ERDDAP > info > bcodmo_dataset_654295

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
	set	data	graph		files	public	GenBank accession numbers for ammonia oxidizer genes collected on the R/V Endeavor (SQO- Delta) in the San Francisco Bay Delta during September and October 2007.		I   M	background			BCO-DMO	bcodmo_dataset_654295

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	Surface sediment was retrieved using a modified Van Veen grab. Duplicate cores were taken from each grab sample using sterile, cut-off 5 mL syringes and immediately placed on dry ice prior to storage at \u201380 degrees celsius. Bottom water nutrient samples were collected in triplicate using a hand-held Niskin bottle, immediately filtered (0.2 um pore size), and frozen on dry ice prior to storage at \u201320 degrees celsius. Nutrient (NH4+, NO2-, and NO3-) concentrations were measured using a QuikChem 8000 Flow Injection Analyzer (Lachat Instruments).\u00a0 Sediment samples for potential nitrification rate measurements were collected in triplicate into the barrels of cut-off 60 mL syringes, which were sealed with parafilm and transported to the laboratory on ice. Potential rates were measured using amended sediment slurries. Slurries included 5 g of sediment (top 1 cm) homogenized in 100 mL of filtered bottom water augmented with NH4+ and phosphate to final additional concentrations of 500 and 100 uM, respectively. Amended slurries were shaken (200 rpm) in the dark for 24 hours at room temperature (about 22 degrees celsius). Aliquots for the determination of NO3- plus NO2- (NOX) were collected at evenly spaced intervals through the incubation period and stored at \u201320 degrees celsius. Prior to analysis, aliquots were thawed and passed through Whatman No. 42 filter paper, and the filtrate was analyzed for the accumulation of NOx over time, using a SmartChem 200 Discrete Analyzer (Unity Scientific). Rates were determined by linear regression of NOx concentrations over time. DNA was extracted from approximately 0.5 g of surface sediments by extruding and cutting the top 0.5 cm from frozen cores with a sterile scalpel and immediately proceeding with the FastDNA SPIN Kit for Soil (MP Biomedicals), including a FastPrep bead beating step of 30 s at speed 5.5. AOA and AOB amoA genes were quantified using gene-specific SYBR qPCR assays on a StepOnePlus Real-Time PCR System (Life Technologies). AOA amoA reactions contained iTaq SYBR Green Supermix with ROX (Bio-Rad Laboratories), 0.4 uM primers Arch-amoAF /Arch-amoAR (Francis et al., 2005) and 1 uL template DNA. AOA qPCR program details were identical to previously published protocols (Mosier and Francis, 2008) but with a 10 s detection step at 78.5 degrees celsius. AOB amoA qPCR reactions used primers amoA1F/amoA2R (Rotthauwe et al., 1997), and were set up following Mosier and Francis (2008) but with a 10 s detection step at 83 degress celsius. Each plate included a standard curve (5 to 10^6 copies/reaction) made by serial dilution of linearized plasmids extracted from previously sequenced clones, and negative controls that substituted sterile water for DNA. The diversity of ammonia oxidizing communities was determined by cloning and sequencing of PCR-amplified amoA genes using primers Arch-amoAF /Arch-amoAR (Francis et al., 2005) and amoA1F*/amoA2R (Rotthauwe et al., 1997; Stephen et al., 1999) for AOA and AOB, respectively. Reaction conditions and PCR programs followed previously published protocols (Mosier and Francis, 2008). Triplicate reactions were qualitatively checked by gel electrophoresis, pooled, and purified using the MinElute PCR Purification Kit or MinElute Gel Extraction Kit (Qiagen), following the manufacturer\u2019s instructions. Purified products were cloned using the pGEM-T Vector System II (Promega), and sequenced by Elim Biopharmaceuticals on a 3730xl capillary sequencer (Life Technologies). Sequences were imported into Geneious (version 6.1.6 created by Biomatters, available from [http://www.geneious.com](\\"http://www.geneious.com\\")) and manually cleaned prior to operational taxonomic unit (OTU) grouping (greater than or equal to 95% sequence similarity) using mothur (Schloss et al., 2009). Rarefaction curves and diversity/richness estimators (Chao1 and Shannon indices) were calculated using mothur. OTUs were aligned with reference sequences using the MUSCLE alignment package within Geneious, using