http://lod.bco-dmo.org/id/dataset/565451
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
2015-09-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial and viral cell counts, and nutrients from 5 cruises on the R/V Hugh R. Sharp in Delaware and Chesapeake Bays, 2014-2016 (Coastal Bacterial Growth Rates project)
2016-03-31
publication
2016-03-31
revision
BCO-DMO Linked Data URI
2016-03-31
creation
http://lod.bco-dmo.org/id/dataset/565451
Dr Barbara Campbell
Clemson 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: Campbell, B. (2016) Bacterial and viral cell counts, and nutrients from 5 cruises on the R/V Hugh R. Sharp in Delaware and Chesapeake Bays, 2014-2016 (Coastal Bacterial Growth Rates project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version waiting for validation) Version Date 2016-03-31 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/565451 [access date]
New data and new versions of previous data: Bacterial growth rate ACTivity in Delaware Bay Dataset Description: <p>Standard oceanographic measurements collected from CTD casts during 5 cruises in Delaware and Chesapeake Bays, representing coastal marine ecosystems.&nbsp; Measurements included nutrients, chlorophyll and light attenuation, bacterial and viral production.</p>
<p><strong>This is a new version with both new data and updated older data.&nbsp; March 31, 2016</strong></p>
<p><strong>DMO notes:</strong></p>
<p>changed ND to nd<br />
,, to ,nd,<br />
space between degree_decimal minutes to no space<br />
change nutrient names to chemical symbols<br />
added toplevel to put all three cruises in the same object<br />
got rid of extra lines in ACTII<br />
fixed bad lat/lon points in each cruise with PI input</p> Methods and Sampling: <p>The water samples were collected with a Seabird 911+ CTD.</p>
<p>Nutrient concentrations were measured by standard wet chemical methods using a SEAL Analytical AA3 Continuous Segmented Flow Analyzer.</p>
<p>Samples for chlorophyll a concentrations were collected by filtering 100 ml of water through Whatman GF/F filters and stored at -20 <sup>o</sup>C until analysis. To estimate concentrations, the filters were placed into 90% acetone and 40% dimethyl sulfoxide <em>(</em><em>DMSO</em>) and then the fluorescence in the extract was measured with a Turner Designs 10-AU fluorometer.</p>
<p>The attenuation coefficient was estimated by measuring photosynthetically active radiance with a Biospherical PNF-210 radiometer over a depth profile. In nearly all cases, the downcast and upcast profiles of radiance were indistinguishable and all data were used. When differences between the down and upcasts were apparent, only the downcast data were used.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1261359 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1261359
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
asNeeded
Dataset Version: waiting for validation
Unknown
cruise_informal
cruiseid
date_local
time_local
lat
lon
station
CTD
temp
sal
secchi_depth
PAR
atten
atten_err
depth_sample
cell_counts
counts_sd
counts_se
bact_prod
bact_prod_sd
bact_prod_lt_pt8
bact_prod_lt_pt8_sd
bact_size_frac
chla
chla_sd
NO3
NO3_sd
NH4
NH4_sd
PO4
PO4_sd
SiO4
SiO4_sd
viral_count
viral_count_sd
CTD Seabird 911+
Flow Cytometer
theme
None, User defined
Cruise identfier
date_local
time of day
latitude
longitude
station
cast
temperature of sample or a generic measurement (not in-situ water temp)
salinity
depth
PAR
beam_c
standard error
count
standard deviation
production
No BCO-DMO term
chlorophyll a
Nitrate
Ammonium
reactive phosphorus (PO4)
Silicate (reactive silica)
abundance
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird 911
Flow Cytometer
instrument
BCO-DMO Standard Instruments
HRS1402
HRS1416
HRS1422
HRS1501
HRS1511
service
Deployment Activity
Delaware Bay
Chesapeake 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.
Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems
https://osprey.bco-dmo.org/project/560414
Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems
<p><strong>Description from NSF award abstract:</strong><br />
Prokaryotic organisms in marine systems are highly diverse and carry out many types of metabolic processes important in biogeochemical cycles. However, the contribution of individual bacterial taxa to biochemical processes is not well understood. Similarly, previous studies have had limited success in understanding the regulation of bacterial communities by looking at correlations between abundance of individual taxa and environmental factors. Estimates of growth rates will help understand both problems. The contribution of specific bacterial taxa to biogeochemical cycles is likely to scale with growth rate as well as abundance, and these rates are also likely to be more sensitive to environment fluctuations than abundance.</p>
<p>This project will examine the following questions and hypotheses about a fundamental property of organisms, growth rates: 1) what is the relationship between growth rate and abundance of specific bacterial taxa in controlled experiments? Do 16S rRNA:rDNA ratios or other growth-regulated transcript:gene ratios reflect real differences in growth rates? The PIs hypothesize that growth responsive transcript:gene ratios will correlate with growth rates independent of metabolic strategy and phylogeny, even though ratios and absolute rates will vary among bacterial species or within a taxa growing under different conditions. This hypothesis will be explored in environmentally relevant isolated bacteria whose genomes have been sequenced as well as in individual taxa in natural communities, whose genomes will be sequenced via a single cell approach. 2) What is the relationship between growth rate and abundance in situ? How are variations in the environment reflected in bacterial growth rates? The PIs hypothesize that growth rates, estimated by either 16S rRNA:rDNA ratios or by other growth responsive transcript:gene ratios, will be better correlated to environmental factors than abundance alone. Variation in growth rates within and between taxa will correlate with changes in the environment, especially with light and nutrients. The project will test this hypothesis by analyzing three well-studied diverse marine ecosystems: a coastal Microbial Observatory site which has been sampled since 2006, and the Delaware and Chesapeake Bays.</p>
<p>To investigate the questions and hypotheses outlined above, the PIs will use a combination of single cell genomics, high throughput sequencing, and QPCR approaches to examine levels of 16S rRNA and other growth-regulated transcripts as well as their corresponding genes under various nutrient conditions and different in situ temporal and spatial scales. High throughput sequencing avoids amplification and cloning artifacts and is cost effective. Growth-responsive transcript:gene ratios, microbial abundance, and biogeochemical properties will be examined over hourly, daily, weekly and monthly time scales to investigate the influence of environmental factors on growth rates of individual bacterial taxa and to explore bottom-up control of microbial communities.</p>
<p>The results from this project will do much to alter our perception of microbial processes in the oceans and estuaries by providing answers to long-standing questions about relationships between activity and standing stocks of bacterial populations. It will begin to link quantitative rate measurements of specific bacterial taxa to the extensive genomic data now becoming available.</p>
Coastal Bacterial Growth Rates
largerWorkCitation
project
eng; USA
biota
oceans
Delaware Bay; Chesapeake Bay
2016-03-31
Delaware and Chesapeake Bays, coastal Atlantic Ocean
0
BCO-DMO catalogue of parameters from Bacterial and viral cell counts, and nutrients from 5 cruises on the R/V Hugh R. Sharp in Delaware and Chesapeake Bays, 2014-2016 (Coastal Bacterial Growth Rates 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/641876.rdf
Name: cruise_informal
Units: text
Description: <p>project name for the cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/641877.rdf
Name: cruiseid
Units: text
Description: <p>official name of the cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/641878.rdf
Name: date_local
Units: m/dd/yyyy
Description: <p>date of measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/641879.rdf
Name: time_local
Units: HH:MM
Description: <p>local time of day</p>
http://lod.bco-dmo.org/id/dataset-parameter/641880.rdf
Name: lat
Units: decimal degrees
Description: <p>the latitude of the CTD or station</p>
http://lod.bco-dmo.org/id/dataset-parameter/641881.rdf
Name: lon
Units: decimal degrees
Description: <p>the longitude of the CTD or station; negative means West of Greenwich</p>
http://lod.bco-dmo.org/id/dataset-parameter/641882.rdf
Name: station
Units: number
Description: <p>sequential cruise station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/641883.rdf
Name: CTD
Units: number
Description: <p>sequential CTD cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/641884.rdf
Name: temp
Units: degrees centrigrade
Description: <p>water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/641885.rdf
Name: sal
Units: PSU
Description: <p>water salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/641886.rdf
Name: secchi_depth
Units: meters
Description: <p>depth at which the Secchi disk could no longer be distinguished</p>
http://lod.bco-dmo.org/id/dataset-parameter/641887.rdf
Name: PAR
Units: microEinsteins per square meter per second
Description: <p>Photosynthetically active radiation; designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis</p>
http://lod.bco-dmo.org/id/dataset-parameter/641888.rdf
Name: atten
Units: per meter
Description: <p>attenuation coefficient</p>
http://lod.bco-dmo.org/id/dataset-parameter/641889.rdf
Name: atten_err
Units: calculated number
Description: <p>error for attenuation coefficient</p>
http://lod.bco-dmo.org/id/dataset-parameter/641890.rdf
Name: depth_sample
Units: meters
Description: <p>depth of the sample data</p>
http://lod.bco-dmo.org/id/dataset-parameter/641891.rdf
Name: cell_counts
Units: cells per milliliter
Description: <p>cell counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/641892.rdf
Name: counts_sd
Units: cells per ml
Description: <p>standard deviation of cell counts (i.e.difference from the mean/average)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641893.rdf
Name: counts_se
Units: cells per milliliter
Description: <p>standard error of cell counts (taking into account the number of samples tested. Error is used to get a better representation of the deviation/error with larger numbers of samples; such as cell counts where we average 10 fields of view to get a number)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641894.rdf
Name: bact_prod
Units: nanograms of Carbon per Liter per hour
Description: <p>bacterial production of the whole sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/641895.rdf
Name: bact_prod_sd
Units: nanograms of Carbon per Liter per hour
Description: <p>standard deviation of measurement of bacterial production</p>
http://lod.bco-dmo.org/id/dataset-parameter/641896.rdf
Name: bact_prod_lt_pt8
Units: nanograms of Carbon per Liter per hour
Description: <p>bacterial production of the part of the sample less than 0.8 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/641897.rdf
Name: bact_prod_lt_pt8_sd
Units: nanograms of Carbon per Liter per hour
Description: <p>standard deviation of bacterial production of the part of the sample less than 0.8 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/641898.rdf
Name: bact_size_frac
Units: percentage
Description: <p>percentage of the whole sample that is less than 0.8 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/641899.rdf
Name: chla
Units: micrograms per liter
Description: <p>chlorophyll a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/641900.rdf
Name: chla_sd
Units: micrograms per liter
Description: <p>standard deviation of chlorophyll measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/641901.rdf
Name: NO3
Units: micromoles per liter
Description: <p>Nitrate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/641902.rdf
Name: NO3_sd
Units: micromoles per liter
Description: <p>standard deviation of Nitrate measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/641903.rdf
Name: NH4
Units: micromoles per liter
Description: <p>Ammonium concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/641904.rdf
Name: NH4_sd
Units: micromoles per liter
Description: <p>standard deviation of Ammonium measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/641905.rdf
Name: PO4
Units: micromoles per liter
Description: <p>Phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/641906.rdf
Name: PO4_sd
Units: micromoles per liter
Description: <p>standard deviation of Phosphate measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/641907.rdf
Name: SiO4
Units: micromoles per liter
Description: <p>Silicate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/641908.rdf
Name: SiO4_sd
Units: micromoles per liter
Description: <p>standard deviation of Silicate measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/641909.rdf
Name: viral_count
Units: numbers per milliliter
Description: <p>number of viruses in the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/641910.rdf
Name: viral_count_sd
Units: numbers per milliliter
Description: <p>standard deviation of the count of the number of viruses in the sample</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
55927
https://datadocs.bco-dmo.org/file/p99nDErixNV2Vk/newACT_cruises_rs.csv
newACT_cruises_rs.csv
Primary data file for dataset ID 565451
download
https://osprey.bco-dmo.org/dataset/565451/data/download
download
onLine
dataset
<p>The water samples were collected with a Seabird 911+ CTD.</p>
<p>Nutrient concentrations were measured by standard wet chemical methods using a SEAL Analytical AA3 Continuous Segmented Flow Analyzer.</p>
<p>Samples for chlorophyll a concentrations were collected by filtering 100 ml of water through Whatman GF/F filters and stored at -20 <sup>o</sup>C until analysis. To estimate concentrations, the filters were placed into 90% acetone and 40% dimethyl sulfoxide <em>(</em><em>DMSO</em>) and then the fluorescence in the extract was measured with a Turner Designs 10-AU fluorometer.</p>
<p>The attenuation coefficient was estimated by measuring photosynthetically active radiance with a Biospherical PNF-210 radiometer over a depth profile. In nearly all cases, the downcast and upcast profiles of radiance were indistinguishable and all data were used. When differences between the down and upcasts were apparent, only the downcast data were used.</p>
Specified by the Principal Investigator(s)
<p>Nutrient concentrations were not processed except for converting raw spectrometric or fluorometric readings to concentrations.</p>
<p>Radiance values at very shallow or very deep depths were excluded from the analysis to calculate the attenuation coefficient when these values were clearly not along the ln (radiance) vs. depth line.</p>
<p>Bacterial Production: Assumes average C per cell = 15 fg and 0.125 nmol-C/pmol of leucine.</p>
from Cruise: HRS1501 <p>Originally in BCO-DMO as HSR1502. Changed after consult with CLC plus R2R to HRS1501.</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 Seabird 911+
CTD Seabird 911+
PI Supplied Instrument Name: CTD Seabird 911+ PI Supplied Instrument Description:Standard Seabird CTD911+ Instrument Name: CTD Sea-Bird 911 Instrument Short Name:CTD SBE 911 Instrument Description: The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with 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/TOOL0035/
Flow Cytometer
Flow Cytometer
PI Supplied Instrument Name: Flow Cytometer PI Supplied Instrument Description:Viruses were counted using a flow cytometer at Xiamen University, following their published method: Horizontal and Vertical Distribution of Marine Virioplankton: A Basin Scale Investigation Based on a Global Cruise. Y. Liang, et al. PLOS ONE www.plosone.org November 2014 9:11; e111634 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/
Cruise: HRS1402
HRS1402
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS1402
Dr Barbara Campbell
Clemson University
Cruise: HRS1416
HRS1416
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS1416
Dr Barbara Campbell
Clemson University
Cruise: HRS1422
HRS1422
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS1422
Dr Barbara Campbell
Clemson University
Cruise: HRS1501
HRS1501
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS1501
Dr Barbara Campbell
Clemson University
Cruise: HRS1511
HRS1511
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel
HRS1511
Dr Barbara Campbell
Clemson University
R/V Hugh R. Sharp
Community Standard Description
International Council for the Exploration of the Sea
R/V Hugh R. Sharp
vessel