http://lod.bco-dmo.org/id/dataset/3452
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
2011-03-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Ammonia-nitrite-nitrate assays from R/V Clifford A. Barnes cruises CB921, CB924, CB928, CB933, CB944 from the East Sound, Hood Canal; 2008-2010 (Marine Nitrogen Cycle project)
2011-03-24
publication
2011-03-24
revision
BCO-DMO Linked Data URI
2011-03-24
creation
http://lod.bco-dmo.org/id/dataset/3452
Anitra E. Ingalls
University of Washington
principalInvestigator
Allan Devol
University of Washington
principalInvestigator
Dr David A. Stahl
University of Washington
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: Ingalls, A. E., Devol, A., Stahl, D. A. (2011) Ammonia-nitrite-nitrate assays from R/V Clifford A. Barnes cruises CB921, CB924, CB928, CB933, CB944 from the East Sound, Hood Canal; 2008-2010 (Marine Nitrogen Cycle project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 24 March 2011) Version Date 2011-03-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3452 [access date]
Ammonia-nitrite-nitrate assays Dataset Description: <p>HC Data - Ammonia-nitrite-nitrate assays</p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0623174 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0623174
onGoing
Anitra E. Ingalls
University of Washington
206-221-6748
School of Oceanography Box 355351 4333 Brooklyn Ave NE
Seattle
WA
98195
USA
aingalls@u.washington.edu
pointOfContact
Allan Devol
University of Washington
206-543-1292
School of Oceanography University of Washington, Box 355351
Seattle
WA
98195
USA
devol@u.washington.edu
pointOfContact
Dr David A. Stahl
University of Washington
206-685-6657
Department of Civil and Environmental Engineering 302 More Hall, Box 352700
Seattle
WA
98195-2700
USA
dastahl@uw.edu
pointOfContact
asNeeded
Dataset Version: 24 March 2011
Unknown
Cruise
Station
Date
Time
Longitude
Latitude
Depth
Volume
NO2
NO2_x_10
Temp
Sal
O2
Chl
NO3minus
NH4
NH4plus_x_10
Sigma_t
Transm
PAR
Abs
CTD Sea-Bird SBE 911plus
theme
None, User defined
Cruise identfier
station
date
time of day
longitude
latitude
depth
volume of water filtered
Nitrite
water temperature at measurement depth
salinity
dissolved Oxygen
chlorophyll a
Nitrate
Ammonium
sigma-t
transmission
PAR
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
instrument
BCO-DMO Standard Instruments
CB921
CB924
CB928
CB933
CB944
service
Deployment Activity
East Sound
Hood Canal
Near main basin
Near main basin and Hood Canal
Hood Canal P12
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.
Quantifying the role of Group I Crenarchaeota in the marine nitrogen cycle using cultures and environmental monitoring of ammonia oxidation, 16S rRNA genes and lipid biomarkers
https://osprey.bco-dmo.org/project/2142
Quantifying the role of Group I Crenarchaeota in the marine nitrogen cycle using cultures and environmental monitoring of ammonia oxidation, 16S rRNA genes and lipid biomarkers
<p><b>Project Summary</b> <br />
Recent advances in molecular microbial ecology have overturned canonical paradigms of the marine nitrogen cycle. Estimates of global nitrogen fixation are regularly revised upward, the non-traditional bacterial denitrification pathway known as anammox is now thought to be responsible for a significant portion of global denitrification, and the discovery of ammonia-oxidizing <i>Archaea </i>necessitates a reevaluation of the contribution of traditional nitrifying bacteria to the global nitrogen cycle. While environmental gene sequencing and geochemical studies were critical to these discoveries, much of our understanding could not have been gained without the aid of studies on representative organisms in pure culture. Since their discovery in 1992, the ecological role of mesophilic marine <i>Archaea </i> has remained a mystery due in large part to the lack of a cultured representative.</p>
<p>We now have a mesophilic marine <i>Crenarchaea</i> in culture along with several lines of evidence that this and many other pelagic marine <i>Crenarchaea</i> oxidize ammonia to obtain the energy needed to sustain autotrophic carbon fixation. The distribution of marine <i>Crenarchaea</i> and their genes encoding ammonia-oxidizing enzymes, suggests that these organisms are responsible for the oxidation of a significant portion of the ocean's reduced nitrogen pools.</p>
<p>Here we propose to begin to better understand the physiological capabilities, distribution and quantitative significance of ammonia-oxidizing <i>Crenarchaea</i>. Our group is uniquely positioned to launch a comprehensive set of studies that will use cutting edge techniques to answer the following questions:<br />
1) What factors control the rate and efficiency of <i>Archaeal</i> ammonia-oxidation?</p>
<p>2) What is the relative role of <i>Bacteria</i> and <i>Archaea</i> in ammonia-oxidation in the marine environment?</p>
<p>3) How can biomarkers be used to detect and assess the physiological status of living ammonia-oxidizing <i>Bacteria</i> and <i>Archaea</i>?</p>
<p>Our study uniquely combines culture work, molecular biology, organic geochemistry and field investigations into one of the first studies of the role of marine <i>Crenarchaea</i> in the biogeochemical cycling of nitrogen.</p>
Marine Nitrogen Cycle
largerWorkCitation
project
eng; USA
oceans
East Sound; Hood Canal; Near main basin; Near main basin and Hood Canal; Hood Canal P12
2011-03-24
Hood Canal, Puget Sound, Washington
0
BCO-DMO catalogue of parameters from Ammonia-nitrite-nitrate assays from R/V Clifford A. Barnes cruises CB921, CB924, CB928, CB933, CB944 from the East Sound, Hood Canal; 2008-2010 (Marine Nitrogen Cycle 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/23937.rdf
Name: Cruise
Units: text
Description: <p>Cruise Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/23938.rdf
Name: Station
Units: text
Description: <p>Station Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/23939.rdf
Name: Date
Units: YYYYMMDD
Description: <p>Date (GMT)</p>
http://lod.bco-dmo.org/id/dataset-parameter/23940.rdf
Name: Time
Units: HHMMSS
Description: <p>Time (GMT)</p>
http://lod.bco-dmo.org/id/dataset-parameter/23941.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Station longitude (West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/23942.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Station latitude (South is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/23943.rdf
Name: Depth
Units: meters
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/23944.rdf
Name: Volume
Units: liters(?)
Description: <p>Volume</p>
http://lod.bco-dmo.org/id/dataset-parameter/23945.rdf
Name: NO2
Units: microM
Description: <p>NO2</p>
http://lod.bco-dmo.org/id/dataset-parameter/23946.rdf
Name: NO2_x_10
Units: (tbd)
Description: <p>NO2 * 10</p>
http://lod.bco-dmo.org/id/dataset-parameter/23947.rdf
Name: Temp
Units: Degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/23948.rdf
Name: Sal
Units: PSU
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/23949.rdf
Name: O2
Units: mg/L
Description: <p>O2</p>
http://lod.bco-dmo.org/id/dataset-parameter/23950.rdf
Name: Chl
Units: mg/m3
Description: <p>Chl</p>
http://lod.bco-dmo.org/id/dataset-parameter/23951.rdf
Name: NO3minus
Units: microM
Description: <p>NO3-</p>
http://lod.bco-dmo.org/id/dataset-parameter/23952.rdf
Name: NH4
Units: microM
Description: <p>NH4</p>
http://lod.bco-dmo.org/id/dataset-parameter/23953.rdf
Name: NH4plus_x_10
Units: (tbd)
Description: <p>NH4+ * 10</p>
http://lod.bco-dmo.org/id/dataset-parameter/23954.rdf
Name: Sigma_t
Units: Kg/m3
Description: <p>Sigma-t</p>
http://lod.bco-dmo.org/id/dataset-parameter/23955.rdf
Name: Transm
Units: percentage
Description: <p>Trans</p>
