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Data server object:  sra_bleach_nonbleach




  
    Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016
    
  
  
    
    

Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016

Website: https://www.bco-dmo.org/dataset/844868
Data Type: experimental, Other Field Results
Version: 1
Version Date: 2021-03-12

Project
» Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling (Moorea Virus Project)
ContributorsAffiliationRole
Thurber, AndrewOregon State University (OSU-CEOAS)Principal Investigator
Messyasz, AdrianaOregon State University (OSU)Student, Contact
York, Amber D.Woods Hole Oceanographic Institution (WHOI BCO-DMO)Data Manager

Abstract
Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016. All sequences are available in the Short Read Archive (SRA) at The National Center for Biotechnology Information (NCBI)under BioProject PRJNA647466 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA647466).


Coverage

Spatial Extent: Lat:-17.28 Lon:-149.49
Temporal Extent: 2016-03

Dataset Description

A processed version of these data were published in Messyasz et al. (2020) (all tables and figures).

All sequences are available in the Short Read Archive (SRA) at The National Center for Biotechnology Information (NCBI).  BioSample and SRA accessions can be accessed from the BioProject PRJNA647466 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA647466).


Acquisition Description

Location: Mo’orea, French Polynesia, Pacific Ocean.

Sampling and analytical procedures: 

Pocillopora spp. coral fragments were collected in situ on SCUBA using bone-cutters. For each coral sample, fragments were airbrushed with 1.5 mL of Qiagen Dneasy Kit lysis buffer and the resulting coral tissue slurry was used for whole community DNA extraction with a Dneasy Kit. For metagenome generation, the extracted DNA from the coral fragments were cleaned with Zymo DNA Clean and Concentrator- 5 Kits and eluted into Ultra-pure H2O for sequencing. DNA from each coral sample was prepared for sequencing with the PrepX DNA Library Kit, then sequenced on the Illumina HiSeq 3000 platform (2 × 150 paired-end).


Processing Description

The only data processing was done by the sequencing facility which included stripping of sequencing primers and bar codes.  No other data manipulation was done.

BCO-DMO Data Manager Notes:
* Data in file "biosample_result.txt" imported into the BCO-DMO data system.
* Sample latitude, longitude, year and month added to the data table from information under the BioSamples at NCBI.
* Modified parameter (column) names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed.  Can not start with a number.  (spaces, +, and - changed to underscores). 
* Converted Date format to ISO 8601 format yyyy-mm-dd


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Related Publications

Messyasz, A., Rosales, S. M., Mueller, R. S., Sawyer, T., Correa, A. M. S., Thurber, A. R., & Vega Thurber, R. (2020). Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses. Frontiers in Marine Science, 7. doi:10.3389/fmars.2020.555474
Results

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Related Datasets

IsRelatedTo
Oregon State University. Comparison of Viral Metagenomes from Bleached and Non-Bleached Pocillopora spp. Corals. 2020/07. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA647466. NCBI:BioProject: PRJNA647466.

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Parameters

ParameterDescriptionUnits
Sample_IDUnique sample identifier consistent within the study. unitless
BioSampleBioSample accession identifier at NCBI. The associated Sequence Read Archive (SRA) sequences can be found by searching by BioSample. unitless
DescriptionType of data (all are environmental metagenomes) unitless
SpeciesSpecies identified. Pocillopora in Mo’orea form a species complex that is morphologically indistinguishable, while these were most similar to Pocillopora meandrina, they are indicated as Pocillopora sp. unitless
TreatmentCorals were either bleached (having lost their photosynthetic symbionts) or non-bleached. unitless
ReplicatePaired corals were collected adjacent to each other with one being bleached and the other not. Corals with the same replicate ID were adjacent to each other on the reef at the time of collection. unitless
YearSample year in format yyyy. unitless
MonthSample month (numeric month) unitless
LatSample latitude (South is negative). decimal degrees
LonSample longitude (West is negative) decimal degrees


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Instruments

Dataset-specific Instrument Name
Illumina HiSeq 3000
Generic Instrument Name
Automated DNA Sequencer
Dataset-specific Description
Sequencing was performed on the Illumina HiSeq 3000 sequencing platform at the Center for Genome Research and Biocomputing at Oregon State University.
Generic 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.


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Project Information

Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling (Moorea Virus Project)

Coverage: Moorea, French Polynesia, Pacific 17 S 150 W


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.

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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)

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This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database.    2021-11-26  21:06:11