ERDDAP > info > bcodmo_dataset_709543

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data			files	public	Oxygen consumption rates/zero valen iron dissolution of FeOB (Ferrozine assay) with Kanamycin addition		I   M	background			BCO-DMO	bcodmo_dataset_709543

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	These data were collected by placing each strain in a 100 mL serum vial with 6 mL of their standard, published media with 30 mg zero valent iron as a source of Fe(II).\u00a0 The headspace was filled with a gas mix of 8% oxygen/10% carbon dioxide/82% nitrogen by using bottled gas mixes and a regulator to flush the headspace without over pressurization.\u00a0 Prior to sealing the serum vials, a\u00a0Presens\u00a0OPTODE dot (sensor) was placed inside the vial, allowing non-invasive gas sampling of the changes in O2 in the headspace.\u00a0 A\u00a0Presens\u00a0four channel system was used to measure changes in oxygen concentration in real-time in each bottle.\u00a0 A total of four channels were measured during each experiment: channels 1 through 3 are the biological treatments and channel 4 was a\u00a0kill\u00a0control (microbes were by placing on a heat block at 100 degrees C for 5 minutes). After 3 days of incubation, the concentration of Fe(II) in the media was measured by ferrozine assay. Old media was then removed and replaced with fresh media containing 30 ng/ml kanamycin to prevent\u00a0growth\u00a0of remaining cells. The headspace was again filled with the same gas mix and oxygen concentrations were measured in real-time in each vial. Fe(II) concentration was determined daily by ferrozine assay for 3 more days.
attribute	NC_GLOBAL	awards_0_award_nid	String	626092
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1459252
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward?AWD_ID=1459252
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	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Ferrozine Vial Data P. Girguis and D. Emerson, PIs Version 21 July 2017
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	date_created	String	2017-07-24T19:06:05Z
attribute	NC_GLOBAL	date_modified	String	2019-03-26T18:16:08Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.709543.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/709543
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Spectrophotometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to measure ferrozine assay
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	709569
attribute	NC_GLOBAL	instruments_0_description	String	An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB20/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Spectrophotometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	707
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Cary 100 UV-Vis Spectrophotometer (Agilent Technologies)
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Used with air saturated water and 100% nitrogen gas.
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	709570
attribute	NC_GLOBAL	instruments_1_description	String	An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Optode
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	727
attribute	NC_GLOBAL	instruments_1_supplied_name	String	PreSens OXY-4 SMA four channel optode and PreSens Pst3 optode sensor spots
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, concentration, data, dataset, date, deviation, dmo, elapsed, erddap, Fe_II_concentration, management, oceanography, office, preliminary, standard, standard_deviation, time, time_elapsed, treatment, vial
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/709543/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/709543
attribute	NC_GLOBAL	param_mapping	String	{'709543': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/709543/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Harvard University
attribute	NC_GLOBAL	people_0_person_name	String	Peter Girguis
attribute	NC_GLOBAL	people_0_person_nid	String	544586
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	Bigelow Laboratory for Ocean Sciences
attribute	NC_GLOBAL	people_1_person_name	String	David Emerson
attribute	NC_GLOBAL	people_1_person_nid	String	544585
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	Harvard University
attribute	NC_GLOBAL	people_2_person_name	String	Jacob Cohen
attribute	NC_GLOBAL	people_2_person_nid	String	650331
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_3_person_nid	String	650173
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	SedimentaryIronCycle
attribute	NC_GLOBAL	projects_0_acronym	String	SedimentaryIronCycle
attribute	NC_GLOBAL	projects_0_description	String	Iron is a critical element for life that serves as an essential trace element for eukaryotic organisms. It is also able to support the growth of a cohort of microbes that can either gain energy for growth via oxidation of ferrous (Fe(II)) to ferric (Fe(III)) iron, or by utilizing Fe(III) for anaerobic respiration coupled to oxidation of simple organic matter or H2. This coupled process is referred to as the microbial iron cycle. One of the primary sources of iron to the ocean comes from dissolved iron (dFe) that is produced through oxidation and reduction processes in the sediment where iron is abundant. The dFe is transported into the overlaying water where it is an essential nutrient for phytoplankton responsible for primary production in the world’s oceans. In fact, iron limitation significantly impacts production in as much as a third of the world’s open oceans. The basic geochemistry of this process is understood; however important gaps exist in our knowledge about the details of how the iron cycle works, and how critical a role bacteria play in it. Intellectual Merit. Conventional wisdom holds that most of the iron oxidation in sediments is abiological, as a result of the rapid kinetics of chemical iron oxidation in the presence of oxygen. This proposal aims to question this conventional view and enhance our understanding of the microbes involved in the sedimentary iron cycle, with an emphasis on the bacteria that catalyze the oxidation of iron. These Fe-oxidizing bacteria (FeOB) utilize iron as a sole energy source for growth, and are autotrophic.  