http://lod.bco-dmo.org/id/dataset/652259
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)
Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014
2016-07-21
publication
2016-07-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-06-06
publication
https://doi.org/10.1575/1912/bco-dmo.652259.1
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) Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-07-21 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.652259.1 [access date]
Bacteria and virus abundance data from the MV1405 cruise. Dataset Description: <p>Bacteria and virus abundance data from the MV1405 cruise. Samples were collected by CTD.</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 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 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>TE buffer with SYBR Gold recipe</strong></p>
<p><u>1X TE (for 100&nbsp;mls)</u><br />
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 stock (Molecular Probes) (0.5 ul stock to 10&nbsp;mls&nbsp;TE buffer)&nbsp;</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
cruise_id
station
CTD
depth
date_GMT
yearday_GMT
time_GMT
lat
lon
bacteria
virus
ISO_DateTime_UTC
Influx Model 209S Mariner Flow Cytometer
theme
None, User defined
Cruise identfier
station
cast
depth
date_gmt
year day (Day of Year, or day of year and decimal time)
time_gmt
latitude
longitude
abundance
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Flow Cytometer
instrument
BCO-DMO Standard Instruments
MV1405
service
Deployment Activity
California Coastline
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
California Coastline
-126.6157
-120.02587
34.23125
42.6495
2014-07-04
2014-07-24
Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
0
BCO-DMO catalogue of parameters from Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014
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/652277.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/652278.rdf
Name: station
Units: unitless
Description: <p>station where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/652279.rdf
Name: CTD
Units: unitless
Description: <p>CTD cast</p>
http://lod.bco-dmo.org/id/dataset-parameter/652280.rdf
Name: depth
Units: meters
Description: <p>depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/652281.rdf
Name: date_GMT
Units: unitless
Description: <p>GMT date of cast; mm/dd/yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/652282.rdf
Name: yearday_GMT
Units: unitless
Description: <p>GMT day of year.</p>
http://lod.bco-dmo.org/id/dataset-parameter/652283.rdf
Name: time_GMT
Units: unitless
Description: <p>GMT time of cast; HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/652284.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/652285.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/652286.rdf
Name: bacteria
Units: bacteria per milliliter
Description: <p>bacteria-like particle abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/652287.rdf
Name: virus
Units: VLP per milliliter
Description: <p>virus-like particle abundance (VLP)</p>
http://lod.bco-dmo.org/id/dataset-parameter/652288.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>DateTime (UTC) ISO formatted</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
2611
https://darchive.mblwhoilibrary.org/bitstream/1912/24204/1/dataset-652259_irnbru-mv1405-bacteria-and-virus-abundance__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.652259.1
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 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 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>TE buffer with SYBR Gold recipe</strong></p>
<p><u>1X TE (for 100&nbsp;mls)</u><br />
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 stock (Molecular Probes) (0.5 ul stock to 10&nbsp;mls&nbsp;TE buffer)&nbsp;</li>
</ol>
Specified by the Principal Investigator(s)
<p><span style="font-size:11px"><strong>DMO notes:</strong></span></p>
<p><span style="font-size:11px">- added cruise_id column<br />
- changed column names to meet BCO-DMO standards<br />
- added ISO_DateTime_UTC column<br />
- reformatted lat/</span><span style="font-size:11px">lon</span><span style="font-size:11px"> to appear in decimal degrees<br />
- removed prefix "stn" and "sta" from numbers in station column</span></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 analyzed on flow cytometer using BD Software (BD Biosciences). 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: MV1405
MV1405
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel
MV1405
Kenneth W. Bruland
University of California-Santa Cruz
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel