http://lod.bco-dmo.org/id/dataset/652223
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
2016-07-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015
2016-07-20
publication
2016-07-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-06-06
publication
https://doi.org/10.1575/1912/bco-dmo.652223.1
Kimberlee Thamatrakoln
Rutgers University
principalInvestigator
Mark A. Brzezinski
University of California-Santa Barbara
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: Thamatrakoln, K., Brzezinski, M. (2016) Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-07-20 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.652223.1 [access date]
Abundance of bacteria viruses and chlorophyll containing cells Dataset Description: <p>Enumeration of Bacteria, viruses, and chlorophyll containing particles using flow cytometry.</p>
<p><strong>For related datasets, click on the project link at the top of the page.</strong></p> Methods and Sampling: <p><strong><em>Environmental Sample Collection</em></strong></p>
<ol>
<li>Transfer 1 ml of whole seawater to a 2 ml cryovial.</li>
<li>Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%.</li>
<li>Incubate at 4 degrees celsius&nbsp;for 30 min.</li>
<li>Flash freeze in liquid N<span style="font-size:10.8333px">2</span>&nbsp;and store at -80 degrees celsius.</li>
</ol>
<p><strong><em>Fluorescent DNA staining (for bacterial and viral abundances)</em></strong></p>
<ol>
<li>Thaw samples.</li>
<li>To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)&nbsp;</li>
<li>Heat to 80 degrees celsius&nbsp;for 10 min in the dark</li>
<li>Cool at RT for 5 min</li>
<li>Analyze via flow cytometry</li>
</ol>
<p><strong><em>Analysis (for bacterial and viral abundances)</em></strong></p>
<p>Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences).</p>
<ol>
<li>An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads.</li>
<li>A gating hierarchy is established using both beads and previously determined virus and bacteria populations as&nbsp;reference&nbsp;(Sybr Gold Fluorescence versus SSC cytogram).</li>
<li>Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission.</li>
</ol>
<p><strong><em>Analysis (for&nbsp;chlorophyll containing&nbsp;cells)</em></strong></p>
<p>Samples are analyzed on a BD Accuri C6. Fixed, frozen samples are thawed and analyzed immediately.</p>
<ol>
<li>An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using various sized fluorescent beads as reference points (1.0, 2.0, 3.0, 6.0 and 10 um).</li>
<li>Gating is established using both beads and previously determined phytoplankton populations as&nbsp;reference&nbsp;(Chlorophyll Fluorescence versus FSC cytogram).</li>
<li>Samples are analyzed using 488nm laser for excitation and the default BD Accuri threshold (80,000 RFU) on FSC is used.</li>
</ol>
<p><strong>TE buffer with SYBR Gold recipe</strong></p>
<p><u>1X TE (for 100&nbsp;mls)</u></p>
<p>1 ml of 1M Tris, pH 8.0<br />
1 ml of 0.5 mM EDTA<br />
98&nbsp;mls&nbsp;MQ water<br />
Store 4 degrees celsius</p>
<p><u>1X TE + SYBR Gold (for 10&nbsp;mls)</u></p>
<ol>
<li>Filter 10&nbsp;mls&nbsp;1 TE buffer, 0.22 um filter</li>
<li>1:20,0000 dilution of SYBR Gold (Molecular Probes) stock (0.5 ul stock to 10&nbsp;mls&nbsp;TE buffer)</li>
</ol>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1333929 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1333929
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1334387 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1334387
completed
Kimberlee Thamatrakoln
Rutgers University
848-932-3464
Department of Marine and Coastal Sciences 71 Dudley Road
New Brunswick
NJ
08901
USA
thamat@marine.rutgers.edu
pointOfContact
Mark A. Brzezinski
University of California-Santa Barbara
805-893-7061
UCSB Marine Science Institute Bldg 520 Rm 4002 Fl 4L
Santa Barbara
CA
93106
USA
mark.brzezinski@lifesci.ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
cast
depth
date_local
time_local
time_utc
date_utc
station
lat
lon
bacteria
virus
chl_total
ISO_DateTime_UTC
cruise_id
Influx Model 209S Mariner Flow Cytometer
BD Accuri C6
theme
None, User defined
cast
depth
date_local
time_local
time_utc
date_utc
station
latitude
longitude
abundance
ISO_DateTime_UTC
Cruise identfier
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Flow Cytometer
instrument
BCO-DMO Standard Instruments
OC1504A
service
Deployment Activity
Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
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.
