http://lod.bco-dmo.org/id/dataset/3872
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
2013-02-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project)
2012-11-19
publication
2012-11-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-11-01
publication
https://doi.org/10.1575/1912/bco-dmo.3872.1
Mary Ann Moran
University of Georgia
principalInvestigator
Ronald P. Kiene
Dauphin Island Sea Lab
principalInvestigator
William Whitman
University of Georgia
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: Moran, M. A., Kiene, R., Whitman, W. (2012) Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2012-11-19 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.3872.1 [access date]
Bacterial production in microcosm experiments. Dataset Description: <p>Bacterial production measurements from control and experimental microcosms from the Dauphin Island Cubitainer Experiment (DICE).</p>
<p><strong>Experimental design, methods, and results are further described in:</strong><br />
<strong>E. C. Howard</strong>, S. Sun, C. R. Reisch, D. A. del Valle, R. P. Kiene, and M. A. Moran (2010). Changes in DMSP Demethylase Gene Assemblages in Response to an Induced Phytoplankton Bloom. Applied and Environmental Microbiology, vol. 77, p. 524.<strong> </strong>DOI: <a href="http://dx.doi.org/10.1128/AEM.01457-10" target="_blank">10.1128/AEM.01457-10</a><br />
<strong>Rinta-Kanto</strong>, H. Burgmann, S. M. Gifford, S. Sun, S. Sharma, R. P. Kiene, and M. A. Moran (2011). Analysis of Sulfur-Related Gene Expression by Roseobacter Communities Using a Taxon-Specific Functional Gene Microarray. Environmental Microbiology, vol. 13, p. 453. DOI: <a href="http://dx.doi.org/10.1111/j.1462-2920.2010.02350.x" target="_blank">10.1111/j.1462-2920.2010.02350.x</a><br />
<strong>Vila-Costa</strong>, M., J. M. Rinta-Kanto, S. Sun, S. Sharma, R. Poretsky, and M. A. Moran. (2010). Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME Journal, vol. 4, p. 1410.<strong> </strong>DOI: <a href="http://dx.doi.org/10.1038/ismej.2010.62" target="_blank">10.1038/ismej.2010.62</a></p> Methods and Sampling: <p>See Howard et al. (2010), Rinta-Kanto et al. (2011), and Vila-Coast et al. (2010) for detailed methods, summarized below:</p>
<p>"In October 2006, seawater was collected from surface waters (&lt;1 m deep) in the Gulf of Mexico off the coast of Dauphin Island, AL (lat: 30 03.041N; lon: 87 59.708W). Water was filtered through a 200-um mesh into six 20-liter polyethylene Cubitainers with minimal headspace.</p>
<p>Three microcosms were amended with 10 um sodium nitrate (NaNO3) and 0.6 um potassium phosphate (K2HPO4) to serve as the experimental microcosms. Three microcosms were left untreated to serve as the control. The Cubitainers were maintained at 27 degrees C on a 12-hour light/dark cycle for the duration of the experiment.</p>
<p>Chemical and activity measurements were collected from the microcosms at the beginning of the experiment (Day 0) and every day for the duration of the experiment at the same time. Bacterial production was measured by 3H-leucine incorporation into trichloroacetic acid (TCA) -insoluble material. Incubations were carried out in triplicate in the dark at in situ temperature with additions of 20 nM of 3H-leucine for 4 hours, starting immediately after water collection. One TCA-killed sample was used as a control. Samples were processed by the microcentrifugation method. Bacterial sulfur requirements were estimated through conversion of bacterial heterotrophic production assuming a bacterial C/S molar ratio of 248."</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0724017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0724017
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Ronald P. Kiene
Dauphin Island Sea Lab
pointOfContact
William Whitman
University of Georgia
706-542-4219
Depmartment of Microbiogy 541 Biological Sciences
Athens
GA
30602
USA
whitman@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
exp_id
lat
lon
site_desc
microcosm
microcosm_type
exp_day
mean
mean_minus_blank
stdev
coeff_var
inc_time
leu_inc_per_h
leu_inc_per_d
stdev_calc
bact_prod
bact_prod_err
bact_C_demand
bact_C_demand_err
bact_S_prod
replicate
dpm
bucket
theme
None, User defined
experiment id
latitude
longitude
site description
sample identification
sample description
No BCO-DMO term
replicate
featureType
BCO-DMO Standard Parameters
bucket
instrument
BCO-DMO Standard Instruments
DMSP_Dauphin_Island
service
Deployment Activity
Gulf of Mexico, Alabama
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.
