ERDDAP > info > bcodmo_dataset_788911

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[Incubations: cell abundance, carbon fixation rates, nitrates] - 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 (Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate)		I   M	background			BCO-DMO	bcodmo_dataset_788911

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv
attribute	NC_GLOBAL	acquisition_description	String	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\u02daC and taken out as needed for setting up a new Vent-SID incubation. In total,\u00a0six incubations were conducted, all at 25(+/-2)\u02daC. Microbial cell counts: 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). Carbon fixation rates: 13C-labeled bicarbonate was added to the incubation chambers to assess chemoautotrophic production.\u00a0At 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. Nitrate concentrations:\u00a0\u00a0Vent 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)\u00b0C. Incubations consisted of a vent fluid with added NO3- (10 \u00b5mol/L), NO2- (1 \u00b5mol/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.\u00a0 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. 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. Peak Simple Version 4.49 was used to generate chromatographs from the photodetector and raw data was further processed in Microsoft Excel.
attribute	NC_GLOBAL	awards_0_award_nid	String	685772
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1559198
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559198
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	Michael E. Sieracki
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50446
attribute	NC_GLOBAL	awards_1_award_nid	String	685780
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1559042
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559042
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	Michael E. Sieracki
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50446
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Incubations: cell counts, carbon fixation rates, nitrates R/V Atlantis, AT37-12 shipboard incubations of vent fluids from Crab Spa site, East Pacific Rise, May 2017 PI: S. Sievert (WHOI) version date: 2020-1-30
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2020-01-30T14:33:34Z
attribute	NC_GLOBAL	date_modified	String	2020-07-02T19:28:18Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.788911.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/788911
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	IR Mass Spec
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used for carbon fixation measurements.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	788944
attribute	NC_GLOBAL	instruments_0_description	String	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).
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB16/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Isotope-ratio Mass Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	469
attribute	NC_GLOBAL	instruments_0_supplied_name	String	DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Used for microbial cell counts.
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	788945
attribute	NC_GLOBAL	instruments_1_description	String	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.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB06/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Microscope-Fluorescence
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	695
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Used for carbon fixation measurements
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	788943
attribute	NC_GLOBAL	instruments_2_description	String	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.
attribute	NC_GLOBAL	instruments_2_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB01/
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Elemental Analyzer
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	546339
attribute	NC_GLOBAL	instruments_2_supplied_name	String	• Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel
attribute	NC_GLOBAL	instruments_3_dataset_instrument_description	String	Used to generate chromatographs from the photodetector and thus measure nitrate concentrations.
attribute	NC_GLOBAL	instruments_3_dataset_instrument_nid	String	806816
attribute	NC_GLOBAL	instruments_3_description	String	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.
attribute	NC_GLOBAL	instruments_3_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB01/
attribute	NC_GLOBAL	instruments_3_instrument_name	String	Elemental Analyzer
attribute	NC_GLOBAL	instruments_3_instrument_nid	String	546339
attribute	NC_GLOBAL	instruments_3_supplied_name	String	Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System
attribute	NC_GLOBAL	instruments_4_dataset_instrument_description	String	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/.
attribute	NC_GLOBAL	instruments_4_dataset_instrument_nid	String	788942
attribute	NC_GLOBAL	instruments_4_description	String	A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
attribute	NC_GLOBAL	instruments_4_instrument_name	String	Shipboard Incubator
attribute	NC_GLOBAL	instruments_4_instrument_nid	String	629001
attribute	NC_GLOBAL	instruments_4_supplied_name	String	Vent-SID
attribute	NC_GLOBAL	keywords	String	abund, bco, bco-dmo, biological, carbon, carbon_fix, cell, cell_abund, chemical, data, dataset, dmo, elapsed, erddap, fix, incubation, management, nox, oceanography, office, preliminary, time, time_elapsed
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/788911/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/788911
attribute	NC_GLOBAL	param_mapping	String	{'788911': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/788911/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	WHOI
attribute	NC_GLOBAL	people_0_person_name	String	Stefan M Sievert
attribute	NC_GLOBAL	people_0_person_nid	String	51416
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	University of Maine
attribute	NC_GLOBAL	people_1_person_name	String	Dr Jeremy Rich
attribute	NC_GLOBAL	people_1_person_nid	String	685778
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Nancy Copley
attribute	NC_GLOBAL	people_2_person_nid	String	50396
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	vent O2 NO3 roles
attribute	NC_GLOBAL	projects_0_acronym	String	vent O2 NO3 roles
attribute	NC_GLOBAL	projects_0_description	String	NSF award abstract: 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. 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.
attribute	NC_GLOBAL	projects_0_end_date	String	2019-04
attribute	NC_GLOBAL	projects_0_geolocation	String	Deep-Sea hydrothermal vent field at 9 deg N on the East Pacific Rise
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate
attribute	NC_GLOBAL	projects_0_project_nid	String	685773
attribute	NC_GLOBAL	projects_0_start_date	String	2016-05
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	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 in the Eastern Tropical North Pacific (ETNP) on RV/Atlantis cruise AT37-12, May 2017.
attribute	NC_GLOBAL	title	String	[Incubations: cell abundance, carbon fixation rates, nitrates] - 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 (Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	incubation		byte
attribute	incubation	_FillValue	byte	127
attribute	incubation	actual_range	byte	1, 6
attribute	incubation	bcodmo_name	String	sample
attribute	incubation	description	String	incubation run identifier
attribute	incubation	long_name	String	Incubation
attribute	incubation	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	incubation	units	String	unitless
variable	time_elapsed		byte
attribute	time_elapsed	_FillValue	byte	127
attribute	time_elapsed	actual_range	byte	0, 6
attribute	time_elapsed	bcodmo_name	String	time_elapsed
attribute	time_elapsed	description	String	time since start of incubation
attribute	time_elapsed	long_name	String	Time Elapsed
attribute	time_elapsed	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/
attribute	time_elapsed	units	String	hours
variable	cell_abund		float
attribute	cell_abund	_FillValue	float	NaN
attribute	cell_abund	actual_range	float	469000.0, 3790000.0
attribute	cell_abund	bcodmo_name	String	cell_concentration
attribute	cell_abund	description	String	microbial cell abundance
attribute	cell_abund	long_name	String	Cell Abund
attribute	cell_abund	units	String	cells/milliliter
variable	carbon_fix		short
attribute	carbon_fix	_FillValue	short	32767
attribute	carbon_fix	actual_range	short	0, 336
attribute	carbon_fix	bcodmo_name	String	unknown
attribute	carbon_fix	description	String	carbon fixation rate
attribute	carbon_fix	long_name	String	Carbon Fix
attribute	carbon_fix	units	String	microgram Carbon/liter/day
variable	NOX		float
attribute	NOX	_FillValue	float	NaN
attribute	NOX	actual_range	float	1.07, 18.31
attribute	NOX	bcodmo_name	String	NO3_NO2
attribute	NOX	description	String	Nitrate+nitrite concentration during incubations
attribute	NOX	long_name	String	NOX
attribute	NOX	units	String	micromol/liter

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.