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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 | Institution | Dataset ID |
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set | data | graph | files | public | [Delta Nitrification Study - GenBank Accession Numbers] - 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. (Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary) | F I M | background | BCO-DMO | bcodmo_dataset_654295 |
Row Type | Variable Name | Attribute Name | Data Type | Value |
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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 | [Delta Nitrification Study - GenBank Accession Numbers] - 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. (Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary) |
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.