http://lod.bco-dmo.org/id/dataset/543828
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
2014-12-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project)
2020-05-04
publication
2020-05-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-05-11
publication
https://doi.org/10.26008/1912/bco-dmo.543828.1
Craig A. Carlson
University of California-Santa Barbara
principalInvestigator
Stephen Giovannoni
Oregon State 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: Carlson, C., Giovannoni, S. (2020) Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-05-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.543828.1 [access date]
Virioplankton abundance at BATS site using FISH probe, 2003-2011 Dataset Description: <p>Virioplankton abundances were measured from samples collected from January 2000 to December 2011 as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (<a href="http://bats.bbsr.edu/">http://bats.bios.edu/)</a>. This dataset reports abundances quantified using FISH (Fluorescence <em>in situ</em> hybridization).</p> Methods and Sampling: <p>The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002).</p>
<p>Study site and sample collection:<br />
Samples were collected aboard the&nbsp;RV Weatherbird II&nbsp;or the&nbsp;RV Atlantic Explorer&nbsp;at the BATS site (31° 40′ N, 64°10′ W). All cruises were conducted as part of the larger BATS program and sampled at least monthly with biweekly sampling between February and April. This sampling strategy has been successful in revealing the major temporal microbial and biogeochemical patterns at this site (Carlson and Ducklow, 1996;&nbsp;Steinberg et al., 2001;&nbsp;Morris et al., 2005;&nbsp;Carlson et al., 2009;&nbsp;Treusch et al., 2009;&nbsp;Lomas et al., 2010). A broader assessment of the BATS biogeochemical data is presented in&nbsp;Deep Sea Research II&nbsp;in 1996 (volume 43, issues 2–3) and 2001 (volume 48, issues 8–9).</p>
<p>Samples for virioplankton (0, 20, 40, 60, 80, 100, 140, 160, 200, 250 and 300 m) and bacterioplankton (0, 10, 20, 40, 60, 80, 100, 120, 140, 160, 200, 250 and 300 m) were collected at the BATS site from January 2000 to December 2009 via conductivity, temperature, depth profiling rosette equipped with 12 l Niskin bottles. The 120 m virioplankton sample was added after October 2007. Throughout the entire time-series, all virioplankton samples were fixed with 0.02 μm filtered formalin (1% final concentration), placed in 5 ml cryovials and flash frozen in liquid nitrogen (Wen et al., 2004) until processing (within 12 weeks of collection). Samples for bacterioplankton abundance were fixed with 0.2 μm filtered gluteraldehyde (1% final concentration) and stored at either 4 °C for 72 h or flash frozen and subsequently stored at −80 °C for up to 6 months until processing as described in&nbsp;Steinberg et al (2001). Storage tests demonstrated no appreciable loss of virioplankton or bacterioplankton abundance when stored in liquid nitrogen for periods up to 6 months (unpublished data). Picophytoplankton samples were collected at the same depths through 250 m from October 2001 to December 2009 (Casey et al., 2007). Samples for fluorescence&nbsp;in situ&nbsp;hybridization (FISH) of specific heterotrophic bacterioplankton lineages were collected from the upper 300 m from January 2003 to December 2005 (Carlson et al., 2009).</p>
<p>Biogeochemical and physical data collected at the BATS site are available at&nbsp;http://bats.bios.edu. The MLD was determined as the depth where potential density (sigma-t) of the water was equal to sea surface sigma-t&nbsp;plus the equivalent in sigma-t&nbsp;to a 0.2 °C decrease in temperature (Sprintall and Tomczak, 1992). Contour plots were created in Ocean Data View (R Schlitzer,&nbsp;http://odv.awi.de/) with VG Gridding and linear mapping adjusted to the median of each data set. Statistics (Pearson's correlation and two-tailed Student's&nbsp;t-test for unequal variances), ratios and percent contributions were determined using Microsoft Excel.</p>
<p>Fluorescence&nbsp;in situ&nbsp;hybridization:<br />
FISH was used to quantify the abundance of members of the SAR11 and&nbsp;Rhodobacteraceae&nbsp;clades. The probe and hybridization protocol for members of the SAR11 clade are described in&nbsp;Morris et al. (2002). The probe for&nbsp;Rhodobacteraceae&nbsp;(5′-CAACGCTAACCCCCTCCG-3′) was used at a final concentration of 2 ng μl−1&nbsp;in hybridization buffer (0.9 mol l−1&nbsp;NaCl, 35% formamide, 20 mmol l−1&nbsp;Tris-HCl (pH 7.4) and 0.01% (w/v) sodium dodecyl sulfate). The hybridization wash temperature was 52 °C. Washes were conducted in buffer containing 20 mmol l−1&nbsp;Tris-HCl (pH 7.4), 70 mmol l−1&nbsp;NaCl, 5 mmol l−1&nbsp;EDTA and 0.01% sodium dodecyl sulfate. Filters were mounted with 20 μl of 1.67 μg ml−1&nbsp;DAPI (SIGMA-Aldrich) in citiflour solution (Ted Pella Inc., Redding, CA, USA) and sealed with nail polish. Image analysis was performed using Cy3 and DAPI filter sets as described by&nbsp;Carlson et al (2009).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0802004 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0802004
completed
Craig A. Carlson
University of California-Santa Barbara
(805) 893-2541
University of California Department of Ecology, Evolution and Marine Biology
Santa Barbara
CA
93106-6150
USA
craig_carlson@ucsb.edu
pointOfContact
Stephen Giovannoni
Oregon State University
541-737-1835
OSU/Department of Microbiology Nash Hall Rm 248
Corvallis
OR
97331
United States
stephen.giovannoni@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
station
cruise_ID
date_in
decyear
lat_in
lon_in
depth
depth_nom
depth_mixed
abund_Probe_Bact
abund_Probe_Bact_sd
abund_Eubac
abund_Cyano
abund_SAR11
abund_Cyt
abund_Rose
CTD
Flow Cytometer
Epifluorescence Microscope
Niskin bottle
theme
None, User defined
station
Cruise identfier
date
year_decimal
latitude
longitude
depth
depth nominal
mixed layer depth
abundance
featureType
BCO-DMO Standard Parameters
CTD - profiler
Flow Cytometer
Fluorescence Microscope
Niskin bottle
instrument
BCO-DMO Standard Instruments
BATS_cruises
service
Deployment Activity
Sargasso Sea
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.
Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory
http://www.bios.edu/research/projects/oceanic-microbial-observatory/
Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory
<p>(<em>Adapted from the NSF award abstract</em>)</p>
<p>The premise of this project is that stratified bacterioplankton clades engage in specialized biogeochemical activities that can be identified by integrated oceanographic and microbiological approaches. Specifically, the objective of this project is to assess if the mesopelagic microbial community rely on diagenetically altered organic matter and subcellular fragments that are produced by microbial processes in the euphotic zone and delivered into the upper mesopelagic by sinking or mixing. In past efforts this microbial observatory had greater success cultivating members of the euphotic zone microbial community, and revealed an unanticipated growth requirement for reduced sulfur compounds in alphaproteobacteria of the SAR11 clade. Genomic information showed that intense competition for substrates imposes trade-offs on bacterioplankton - there are regions of N dimensional nutrient space where specialists win. We postulate that specific growth requirements may explain some the regular spatial and temporal patterns that have been observed in upper mesopelagic bacterioplankton communities, and the difficulties of culturing some of these organisms.</p>
<p>The specific objectives of this project are: 1) to produce 13C and 15N labeled subcellular (e.g., soluble, cell wall, and membrane) and DOM fractions from photosynthetic plankton cultures and use stable isotope probing to identify specific clades in the surface and upper mesopelagic microbial community that assimilate fractions of varying composition and lability. 2) to use fluorescence in situ hybridization approaches to monitor temporal and spatial variability of specific microbial populations identified from the SIP and HTC experiments. To increase resolution we will use CARD-FISH protocols. 3) to measure the proteomes of bacterioplankton communities to identify highly translated genes in the surface layer and upper mesopelagic, and community responses to seasonal nutrient limitation. 4) and, to cultivate these organisms via high throughput culturing (HTC) by pursuing the hypothesis that they require specific nutrient factors and/or diagenetically altered organic substrates. Complete genome sequences from key organisms will be sought and used as queries to study patterns of natural variation in genes and populations that have been associated with biogeochemically important functions.</p>
