1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:T46a,

Light attenuation was calculated from light intensities from linear regression analyses of ln(PAR) vs. depth.

Related files and references:

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.

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.

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.

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.

1d:Tfab,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. This project will address the following questions and hypotheses: 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. 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. 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. 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. 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 The project is affiliated with the Bermuda Atlantic Time-Series Study (BATS), http://bats.bios.edu.6:["$","$L1b",null,{"dataset":{"_id":"3866","description":"

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.

\n","problem":"","acquisition":"

The estuary was sampled with Niskin bottles in a CTD rosette from about 0.5 m. Salinity was taken from the CTD while light intensity at various depths was measured with a Biospherical light meter (model PNF-2102P).

Total microbial abundance and average cell size were determined by epifluorescence microscopy as described previously (Nikrad et al. 2012). 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).

The concentrations of ammonium, nitrate, phosphate, and silicate were measured with a Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009).
\n

\n","processing":"$1c","bcodmoProcessing":"","title":"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)","nickname":"active surface bacteria","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"","version_date":"2013-01-22T10:00:00.000Z","abstract":"","citation":"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]","citationParts":{"identifier":"http://lod.bco-dmo.org/id/dataset/3866","versionDate":"2013-01-22","versionId":"","year":"2013","title":"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)","authors":"Campbell, B., Kirchman, D. 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Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.","type_acronym":"Niskin bottle"},{"_id":"6073","name":"Nutrient Autoanalyzer","description":"Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009)","type_id":"558","type_name":"Nutrient Autoanalyzer","type_desc":"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.","type_acronym":"Nutrient Autoanalyzer"},{"_id":"6066","name":"Photosynthetically Available Radiation Sensor","description":"Biospherical light meter (model PNF-2102P)\nProfiling Natural Fluorescence Radiometer: Unlike strobe fluorometers, a natural fluorometer measures fluorescence emitted under the ambient light conditions that are driving photosynthesis in situ.","type_id":"439","type_name":"Photosynthetically Available Radiation Sensor","type_desc":"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.","type_acronym":"PAR sensor"},{"_id":"6067","name":"Secchi Disc","description":"","type_id":"609","type_name":"Secchi Disc","type_desc":"Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity","type_acronym":"Secchi Disc"}],"parameters":[{"_id":"32283","name":"cruise_id","format":"","frictionlessType":"","description":"

cruise identification; official R2R name

","units":{"_id":"","name":"text"},"type":{"_id":"1102","name":"cruise_id","description":"

cruise designation; name

"}},{"_id":"32284","name":"cruise_name","format":"","frictionlessType":"","description":"

cruise identification; project-based name

","units":{"_id":"","name":"text"},"type":{"_id":"1929","name":"Cruise Name","description":"

The cruise_name is a local name chosen by project investigators for a research expedition on a vessel, as opposed to the formal/official cruise ID asserted by the vessel operator.

"}},{"_id":"32285","name":"sta","format":"","frictionlessType":"","description":"

station identifier

","units":{"_id":"","name":"text"},"type":{"_id":"987","name":"station","description":"

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

"}},{"_id":"32286","name":"date_local","format":"","frictionlessType":"","description":"

local date of sample collection

","units":{"_id":"","name":"yyyymmdd"},"type":{"_id":"799","name":"date_local","description":"

local month, day and year, usually as a text string, e.g. feb10_1995. It is better to use one of the other forms of presenting date and time data so that the data can be used in computations and for comparisons. Note, if the string begins with numbers but also includes letters, there may be problems using the field name for retrieval.

"}},{"_id":"32287","name":"time_local","format":"","frictionlessType":"","description":"

local time of sample collection

","units":{"_id":"","name":"HH:MM:SS"},"type":{"_id":"1007","name":"time_local","description":"

time of day, local time, using 2400 clock format

"}},{"_id":"32288","name":"lat","format":"","frictionlessType":"","description":"

latitude; north is positive

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"32289","name":"lon","format":"","frictionlessType":"","description":"

longitude; east is positive

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"32290","name":"temp","format":"","frictionlessType":"","description":"

temperature

","units":{"_id":"","name":"degrees Celsius"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"32291","name":"sal","format":"","frictionlessType":"","description":"

salinity

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"32292","name":"PAR","format":"","frictionlessType":"","description":"

Photosynthetically Available [Active] Radiation; downwelling irradiance

","units":{"_id":"","name":"q/cm2/s"},"type":{"_id":"913","name":"PAR","description":"

Photosynthetically Available [Active] Radiation; downwelling irradiance; units vary: often microEinsteins/meter^2/second, microEinsteins/centimeter^2/second, or micromoles photons/meter/second

"}},{"_id":"32293","name":"depth_secchi","format":"","frictionlessType":"","description":"

depth at which a Secchi disk disappears

","units":{"_id":"","name":"meters"},"type":{"_id":"1953","name":"depth_secchi","description":"

The depth at which a Secchi disk disappears, a measure of water clarity.

"}},{"_id":"32294","name":"atten_secchi","format":"","frictionlessType":"","description":"

light attenuation from Secchi reading

","units":{"_id":"","name":"per meter"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32295","name":"atten_err","format":"","frictionlessType":"","description":"

light attenuation standard error

","units":{"_id":"","name":"per meter"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32296","name":"NO3","format":"","frictionlessType":"","description":"

nitrate concentration

","units":{"_id":"","name":"uM"},"type":{"_id":"1194","name":"NO3","description":"

Nitrate concentration in the water column

"}},{"_id":"32297","name":"NO3_sd","format":"","frictionlessType":"","description":"

nitration standard deviation

","units":{"_id":"","name":"uM"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32298","name":"PO4","format":"","frictionlessType":"","description":"

phosphate concentration

","units":{"_id":"","name":"uM"},"type":{"_id":"937","name":"PO4","description":"

Orthophosphate (phosphate, reactive phosphorus), Various units.

"}},{"_id":"32299","name":"PO4_sd","format":"","frictionlessType":"","description":"

phosphate standard deviation

","units":{"_id":"","name":"uM"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32300","name":"NH4","format":"","frictionlessType":"","description":"

ammonium concentration

","units":{"_id":"","name":"uM"},"type":{"_id":"901","name":"Ammonium","description":"

Ammonium and ammonia concentration parameters in any body of fresh or salt water.

"}},{"_id":"32301","name":"NH4_sd","format":"","frictionlessType":"","description":"

ammonium standard deviation

","units":{"_id":"","name":"uM"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32302","name":"Si","format":"","frictionlessType":"","description":"

silicate concentration

","units":{"_id":"","name":"uM"},"type":{"_id":"490515","name":"Si","description":"

Silicon (Si). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.

"}},{"_id":"32303","name":"Si_sd","format":"","frictionlessType":"","description":"

silicate standard deviation

","units":{"_id":"","name":"uM"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32304","name":"chl_a","format":"","frictionlessType":"","description":"

chlorophyl-a concentration

","units":{"_id":"","name":"micrograms/liter"},"type":{"_id":"766","name":"chlorophyll a","description":"

Total chlorophyll a pigment. See dataset for units of measurement; often reported in: milligrams per cubic meter (mg/m3); micrograms/liter (ug/L); nanograms/liter (ng/L).

CAUTION Within JGOFS MERGED water column products: this parameter is derived from HPLC methodology and the units are nanograms/liter; however; this parameter name is also used for a variety of water and nonwater column sampling; derived via the fluorometric method; units will also vary.

"}},{"_id":"32305","name":"chl_a_sd","format":"","frictionlessType":"","description":"

chlorophyl-a standard deviation

","units":{"_id":"","name":"micrograms/liter"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32306","name":"bact_cm3","format":"","frictionlessType":"","description":"

microbial abundance

","units":{"_id":"","name":"cells/ml"},"type":{"_id":"1470","name":"bact_abun_sed","description":"

bacterial abundance in sediment volume

"}},{"_id":"32307","name":"bact_cm3_sd","format":"","frictionlessType":"","description":"

microbial abundance standard deviation

","units":{"_id":"","name":"cells/ml"},"type":{"_id":"1471","name":"bacteria abundance std error","description":"

bacteria abundance; error within one standard deviation

"}},{"_id":"32308","name":"cell_size","format":"","frictionlessType":"","description":"

microbial cell size (volume)

","units":{"_id":"","name":"micrometers^3"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32309","name":"cell_size_se","format":"","frictionlessType":"","description":"

microbial cell size standard error

","units":{"_id":"","name":"micrometers^3"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32310","name":"bact_aap","format":"","frictionlessType":"","description":"

percent aerobic anoxygenic phototrophic bacteria of total

","units":{"_id":"","name":"percent"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32311","name":"bact_aap_sd","format":"","frictionlessType":"","description":"

aerobic anoxygenic phototrophic bacteria standard deviation

","units":{"_id":"","name":"percent"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32312","name":"Synech","format":"","frictionlessType":"","description":"

Synechococcus abundance

","units":{"_id":"","name":"cells/ml"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32313","name":"PicoEuk","format":"","frictionlessType":"","description":"

picoeukaryotes abundance

","units":{"_id":"","name":"cells/ml"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32314","name":"Prochlo","format":"","frictionlessType":"","description":"

Prochlorococcus abundance

","units":{"_id":"","name":"cells/ml"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32315","name":"leu_incorp","format":"","frictionlessType":"","description":"

3H-leucine incorporation rate

","units":{"_id":"","name":"picoMolar/h"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"32316","name":"leu_incorp_sd","format":"","frictionlessType":"","description":"

3H-leucine incorporation standard deviation

","units":{"_id":"","name":"picoMolar/h"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

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