozen until analysis back in the shore lab. Gas chromatography combustion (Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel) coupled to an isotope ratio mass spectrometer (GC-IRMS) (Finnigan-MAT Conflo-II interface attached to a DeltaPlus Isotope Ratio Mass Spectrometer) was used to measure the incorporation of 13C-labelled bicarbonate into biomass during the incubations to determine chemoautotrophic production.</p>
<p><strong>Nitrate concentrations</strong>:&nbsp;&nbsp;Vent fluid from the Crab Spa site was incubated on the deck of the ship in the Vent-SID reaction chamber, in the dark at a temperature of 25(+/- 2)°C. Incubations consisted of a vent fluid with added NO3- (10 µmol/L), NO2- (1 µmol/L) and H13CO3- (0.7 mmol/L) and time-point samples were taken for nitrate+nitrite measurements at 0, 3, and 6 hours. Six incubations were conducted that varied in combinations of 15NO3-/14NO3 or 15NO2-/14NO2-, keeping the total concentration of added NO3- and NO2- constant across incubations.&nbsp;</p>
<p>Nitrate concentrations were measured in time-point samples utilizing the vanadium(III) reduction of nitrate and nitrite method described by Braman and Hendrix, 1989. Samples were injected into a heated Vanadium acid solution whereby NO3- and NO2- were reduced to NOx gases. The NOx then passed into a Teledyne T200 NOx analyzer where a photodetector measured the light produced from the chemiluminescent reaction of NOx and instrument generated ozone.</p>
<p>After initial collection, vent fluid samples were stored in 15 mL conical tubes at -20C until analyzed on the Teledyne NOx analyzer. Once thawed, samples were injected using Hamilton 1700 series gastight syringes and Nitrate concentrations were calculated alongside standards generated from a Ricca Nitrate Nitrogen Standard (CAT#5459-16, 1000 ppm N, 4427 ppm NO3). The series of standards ranged from 1 uM to 50 uM and were made up by diluting the Ricca standard in Milli-Q water.</p>
<p>Peak Simple Version 4.49 was used to generate chromatographs from the photodetector and raw data was further processed in Microsoft Excel.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing</strong><br />
- combined cell abundance, carbon fixation rates, and nitrate concentration excel tables into a single table</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
DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface
DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface
PI Supplied Instrument Name: DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface PI Supplied Instrument Description:Used for carbon fixation measurements. Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
PI Supplied Instrument Name: PI Supplied Instrument Description:Used for microbial cell counts. Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
•Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel
•Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel
PI Supplied Instrument Name: •Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel PI Supplied Instrument Description:Used for carbon fixation measurements 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/
Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System
Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System
PI Supplied Instrument Name: Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System PI Supplied Instrument Description:Used to generate chromatographs from the photodetector and thus measure nitrate concentrations. 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/
Vent-SID
Vent-SID
PI Supplied Instrument Name: Vent-SID PI Supplied Instrument Description:A Vent-SID, Vent-Submersible Incubation Device, was used for on-deck incubations. It draws seawater and microbes into incubation chambers and measures the biochemical business going on under natural conditions. For further description of this device, see https://www.whoi.edu/oceanus/feature/bringing-a-lab-to-the-seafloor/. Instrument Name: Shipboard Incubator Instrument Short Name: Instrument Description: A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Cruise: AT37-12
AT37-12
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT37-12
Stefan M. Sievert
Woods Hole Oceanographic Institution
http://datadocs.bco-dmo.org/docs/Vent_O2_NO3_Roles/data_docs/AT37-12_Cruise_Report.pdf
Report describing AT37-12
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel