http://lod.bco-dmo.org/id/dataset/684207
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-03-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Spatiotemporal characterization of nirK and nirS abundance from R/V Polaris monthly San Francisco Bay USGS Water Quality cruises from July of 2011 to June of 2012 (N-Cycling Microbial Communities project)
2017-07-03
publication
2017-07-03
revision
BCO-DMO Linked Data URI
2017-07-03
creation
http://lod.bco-dmo.org/id/dataset/684207
Christopher Francis
Stanford University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Francis, C. (2017) Spatiotemporal characterization of nirK and nirS abundance from R/V Polaris monthly San Francisco Bay USGS Water Quality cruises from July of 2011 to June of 2012 (N-Cycling Microbial Communities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-07-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/684207 [access date]
Spatiotemporal characterization of nirK and nirS abundance in San Francisco Bay Dataset Description: <p>This dataset contains data related to spatiotemporal characterization of nirK and nirS Abundance in San Francisco Bay. Data include sampling information (e.g. latitude, longitude, date, water temperature), bottom chemistry (e.g. salinity, nitrate, ammonium), sediment chemistry (e.g. porosity, total carbon, Mg, C/N), and sediment nirK and nirS gene abundance per ng DNA and per gram dry sediment.</p>
<p>nirK = copper-containing nitrite reductase<br />
nirS = cytochrome-cd1 nitrite reductase</p>
<p><strong>These data were published in Lee and </strong><strong>Franics</strong><strong>, 2017:</strong><br />
Lee, J. A., and C. A. Francis. 2017. Spatiotemporal characterization of San Francisco Bay denitrifying communities: a comparison of <em>nirK</em> and <em>nirS</em> diversity and abundance. <em>Microbial Ecology</em> 73(2): 271-284. doi: <a href="http://doi.org/10.1007/s00248-016-0865-y" target="_blank">10.1007/s00248-016-0865-y</a></p>
<p><strong>For related datasets, click on the project link at the top of the page.</strong></p> Methods and Sampling: <div>
<p><strong>Field sampling<em>:</em></strong></p>
<p>Sampling was conducted between July 2011 and June 2012 aboard&nbsp;monthly full-bay cruises on the R/V <em>Polaris </em>carried out by the US Geological Survey (USGS; Menlo Park, CA,&nbsp;<a href="https://sfbay.wr.usgs.gov/access/wqdata/overview/wherewhen/where.html" target="_blank">external link</a>). Sediment samples were collected by overboard Van Veen grab. Surface cores were collected using sterile 1-cc and 6-cc cut-off syringes, placed immediately on dry ice, and stored at -80C until processing. Bottom water was caught in the grab simultaneously with the sediment. Due to logistical difficulties, no samples were collected at site 21 in December 2011, or at any sites in April 2012.</p>
<p><strong>Sediment and water chemical measurements. </strong>Salinity and temperature were measured</p>
<p>on-site using a YSI 556 MPS handheld multiparameter instrument (YSI Inc, OH). Subsamples of water for nutrient analyses were filtered through a 0.2 um PES syringe filter, placed on dry ice, and then stored at -80C until processing. Bottom water NO2-&nbsp;and NO3-<sup>&nbsp;</sup>concentrations were measured using a WestCo SmartChem 200 Discrete Analyzer (Unity Scientific, Brookfield, CT), and NH4+&nbsp;was measured using the salicylate-hypochlorite method. In preparation for sediment chemical measurements, frozen sediment samples were thawed and air-dried, then ground, sieved, and homogenized. Total C and N were measured on a Carlo Erba NA1500 Elemental Analyzer (Val de Reuil, France) using an atropine standard curve, and total content of specific elements (Al, Cl, Mg, Na, P, S, Cu, Fe, Mn, Pb) was measured on a Spectro Xepos HE XRF Spectrometer (Kleve, Germany). Sediment samples were weighed before and after drying for calculation of gravimetric water content.</p>
<p><strong>Nucleic acid extraction and gene abundance measurements<em>:</em> </strong></p>
