http://lod.bco-dmo.org/id/dataset/845039
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
2021-03-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral associated microbes on coral, sediment and water sampled from coral reefs in Mo'orea, French Polynesia in 2017 and 2018
2021-03-14
publication
2021-03-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-04-23
publication
https://doi.org/10.26008/1912/bco-dmo.845039.1
Andrew Thurber
Oregon State University
principalInvestigator
Adrienne Simoes Correa
Rice University
principalInvestigator
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
documentDigital
Cite this dataset as: Thurber, A., Vega Thurber, R., Correa, A. S. (2021) Coral associated microbes on coral, sediment and water sampled from coral reefs in Mo'orea, French Polynesia in 2017 and 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-03-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.845039.1 [access date]
Bacteria and Archaea found on coral, sediment, and water in Mo’orea, French Polynesia Dataset Description: Acquisition Description: <p><strong>Coral, water and sediment were sampled at 21 sites around the island of Mo’orea, French Polynesia in September 2017 and March 2018.&nbsp; </strong>Locations included Forereef on the oceanic side of the reef crest, Backreef on the lagoonal side of the reef crest, and Fringing Reef adjacent to the shoreline.&nbsp;</p>
<p><strong>Coral:</strong> Individual corals from three&nbsp;species&nbsp;(<em>Acropora hyacinthus</em>, <em>Porites lobata</em>, and <em>Pocillopora</em> <em>sp.</em>)&nbsp;were tagged and repeatedly sampled twice a year in the rainy and dry seasons at&nbsp;depths between 1 and 10 meter water depth.&nbsp;&nbsp;Note that <em>Pocillopora</em> are a species complex on the Island of Mo’orea and while all individuals appeared to be <em>Pocillopora meandrina</em>, different species of this genus are morphologically indistinguishable at the size of these corals.&nbsp; Sampling was done free-diving or&nbsp;on SCUBA, with individual corals sampled using bone cutters (or chisels for <em>P. lobata</em>)&nbsp;that had been flame sterilized prior to each day's collection and were used only for that species to eliminate cross-species contamination. Corals with the same ID are the same individual sampled over time.&nbsp;All collections were done while wearing nitrile gloves. Upon return to the boat, coral fragments were placed in Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees C) until processing.&nbsp;<br />
<br />
<strong>Sediment</strong>: 2 milliliters of sediment were collected by gloved hands in sterile ‘snap-cap’ vials. Upon return to the boat samples were added to Zymo DNA/RNA shield and kept cold on Techni ice (frozen to –80 degrees C) until processing.&nbsp;&nbsp;</p>
<p><strong>Water:</strong> 500 milliliters of seawater was collected and kept chilled until it was filtered onto a 0.1 micron&nbsp;filter, then put into Zymo DNA/RNA shield and kept cold on Techni ice (frozen to –80 degrees C) until processing.</p>
<p><strong>Sample&nbsp;processing:</strong><br />
Initial processing included bead beating of all samples prior to them being frozen at -80 degrees C and shipped back to either Rice University or Oregon State University. Coral and sediment were extracted using the ZYMO quick-DNA extraction kit and water samples with Qiagen Powerwater DNA extraction kit. DNA was amplified (at OSU) following the Earth Microbiome Project protocols, using the updated primers of 515f (Parada et al. 2016) and 806r (Apprill et al. 2015). Due to co-amplification of eukaryotic 12S rRNA genes, DNA was size selected using Blue Pippin (Sage Scientific) prior to sequencing to minimize 12S sequence generation.&nbsp;Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.&nbsp; While we used forward and reverse barcoding for sequencing, reverse read quality scores were not acceptable and only forward reads were used and uploaded to the SRA.&nbsp; In certain cases, there were repeated sequencing runs for individual samples.&nbsp; That is indicated with different numbers.</p>
<p dir="ltr">Accession numbers of DNA sequences generated as part of this project are archived and available in the National Center for Biotechnology Information (NCBI)&nbsp;Short Read Archive under BioProject Identifier PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635798 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1635798
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635913 Award URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1635913
completed
Andrew Thurber
Oregon State University
5417374500
103 CEAOS Admin Bldg.
Corvallis
OR
973318507
US
athurber@coas.oregonstate.edu
pointOfContact
Adrienne Simoes Correa
Rice University
713-348-3054
6100 Main St, MS-170
Houston
TX
77005
US
ac53@rice.edu
pointOfContact
Rebecca Vega Thurber
Oregon State University
541-737-1851
220 Nash Hall Oregon State University
Corvallis
OR
97331
USA
Rebecca.Vega-Thurber@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioSample_accession
Sample_name
Organism
Year
Month
Depth
Env_Local_Scale
Geo_Loc_Name
Latitude
Longitude
Host
Host_Subject_ID
Sequencing_Replicate
Illumina MiSeq platform
SCUBA
BluePippin
theme
None, User defined
accession number
sample identification
sample type
year
month of year
depth
site description
region
latitude
longitude
replicate
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Diving Mask and Snorkel
Self-Contained Underwater Breathing Apparatus
Agarose Gel Electrophoresis System
instrument
BCO-DMO Standard Instruments
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.
Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling
https://www.bco-dmo.org/project/713328
Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling
<p>Ecologically and economically, coral reefs are among the most valuable ecosystems on Earth. These habitats are estimated to harbor up to nine million species, contribute ~30 billion US dollars annually to the global economy, and are tropical epicenters of biogeochemical cycling. Global (climate change) and local (nutrient pollution and overfishing) stressors are drivers of coral reef decline that can disrupt the symbiotic associations among corals and resident microbial communities, including dinoflagellate algae, bacteria, and viruses. Viruses interact with all living cellular organisms, are abundant in oceans, and integral to marine ecosystem functioning. This project will be the first to quantify the variability of viral infection in corals across different reef habitats and across time. This will increase our understanding of the total diversity of coral viruses and illuminate the full suite of factors that trigger viral outbreaks on reefs. At the same time the project will evaluate how carbon and nitrogen cycling are altered on coral reefs as a result of global and local stressors that trigger viral infection. This project will ultimately broaden our understanding of the impacts of viruses on reefs beyond their role as putative disease agents. Results of the project will be communicated broadly in scientific arenas, in K-12, undergraduate, and graduate education and training programs, and to the general public through video and multimedia productions, as well as outreach events. 2-D Reef Replicas from our field sites across Moorea will be constructed, allowing children and adults in the US and French Polynesia to 'become' marine scientists and use quadrats, transect tapes, and identification guides to quantify metrics of reef change. Three graduate students will be involved in all aspects of the research and an effort will be made to recruit and support minority students. All datasets will be made freely available to the public and newly developed methods from this project will serve as an important set of springboard tools and baselines for future lines of inquiry into the processes that influence reef health.</p>
<p>Coral reefs, found in nutrient-poor shallow waters, are biodiversity and productivity hotspots that provide substantial ecological and societal benefits. Corals energetically subsidize these oligotrophic ecosystems by releasing significant amounts of mucus (an organic carbon and nitrogen-rich matrix) into the surrounding seawater. Viral production in reef waters can be a significant portion of total reef carbon cycling, accounting for ~10% of gross benthic carbon fixation in reef ecosystems. Viruses are also ~10 times more abundant on coral surfaces than in the water column meaning that viral infection experienced by corals during stress likely results is an increase in carbon and perhaps nitrogen flux to the water column. Thus phages and eukaryotic viruses may be responsible for shifting reef health and function directly via coral and symbiont infection and by altering biogeochemical cycling in host colonies and the adjacent reef system. The main goal of this project is to experimentally interrogate and then model the links among viral infections, declines in coral and reef health, and associated shifts in biogeochemical cycling in reef ecosystems. Lab and field experiments will be conducted at the Moorea Coral Reef LTER to characterize the spatiotemporal dynamics of viruses within two dominant reef-building coral species that differ in their susceptibility to abiotic stress. A novel viral infection and induction approach will be coupled with stable isotopic pulse-chase experiments to quantify and track carbon and nitrogen flux out of coral holobionts (host and microbial symbionts) and into dissolved and particulate pools. In these experiments, virus, bacteria, and symbiont abundance, diversity, and function will be measured simultaneously with the health and activity of the host. Pulse-chase techniques, as well as flux- and niche-based modeling, will result in a holistic understanding of how corals and associated viruses impact reef energy budgets and the ramifications of carbon and nitrogen flux for reef communities. Ultimately, this project will quantify and describe an integrated mechanism by which environmental stressors alter viral, microbial, and coral diversity and, consequently, ecosystem function.</p>
Moorea Virus Project
largerWorkCitation
project
eng; USA
biota
oceans
-149.921
-149.762
-17.58
-17.4721
2017-09-01
2018-03-31
Moorea, French Polynesia, Pacific 17 S 150 W
0
BCO-DMO catalogue of parameters from Coral associated microbes on coral, sediment and water sampled from coral reefs in Mo'orea, French Polynesia in 2017 and 2018
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/846926.rdf
Name: BioSample_accession
Units: unitless
Description: NCBI Short Read Archive BioSample accession identifier
http://lod.bco-dmo.org/id/dataset-parameter/846927.rdf
Name: Sample_name
Units: unitless
Description: Unique Sample ID
http://lod.bco-dmo.org/id/dataset-parameter/846928.rdf
Name: Organism
Units: unitless
Description: Host organism from which environmental metagenome was made
http://lod.bco-dmo.org/id/dataset-parameter/846929.rdf
Name: Year
Units: dimensionless
Description: Year of sample collection from environment
http://lod.bco-dmo.org/id/dataset-parameter/846930.rdf
Name: Month
Units: dimensionless
Description: Month of sample collection from environment
http://lod.bco-dmo.org/id/dataset-parameter/846931.rdf
Name: Depth
Units: meters
Description: Seawater depth from which the sample was collected
http://lod.bco-dmo.org/id/dataset-parameter/846932.rdf
Name: Env_Local_Scale
Units: unitless
Description: Reef type (forereef= oceanic side of the reef crest, backreef= lagoonal side of the reef crest, fringing reef= adjacent to the shoreline)
http://lod.bco-dmo.org/id/dataset-parameter/846933.rdf
Name: Geo_Loc_Name
Units: unitless
Description: Geographic location
http://lod.bco-dmo.org/id/dataset-parameter/846934.rdf
Name: Latitude
Units: decimal degrees
Description: Latitude of sample collection
http://lod.bco-dmo.org/id/dataset-parameter/846935.rdf
Name: Longitude
Units: decimal degrees
Description: Longitude of sample collection
http://lod.bco-dmo.org/id/dataset-parameter/846936.rdf
Name: Host
Units: unitless
Description: Sediment, Water, or Coral species
http://lod.bco-dmo.org/id/dataset-parameter/846937.rdf
Name: Host_Subject_ID
Units: unitless
Description: Identification of individual tagged corals that were repeatedly sampled. (Water and sediment have only one sample at each site)
http://lod.bco-dmo.org/id/dataset-parameter/846938.rdf
Name: Sequencing_Replicate
Units: unitless
Description: Repeated sequencing runs for individual samples
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://www.bco-dmo.org/dataset/845039/data/download
download
onLine
dataset
<p><strong>Coral, water and sediment were sampled at 21 sites around the island of Mo’orea, French Polynesia in September 2017 and March 2018.&nbsp; </strong>Locations included Forereef on the oceanic side of the reef crest, Backreef on the lagoonal side of the reef crest, and Fringing Reef adjacent to the shoreline.&nbsp;</p>
<p><strong>Coral:</strong> Individual corals from three&nbsp;species&nbsp;(<em>Acropora hyacinthus</em>, <em>Porites lobata</em>, and <em>Pocillopora</em> <em>sp.</em>)&nbsp;were tagged and repeatedly sampled twice a year in the rainy and dry seasons at&nbsp;depths between 1 and 10 meter water depth.&nbsp;&nbsp;Note that <em>Pocillopora</em> are a species complex on the Island of Mo’orea and while all individuals appeared to be <em>Pocillopora meandrina</em>, different species of this genus are morphologically indistinguishable at the size of these corals.&nbsp; Sampling was done free-diving or&nbsp;on SCUBA, with individual corals sampled using bone cutters (or chisels for <em>P. lobata</em>)&nbsp;that had been flame sterilized prior to each day's collection and were used only for that species to eliminate cross-species contamination. Corals with the same ID are the same individual sampled over time.&nbsp;All collections were done while wearing nitrile gloves. Upon return to the boat, coral fragments were placed in Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees C) until processing.&nbsp;<br />
<br />
<strong>Sediment</strong>: 2 milliliters of sediment were collected by gloved hands in sterile ‘snap-cap’ vials. Upon return to the boat samples were added to Zymo DNA/RNA shield and kept cold on Techni ice (frozen to –80 degrees C) until processing.&nbsp;&nbsp;</p>
<p><strong>Water:</strong> 500 milliliters of seawater was collected and kept chilled until it was filtered onto a 0.1 micron&nbsp;filter, then put into Zymo DNA/RNA shield and kept cold on Techni ice (frozen to –80 degrees C) until processing.</p>
<p><strong>Sample&nbsp;processing:</strong><br />
Initial processing included bead beating of all samples prior to them being frozen at -80 degrees C and shipped back to either Rice University or Oregon State University. Coral and sediment were extracted using the ZYMO quick-DNA extraction kit and water samples with Qiagen Powerwater DNA extraction kit. DNA was amplified (at OSU) following the Earth Microbiome Project protocols, using the updated primers of 515f (Parada et al. 2016) and 806r (Apprill et al. 2015). Due to co-amplification of eukaryotic 12S rRNA genes, DNA was size selected using Blue Pippin (Sage Scientific) prior to sequencing to minimize 12S sequence generation.&nbsp;Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.&nbsp; While we used forward and reverse barcoding for sequencing, reverse read quality scores were not acceptable and only forward reads were used and uploaded to the SRA.&nbsp; In certain cases, there were repeated sequencing runs for individual samples.&nbsp; That is indicated with different numbers.</p>
<p dir="ltr">Accession numbers of DNA sequences generated as part of this project are archived and available in the National Center for Biotechnology Information (NCBI)&nbsp;Short Read Archive under BioProject Identifier PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406).&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Data processing:</strong><br />
The only data processing was done by the sequencing facility which included stripping of sequencing primers and bar codes.&nbsp; No other data manipulation was done.</p>
<p dir="ltr"><strong>BCO-DMO processing description:</strong><br />
The original data submitted in CSV file "AroundIsland_Metadata_final.csv" was modified during processing:<br />
-&nbsp;Adjusted field/parameter names to comply with database requirements<br />
- Added a conventional header with dataset name, PI names, version date, and BioProject<br />
- Added separate columns for Latitude and Longitude and converted to decimal degrees<br />
- Split column "collection_date" to show separate "Month" and Year" columns</p>
<p dir="ltr">&nbsp;</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
Illumina MiSeq platform
Illumina MiSeq platform
PI Supplied Instrument Name: Illumina MiSeq platform PI Supplied Instrument Description:Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
PI Supplied Instrument Name: PI Supplied Instrument Description:Samples were collected by free diving Instrument Name: Diving Mask and Snorkel Instrument Short Name: Instrument Description: A diving mask (also half mask, dive mask or scuba mask) is an item of diving equipment that allows underwater divers, including, scuba divers, free-divers, and snorkelers to see clearly underwater.
Snorkel: A breathing apparatus for swimmers and surface divers that allows swimming or continuous use of a face mask without lifting the head to breathe, consisting of a tube that curves out of the mouth and extends above the surface of the water.
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: http://oceanexplorer.noaa.gov/technology/diving/diving.html
BluePippin
BluePippin
PI Supplied Instrument Name: BluePippin PI Supplied Instrument Description:BluePippin is a an automated DNA Size Selection System, a preparative electrophoresis platform that uses agarose gel plates.
For this dataset, DNA was size selected using Blue Pippin (Sage Scientific) prior to sequencing to minimize 12S sequence generation
Instrument Name: Agarose Gel Electrophoresis System Instrument Short Name:agarose gel electrophoresis system Instrument Description: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.