http://lod.bco-dmo.org/id/dataset/752722
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
2019-01-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacteria cell counts and virus-like particle abundances from Espelandsvegen Fjord, Bergen Norway, May 2017
2021-01-06
publication
2021-01-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-01-06
publication
https://doi.org/10.26008/1912/bco-dmo.752722.1
Kimberlee Thamatrakoln
Rutgers University
principalInvestigator
Kay D. Bidle
Rutgers 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: Thamatrakoln, K., Bidle, K. D. (2021) Bacteria cell counts and virus-like particle abundances from Espelandsvegen Fjord, Bergen Norway, May 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-01-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.752722.1 [access date]
Bergen MesoHux 2017 Bacteria and Virus Abundance Dataset Description: <p>This dataset includes bacterial and virus abundances using flow cytometry from seawater collected in the Norwegian National Mesocosm Centre at the Espegrend (Espeland) Marine Biological Station near Bergen, Norway, in May 2017.</p> Methods and Sampling: <p><strong>Environmental Sample Collection</strong></p>
<ol>
<li>Transfer 1 ml of whole seawater to a 2 ml cryovial.</li>
<li>Add 20 µl of 25% glutaraldehyde for a final concentration of 0.5%.</li>
<li>Incubate at 4°C for 15 min.</li>
<li>Flash freeze in liquid N<sub>2</sub> and store at -80°C.</li>
</ol>
<p><strong>Fluorescent DNA staining (for bacterial and viral abundances)</strong></p>
<ol>
<li>Thaw samples.</li>
<li>To 20 µl of sample, add 980 µl 1X TE buffer with SYBR Gold (see recipe below)</li>
<li>Heat to 80°C for 10 min in the dark</li>
<li>Cool at RT for 10 min in the dark</li>
<li>Analyze via flow cytometry</li>
</ol>
<p><strong>Analysis (for bacterial and viral abundances)</strong></p>
<p>Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Sortware (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 µm fluorescent beads.</li>
<li>A gating hierarchy is established using both beads and previously determined virus and bacteria populations as reference (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. Flow rates are determined using the volumetric method.</li>
<li>Collected data are analyzed using FlowJo v9.9.6. Virus Like Particles (VLPs) are differentiated from bacteria using the gating hierarchy established at time of collection.</li>
</ol>
<p><strong>TE buffer with SYBR Gold recipe</strong><br />
<u>1X TE (for 100 mls)</u><br />
1 ml of 1M Tris, pH 8.0<br />
1 ml of 0.5 mM EDTA<br />
98 mls MQ water<br />
Store 4ºC</p>
<p><u>1X TE + SYBR Gold (for 10 mls)</u><br />
1. Filter 10 mls 1 TE buffer, 0.22 μm filter<br />
2. 1:20,000 dilution of SYBR Gold stock (Molecular Probes) (0.5 μl stock to 10 mls TE buffer)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559179 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559179
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
Kay D. Bidle
Rutgers University
848-932-3467
Department of Marine and Coastal Sciences 71 Dudley Road
New Brunswick
NJ
08901
USA
bidle@marine.rutgers.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Treatment
Bag
Date
Bacteria_abund
Virus_like_particles_abund
Depth
Depth_description
Influx Model 209S Mariner Flow Cytometer
theme
None, User defined
treatment
sample identification
date
abundance
depth
Depth_Loc
featureType
BCO-DMO Standard Parameters
Flow Cytometer
instrument
BCO-DMO Standard Instruments
MesoHux_2017
service
Deployment Activity
Raunefjord, 20 miles south of Bergen
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.
Light-dependent regulation of coccolithophore host-virus interactions: mechanistic insights and implications for structuring infection in the surface ocean
https://osprey.bco-dmo.org/project/632624
Light-dependent regulation of coccolithophore host-virus interactions: mechanistic insights and implications for structuring infection in the surface ocean
<p><em>Description from the NSF award abstract:</em><br />
Phytoplankton, microscopic photosynthetic algae, form the basis of marine foodwebs and are responsible for producing nearly half the oxygen on the planet, yet represent <1% of Earth's biomass. Steady-state maintenance of a high production to biomass ratio implies that, on average, these organisms grow, die and are replaced once every week. Predatory infection by viruses has emerged as the primary mechanism responsible for the high mortality rates of phytoplankton populations. Despite the importance of viral mortality in structuring marine microbial ecosystems, little is known about the fundamental mechanisms that regulate host-virus interactions. Phytoplankton are inherently dependent on light and photosynthesis. Given the need for host resources, the viruses that infect these organisms must, therefore, also fundamentally depend on light and photosynthesis. This project will explore the relationship between light and viral infection to develop a framework for how light influences viral infection and phytoplankton mortality in the surface ocean. The widespread phytoplankton species Emiliania huxleyi, and its associated virus, Coccolithovirus, has emerged as the prominent model system for investigating algal-viral interactions due to its ecological relevance and collective mechanistic insight from numerous physiological, molecular, biochemical, genomic, and field studies. Laboratory-based culture studies will be used to elucidate the role light plays in mediating infection in E. huxleyi, specifically addressing whether light is required for viral infection as well as identifying the light-regulated host metabolic processes that viruses may co-opt for successful infection and production. These observations will then be extended to natural populations using manipulative, field-based experiments to elucidate the role light plays in structuring infection in the surface ocean. This project provides hands-on training for a Rutgers University undergraduate student, as well as a postdoctoral researcher. To facilitate ocean literacy, researchers will work with the Education and Public Outreach staff and Tilapia Film, LLC to develop an educational video based on research findings and the Next Generation Science Standards. This video, aimed at middle, high school, and undergraduate students, expands on an already successful video series that highlights scientific practices through real research investigations. It will be open access and disseminated through existing connections to the New Jersey Science Teacher Association, the National Science Teachers Association, the National Marine Educators Association, and the National Biology Teachers Association. </p>
<p>Predatory infection by viruses is the primary mechanism responsible for the high lysis rates observed in phytoplankton populations. As the most abundant biological entities in aquatic environments, viruses turn over more than a quarter of the photosynthetically-fixed carbon, thereby fueling microbial foodwebs and short-circuiting carbon export to higher trophic levels and the deep sea. Despite its importance, estimates of viral-induced mortality are rarely included in global models of net primary productivity and deep carbon export, in part because we lack a mechanistic understanding of the fundamental factors that regulate host-virus interactions. For viruses infecting obligate photoautotrophs, there is an inherent and fundamental interaction between light and the infection process, as well as a dependence on light-regulated host metabolic processes that may be required for viral replication. Using the model algal host, Emiliania huxleyi and its associated Coccolithovirus, this project addresses the hypotheses that: 1) infection dynamics in E. huxleyi are driven through light-dependent processes, specifically that light mediates viral entry and replication, and that viruses redirect host energy to maximize viral replication, and 2) light increases viral decay relieving hosts of viral pressure. This mechanistic, cellular framework will then be used to elucidate the role light plays in structuring infection in natural coccolithophore populations using manipulative field-based experiments. Given that light is one of the most fundamental, readily, and easily measured features of the ocean, this work will ultimately provide a context for modeling the biogeochemical impact of viral infection in the global ocean.</p>