Ocean Microbial Observatory
largerWorkCitation
project
eng; USA
biota
oceans
Sargasso Sea
-64.17
-64.17
31.67
31.67
2003-01-23
2005-12-09
Bermuda Atlantic Time-Series study site
0
BCO-DMO catalogue of parameters from Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory 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/810680.rdf
Name: station
Units: unitless
Description: <p>BATS cruise number during which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/810681.rdf
Name: cruise_ID
Units: unitless
Description: <p>BATS cruise ID for the sample that matches the BATS sample collected from the same niskin</p>
http://lod.bco-dmo.org/id/dataset-parameter/810682.rdf
Name: date_in
Units: unitless
Description: <p>date of collection at the time of CTD entry year month day</p>
http://lod.bco-dmo.org/id/dataset-parameter/810683.rdf
Name: decyear
Units: unitless
Description: <p>decimal year</p>
http://lod.bco-dmo.org/id/dataset-parameter/810684.rdf
Name: lat_in
Units: decimal degrees
Description: <p>Latitude at the time of CTD entry in degrees N</p>
http://lod.bco-dmo.org/id/dataset-parameter/810685.rdf
Name: lon_in
Units: decimal degrees
Description: <p>Longitude at the time of CTD entry in degrees W</p>
http://lod.bco-dmo.org/id/dataset-parameter/810686.rdf
Name: depth
Units: meters
Description: <p>the actual depth in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/810687.rdf
Name: depth_nom
Units: meters
Description: <p>bottle target depths in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/810688.rdf
Name: depth_mixed
Units: meters
Description: <p>mixed layer depth in meters; MLD was determined as the depth where potential density (sigma-t) of the water was equal to sea surface sigma-t plus the equivalent in sigma-t to a 0.2 1C decrease in temperature (Sprintall and Tomczak 1992).</p>
http://lod.bco-dmo.org/id/dataset-parameter/810689.rdf
Name: abund_Probe_Bact
Units: 10^8 cells/liter
Description: <p>Abundance of Bacteria and Archaea as determined by DAPI staining and microscopy counts using the same filter as the probe data</p>
http://lod.bco-dmo.org/id/dataset-parameter/810690.rdf
Name: abund_Probe_Bact_sd
Units: 10^8 cells/liter
Description: <p>standard deviation of Bacteria and Archaea abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/810691.rdf
Name: abund_Eubac
Units: 10^8 cells/liter
Description: <p>Abundance of Bacteria as determined by the Eubacteria prob</p>
http://lod.bco-dmo.org/id/dataset-parameter/810692.rdf
Name: abund_Cyano
Units: 10^7 cells/liter
Description: <p>Abundance of Cyanobacteria mainly Synechococcus as determined by microscopy</p>
http://lod.bco-dmo.org/id/dataset-parameter/810693.rdf
Name: abund_SAR11
Units: 10^8 cells/liter
Description: <p>Abundance of SAR11 bacterioplankton; FISH Probe = Morris et al. 2002</p>
http://lod.bco-dmo.org/id/dataset-parameter/810694.rdf
Name: abund_Cyt
Units: 10^7 cells/liter
Description: <p>Abundance of Bacteriodetes bacterioplankton; FISH Probe = CF319a; CF319b</p>
http://lod.bco-dmo.org/id/dataset-parameter/810695.rdf
Name: abund_Rose
Units: 10^7 cells/liter
Description: <p>Abundance of Rhodobacteraceae bacterioplankton; FISH Probe = 536R</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
37183
https://darchive.mblwhoilibrary.org/bitstream/1912/25758/1/dataset-543828_mo-virioplankton-abund-fish-probe__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.543828.1
download
onLine
dataset
<p>The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002).</p>
<p>Study site and sample collection:<br />
Samples were collected aboard the&nbsp;RV Weatherbird II&nbsp;or the&nbsp;RV Atlantic Explorer&nbsp;at the BATS site (31° 40′ N, 64°10′ W). All cruises were conducted as part of the larger BATS program and sampled at least monthly with biweekly sampling between February and April. This sampling strategy has been successful in revealing the major temporal microbial and biogeochemical patterns at this site (Carlson and Ducklow, 1996;&nbsp;Steinberg et al., 2001;&nbsp;Morris et al., 2005;&nbsp;Carlson et al., 2009;&nbsp;Treusch et al., 2009;&nbsp;Lomas et al., 2010). A broader assessment of the BATS biogeochemical data is presented in&nbsp;Deep Sea Research II&nbsp;in 1996 (volume 43, issues 2–3) and 2001 (volume 48, issues 8–9).</p>