http://lod.bco-dmo.org/id/dataset-parameter/23956.rdf
Name: PAR
Units: percentage
Description: <p>PAR</p>
http://lod.bco-dmo.org/id/dataset-parameter/23957.rdf
Name: Abs
Units: (tbd)
Description: <p>Abs</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
19008
https://datadocs.bco-dmo.org/file/1VVMoy8fOnQ2v6/HC_Data.csv
HC_Data.csv
Primary data file for dataset ID 3452
download
https://osprey.bco-dmo.org/dataset/3452/data/download
download
onLine
dataset
<p><strong>OPA ammonia assay</strong><br />
Prepare all solutions in acid-washed (0.1% HCl), triple-rinsed (MilliQ H2O) brown HDPE bottles. Prepare stock solutions with freshly drawn ultra-pure deionized Milli-Q water. For the OPA solution use ethanol of the highest purity available.<br />
<br />
SOLUTIONS:<br />
Sodium sulfite solution: Dissolve 1 g sodium sulfite in 125 ml MilliQ water.<br />
&nbsp;<br />
Borate buffer solution: Dissolve 40 g disodium tetraborate decahydrate in 1000 ml MilliQ water. If necessary, filter the solution to remove turbitity. The solution is stable.<br />
<br />
OPA solution: Dissolve 2 g of standard grade o-phtaldialdehyde (P- 1378 Sigma) in 50 ml of ethanol in the dark.<br />
<br />
Ammonium chloride stock solution (10mM): Dissolve 535 mg dried NH4Cl in 1000 ml of MilliQ water.<br />
<br />
WORKING REAGENT:<br />
In a HDPE bottle mix 1000 ml of borate buffer with 50 ml of OPA solution and 5 ml of sodium sulfite. This reagent is light-sensitive. Let the reagent age at least one day before use. Store dark for at least 2 month.<br />
&nbsp;<br />
PROTOCOL:<br />
Prepare 2 µM ammonium standard in a 250ml HDPE bottle: Add 40 µl of ammonium chloride stock solution (10 mM) to 200 ml Milli-Q water.<br />
&nbsp;<br />
Prepare standard curve as follows:<br />
Standard [nM] MilliQ water 2 µM NH4Cl<br />
0 80 0<br />
0 80 0<br />
10 79.6 0.4<br />
25 79 1<br />
500 60 20<br />
1000 40 40<br />
2000 0 80<br />
&nbsp;<br />
Fill 80 ml of water sample into a 250-ml HDPE bottle.<br />
Add 20 ml of working reagent to all samples and standards.<br />
Incubate for accurately 30 min at 65°C and cool to room temperature.<br />
Analyze fluorescence intensity in Turner fluorometer with CDOM/Ammonia kit.<br />
&nbsp;<br />
Reference:<br />
Holmes, R. M., A. Aminot, R. Kerouel, B. A. Hooker and B. J. Peterson (1999). A simple and precise method for measuring ammonium and marine and freshwater ecosystems. Canadian Journal of Fisheries and Aquatic Sciences 56(10): 1801-1809. Keroul &amp; Aminot (1997) Fluorometric determination of ammonia in sea and estuarine waters by direct segmented flow analysis. Marine Chemistry 57: 265-275.<br />
&nbsp;<br />
&nbsp;<br />
<strong>Nitrite Determination </strong><br />
REAGENTS:<br />
Sulfanilamide reagent: Add 100 ml conc. HCl to 700ml MilliQ water<br />
Add 10g Sulfanilamide, stir to dissolve.<br />
Make up volume to 1000 ml<br />
Store at 4?C in the dark, stable for several weeks.<br />
&nbsp;<br />
Naphthylethylenediamine (NED) reagent: Dissolve 1 g of N-(1-Naphthyl)-ethylendiamin-dihydrochloride in 1000 ml of MilliQ water. Store at 4?C in the dark, stable for several weeks.<br />
&nbsp;<br />
Nitrite standard stock solution (10 mM): Dissolve 0.690 g dried NaNO2 in 1000 ml MilliQ water.<br />
&nbsp;<br />
PROCEDURE:<br />
Prepare 2 µM nitrite standard in a 250ml HDPE bottle: Add 40 µl of nitrite standard stock solution (10 mM) to 200 ml artificial seawater (SCM salts).<br />
&nbsp;<br />
Prepare nitrite standard curve as follows:<br />
Standard [nM] SCM salts [ml] 2 µM Nitrite Standard [ml]<br />
0 100 0<br />
0 100 0<br />
10 99.5 0.5<br />
25 98.75 1.25<br />
500 75 25<br />
1000 50 50<br />
2000 0 100<br />
&nbsp;<br />
Fill 100 ml of sample water into 250ml HDPE bottles.<br />
Add 2 ml of sulfanilamide reagent, swirl and let stand for 1 min.<br />
Add 2 ml of NED reagent and swirl again.<br />