<p>Total DNA was extracted&nbsp;in triplicate, from the surface 1-cm of sediment of each of 3 cores from each site, using the FastDNA Spin Kit for Soil (MP Biomedicals, Solon, OH) following the manufacturer’s instructions. Abundances of <em>nirK</em>, <em>nirS</em>, and bacterial 16S rRNA genes were measured using quantitative real-time PCR on the StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA), as described in Lee and Francis (2017). Each of the three DNA extractions from each sample was quantified in a separate reaction, with each reaction run in triplicate. A fresh 8-point standard curve was run on each reaction plate using 10-fold dilutions of a linearized plasmid containing an amplicon of the appropriate gene that had previously been PCR-amplified from San Francisco Bay sediment and sequenced.</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; From DNA samples collected at each site in July 2011, October 2011, January 2012, and May 2012, <em>nirK </em>and <em>nirS </em>gene fragments were PCR amplified, cloned, and sequenced, as described in Lee and Francis (2017). The nucleotide sequences reported in this study have been deposited in GenBank under accession numbers KR060094 - KR060621 (for <em>nirK</em>) and KR060622 - KR061281 (for <em>nirS</em>).</p>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0847266 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0847266
completed
Christopher Francis
Stanford University
650-724-0301
Environmental Earth System Science 473 Via Ortega, Y2E2 Bldg
Stanford
CA
94305-4216
USA
caf@stanford.edu
pointOfContact
asNeeded
Unknown
Site
Month
Year
Date
Latitude
Longitude
Temp
Sal
NO3
NH4
porosity
Ctot
Ntot
C_N
Al
Cl
Mg
Na
P
S
Cu
Fe
Mn
Pb
nirK_mean_DNA
nirK_sd_DNA
nirS_mean_DNA
nirS_sd_DNA
bacterial_16S_mean_DNA
bacterial_16S_sd_DNA
nirK_mean_dry
nirK_sd_dry
nirS_mean_dry
nirS_sd_dry
bacterial_16S_mean_dry
bacterial_16S_sd_dry
Van Veen grab
Carlo Erba NA1500 Elemental Analyzer
WestCo SmartChem 200 Discrete Analyzer
StepOnePlus Real-Time PCR system
Spectro Xepos HE XRF Spectrometer
YSI 556 MPS handheld multiparameter instrument
theme
None, User defined
site
month of year
year
date
latitude
longitude
water temperature at measurement depth
salinity
Nitrate
Ammonium
sediment porosity
Elemental carbon (C)
Nitrogen
Carbon to Nitrogen ratio (C:N)
Aluminum
chlorine
Magnesium
Sodium
Phosphorus
Sulfur (S)
Copper
Iron
Manganese
Lead
genetic material concentration
featureType
BCO-DMO Standard Parameters
Bottom Sediment Grab Samplers
Carlo-Erba NA-1500 Elemental Analyzer
Discrete Analyzer
qPCR Thermal Cycler
Spectrometer
YSI Professional Plus Multi-Parameter Probe
instrument
BCO-DMO Standard Instruments
USGS_WQ_SanFrancisco_2011-2012
service
Deployment Activity
San Francisco Bay
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary
https://osprey.bco-dmo.org/project/546278
Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary
<p><em>Description from the NSF award abstract:</em></p>
<p>This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).</p>
<p>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.</p>
<p>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.</p>
N-Cycling Microbial Communities
largerWorkCitation
project
eng; USA
oceans
San Francisco Bay
-122.37
-121.152
37.698
38.048
2011-07-13
2012-06-20
San Francisco Bay
0
BCO-DMO catalogue of parameters from Spatiotemporal characterization of nirK and nirS abundance from R/V Polaris monthly San Francisco Bay USGS Water Quality cruises from July of 2011 to June of 2012 (N-Cycling Microbial Communities project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/707616.rdf
Name: Site
Units: unitless
Description: <p>Site identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/707617.rdf
Name: Month
Units: unitless
Description: <p>Month of sampling in format mmm</p>
http://lod.bco-dmo.org/id/dataset-parameter/707618.rdf
Name: Year
Units: unitless
Description: <p>Year of sampling in format yyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/707619.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling in format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/707620.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/707621.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling location; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/707622.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperture of bottom water where sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/707623.rdf
Name: Sal
Units: Practical Salinity Units (PSU)
Description: <p>Salinity of bottom water where sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/707624.rdf
Name: NO3
Units: micromolar (mM)
Description: <p>Dissolved nitrate concentration in bottom water</p>
http://lod.bco-dmo.org/id/dataset-parameter/707625.rdf
Name: NH4
Units: micromolar (mM)
Description: <p>Dissolved ammonium concentration in bottom water</p>
http://lod.bco-dmo.org/id/dataset-parameter/707626.rdf
Name: porosity
Units: percent (%) by mass
Description: <p>Gravimetric water content of sediments</p>
http://lod.bco-dmo.org/id/dataset-parameter/707627.rdf
Name: Ctot
Units: percent (%) by mass
Description: <p>Total carbon content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707628.rdf
Name: Ntot
Units: percent (%) by mass
Description: <p>Total nitrogen content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707629.rdf
Name: C_N
Units: dimensionless
Description: <p>Carbon to nitrogen ratio (by mass) of sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707630.rdf
Name: Al
Units: percent (%) by mass
Description: <p>Total aluminium content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707631.rdf
Name: Cl
Units: percent (%) by mass
Description: <p>Total chlorine content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707632.rdf
Name: Mg
Units: percent (%) by mass
Description: <p>Total magnesium content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707633.rdf
Name: Na
Units: percent (%) by mass
Description: <p>Total sodium content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707634.rdf
Name: P
Units: percent (%) by mass
Description: <p>Total phosphorus content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707635.rdf
Name: S
Units: percent (%) by mass
Description: <p>Total sulfur content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707636.rdf
Name: Cu
Units: migrograms per gram (ug/g)
Description: <p>Total copper content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707637.rdf
Name: Fe
Units: migrograms per gram (ug/g)
Description: <p>Total iron content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707638.rdf
Name: Mn
Units: migrograms per gram (ug/g)
Description: <p>Total manganese content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707639.rdf
Name: Pb
Units: migrograms per gram (ug/g)
Description: <p>Total lead content in dried sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707640.rdf
Name: nirK_mean_DNA
Units: genes per ng DNA
Description: <p>Average sediment nirK gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707641.rdf
Name: nirK_sd_DNA
Units: genes per ng DNA
Description: <p>Standared deviation of sediment nirK gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707642.rdf
Name: nirS_mean_DNA
Units: genes per ng DNA
Description: <p>Average sediment nirS gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707643.rdf
Name: nirS_sd_DNA
Units: genes per ng DNA
Description: <p>Standared deviation of sediment nirS gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707644.rdf
Name: bacterial_16S_mean_DNA
Units: genes per ng DNA
Description: <p>Average bacterial 16S gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707645.rdf
Name: bacterial_16S_sd_DNA
Units: genes per ng DNA
Description: <p>Standard deviation of bacterial 16S gene abundance per ng DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/707646.rdf
Name: nirK_mean_dry
Units: genes per g dry sediment
Description: <p>Average sediment nirK gene abundance per gram of dry sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707647.rdf
Name: nirK_sd_dry
Units: genes per g dry sediment
Description: <p>Standared deviation of sediment nirK gene abundance per gram of dry sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707648.rdf