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
https://osprey.bco-dmo.org/project/2244
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
<p>The recent discovery of key genes that mediate competing pathways at a critical juncture in the marine sulfur cycle has allowed biogeochemists to make rapid advances in understanding where and when sulfur transformations occur in the ocean, and most importantly, what factors regulate them. This project describes an environmental functional genomics project that will rapidly increase our knowledge of the role that bacterioplankton play in dimethylsulfoniopropionate (DMSP) cycling in ocean surface waters, focusing particularly on biological controls of volatile sulfur exchange across the ocean/atmosphere boundary.</p>
<p>The investigators have asked three critical hypotheses to explain the regulation of bacterial DMSP degradation: that involve investigations on the energy constraints of DMSP cycling, the role that DMSP concentration in the oceans plays, and the sulfur requirements for bacterial growth. These research areas serve as the focus for hypothesis-driven laboratory and field studies using functional genomics approaches that will track patterns in gene expression in relation to sulfur metabolism. The hypotheses will be tested with:<br />
1) chemostat systems with a model marine bacterium Silicibacter pomeroyi;<br />
2) microcosm experiments with Gulf of Mexico seawater; and<br />
3) field studies at various sites in the Gulf of Mexico. Marine bacterioplankton play a key role in regulating the flux of DMSP-derived sulfur to the atmosphere, a process of great importance for global climate regulation and marine productivity.</p>
<p>The investigators will also be involved in graduate and undergraduate student education, and two post-doctoral associates will be trained to address multidisciplinary challenges in environmental microbiology. High school biology students in Athens, GA will participate in marine microbial biology research that includes bacterial diversity and discovery studies in coastal Georgia, follow-up training in molecular tools and bioinformatics in their own classroom, and summer internships at the University of Georgia and Dauphin Island Sea Laboratory.</p>
<p>(The description above is from the NSF Award Abstract).</p>
En-Gen DMSP Cycling
largerWorkCitation
project
eng; USA
oceans
Gulf of Mexico, Alabama
-87.99513
-87.99513
30.05068
30.05068
2006-10-01
2006-10-31
Sapelo Island, GA, USA, 31.4° N Lat, 81.3° W Lon / Dauphin Island, AL, USA, 30.3 ° N Lat, 88.1° W Lon
0
BCO-DMO catalogue of parameters from Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling 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/32844.rdf
Name: exp_id
Units: text
Description: <p>Name of the experiment. DICE = Dauphin Island Cubitainer Experiment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32845.rdf
Name: lat
Units: decimal degree
Description: <p>Latitude of the sample collection site. North = Positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32846.rdf
Name: lon
Units: decimal degree
Description: <p>Longitude of the sample collection. West = Negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32847.rdf
Name: site_desc
Units: text
Description: <p>Description of the sample collection site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32848.rdf
Name: microcosm
Units: text
Description: <p>Identifier for the microcosm experiment.<br /><br />
C1 and C2 were control microcosms containing Gulf of Mexico seawater.<br /><br />
E1 and E2 were experimental microcosms containing Gulf of Mexico seawater amended with inorganic N and P.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32849.rdf
Name: microcosm_type
Units: text
Description: <p>Type of microcosm. Experimental or Control.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32850.rdf
Name: exp_day
Units: integer
Description: <p>Sequential day of the experiment. Day 0 = start of the experiment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32851.rdf
Name: mean
Units: dpm
Description: <p>Calculated average of triplicates (including the blank).</p>
http://lod.bco-dmo.org/id/dataset-parameter/32852.rdf
Name: mean_minus_blank
Units: dpm
Description: <p>Average corrected for the blank.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32853.rdf
Name: stdev
Units: dpm
Description: <p>Standard deviation of the mean.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32854.rdf
Name: coeff_var
Units: %
Description: <p>Coefficient of variation of the mean.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32855.rdf
Name: inc_time
Units: hours
Description: <p>Incubation time.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32856.rdf
Name: leu_inc_per_h