Incubate for 10 to 15 min.<br />
Read absorbance at 540nm in a 5cm cuvette<br />
&nbsp;<br />
Grasshoff, Kremling, Erhard (1999) Methods of Seawater Analysis, 3 edn. Wiley-VCH<br />
&nbsp;<br />
<strong>Nitrate Assay for Seawater</strong><br />
Deionized water and standards<br />
For preparing standard and reagent solutions use deionized water purified by a distilling unit followed by the Millipore Synergy 185 Water System that produces water with 18 MΩ resistance.<br />
&nbsp;<br />
REAGENTS:<br />
2% (w/v) resorcinol solution: prepare fresh daily by dissolving 2.0 g of ACS reagent grade resorcinol crystals in 100 ml Milli-Q water.<br />
&nbsp;<br />
Concentrated sulfuric acid<br />
Nitrate stock standard solution (10 mM): Dissolve 0.85 g NaNO3 in 1 L of MilliQ water. Store stock solutions in a 1L polyethylene bottle at 4 °C in a refrigerator.<br />
Prepare working standard solutions from serial dilutions of stock solution with artificial sea water (SCM media – 26 g NaCl, 5 g MgSO4•7H2O, 5 g MgCl2•6H2O, 1.5 g CaCl2•2H2O, 0.1 g KBr in 1 L Milli-Q water).<br />
&nbsp;<br />
PROCEDURE:<br />
Prepare 40 µM nitrate standard in a 250ml HDPE bottle by adding 400 µl of nitrate standard stock solution (10 mM) to 99.6 ml of artificial seawater (SCM media).<br />
&nbsp;<br />
Prepare nitrate standard curve as follows:<br />
Standard [µM] SCM salts [ml] 40 µM Nitrate Standard [ml]<br />
0 20 0<br />
0 20 0<br />
0.25 19.875 0.125<br />
0.5 19.75 0.25<br />
10 15 5<br />
20 10 10<br />
40 0 20<br />
&nbsp;<br />
Transfer 20.0 ml of a seawater sample or standard into a 250 ml brown PE bottle.<br />
Add 2.4 ml of 2% resorcinol solution and swirl to mix the resorcinol with the sample.<br />
Carefully add 20.0 ml of concentrated sulfuric acid, close the bottle with its lid and then gently swirl to mix the solution. Let the bottles stand for 30 min.<br />
Place the bottles in a water bath until it reaches room temperature.<br />
Measure the absorbance of the sample at 505 nm in a 5 cm cuvette against a blank with acidified seawater.<br />
&nbsp;<br />
Reference:<br />
Zhang, J.Z. &amp; Fischer, C.J., 2006. A simplified resorcinol method for direct spectrophotometric determination of nitrate in seawater. Mar. Chem. 99, 220-226.</p>
<p><strong>BCO-DMO Processing Notes</strong><br />
Generated from original .xls file "Ingalls_HC_Data for NODC.xls" contributed by Anitra Ingalls<br />
<br />
<strong>BCO-DMO Edits</strong><br />
- Multiple sheet spreadsheet converted to individual, single sheet spreadsheets by cruise<br />
- Cruise Id standardized to R2R Catalog<br />
- Cruise Id and station metadata added to each data record<br />
- Parameters edited to conform to BCO-DMO parameter naming convention<br />
- "Date (euro)" removed<br />
- Decimal data values padded to consistent decimal places as reported<br />
- "nd" (no data) value inserted in blank cells</p>
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
CTD Sea-Bird SBE 911plus
CTD Sea-Bird SBE 911plus
PI Supplied Instrument Name: CTD Sea-Bird SBE 911plus Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Cruise: CB921
CB921
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel
CB921
Anitra E. Ingalls
University of Washington
Cruise: CB924
CB924
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel
CB924
Anitra E. Ingalls
University of Washington
Cruise: CB928
CB928
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel
CB928
Anitra E. Ingalls
University of Washington
Cruise: CB933
CB933
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel
CB933
Anitra E. Ingalls
University of Washington
Cruise: CB944
CB944
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel
CB944
Dr David A. Stahl
University of Washington
R/V Clifford A. Barnes
Community Standard Description
International Council for the Exploration of the Sea
R/V Clifford A. Barnes
vessel