They were only discovered in the ocean about forty-five years ago, and are now known to be abundant at hydrothermal vents that emanate ferrous-rich fluids. More recently, the first evidence was published that they could inhabit coastal sediments, albeit at reduced numbers, and even be abundant in some continental shelf sediments. These habitats are far removed from hydrothermal vents, and reveal the sediments may be an important habitat for FeOB that live on ferrous iron generated in the sediment. This begs the question: are FeOB playing an important role in the oxidative part of the sedimentary Fe-cycle? One important attribute of FeOB is their ability to grow at very low levels of O2, an essential strategy for them to outcompete chemical iron oxidation. How low a level of O2 can sustain them, and how this might affect their distribution in sediments is unknown. In part, this is due to the technical challenges of measuring O2 concentrations and dynamics at very low levels; yet these concentrations could be where FeOB flourish. The central hypothesis of this proposal is that FeOB are more common in marine sedimentary environments than previously recognized, and play a substantive role in governing the iron flux from the sediments into the water column by constraining the release of dFe from sediments. A set of experimental objectives are proposed to test this. A survey of near shore regions in the Gulf of Maine, and a transect along the Monterey Canyon off the coast of California will obtain cores of sedimentary muds and look at the vertical distribution of FeOB and putative Fe-reducing bacteria using sensitive techniques to detect their presence and relative abundance. Some of these same sediments will be used in a novel reactor system that will allow for precise control of O2 levels and iron concentration to measure the dynamics of the iron cycle under different oxygen regimens. Finally pure cultures of FeOB with different O2 affinities will be tested in a bioreactor coupled to a highly sensitive mass spectrometer to determine the lower limits of O2 utilization for different FeOB growing on iron, thus providing mechanistic insight into their activity and distribution in low oxygen environments. Broader Impacts. An important impact of climate change on marine environments is a predicted increase in low O2 or hypoxic zones in the ocean. Hypoxia in association with marine sediments will have a profound influence on the sedimentary iron cycle, and is likely to lead to greater inputs of dFe into the ocean. In the longer term, this increase in dFe flux could alleviate iron-limitation in some regions of the ocean, thereby enhancing the rate of CO2-fixation and draw down of CO2 from the atmosphere. This is one important reason for developing a better understanding of microbial control of sedimentary iron cycle. This project will also provide training to a postdoctoral scientist, graduate students and undergraduates. This project will contribute to a student initiated exhibit, entitled ‘Iron and the evolution of life on Earth’ at the Harvard Museum of Natural History providing a unique opportunity for undergraduate training and outreach.
attribute	NC_GLOBAL	projects_0_geolocation	String	Intertidal coastal river and coastal shelf sediments, mid-coast, Maine, USA; Monteray Bay Canyon, sediments, CA, USA
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications
attribute	NC_GLOBAL	projects_0_project_nid	String	544584
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	Oxygen consumption rates/zero valen iron dissolution of FeOB (Ferrozine assay) with Kanamycin addition
attribute	NC_GLOBAL	title	String	Oxygen consumption rates/zero valen iron dissolution of FeOB (Ferrozine assay) with Kanamycin addition
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	vial		String
attribute	vial	bcodmo_name	String	sample
attribute	vial	description	String	[strain] ASWkan ferrozine sample description
attribute	vial	long_name	String	Vial
attribute	vial	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	vial	units	String	unitless
variable	date		String
attribute	date	bcodmo_name	String	date
attribute	date	description	String	Date measurement was taken; YYYY/MM/DD
attribute	date	long_name	String	Date
attribute	date	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	date	source_name	String	date
attribute	date	time_precision	String	1970-01-01
attribute	date	units	String	unitless
variable	treatment		String
attribute	treatment	bcodmo_name	String	treatment
attribute	treatment	description	String	Whether measurement was of starting media (ASW) or replacement media (ASW + Kan)
attribute	treatment	long_name	String	Treatment
attribute	treatment	units	String	unitless
variable	time_elapsed		float
attribute	time_elapsed	_FillValue	float	NaN
attribute	time_elapsed	actual_range	float	72.0, 145.5
attribute	time_elapsed	bcodmo_name	String	time_elapsed
attribute	time_elapsed	description	String	Time since start of experiment
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	Fe_II_concentration		String
attribute	Fe_II_concentration	bcodmo_name	String	Fe
attribute	Fe_II_concentration	description	String	Concentration of Fe(II) in media (average of triplicate samples)
attribute	Fe_II_concentration	long_name	String	Fe II Concentration
attribute	Fe_II_concentration	units	String	mM
variable	standard_deviation		String
attribute	standard_deviation	bcodmo_name	String	standard deviation
attribute	standard_deviation	description	String	Standard deviation of triplicate samples
attribute	standard_deviation	long_name	String	Standard Deviation
attribute	standard_deviation	units	String	mM

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.