Name: nirS_mean_dry
Units: genes per g dry sediment
Description: <p>Average sediment nirS gene abundance per gram of dry sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707649.rdf
Name: nirS_sd_dry
Units: genes per g dry sediment
Description: <p>Standared deviation of sediment nirS gene abundance per gram of dry sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707650.rdf
Name: bacterial_16S_mean_dry
Units: genes per g dry sediment
Description: <p>Average bacterial 16S gene abundance per gram of dry sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/707651.rdf
Name: bacterial_16S_sd_dry
Units: genes per g dry sediment
Description: <p>Standard deviation of bacterial 16S gene abundance per gram of dry sediment</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
13497
https://datadocs.bco-dmo.org/file/EKKyElMIpOMNj8/nirK_nirS.csv
nirK_nirS.csv
Primary data file for dataset ID 684207
download
https://osprey.bco-dmo.org/dataset/684207/data/download
download
onLine
dataset
<div>
<p><strong>Field sampling<em>:</em></strong></p>
<p>Sampling was conducted between July 2011 and June 2012 aboard&nbsp;monthly full-bay cruises on the R/V <em>Polaris </em>carried out by the US Geological Survey (USGS; Menlo Park, CA,&nbsp;<a href="https://sfbay.wr.usgs.gov/access/wqdata/overview/wherewhen/where.html" target="_blank">external link</a>). Sediment samples were collected by overboard Van Veen grab. Surface cores were collected using sterile 1-cc and 6-cc cut-off syringes, placed immediately on dry ice, and stored at -80C until processing. Bottom water was caught in the grab simultaneously with the sediment. Due to logistical difficulties, no samples were collected at site 21 in December 2011, or at any sites in April 2012.</p>
<p><strong>Sediment and water chemical measurements. </strong>Salinity and temperature were measured</p>
<p>on-site using a YSI 556 MPS handheld multiparameter instrument (YSI Inc, OH). Subsamples of water for nutrient analyses were filtered through a 0.2 um PES syringe filter, placed on dry ice, and then stored at -80C until processing. Bottom water NO2-&nbsp;and NO3-<sup>&nbsp;</sup>concentrations were measured using a WestCo SmartChem 200 Discrete Analyzer (Unity Scientific, Brookfield, CT), and NH4+&nbsp;was measured using the salicylate-hypochlorite method. In preparation for sediment chemical measurements, frozen sediment samples were thawed and air-dried, then ground, sieved, and homogenized. Total C and N were measured on a Carlo Erba NA1500 Elemental Analyzer (Val de Reuil, France) using an atropine standard curve, and total content of specific elements (Al, Cl, Mg, Na, P, S, Cu, Fe, Mn, Pb) was measured on a Spectro Xepos HE XRF Spectrometer (Kleve, Germany). Sediment samples were weighed before and after drying for calculation of gravimetric water content.</p>
<p><strong>Nucleic acid extraction and gene abundance measurements<em>:</em> </strong></p>
<p>Total DNA was extracted&nbsp;in triplicate, from the surface 1-cm of sediment of each of 3 cores from each site, using the FastDNA Spin Kit for Soil (MP Biomedicals, Solon, OH) following the manufacturer’s instructions. Abundances of <em>nirK</em>, <em>nirS</em>, and bacterial 16S rRNA genes were measured using quantitative real-time PCR on the StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA), as described in Lee and Francis (2017). Each of the three DNA extractions from each sample was quantified in a separate reaction, with each reaction run in triplicate. A fresh 8-point standard curve was run on each reaction plate using 10-fold dilutions of a linearized plasmid containing an amplicon of the appropriate gene that had previously been PCR-amplified from San Francisco Bay sediment and sequenced.</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; From DNA samples collected at each site in July 2011, October 2011, January 2012, and May 2012, <em>nirK </em>and <em>nirS </em>gene fragments were PCR amplified, cloned, and sequenced, as described in Lee and Francis (2017). The nucleotide sequences reported in this study have been deposited in GenBank under accession numbers KR060094 - KR060621 (for <em>nirK</em>) and KR060622 - KR061281 (for <em>nirS</em>).</p>