<p>Samples for virioplankton (0, 20, 40, 60, 80, 100, 140, 160, 200, 250 and 300 m) and bacterioplankton (0, 10, 20, 40, 60, 80, 100, 120, 140, 160, 200, 250 and 300 m) were collected at the BATS site from January 2000 to December 2009 via conductivity, temperature, depth profiling rosette equipped with 12 l Niskin bottles. The 120 m virioplankton sample was added after October 2007. Throughout the entire time-series, all virioplankton samples were fixed with 0.02 μm filtered formalin (1% final concentration), placed in 5 ml cryovials and flash frozen in liquid nitrogen (Wen et al., 2004) until processing (within 12 weeks of collection). Samples for bacterioplankton abundance were fixed with 0.2 μm filtered gluteraldehyde (1% final concentration) and stored at either 4 °C for 72 h or flash frozen and subsequently stored at −80 °C for up to 6 months until processing as described in&nbsp;Steinberg et al (2001). Storage tests demonstrated no appreciable loss of virioplankton or bacterioplankton abundance when stored in liquid nitrogen for periods up to 6 months (unpublished data). Picophytoplankton samples were collected at the same depths through 250 m from October 2001 to December 2009 (Casey et al., 2007). Samples for fluorescence&nbsp;in situ&nbsp;hybridization (FISH) of specific heterotrophic bacterioplankton lineages were collected from the upper 300 m from January 2003 to December 2005 (Carlson et al., 2009).</p>
<p>Biogeochemical and physical data collected at the BATS site are available at&nbsp;http://bats.bios.edu. The MLD was determined as the depth where potential density (sigma-t) of the water was equal to sea surface sigma-t&nbsp;plus the equivalent in sigma-t&nbsp;to a 0.2 °C decrease in temperature (Sprintall and Tomczak, 1992). Contour plots were created in Ocean Data View (R Schlitzer,&nbsp;http://odv.awi.de/) with VG Gridding and linear mapping adjusted to the median of each data set. Statistics (Pearson's correlation and two-tailed Student's&nbsp;t-test for unequal variances), ratios and percent contributions were determined using Microsoft Excel.</p>
<p>Fluorescence&nbsp;in situ&nbsp;hybridization:<br />
FISH was used to quantify the abundance of members of the SAR11 and&nbsp;Rhodobacteraceae&nbsp;clades. The probe and hybridization protocol for members of the SAR11 clade are described in&nbsp;Morris et al. (2002). The probe for&nbsp;Rhodobacteraceae&nbsp;(5′-CAACGCTAACCCCCTCCG-3′) was used at a final concentration of 2 ng μl−1&nbsp;in hybridization buffer (0.9 mol l−1&nbsp;NaCl, 35% formamide, 20 mmol l−1&nbsp;Tris-HCl (pH 7.4) and 0.01% (w/v) sodium dodecyl sulfate). The hybridization wash temperature was 52 °C. Washes were conducted in buffer containing 20 mmol l−1&nbsp;Tris-HCl (pH 7.4), 70 mmol l−1&nbsp;NaCl, 5 mmol l−1&nbsp;EDTA and 0.01% sodium dodecyl sulfate. Filters were mounted with 20 μl of 1.67 μg ml−1&nbsp;DAPI (SIGMA-Aldrich) in citiflour solution (Ted Pella Inc., Redding, CA, USA) and sealed with nail polish. Image analysis was performed using Cy3 and DAPI filter sets as described by&nbsp;Carlson et al (2009).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
- converted longitudes to negative values to represent degrees West</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
CTD
PI Supplied Instrument Name: CTD 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 PI Supplied Instrument Description:Becton Dickenson (Franklin Lakes, NJ, USA; formerly Cytopeia) high speed jet-in-air InFlux flow cytometer, using a 488 nm blue excitation laser, appropriate Chl-a (692±20 nm) and phycoerythrin (580±15 nm) bandpass filters. 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 PI Supplied Instrument Description:Olympus AX70 microscope (Olympus, Tokyo, Japan) equipped with a Toshiba CCD video camera (Irvine, CA, USA) 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 PI Supplied Instrument Description:12 liter Niskin bottles 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/
Cruise: BATS_cruises
BATS_cruises
Multiple Vessels
vessel
BATS_cruises
Nicholas R. Bates
Bermuda Institute of Ocean Sciences
http://bats.bios.edu/bats-data/
Report describing BATS_cruises
Multiple Vessels
vessel