Linking physiological and molecular aspects of diatom silicification in field populations
https://osprey.bco-dmo.org/project/558198
Linking physiological and molecular aspects of diatom silicification in field populations
<p><em>Description from NSF award abstract:</em><br />
Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.</p>
<p>It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.</p>
Diatom Silicification
largerWorkCitation
project
eng; USA
oceans
Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
-124.48169
-120.81017
34.55467
43.65434
2015-04-20
2015-05-01
Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
0
BCO-DMO catalogue of parameters from Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015
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/652236.rdf
Name: cast
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/652237.rdf
Name: depth
Units: meters
Description: <p>depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/652238.rdf
Name: date_local
Units: unitless
Description: <p>local date of cast; mm-bbb-yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/652239.rdf
Name: time_local
Units: unitless
Description: <p>local time of cast; HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/652240.rdf
Name: time_utc
Units: unitless
Description: <p>UTC time of cast; HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/652241.rdf
Name: date_utc
Units: unitless
Description: <p>UTC date of cast; mm-bbb-yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/652242.rdf
Name: station
Units: unitless
Description: <p>consecutive station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/652243.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/652244.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/652245.rdf
Name: bacteria
Units: bacteria per milliliter
Description: <p>bacteria-like particle abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/652246.rdf
Name: virus
Units: VLP per milliliter
Description: <p>virus-like particle abundance (VLP)</p>
http://lod.bco-dmo.org/id/dataset-parameter/652247.rdf
Name: chl_total
Units: cells per milliliter
Description: <p>chlorophyll containing cells</p>
http://lod.bco-dmo.org/id/dataset-parameter/652248.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>DateTime (UTC) ISO formatted</p>
http://lod.bco-dmo.org/id/dataset-parameter/652249.rdf
Name: cruise_id
Units: unitless
Description: <p>The name of the cruise that collected these data.</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
6059
https://darchive.mblwhoilibrary.org/bitstream/1912/24207/1/dataset-652223_musicc-oc1504a-bacteria-virus-and-chlorophyll-containing-cell-abundance__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.652223.1
download
onLine
dataset
<p><strong><em>Environmental Sample Collection</em></strong></p>
<ol>
<li>Transfer 1 ml of whole seawater to a 2 ml cryovial.</li>
<li>Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%.</li>
<li>Incubate at 4 degrees celsius&nbsp;for 30 min.</li>
<li>Flash freeze in liquid N<span style="font-size:10.8333px">2</span>&nbsp;and store at -80 degrees celsius.</li>
</ol>
<p><strong><em>Fluorescent DNA staining (for bacterial and viral abundances)</em></strong></p>
<ol>
<li>Thaw samples.</li>
<li>To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)&nbsp;</li>
<li>Heat to 80 degrees celsius&nbsp;for 10 min in the dark</li>
<li>Cool at RT for 5 min</li>
<li>Analyze via flow cytometry</li>
</ol>
<p><strong><em>Analysis (for bacterial and viral abundances)</em></strong></p>
<p>Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences).</p>
<ol>
<li>An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads.</li>
<li>A gating hierarchy is established using both beads and previously determined virus and bacteria populations as&nbsp;reference&nbsp;(Sybr Gold Fluorescence versus SSC cytogram).</li>
<li>Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission.</li>
</ol>
<p><strong><em>Analysis (for&nbsp;chlorophyll containing&nbsp;cells)</em></strong></p>
<p>Samples are analyzed on a BD Accuri C6. Fixed, frozen samples are thawed and analyzed immediately.</p>
<ol>
<li>An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using various sized fluorescent beads as reference points (1.0, 2.0, 3.0, 6.0 and 10 um).</li>
<li>Gating is established using both beads and previously determined phytoplankton populations as&nbsp;reference&nbsp;(Chlorophyll Fluorescence versus FSC cytogram).</li>
<li>Samples are analyzed using 488nm laser for excitation and the default BD Accuri threshold (80,000 RFU) on FSC is used.</li>
</ol>
<p><strong>TE buffer with SYBR Gold recipe</strong></p>
<p><u>1X TE (for 100&nbsp;mls)</u></p>
<p>1 ml of 1M Tris, pH 8.0<br />
1 ml of 0.5 mM EDTA<br />
98&nbsp;mls&nbsp;MQ water<br />
Store 4 degrees celsius</p>
<p><u>1X TE + SYBR Gold (for 10&nbsp;mls)</u></p>
<ol>
<li>Filter 10&nbsp;mls&nbsp;1 TE buffer, 0.22 um filter</li>
<li>1:20,0000 dilution of SYBR Gold (Molecular Probes) stock (0.5 ul stock to 10&nbsp;mls&nbsp;TE buffer)</li>
</ol>
Specified by the Principal Investigator(s)
<p><span style="font-size:11px"><strong>DMO notes:</strong></span></p>
<p>-Changed parameter names to meet BCO-DMO naming conventions<br />
-Added ISO_DateTime column<br />
-Removed 4 unnecessary lat/lon columns (2 remain).</p>
<p>&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
Influx Model 209S Mariner Flow Cytometer
Influx Model 209S Mariner Flow Cytometer
PI Supplied Instrument Name: Influx Model 209S Mariner Flow Cytometer PI Supplied Instrument Description:Samples were analyzed on flow cytometer using BD Software (BD Biosciences). Bacterial and viral abundances were analyzed on this 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/
BD Accuri C6
BD Accuri C6
PI Supplied Instrument Name: BD Accuri C6 PI Supplied Instrument Description:Chlorophyll containing cells analyzed on this 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/
Cruise: OC1504A
OC1504A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1504A
Kimberlee Thamatrakoln
Rutgers University
https://musicc2015.wordpress.com
Report describing OC1504A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel