http://lod.bco-dmo.org/id/dataset/3866
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
2013-01-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial abundance, activity, and nutrient concentrations in Delaware Bay from R/V Hugh R. Sharp HRS090706DK in the Delaware Bay from July 2009 (Active bacteria in surface waters project)
2013-01-22
publication
2013-01-22
revision
BCO-DMO Linked Data URI
2013-01-22
creation
http://lod.bco-dmo.org/id/dataset/3866
Dr Barbara Campbell
Clemson University
principalInvestigator
David L. Kirchman
University of Delaware
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: Campbell, B., Kirchman, D. L. (2013) Microbial abundance, activity, and nutrient concentrations in Delaware Bay from R/V Hugh R. Sharp HRS090706DK in the Delaware Bay from July 2009 (Active bacteria in surface waters project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2013-01-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3866 [access date]
Microbial abundance, activity, and nutrient concentrations in Delaware Bay Dataset Description: <p>The data set includes salinity, light intensity and attenuation, microbial abundance, microbial heterotrophic activity, and inorganic nutrient concentrations along the salinity gradient of the Delaware estuary in July 2009.</p> Methods and Sampling: <p>The estuary was sampled with Niskin bottles in a CTD rosette from about 0.5 m.&nbsp; Salinity was taken from the CTD while light intensity at various depths was measured with a Biospherical light meter (model PNF-2102P).<br />
<br />
Total microbial abundance and average cell size were determined by epifluorescence microscopy as described previously (Nikrad et al. 2012).&nbsp; The abundance of autotrophic microbes (Synechococcus, picoeukaryotes, and Prochlorococcus) was determined by flow cytometry as previously described (Straza and Kirchman 2011). Incorporation of 3H-leucine was measured in 30 minute incubations using standard methods described elsewhere (Kirchman 2001).<br />
<br />
The concentrations of ammonium, nitrate, phosphate, and silicate were measured with a Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009). <br />
&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0825468 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0825468
completed
Dr Barbara Campbell
Clemson University
864-656-0559
Department of Biological Sciences 155B Life Science Facility, 190 Collings St.
Clemson
SC
29634
USA
bcampb7@clemson.edu
pointOfContact
David L. Kirchman
University of Delaware
302-645-4375
School of Marine Science and Policy 700 Pilottown Road
Lewes
DE
19958
USA
kirchman@udel.edu
pointOfContact
asNeeded
Unknown
cruise_id
cruise_name
sta
date_local
time_local
lat
lon
temp
sal
PAR
depth_secchi
atten_secchi
atten_err
NO3
NO3_sd
PO4
PO4_sd
NH4
NH4_sd
Si
Si_sd
chl_a
chl_a_sd
bact_cm3
bact_cm3_sd
cell_size
cell_size_se
bact_aap
bact_aap_sd
Synech
PicoEuk
Prochlo
leu_incorp
leu_incorp_sd
CTD profiler
Flow Cytometer
Epifluorescence Microscope
Niskin bottle
Nutrient Autoanalyzer
Photosynthetically Available Radiation Sensor
Secchi Disc
theme
None, User defined
Cruise identfier
cruise name
station
date_local
time_local
latitude
longitude
water temperature at measurement depth
salinity
PAR
depth_secchi
No BCO-DMO term
Nitrate
reactive phosphorus (PO4)
Ammonium
Silicon
chlorophyll a
bacterial abundance sediment
bacteria abundance standard error
featureType
BCO-DMO Standard Parameters
CTD - profiler
Flow Cytometer
Fluorescence Microscope
Niskin bottle
Nutrient Autoanalyzer
Photosynthetically Available Radiation Sensor
Secchi Disc
instrument
BCO-DMO Standard Instruments
HRS090706DK
service
Deployment Activity
Delaware 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.
Are abundant bacteria more active than rare bacteria in the Sargasso Sea?
https://osprey.bco-dmo.org/project/2253
Are abundant bacteria more active than rare bacteria in the Sargasso Sea?
<p>Marine prokaryotic communities are now known to be highly diverse and may be carrying out new types of metabolisms that, if confirmed, could fundamentally alter models of energy and material flow through the oceans. These metabolisms include photoheterotrophic and chemolithotrophic pathways that are entirely novel or were not thought to be occurring in the surface layer of the oceans. The problem is, we do not know which fraction of this diverse community is actually active in biogeochemical processes and whether the metabolic functions, especially the new ones suggested by genomic data, are actually being carried out by marine prokaryotic communities.</p>
<p>This project will address the following questions and hypotheses:</p>
<p>1. What bacteria are most active in open oceanic environments like the Sargasso Sea? The investigators hypothesize that the most abundant bacterioplankton groups are also the most active whereas the rare groups will be less active. This hypothesis will be explored using four indices of activity: i) levels of 16S rRNA vs. 16S rRNA genes; ii) replicating cells as measured by the incorporation of the thymidine analog, BrdU; iii) incorporation of key dissolved compounds by abundant bacterial groups as revealed by microautoradiography combined with fluorescence in situ hybridization (Micro-FISH), and iv) transcript levels of growth-dependent phylogenetic markers other than 16S rRNA (e.g. tuf, rpoB and dnaE). The investigators are especially interested in whether rare bacteria are inactive and are potentially part of a 'seed bank' that serves as the inoculum for future communities.</p>
<p>2. What metabolic processes are represented by the most commonly expressed genes? The investigators hypothesize that the most commonly expressed genes will be those associated with the processing of dissolved organic matter rather than other energy generating mechanisms, including photoheterotrophy and chemolithotrophy. Expression will be examined by pyrosequencing mRNA (metatranscriptome) from the Sargasso Sea. We will map the metatranscriptome onto metagenomic assemblies from the Sargasso Sea and explore which genes called in metagenomic studies are real rather than bioinformatic artifacts.</p>
<p>The project will use a combination of pyrosequencing and QPCR approaches to examine rRNA:rDNA ratios, BrdU incorporating cells, and transcript types and amounts in the metatranscriptome of Sargasso Sea surface water. Pyrosequencing (454) avoids amplification and cloning artifacts and it is cost effective. Preliminary analyses indicate that the sequence length of 454 reads and the proposed number of sequences are ideal for addressing the questions raised here. The investigators will also use Micro-FISH to examine incorporation of thymidine, leucine, and PO4. Samples will be collected twice yearly during the spring phytoplankton bloom when heterotrophic bacterial production is lowest and during the peak of bacterial production in summer.</p>
<p>This project will do much to alter our perception of microbial processes in the oligotrophic ocean by providing answers to long-standing questions about activity and standing stocks of bacterial populations and by linking metabolic processes to the extensive environmental genomic data now becoming available.</p>
<p>The project will support a graduate student and involve underrepresented undergraduates in summer research projects, including at sea field work. The results from this project will be incorporated into an environmental genomics web site and used in courses taught by Kirchman. The Kirchman and Heidelberg labs are featured in lab tours open to the public (~ 1000 visitors per year) and Campbell and Kirchman are also involved in Coast Day, an annual open house that attracts about 10,000 visitors. Finally, the PIs will be involved in K-12 teacher training workshops and other Delaware Center for Critical Zone Research outreach activities</p>
<p>The project is affiliated with the Bermuda Atlantic Time-Series Study (BATS), <a href="http://bats.bios.edu/">http://bats.bios.edu</a>.</p>
Active bacteria in surface waters
largerWorkCitation
project
eng; USA
oceans
Delaware Bay
2013-01-22
Coastal Delaware, Delaware Bay, Sargasso Sea
0
BCO-DMO catalogue of parameters from Microbial abundance, activity, and nutrient concentrations in Delaware Bay from R/V Hugh R. Sharp HRS090706DK in the Delaware Bay from July 2009 (Active bacteria in surface waters 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/32283.rdf
Name: cruise_id
Units: text
Description: <p>cruise identification; official R2R name</p>
http://lod.bco-dmo.org/id/dataset-parameter/32284.rdf
Name: cruise_name
Units: text
Description: <p>cruise identification; project-based name</p>
http://lod.bco-dmo.org/id/dataset-parameter/32285.rdf
Name: sta
Units: text
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/32286.rdf
Name: date_local
Units: yyyymmdd
Description: <p>local date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/32287.rdf
Name: time_local
Units: HH:MM:SS
Description: <p>local time of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/32288.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/32289.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/32290.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/32291.rdf
Name: sal
Units: dimensionless
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/32292.rdf
Name: PAR
Units: q/cm2/s
Description: <p>Photosynthetically Available [Active] Radiation; downwelling irradiance</p>
http://lod.bco-dmo.org/id/dataset-parameter/32293.rdf
Name: depth_secchi
Units: meters
Description: <p>depth at which a Secchi disk disappears</p>
http://lod.bco-dmo.org/id/dataset-parameter/32294.rdf
Name: atten_secchi
Units: per meter
Description: <p>light attenuation from Secchi reading</p>
http://lod.bco-dmo.org/id/dataset-parameter/32295.rdf
Name: atten_err
Units: per meter
Description: <p>light attenuation standard error</p>
http://lod.bco-dmo.org/id/dataset-parameter/32296.rdf
Name: NO3
Units: uM
Description: <p>nitrate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/32297.rdf
Name: NO3_sd
Units: uM
Description: <p>nitration standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32298.rdf
Name: PO4
Units: uM
Description: <p>phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/32299.rdf
Name: PO4_sd
Units: uM
Description: <p>phosphate standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32300.rdf
Name: NH4
Units: uM
Description: <p>ammonium concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/32301.rdf
Name: NH4_sd
Units: uM
Description: <p>ammonium standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32302.rdf
Name: Si
Units: uM
Description: <p>silicate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/32303.rdf
Name: Si_sd
Units: uM
Description: <p>silicate standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32304.rdf
Name: chl_a
Units: micrograms/liter
Description: <p>chlorophyl-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/32305.rdf
Name: chl_a_sd
Units: micrograms/liter
Description: <p>chlorophyl-a standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32306.rdf
Name: bact_cm3
Units: cells/ml
Description: <p>microbial abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/32307.rdf
Name: bact_cm3_sd
Units: cells/ml
Description: <p>microbial abundance standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32308.rdf
Name: cell_size
Units: micrometers^3
Description: <p>microbial cell size (volume)</p>
http://lod.bco-dmo.org/id/dataset-parameter/32309.rdf
Name: cell_size_se
Units: micrometers^3
Description: <p>microbial cell size standard error</p>
http://lod.bco-dmo.org/id/dataset-parameter/32310.rdf
Name: bact_aap
Units: percent
Description: <p>percent aerobic anoxygenic phototrophic bacteria of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/32311.rdf
Name: bact_aap_sd
Units: percent
Description: <p>aerobic anoxygenic phototrophic bacteria standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/32312.rdf
Name: Synech
Units: cells/ml
Description: <p>Synechococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/32313.rdf
Name: PicoEuk
Units: cells/ml
Description: <p>picoeukaryotes abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/32314.rdf
Name: Prochlo
Units: cells/ml
Description: <p>Prochlorococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/32315.rdf
Name: leu_incorp
Units: picoMolar/h
Description: <p>3H-leucine incorporation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/32316.rdf
Name: leu_incorp_sd
Units: picoMolar/h
Description: <p>3H-leucine incorporation standard deviation</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
3574
https://datadocs.bco-dmo.org/file/oAAmBx7uv6LGlX/active_bact.csv
active_bact.csv
Primary data file for dataset ID 3866
download
https://osprey.bco-dmo.org/dataset/3866/data/download
download
onLine
dataset
<p>The estuary was sampled with Niskin bottles in a CTD rosette from about 0.5 m.&nbsp; Salinity was taken from the CTD while light intensity at various depths was measured with a Biospherical light meter (model PNF-2102P).<br />
<br />
Total microbial abundance and average cell size were determined by epifluorescence microscopy as described previously (Nikrad et al. 2012).&nbsp; The abundance of autotrophic microbes (Synechococcus, picoeukaryotes, and Prochlorococcus) was determined by flow cytometry as previously described (Straza and Kirchman 2011). Incorporation of 3H-leucine was measured in 30 minute incubations using standard methods described elsewhere (Kirchman 2001).<br />
<br />
The concentrations of ammonium, nitrate, phosphate, and silicate were measured with a Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009). <br />
&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Light attenuation was calculated from light intensities from linear regression analyses of ln(PAR) vs. depth.</p>
<p><br />
<b>Related files and references:&nbsp; </b><br />
<br />
Kirchman, D. L. 2001. Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. Pages 227-237 in J. H. Paul, editor. Marine Microbiology. Academic Press, San Diego.</p>
<p>Nikrad, M. P., M. T. Cottrell, and D. L. Kirchman. 2012. Abundance and Single-Cell Activity of Heterotrophic Bacterial Groups in the Western Arctic Ocean in Summer and Winter. Applied and Environmental Microbiology 78:2402-2409.</p>
<p>Sharp, J. H., K. Yoshiyama, A. E. Parker, M. C. Schwartz, S. E. Curless, A. Y. Beauregard, J. E. Ossolinski, and A. R. Davis. 2009. A biogeochemical view of estuarine eutrophication:Seasonal and spatial trends and correlations in the Delaware Estuary. Estuaries and Coasts 32:1023-1043.</p>
<p>Straza, T. R. A. and D. L. Kirchman. 2011. Single-cell response of bacterial groups to light and other environmental factors in the Delaware Bay, USA. Aquatic Microbial Ecology 62:267-277.<br />
&nbsp;</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 profiler
CTD profiler
PI Supplied Instrument Name: CTD profiler Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Flow Cytometer
Flow Cytometer
PI Supplied Instrument Name: Flow Cytometer Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Epifluorescence Microscope
Epifluorescence Microscope
PI Supplied Instrument Name: Epifluorescence Microscope Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Nutrient Autoanalyzer
Nutrient Autoanalyzer
PI Supplied Instrument Name: Nutrient Autoanalyzer PI Supplied Instrument Description:Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009) Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Photosynthetically Available Radiation Sensor
Photosynthetically Available Radiation Sensor
PI Supplied Instrument Name: Photosynthetically Available Radiation Sensor PI Supplied Instrument Description:Biospherical light meter (model PNF-2102P)
Profiling Natural Fluorescence Radiometer: Unlike strobe fluorometers, a natural fluorometer measures fluorescence emitted under the ambient light conditions that are driving photosynthesis in situ. Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
Secchi Disc
Secchi Disc
PI Supplied Instrument Name: Secchi Disc Instrument Name: Secchi Disc Instrument Short Name:Secchi Disc Instrument Description: Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0430/
Cruise: HRS090706DK
HRS090706DK
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS090706DK
David L. Kirchman
University of Delaware
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel