ERDDAP > info > bcodmo_dataset_650324

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
	set	data	graph		files	public	[Oxygen Consumption Rates of Iron Oxidizing Bacteria - FeOB] - Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project) (Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications)		I   M	background			BCO-DMO	bcodmo_dataset_650324

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	The cultivars of the neutrophilic iron oxidizers Mariprofundus ferrooxydans PV-1 and \"TAG-1\" were obtained from the Emerson lab at Bigelow laboratories.
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	O2 consumption; Iron Oxidizing bacteria MultiChannelStudio Version 1.0.16.0 P. Girguis and D. Emerson, PIs version 29 June 2016
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	2016-06-29T19:59:40Z
attribute	NC_GLOBAL	date_modified	String	2019-06-06T19:05:08Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.650324.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/650324
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	A Presens™ OPTODE dot (sensor) was placed inside the sample vial, allowing non-invasive gas sampling of the changes in O2 in the headspace. For more information about the PreSens OPTODE sensor, read this.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	650372
attribute	NC_GLOBAL	instruments_0_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_0_instrument_name	String	Optode
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	727
attribute	NC_GLOBAL	instruments_0_supplied_name	String	PreSens OPTODE dot
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, conc, consume, data, dataset, date, date_local, dmo, erddap, FeOB_strain, iso, local, management, O2, O2_conc, O2_consume, oceanography, office, oxygen, preliminary, strain, temperature, time, time_local, treatment, yrday, yrday_local
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/650324/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/650324
attribute	NC_GLOBAL	param_mapping	String	{'650324': {'ISO_DateTime_Local': 'flag - time'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/650324/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	David Johnston
attribute	NC_GLOBAL	people_2_person_nid	String	650329
attribute	NC_GLOBAL	people_2_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_2_role_type	String	originator
attribute	NC_GLOBAL	people_3_affiliation	String	Harvard University
attribute	NC_GLOBAL	people_3_person_name	String	Jacob Cohen
attribute	NC_GLOBAL	people_3_person_nid	String	650331
attribute	NC_GLOBAL	people_3_role	String	Contact
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	people_4_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_4_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_4_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_4_person_nid	String	650173
attribute	NC_GLOBAL	people_4_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_4_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	subsetVariables	String	temp
attribute	NC_GLOBAL	summary	String	Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)
attribute	NC_GLOBAL	time_coverage_end	String	2016-05-23T03:53:24Z
attribute	NC_GLOBAL	time_coverage_start	String	2016-03-16T06:42:12Z
attribute	NC_GLOBAL	title	String	[Oxygen Consumption Rates of Iron Oxidizing Bacteria - FeOB] - Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project) (Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	FeOB_strain		String
attribute	FeOB_strain	bcodmo_name	String	brief_desc
attribute	FeOB_strain	description	String	strain of iron oxidizing bacteria (PV-1 or TAG-1)
attribute	FeOB_strain	long_name	String	Fe OB Strain
attribute	FeOB_strain	units	String	unitless
variable	temp		byte
attribute	temp	_FillValue	byte	127
attribute	temp	actual_range	byte	20, 20
attribute	temp	bcodmo_name	String	temperature
attribute	temp	description	String	the temperature at which the experiments were conducted; the whole experiment was conducted at 20 degrees
attribute	temp	long_name	String	Temperature
attribute	temp	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/
attribute	temp	units	String	degrees celsius
variable	O2_conc		byte
attribute	O2_conc	_FillValue	byte	127
attribute	O2_conc	actual_range	byte	25, 100
attribute	O2_conc	bcodmo_name	String	O2_umol_L
attribute	O2_conc	description	String	the oxygen concentration to which the bacteria were exposed
attribute	O2_conc	long_name	String	O2 Conc
attribute	O2_conc	units	String	micromoles per liter
variable	treatment		String
attribute	treatment	bcodmo_name	String	treatment
attribute	treatment	description	String	original name: channel; channels 1 through 3 are the biological treatments and channel 4 was a kill control
attribute	treatment	long_name	String	Treatment
attribute	treatment	units	String	unitless
variable	date_local		String
attribute	date_local	bcodmo_name	String	date_local
attribute	date_local	description	String	the range of dates the experiment took place
attribute	date_local	long_name	String	Date Local
attribute	date_local	time_precision	String	1970-01-01
attribute	date_local	units	String	unitless
variable	time_local		String
attribute	time_local	bcodmo_name	String	time_local
attribute	time_local	description	String	time at which measurements were recorded (hour:minutes)
attribute	time_local	long_name	String	Time Local
attribute	time_local	units	String	unitless
variable	O2_consume		float
attribute	O2_consume	_FillValue	float	NaN
attribute	O2_consume	actual_range	float	8.677, 104.391
attribute	O2_consume	bcodmo_name	String	O2_umol_L
attribute	O2_consume	description	String	oxygen consumption
attribute	O2_consume	long_name	String	O2 Consume
attribute	O2_consume	units	String	micromoles per liter
variable	yrday_local		double
attribute	yrday_local	_FillValue	double	NaN
attribute	yrday_local	actual_range	double	75.27931, 143.16208
attribute	yrday_local	bcodmo_name	String	yrday_local
attribute	yrday_local	description	String	day of the year including decimals; added by DMO
attribute	yrday_local	long_name	String	Yrday Local
attribute	yrday_local	units	String	decimal day
variable	time		double
attribute	time	_CoordinateAxisType	String	Time
attribute	time	actual_range	double	1.458110532E9, 1.463975604E9
attribute	time	axis	String	T
attribute	time	bcodmo_name	String	ISO_DateTime_Local
attribute	time	description	String	date and time formatted to ISO 8601 standard; added by DMO. in the format YYYY-mm-ddTHH:MM:SS.xx.
attribute	time	ioos_category	String	Time
attribute	time	long_name	String	ISO Date Time Local
attribute	time	source_name	String	ISO_DateTime_Local
attribute	time	standard_name	String	time
attribute	time	time_origin	String	01-JAN-1970 00:00:00
attribute	time	time_precision	String	1970-01-01T00:00:00Z
attribute	time	units	String	seconds since 1970-01-01T00:00:00Z

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.