Light-dependent host virus interactions
largerWorkCitation
project
eng; USA
biota
oceans
Raunefjord, 20 miles south of Bergen
5.218738
5.218738
60.269602
60.269602
2017-05-08
2017-05-30
Norwegian National Mesocosm Centre at the Espegrend Marine Biological Station (60 16'25N, 5 14'10E)
0
BCO-DMO catalogue of parameters from Bacteria cell counts and virus-like particle abundances from Espelandsvegen Fjord, Bergen Norway, May 2017
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/752732.rdf
Name: Treatment
Units: unitless
Description: <p>nutrient amendment and/or manipulation:<br />
Fjord = water sampled directly from fjord adjacent to mesocosm bags<br />
Ambient = unamended<br />
P-limited=N:P (66:1; 4 µmol L-1 sodium nitrate:0.06 µmol L-1 sodium phosphate) added on 13-May, 14-May, 15-May-<br />
Redfield = N:P (16:1; 4 µmol L-1 sodium nitrate:0.25 µmol L-1 sodium phosphate ) added on 13-May, 14-May, 15-May<br />
Redfield/Shaded = N:P (16:1; 4 µmol L-1 sodium nitrate:0.25 µmol L-1 sodium phosphate) added on 13-May, 14-May, 15-May-; bags shaded to 20% surface irradiance on 24-May-2017)</p>
http://lod.bco-dmo.org/id/dataset-parameter/752733.rdf
Name: Bag
Units: unitless
Description: <p>Bag #</p>
http://lod.bco-dmo.org/id/dataset-parameter/752734.rdf
Name: Date
Units: unitless
Description: <p>Date formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/752735.rdf
Name: Bacteria_abund
Units: cells/milliliter
Description: <p>Bacteria cell counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/752736.rdf
Name: Virus_like_particles_abund
Units: viruses/milliliter
Description: <p>virus-like particle counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/835426.rdf
Name: Depth
Units: meters
Description: <p>sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/835427.rdf
Name: Depth_description
Units: unitless
Description: <p>depth of sampling: surface = ~1 m; deep = ~5 m</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
20350
https://darchive.mblwhoilibrary.org/bitstream/1912/26533/1/dataset-752722_bergen-mesohux-2017-bacteria-and-virus-abundance__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.752722.1
download
onLine
dataset
<p><strong>Environmental Sample Collection</strong></p>
<ol>
<li>Transfer 1 ml of whole seawater to a 2 ml cryovial.</li>
<li>Add 20 µl of 25% glutaraldehyde for a final concentration of 0.5%.</li>
<li>Incubate at 4°C for 15 min.</li>
<li>Flash freeze in liquid N<sub>2</sub> and store at -80°C.</li>
</ol>
<p><strong>Fluorescent DNA staining (for bacterial and viral abundances)</strong></p>
<ol>
<li>Thaw samples.</li>
<li>To 20 µl of sample, add 980 µl 1X TE buffer with SYBR Gold (see recipe below)</li>
<li>Heat to 80°C for 10 min in the dark</li>
<li>Cool at RT for 10 min in the dark</li>
<li>Analyze via flow cytometry</li>
</ol>
<p><strong>Analysis (for bacterial and viral abundances)</strong></p>
<p>Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Sortware (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 µm fluorescent beads.</li>
<li>A gating hierarchy is established using both beads and previously determined virus and bacteria populations as reference (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. Flow rates are determined using the volumetric method.</li>
<li>Collected data are analyzed using FlowJo v9.9.6. Virus Like Particles (VLPs) are differentiated from bacteria using the gating hierarchy established at time of collection.</li>
</ol>
<p><strong>TE buffer with SYBR Gold recipe</strong><br />
<u>1X TE (for 100 mls)</u><br />
1 ml of 1M Tris, pH 8.0<br />
1 ml of 0.5 mM EDTA<br />
98 mls MQ water<br />
Store 4ºC</p>
<p><u>1X TE + SYBR Gold (for 10 mls)</u><br />
1. Filter 10 mls 1 TE buffer, 0.22 μm filter<br />
2. 1:20,000 dilution of SYBR Gold stock (Molecular Probes) (0.5 μl stock to 10 mls TE buffer)</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- re-formatted date from d-Mon-yy to yyyy-mm-dd<br />
- replaced commas with semicolons<br />
- reordered columns; sorted records by Treatment, Bag#, Depth<br />
-&nbsp;changed column name Depth to Depth_description (shallow, deep) and added column Depth (1, 5)</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:Use to make cell counts of bacteria and virus particles. 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/
Deployment: MesoHux_2017
MesoHux_2017
National Mesocosm Centre
National Mesocosm Centre
National Mesocosm Centre
National Mesocosm Centre