http://lod.bco-dmo.org/id/dataset/558294
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
2015-05-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral analyzed in the Vega Thurber lab at Florida International University, North Miami, FL (Coral Virus project)
2015-05-12
publication
2015-05-12
revision
BCO-DMO Linked Data URI
2015-05-12
creation
http://lod.bco-dmo.org/id/dataset/558294
Rebecca Vega Thurber
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: Vega Thurber, R. (2015) Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral analyzed in the Vega Thurber lab at Florida International University, North Miami, FL (Coral Virus project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 12 May 2015) Version Date 2015-05-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/558294 [access date]
Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral. Dataset Description: <p>These two viral metagenomes were derived from 1) an apparently healthy <em>Montastrea cavernosa</em> coral maintained in 28.0 degrees C, and 2) a heat stressed <em>M. cavernosa</em> coral which was exposed to 31.5 degrees C for 12 hours.</p>
<p>The experiment was conducted in North Miami, Florida, USA, at Florida International University. Specimens were collected at Key West, FL, USA.</p>
<p><strong>Status Note [ 12 May 2015 ]:</strong> These data are stored at the MG-RAST Server <a href="http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeSearch" target="_blank">http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeSearch</a> under ID numbers: 44551158.3 and 44551159.3. However, at this time, these data are not publicly available. Links will be provided here once the data are available online through MG-RAST.</p> Methods and Sampling: <p>For complete details see Correa et al. (2012).</p>
<p>Following treatment, the tissue layer from each fragment was removed using an airbrush and 0.02 mm filtered viral-free 1_ PBS (pH 7.8). Coral and coral symbiont homogenates were collected in sterile tri-pour containers and pre-filtered with an 1-mm nucleopore filter (Whatman, Piscataway, NJ,USA). VLPs were concentrated from 27 ml of homogenate using ultracentrifugation of four-layer (1.2, 1.35, 1.5 and 1.7 g ml<sup>-1</sup>) cesium chloride density gradients (Vega Thurber et al., 2009). A gray band formed in the 1.2 g ml<sup>-1</sup> density layer (Supplementary Figure 1a) and was harvested using an 18-gage needle and sterile syringe. Before and following a 0.22-mm Sterivex (Millipore, Billerica,MA, USA) filtration step (for details, see Vega Thurber et al. (2009)), this fraction was visualized using epifluorescence microscopy and SYBR Gold (Invitrogen, Carlsbad, CA, USA) staining (Noble and Fuhrman, 1998; Vega Thurber et al., 2009).</p>
<p><strong>Related publications:</strong><br />
Correa, A.M., Welsh, R.M., and Vega Thurber, R.L. 2012. Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals. ISME J., 7(1): 13-27. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.75" target="_blank">10.1038/ismej.2012.75</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1242064 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1242064
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0960937 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0960937
onGoing
Rebecca Vega Thurber
Oregon State University
rvegathurber@gmail.com
pointOfContact
asNeeded
Dataset Version: 12 May 2015
Unknown
Vega_Thurber_Coral_Virus
service
Deployment Activity
Florida International University, North Miami, FL
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.
Effects of Viruses on Coral Fitness
https://osprey.bco-dmo.org/project/527434
Effects of Viruses on Coral Fitness
<p><em>Description from NSF Award Abstract:</em><br />
Corals are important ecosystem engineers, providing habitat and nutrient recycling to tropical reefs. However, coral species richness and abundance are in decline world-wide, due in large part to anthropogenic impacts stemming from global industrialization and human population growth. Over the past several decades, global coral cover is estimated to have declined between ~20 to 60%, and approximately one-third of all known reef-building corals currently face an elevated risk of extinction. Coral disease is a major contributor to this decline of tropical reefs, and therefore, investigations into the causes of and remedies to these diseases are of critical importance. Currently little is known about viruses that infect corals. This project will address this issue.</p>
<p>Herpes-like viruses have been shown to be produced in coral tissues after acute episodes of stress.Viral diversity characterization, however, does not inform scientists about the effects of viral infection on coral hosts. This project will investigate whether viral infection in corals leads to disease and/or reductions in coral reproductive fitness. Specifically, this project aims to compare and contrast the relative abundance and diversity of viruses present in coral tissues during episodes of diseases, particularly, growth anomalies in Porites species and white plague disease in Montastraea species. Pyrosequencing of viral DNA will be conducted on healthy and diseased corals to: i) characterize new viral types, ii) determine whether viral types are associated with particular diseases, and iii) address the central hypothesis that viruses contribute to reduced coral fitness. Sequence analysis and functional annotation of coral viromes will determine the phylogenetic and evolutionary relationships of these viruses and identify viral mechanisms of host infection and disease. The role of viruses in host fitness will be further explored using coral fecundity and larval survivorship and settlement experiments on the model coral, Acropora millepora. Viruses will be isolated from adults, egg bundles, and larvae, in order to determine the transmission mode and ontogenic fitness effects of viral infection.</p>
<p>This proposal will expand the coral taxa, diseases, developmental stages, and geographic regions from which viruses have been characterized, broadening our general knowledge about the diversity of these coral parasites. The examination of viral consortia in healthy and diseased corals combined with viral inoculation experiments will then take the next step and provide scientists clues about the ecological roles that viruses play in coral reef ecosystems. This combination of high-throughput sequencing and microscopy-based methods will lead to a more comprehensive picture of the diversity and role(s) of coral viruses in holobiont fitness and disease. Lastly, insight into how viruses are transmitted will give policymakers better information about how to control viral outbreaks, including limiting the spread of infection and disease.</p>
<p>Recent metagenomics work has begun to uncover unique viral assemblages associated with a variety of ecosystems. To a large extent, this work has focused on phages from the open ocean and temperate coasts. This project will use similar methods to investigate viruses in tropical stony corals, a group of highly threatened organisms which provide a multitude of ecosystem services to marine organisms and local communities. The characterization of viral consortia in healthy, diseased, and different life stages of corals will provide scientists clues about the roles that viruses play in the establishment, health, and resilience of these critical ecosystem engineers.</p>
<p><strong>Note:</strong> Funding for this project has transferred from award OCE-0960937 to OCE-1242064, coincident with Principal Investigator's affiliation change.</p>
Coral Virus
largerWorkCitation
project
eng; USA
oceans
Florida International University, North Miami, FL
2015-05-12
St. Thomas, US Virgin Islands, USA; Heron Island, QLD, Australia; Orpheus Island, QLD, Australia; Kona ,Hawaii, USA; Moorea, French Polynesia.
0
BCO-DMO catalogue of parameters from Viral metagenomes derived from an apparently healthy M. cavernosa coral and a heat-stressed M. cavernosa coral analyzed in the Vega Thurber lab at Florida International University, North Miami, FL (Coral Virus 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
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
https://osprey.bco-dmo.org/dataset/558294/data/download
download
onLine
dataset
<p>For complete details see Correa et al. (2012).</p>
<p>Following treatment, the tissue layer from each fragment was removed using an airbrush and 0.02 mm filtered viral-free 1_ PBS (pH 7.8). Coral and coral symbiont homogenates were collected in sterile tri-pour containers and pre-filtered with an 1-mm nucleopore filter (Whatman, Piscataway, NJ,USA). VLPs were concentrated from 27 ml of homogenate using ultracentrifugation of four-layer (1.2, 1.35, 1.5 and 1.7 g ml<sup>-1</sup>) cesium chloride density gradients (Vega Thurber et al., 2009). A gray band formed in the 1.2 g ml<sup>-1</sup> density layer (Supplementary Figure 1a) and was harvested using an 18-gage needle and sterile syringe. Before and following a 0.22-mm Sterivex (Millipore, Billerica,MA, USA) filtration step (for details, see Vega Thurber et al. (2009)), this fraction was visualized using epifluorescence microscopy and SYBR Gold (Invitrogen, Carlsbad, CA, USA) staining (Noble and Fuhrman, 1998; Vega Thurber et al., 2009).</p>
<p><strong>Related publications:</strong><br />
Correa, A.M., Welsh, R.M., and Vega Thurber, R.L. 2012. Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals. ISME J., 7(1): 13-27. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.75" target="_blank">10.1038/ismej.2012.75</a></p>
Specified by the Principal Investigator(s)
<p>Approximately 2 ug of cDNA of each sample was pyrosequenced on a Roche Titanium 454 platform at the Broad Institute (Massachusetts Institute of Technology, Cambridge, MA, USA). SFF files were converted to FASTA and FASTAQ files, and each read was parsed and assigned an alphanumeric name. Reads were archived at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) (ID SRA052068), as well as at CAMERA (IDs CAM_SMPL_000711 and CAM_SMPL_000712) (Sun et al., 2011) and MG-RAST (IDs 4455158.3 and 4455159.3).</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
Deployment: Vega_Thurber_Coral_Virus
Vega_Thurber_Coral_Virus
lab_FIU
laboratory
lab_FIU
laboratory