ERDDAP > info > bcodmo_dataset_747948

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	[Illumina Sequences] - Illumina sequencing data from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin (Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications)		F   I   M	background			BCO-DMO	bcodmo_dataset_747948

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,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	This study included cold seep and hydrothermal vent sediments from along the Pacific coast of North America. Sediments were collected via 30 cm long polycarbonate pushcores from a cold methane seep at Hydrate Ridge (44\u00b034'10. 20\"N, 125\u00b0 8'48. 48\"W) at 777 m water depth with the ROV Ropos (Dive 1458); hydrothermal vents at Guaymas Basin, Gulf of California (27\u00b00'27.84\"N, 111\u00b024'27.84\"W) at 2000 m with the DSV Alvin (Dive 4486); and hydrothermal vents at Middle Valley, Juna de Fuca Ridge (48\u00b027'26.40\"N, 128\u00b042'30.60\"W) at 2413 m with the DSV Alvin (Dive 4625). For this study, a total of three pushcores were collected from Hydrate Ridge at 4\u00b0C, one from Guaymas Basin at 30-35\u00b0C, and one from Middle Valley at 5\u201357\u00b0C (Table 4.1). Total genomic DNA was extracted using a phenol-chloroform protocol modified to prevent nucleic acid loss and eliminate potential inhibitors of downstream PCR, and which has been very successful in studies of low biomass sediments (Adams et al. 2013). PCR amplification was performed with primers designed to be universal to both archaea and bacteria (515F/806R) (Caporaso et al., 2012), containing attached Illumina adaptors and barcodes (Kozich et al., 2013). All DNA extracts were amplified in duplicate with OmniTaq (Taq mutant) polymerase according to the manufacturer\u2019s instructions (DNA Polymerase Technologies, St. Louis, MO, USA), with a final concentration of 0.2 \u03bcM for each primer. For each PCR, 1 \u03bcL template DNA was added to the final reaction mixture for a final volume of 50 \u03bcl. Amplification conditions were as follows: 94\u00b0C for 3 min to denature DNA; 30 cycles at 94\u00b0C for 45 s, 50\u00b0C for 60 s, and 72\u00b0C for 60 s; and a final extension of 10 min at 72 \u00b0C.
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	Illumina Sequencing From Deep Sea Sediments PI: Peter Girguis (Harvard) Contributor: Melissa Adams Version date: 12 October 2018
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	2018-10-12T18:57:48Z
attribute	NC_GLOBAL	date_modified	String	2019-03-15T18:04:04Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.747948.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-111.4078
attribute	NC_GLOBAL	geospatial_lat_max	double	48.45722
attribute	NC_GLOBAL	geospatial_lat_min	double	27.0078
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-111.4078
attribute	NC_GLOBAL	geospatial_lon_min	double	-128.70861
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/747948
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	747953
attribute	NC_GLOBAL	instruments_0_description	String	General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute	NC_GLOBAL	instruments_0_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	471582
attribute	NC_GLOBAL	keywords	String	accession, analysis, Analysis_methods, bco, bco-dmo, biological, chemical, collected, data, dataset, description, description_of_the_types_of_sequences, dive, Dive_number, dmo, erddap, instrument, instrument_and_model, latitude, latitude_dms, link, locations, locations_where_species_were_collected, longitude, longitude_dms, management, methods, model, names, number, oceanography, office, preliminary, sequence, sequence_accession_number, sequences, sequencing, sequencing_and_analysis_methods, species, Species_Names, types, vessel, where
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/747948/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/747948
attribute	NC_GLOBAL	Northernmost_Northing	double	48.45722
attribute	NC_GLOBAL	param_mapping	String	{'747948': {'latitude': 'flag - latitude', 'longitude': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/747948/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	Harvard University
attribute	NC_GLOBAL	people_1_person_name	String	Melissa Adams
attribute	NC_GLOBAL	people_1_person_nid	String	747964
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
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	Shannon Rauch
attribute	NC_GLOBAL	people_2_person_nid	String	51498
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	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	Southernmost_Northing	double	27.0078
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	Species_Names,description_of_the_types_of_sequences,sequencing_and_analysis_methods,instrument_and_model,Analysis_methods
attribute	NC_GLOBAL	summary	String	Illumina sequencing data (NCBI accession numbers) from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin.
attribute	NC_GLOBAL	title	String	[Illumina Sequences] - Illumina sequencing data from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin (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	Westernmost_Easting	double	-128.70861