Units: nM Leu per hour
Description: <p>Measure of bacterial production in nanomoles of radiolabeled leucine incorporated per hour of incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32857.rdf
Name: leu_inc_per_d
Units: nM Leu per day
Description: <p>Measure of bacterial production in nanomoles of radiolabeled leucine incorporated per day of incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32858.rdf
Name: stdev_calc
Units: nM Leu per day
Description: <p>Estimated variation about the mean based on % CV in specific activity measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32859.rdf
Name: bact_prod
Units: nM Carbon per day
Description: <p>Measure of bacterial Carbon production in nanomoles of carbon substrate converted to bacterial biomass each day.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32860.rdf
Name: bact_prod_err
Units: nM Carbon per day
Description: <p>Estimated variation about the mean of bacterial production based on % CV in specific activity measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32861.rdf
Name: bact_C_demand
Units: nM Carbon per day
Description: <p>Nanomoles of carbon substrate needed by bacteria each day, including bacterial production and bacterial respiration. This assumes a bacterial growth efficiency of 15%.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32862.rdf
Name: bact_C_demand_err
Units: nM Carbon per day
Description: <p>Estimated variation about the mean of bacterial carbon demand based on % CV in specific activity measurements. </p>
http://lod.bco-dmo.org/id/dataset-parameter/32863.rdf
Name: bact_S_prod
Units: nM Sulfur per day
Description: <p>Nanomoles of sulfur substrate needed by bacteria each day. This assumes a C:S ratio of 248 in bacterial biomass.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32864.rdf
Name: replicate
Units: unitless
Description: <p>Replicate identifier.<br /><br />
a, b, and c are replicate samples from the same treatment.<br /><br />
blank is a killed control, with formaldehyde added prior to addition of isotope.</p>
http://lod.bco-dmo.org/id/dataset-parameter/32865.rdf
Name: dpm
Units: dpm
Description: <p>Disintegrations per minute (dpm) measured per replicate.</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
19740
https://darchive.mblwhoilibrary.org/bitstream/1912/24762/1/dataset-3872_bacterialproduction__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.3872.1
download
onLine
dataset
<p>See Howard et al. (2010), Rinta-Kanto et al. (2011), and Vila-Coast et al. (2010) for detailed methods, summarized below:</p>
<p>"In October 2006, seawater was collected from surface waters (&lt;1 m deep) in the Gulf of Mexico off the coast of Dauphin Island, AL (lat: 30 03.041N; lon: 87 59.708W). Water was filtered through a 200-um mesh into six 20-liter polyethylene Cubitainers with minimal headspace.</p>
<p>Three microcosms were amended with 10 um sodium nitrate (NaNO3) and 0.6 um potassium phosphate (K2HPO4) to serve as the experimental microcosms. Three microcosms were left untreated to serve as the control. The Cubitainers were maintained at 27 degrees C on a 12-hour light/dark cycle for the duration of the experiment.</p>
<p>Chemical and activity measurements were collected from the microcosms at the beginning of the experiment (Day 0) and every day for the duration of the experiment at the same time. Bacterial production was measured by 3H-leucine incorporation into trichloroacetic acid (TCA) -insoluble material. Incubations were carried out in triplicate in the dark at in situ temperature with additions of 20 nM of 3H-leucine for 4 hours, starting immediately after water collection. One TCA-killed sample was used as a control. Samples were processed by the microcentrifugation method. Bacterial sulfur requirements were estimated through conversion of bacterial heterotrophic production assuming a bacterial C/S molar ratio of 248."</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO made the following changes:<br />
- Modified parameter names to conform with BCO-DMO naming conventions.<br />
- Replaced blanks with 'nd' to indicate 'no data'.<br />
- Added the site coordinates provided in the publications above.</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
bucket
bucket
PI Supplied Instrument Name: bucket PI Supplied Instrument Description:Water was collected in the field using a clean bucket. Instrument Name: bucket Instrument Short Name:bucket Instrument Description: A bucket used to collect surface sea water samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0536/
Cruise: DMSP_Dauphin_Island
DMSP_Dauphin_Island
R/V E.O. Wilson
R/V E.O. Wilson
vessel
DMSP_Dauphin_Island
Mary Ann Moran
University of Georgia
R/V E.O. Wilson
R/V E.O. Wilson
vessel