</div>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Van Veen grab
Van Veen grab
PI Supplied Instrument Name: Van Veen grab Instrument Name: Bottom Sediment Grab Samplers Instrument Short Name:BSGS Instrument Description: These samplers are designed to collect an accurate representative sample of the sediment bottom. The bite of the sampler should be deep enough so all depths are sampled equally. The closing mechanism is required to completely close and hold the sample as well as prevent wash-out during retrieval. Likewise, during descent the sampler should be designed to minimize disturbance of the topmost sediment by the pressure wave as it is lowered to the bottom. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/50/
Carlo Erba NA1500 Elemental Analyzer
Carlo Erba NA1500 Elemental Analyzer
PI Supplied Instrument Name: Carlo Erba NA1500 Elemental Analyzer PI Supplied Instrument Description:. Total C and N were measured on a Carlo Erba NA1500 Elemental Analyzer (Val de Reuil, France) Instrument Name: Carlo-Erba NA-1500 Elemental Analyzer Instrument Short Name:Carlo-Erba NA-1500 Instrument Description: A laboratory instrument that simultaneously determines total nitrogen and total carbon from a wide range of organic and inorganic sediment samples. The sample is completely and instantaneously oxidised by flash combustion, which converts all organic and inorganic substances into combustion products. The resulting combustion gases pass through a reduction furnace and are swept into the chromatographic column by the carrier gas which is helium. The gases are separated in the column and detected by the thermal conductivity detector which gives an output signal proportional to the concentration of the individual components of the mixture. The instrument was originally manufactured by Carlo-Erba, which has since been replaced by Thermo Scientific (part of Thermo Fisher Scientific). This model is no longer in production. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0470/
WestCo SmartChem 200 Discrete Analyzer
WestCo SmartChem 200 Discrete Analyzer
PI Supplied Instrument Name: WestCo SmartChem 200 Discrete Analyzer PI Supplied Instrument Description:Bottom water NO2 and NO3 concentrations were measured using a WestCo SmartChem 200 Discrete Analyzer (Unity Scientific, Brookfield, CT). Instrument Name: Discrete Analyzer Instrument Short Name:Discrete Analyzer Instrument Description: 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.
StepOnePlus Real-Time PCR system
StepOnePlus Real-Time PCR system
PI Supplied Instrument Name: StepOnePlus Real-Time PCR system PI Supplied Instrument Description:StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA) Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
Spectro Xepos HE XRF Spectrometer
Spectro Xepos HE XRF Spectrometer
PI Supplied Instrument Name: Spectro Xepos HE XRF Spectrometer PI Supplied Instrument Description:Total content of specific elements (Al, Cl, Mg, Na, P, S, Cu, Fe, Mn, Pb) was measured on a Spectro Xepos HE XRF Spectrometer (Kleve, Germany) Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/
YSI 556 MPS handheld multiparameter instrument
YSI 556 MPS handheld multiparameter instrument
PI Supplied Instrument Name: YSI 556 MPS handheld multiparameter instrument PI Supplied Instrument Description:YSI 556 MPS handheld multiparameter instrument (YSI Inc, OH). Instrument Name: YSI Professional Plus Multi-Parameter Probe Instrument Short Name:YSI ProPlus Instrument Description: The YSI Professional Plus handheld multiparameter meter provides for the measurement of a variety of combinations for dissolved oxygen, conductivity, specific conductance, salinity, resistivity, total dissolved solids (TDS), pH, ORP, pH/ORP combination, ammonium (ammonia), nitrate, chloride and temperature. More information from the manufacturer.
Cruise: USGS_WQ_SanFrancisco_2011-2012
USGS_WQ_SanFrancisco_2011-2012
R/V Polaris
R/V Polaris
vessel
R/V Polaris
R/V Polaris
vessel