a gap open score of \u2013750. Alignments were manually checked and used to build neighbor-joining bootstrap trees (Jukes-Cantor distance model, 1000 neighbor joining bootstrap replicates) within Geneious. The amoA sequences generated in this study have been deposited into GenBank with accession numbers KM000240 to KM000508 (AOB) and KM000509 to KM000784 (AOA). Two-tailed Spearman rank correlation coefficients (\u03c1) were calculated using R (R Core Team, 2014) to determine correlations between variables, using the suggested critical value of 0.786 for 5% significance with a sample size of 7 (Zar, 1972). Principal component and non-metric multidimensional scaling analyses were performed using the vegan package in R (Oksanen, 2013). Environmental variables were z-transformed to standardize across different scales and units by subtracting the population mean from each measurement and dividing by the standard deviation. OTU count data were Hellinger-transformed to standardize to relative abundances (Legendre and Legendre, 2012). Other than unweighted UniFrac distances, which were calculated using the online UniFrac portal (Lozupone et al., 2006), distance/dissimilarity indices were calculated using the vegan package in R. All principle component analyses are presented using scaling 1; therefore, the distance between sites on the biplot represents their Euclidean distance, and the right-angle projection of a site onto a descriptor vector shows the approximate position of that site on the vector (Legendre and Legendre, 2012).\u00a0
attribute	NC_GLOBAL	awards_0_award_nid	String	546277
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-0847266
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0847266
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	GenBank Accession Numbers Christopher A. Francis, PI Version 17 August 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	2016-08-18T16:40:26Z
attribute	NC_GLOBAL	date_modified	String	2019-05-20T17:35:41Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.654295.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-121.597033
attribute	NC_GLOBAL	geospatial_lat_max	double	38.167117
attribute	NC_GLOBAL	geospatial_lat_min	double	38.017617
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-121.597033
attribute	NC_GLOBAL	geospatial_lon_min	double	-121.850917
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/654295
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Hand-held Niskin bottle
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	654335
attribute	NC_GLOBAL	instruments_0_description	String	A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	413
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Niskin bottle
attribute	NC_GLOBAL	instruments_1_acronym	String	FIA
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Concentrations measured via QuikChem 8000 Flow Injection Analyzer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	654336
attribute	NC_GLOBAL	instruments_1_description	String	An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB36/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Flow Injection Analyzer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	657
attribute	NC_GLOBAL	instruments_1_supplied_name	String	QuikChem 8000
attribute	NC_GLOBAL	instruments_2_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Genes quantified using gene-specific SYBR qPCR assays
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	654342
attribute	NC_GLOBAL	instruments_2_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_2_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	471582
attribute	NC_GLOBAL	instruments_2_supplied_name	String	StepOnePlus Real-Time PCR System
attribute	NC_GLOBAL	instruments_3_acronym	String	Discrete Analyzer
attribute	NC_GLOBAL	instruments_3_dataset_instrument_description	String	Filtrate analyzed from the accumulation of NOx over time using this discrete analyzer.
attribute	NC_GLOBAL	instruments_3_dataset_instrument_nid	String	654338
attribute	NC_GLOBAL	instruments_3_description	String	Discrete analyzers utilize discrete reaction wells to mix and develop the colorimetric reaction, allowing for a wide variety of assays to be performed from one sample. These instruments are ideal for drinking water, wastewater, soil testing, environmental and university or research applications where multiple assays and high throughput are required.
attribute	NC_GLOBAL	instruments_3_instrument_name	String	Discrete Analyzer
attribute	NC_GLOBAL	instruments_3_instrument_nid	String	654337
attribute	NC_GLOBAL	instruments_3_supplied_name	String	SmartChem 200 Discrete Analyzer
attribute	NC_GLOBAL	keywords	String	accession, accession_numbers, bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, gene, latitude, longitude, management, numbers, oceanography, office, organism, preliminary, station
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/654295/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/654295
attribute	NC_GLOBAL	Northernmost_Northing	double	38.167117
attribute	NC_GLOBAL	param_mapping	String	{'654295': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/654295/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Stanford University
attribute	NC_GLOBAL	people_0_person_name	String	Dr Christopher Francis
attribute	NC_GLOBAL	people_0_person_nid	String	51553
attribute	NC_GLOBAL	people_0_role	String	Lead Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_1_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_1_person_nid	String	650173
attribute	NC_GLOBAL	people_1_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	project	String	N-Cycling Microbial Communities
attribute	NC_GLOBAL	projects_0_acronym	String	N-Cycling Microbial Communities
attribute	NC_GLOBAL	projects_0_description	String	Description from the NSF award abstract: This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). Although nitrogen (N) acts as a limiting nutrient in many marine ecosystems, from estuaries to the open ocean, N in excess can be extremely detrimental. Eutrophication is of particular concern in estuaries, with over half of the estuaries in the United States experiencing its effects. Harmful levels of N in estuaries can be diminished through tightly coupled processes in the microbial nitrogen cycle, including nitrification (chemoautotrophic oxidation of ammonia to nitrite and nitrate) and denitrification (the dissimilatory reduction of nitrate to N2 gas). In fact, coupled nitrification-denitrification can remove up to 50% of external dissolved inorganic nitrogen inputs to estuaries, thereby reducing the risk of eutrophication. Despite the biogeochemical importance of both nitrification and denitrification in estuarine systems, surprisingly little is known regarding the underlying microbial communities responsible for these processes, or how they are influenced by key physical/chemical factors. The investigators will work in San Francisco Bay - the largest estuary on the west coast of the United States - using molecular, biogeochemical and cultivation approaches to explore how the distribution, diversity, abundance, and activities of key N-cycling communities are influenced by environmental gradients over temporal and spatial scales. Denitrifying communities will be studied using functional genes (nirK and nirS) encoding the key denitrification enzyme nitrite reductase, while genes encoding ammonia monooxygenase subunit A (amoA) will be used to study both ammonia-oxidizing bacteria (AOB) and the recently-discovered ammonia-oxidizing archaea (AOA)- members of one of the most ubiquitous and abundant prokaryotic groups on the planet, the mesophilic Crenarchaeota. Analyzing sediments from sites spanning a range of physical and chemical conditions in the Bay, seasonally over the course of several years, will represent an unprecedented opportunity to examine spatial, physical/chemical, and temporal effects on both denitrifier and ammonia-oxidizer communities in this large, urban estuary. Concurrently, an intensive cultivation effort will also be undertaken, in order to compile a novel culture collection of estuarine denitrifiers and ammonia-oxidizers, for which virtually nothing is currently known. Taken together, these complimentary approaches will help reveal how complex physical/chemical gradients influence the diversity and functioning of key estuarine N-cycling communities over time and space.
attribute	NC_GLOBAL	projects_0_end_date	String	2015-05
attribute	NC_GLOBAL	projects_0_geolocation	String	San Francisco Bay
attribute	NC_GLOBAL	projects_0_name	String	Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary
attribute	NC_GLOBAL	projects_0_project_nid	String	546278
attribute	NC_GLOBAL	projects_0_start_date	String	2009-06
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	38.017617
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	gene
attribute	NC_GLOBAL	summary	String	GenBank accession numbers for ammonia oxidizer genes collected on the R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007.
attribute	NC_GLOBAL	title	String	GenBank accession numbers for ammonia oxidizer genes collected on the R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007.
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-121.850917
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	gene		String
attribute	gene	bcodmo_name	String	sample
attribute	gene	description	String	gene analyzed
attribute	gene	long_name	String	Gene
attribute	gene	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	gene	units	String	unitless
variable	station		String
attribute	station	bcodmo_name	String	station
attribute	station	description	String	station where sample was taken
attribute	station	long_name	String	Station
attribute	station	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	38.017617, 38.167117
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
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	-121.850917, -121.597033
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
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	organism		String
attribute	organism	bcodmo_name	String	sample
attribute	organism	description	String	organism analyzed
attribute	organism	long_name	String	Organism
attribute	organism	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	organism	units	String	unitless
variable	accession_numbers		String
attribute	accession_numbers	bcodmo_name	String	accession number
attribute	accession_numbers	description	String	GenBank accession numbers
attribute	accession_numbers	long_name	String	Accession Numbers
attribute	accession_numbers	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.