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	sequence_accession_number		String
attribute	sequence_accession_number	bcodmo_name	String	accession number
attribute	sequence_accession_number	description	String	NCBI accession number
attribute	sequence_accession_number	long_name	String	Sequence Accession Number
attribute	sequence_accession_number	units	String	unitless
variable	link		String
attribute	link	bcodmo_name	String	external_link
attribute	link	description	String	URL to NCBI accession
attribute	link	long_name	String	Link
attribute	link	units	String	unitless
variable	Species_Names		String
attribute	Species_Names	bcodmo_name	String	taxon
attribute	Species_Names	description	String	Description/name of species
attribute	Species_Names	long_name	String	Species Names
attribute	Species_Names	units	String	unitless
variable	description_of_the_types_of_sequences		String
attribute	description_of_the_types_of_sequences	bcodmo_name	String	sample_descrip
attribute	description_of_the_types_of_sequences	description	String	Description of the type of sequence
attribute	description_of_the_types_of_sequences	long_name	String	Description Of The Types Of Sequences
attribute	description_of_the_types_of_sequences	units	String	unitless
variable	locations_where_species_were_collected		String
attribute	locations_where_species_were_collected	bcodmo_name	String	site
attribute	locations_where_species_were_collected	description	String	Location of sample collection
attribute	locations_where_species_were_collected	long_name	String	Locations Where Species Were Collected
attribute	locations_where_species_were_collected	units	String	unitless
variable	latitude_dms		String
attribute	latitude_dms	bcodmo_name	String	latitude
attribute	latitude_dms	description	String	Latitude of sample collection in degrees, minutes, and seconds
attribute	latitude_dms	long_name	String	Latitude
attribute	latitude_dms	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	latitude_dms	standard_name	String	latitude
attribute	latitude_dms	units	String	unitless
variable	longitude_dms		String
attribute	longitude_dms	bcodmo_name	String	longitude
attribute	longitude_dms	description	String	Longitude of sample collection in degrees, minutes, and seconds
attribute	longitude_dms	long_name	String	Longitude
attribute	longitude_dms	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude_dms	standard_name	String	longitude
attribute	longitude_dms	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	27.0078, 48.45722
attribute	latitude	axis	String	Y
attribute	latitude	bcodmo_name	String	latitude
attribute	latitude	colorBarMaximum	double	90.0
attribute	latitude	colorBarMinimum	double	-90.0
attribute	latitude	description	String	Latitude of sample collection in decimal degrees; North = positive values
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		double
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	_FillValue	double	NaN
attribute	longitude	actual_range	double	-128.70861, -111.4078
attribute	longitude	axis	String	X
attribute	longitude	bcodmo_name	String	longitude
attribute	longitude	colorBarMaximum	double	180.0
attribute	longitude	colorBarMinimum	double	-180.0
attribute	longitude	description	String	Longitude of sample collection in degrees, minutes, and seconds; East = positive values
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	Vessel		String
attribute	Vessel	bcodmo_name	String	instrument
attribute	Vessel	description	String	Name of collection vehicle
attribute	Vessel	long_name	String	Vessel
attribute	Vessel	units	String	unitless
variable	Dive_number		short
attribute	Dive_number	_FillValue	short	32767
attribute	Dive_number	actual_range	short	1458, 4625
attribute	Dive_number	bcodmo_name	String	dive_id
attribute	Dive_number	colorBarMaximum	double	100.0
attribute	Dive_number	colorBarMinimum	double	0.0
attribute	Dive_number	description	String	Dive ID number
attribute	Dive_number	long_name	String	Dive Number
attribute	Dive_number	units	String	unitless
variable	sequencing_and_analysis_methods		String
attribute	sequencing_and_analysis_methods	bcodmo_name	String	sampling_method
attribute	sequencing_and_analysis_methods	description	String	Description of sequencing and analysis methods
attribute	sequencing_and_analysis_methods	long_name	String	Sequencing And Analysis Methods
attribute	sequencing_and_analysis_methods	units	String	unitless
variable	instrument_and_model		String
attribute	instrument_and_model	bcodmo_name	String	instrument
attribute	instrument_and_model	description	String	Name of sequencing instruments
attribute	instrument_and_model	long_name	String	Instrument And Model
attribute	instrument_and_model	units	String	unitless
variable	Analysis_methods		String
attribute	Analysis_methods	bcodmo_name	String	sampling_method
attribute	Analysis_methods	description	String	Description of analysis methods
attribute	Analysis_methods	long_name	String	Analysis Methods
attribute	Analysis_methods	units	String	unitless

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.