http://lod.bco-dmo.org/id/dataset/844568
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
2021-03-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments
2021-03-09
publication
2021-03-09
revision
BCO-DMO Linked Data URI
2021-03-09
creation
http://lod.bco-dmo.org/id/dataset/844568
Adrienne M.S. Correa
Rice 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: Correa, A. M.S. (2021) Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-03-09 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/844568 [access date]
Methods and Sampling: <p>Methodology summary:&nbsp;<br />
<br />
ITS-2 rDNA Symbiodiniaceae community libraries were prepared and PE 300bp reads were generated using Illumina MiSeq platform.&nbsp;</p>
<p>Sampling and analytical procedures:&nbsp;<br />
<br />
Samples were preserved in DNA/RNA shield (Zymo Research, CA) and stored at -20℃ until further processing. DNA was extracted using the ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA) from 20-200 mg of feces, small coral tissue sections (~5 mm<sup>2</sup>), 250 ml sediments and ~1890 ml water using a ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA).<br />
<br />
Sample subject list with aphiaIDs for taxonomic names:</p>
<div>Acropora, 205469<br />
Amanses scopas, 212242<br />
Chaetodon citrinellus, 218744<br />
Chaetodon lunulatus, 398549<br />
Chaetodon ornatissimus, 273352<br />
Chaetodon pelewensis, 273353<br />
Chaetodon reticulatus, 273359<br />
Chlorurus spilurus, 712772<br />
Ctenochaetus flavicauda, 277560<br />
Ctenochaetus striatus, 219659<br />
Pocillopora, 206938<br />
Porites, 206485<br />
Sediment<br />
Water</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635798 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635798
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635913 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635913
onGoing
Adrienne M.S. Correa
Rice University
amsc@berkeley.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Illumina MiSeq platform
theme
None, User defined
Automated DNA Sequencer
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://osprey.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
oceans
2019-01-01
2019-01-01
Moorea, French Polynesia, Pacific 17 S 150 W
0
BCO-DMO catalogue of parameters from Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments
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/844568/data/download
download
onLine
dataset
<p>Methodology summary:&nbsp;<br />
<br />
ITS-2 rDNA Symbiodiniaceae community libraries were prepared and PE 300bp reads were generated using Illumina MiSeq platform.&nbsp;</p>
<p>Sampling and analytical procedures:&nbsp;<br />
<br />
Samples were preserved in DNA/RNA shield (Zymo Research, CA) and stored at -20℃ until further processing. DNA was extracted using the ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA) from 20-200 mg of feces, small coral tissue sections (~5 mm<sup>2</sup>), 250 ml sediments and ~1890 ml water using a ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA).<br />
<br />
Sample subject list with aphiaIDs for taxonomic names:</p>
<div>Acropora, 205469<br />
Amanses scopas, 212242<br />
Chaetodon citrinellus, 218744<br />
Chaetodon lunulatus, 398549<br />
Chaetodon ornatissimus, 273352<br />
Chaetodon pelewensis, 273353<br />
Chaetodon reticulatus, 273359<br />
Chlorurus spilurus, 712772<br />
Ctenochaetus flavicauda, 277560<br />
Ctenochaetus striatus, 219659<br />
Pocillopora, 206938<br />
Porites, 206485<br />
Sediment<br />
Water</div>
Specified by the Principal Investigator(s)
<p>The sequencing data were processed using Symportal (Hume et al., 2019). Samples with &lt;1,000 reads were discarded and sequencing depth was assessed using rarefaction curves. ITS2-profiles were reduced to number of reads per Symbiodiniaceae genus and expressed as percentages. All data were analysed using R version 3.6.1 (R Core Team, 2019).<br />
<br />
BCO-DMO data manager processing notes:<br />
* Data submitted in Excel file "Correa Grupstra 121620 metadata.xlsx" extracted to csv.<br />
* Taxonomic names verified using the World Register or Marine Species taxa match tool.&nbsp; All names matched exactly to accepted taxonomic names (as of 2021-03-09).</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 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.