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Title Sum-
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.
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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 (external link)
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/ (external link)
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 (external link)
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/ (external link)
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/ (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/654295 (external link)
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 (external link)
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/ (external link)
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/ (external link)
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/ (external link)
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/ (external link)
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.

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