Microbiome composition of coral species collected from reefs in Mo'orea, French Polynesia and exposed to various experimental treatments in August 2018 (NCEI Accession 0291557)
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title: Microbiome composition of coral species collected from reefs in Mo'orea, French Polynesia and exposed to various experimental treatments in August 2018 (NCEI Accession 0291557)
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abstract: This dataset contains biological and survey - biological data collected in the South Pacific Ocean from 2018-08-01 to 2021-08-31. These data include species. The instruments used to collect these data include Automated DNA Sequencer, Sage Science BluePippin DNA size selection device, and circulating water bath. These data were collected by Andrew Thurber and Rebecca Vega Thurber of Oregon State University as part of the "Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling (Moorea Virus Project)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2022-05-24. The following is the text of the dataset description provided by BCO-DMO: DNA results of Pocillopora cf. meandrina and Acropora hyacinthus Dataset Description: Acquisition Description: Sampling and analytical procedures: Corals of two species ( Pocillopora cf. meandrina and Acropora hyacinthus ) were collected from the reef crest on the north side of the island of Mo'orea, French Polynesia (GPS location: 17.47541 S, 149.8402 W). The fragmented corals were transported to Gump Research Station where they equilibrated for >24 hours in shaded flowing seawater tables. Coral fragments were exposed to slightly elevated bicarbonate (+1 mM) and Ammonium (0.5 mM NH 4 ) for 24 hours prior to being sampled (T0 controls) and then exposed to various experimental treatments to better understand the response of reefs to factors that trigger viral outbreaks. Treatments were: Control: no modification Nutrient: addition of two millimolar nitrate (2mM NO 3 ) Temperature: increase of 3 degrees Celsius (+3 °C ) Coral exudate: addition of a mean of 2 millimolar dissolved organic carbon (DOC) + particulate organic carbon (POC) from a bleaching coral (co-occurring con-specific coral head Exudate: exudate blank is the coral exudate only, with no coral sample added. Blank: water with no coral added Note: Water was filtered (0.2 micron filtration) before being used in the experiment. Corals were kept in individual recirculating water baths. Fragments from a single coral head were exposed to all treatments, with replicate samples of the same coral head sharing the same letter designation. At specified time points (6,12, 24, and 48 hours since exposure to treatment began) corals were sacrificed and water from the water baths (microcosm water) was sampled for microbial community composition by filtering ca. 0.5L water through a 0.2 micron filter (Sterivex-GP 0.22 µm, SVGP01050, Millipore) after which they were frozen. Coral exudate blank clogged the Sterivex filter, resulting in a marked decrease in the amount of water that was filtered. Coral pieces were placed in Zymo DNA/RNA shield. Initial processing of the corals included bead beating and then freezing at -80 °C , followed by shipping to either Rice University or Oregon State University (OSU) for DNA extraction. DNA sequencing DNA was extracted using either the Zymo quick-DNA extraction kit (corals) or the Quigen Powerwater kit (water samples) following manufacturer protocols. 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 sequencing. While we used dual indexed primers during sequencing, reverse read quality scores were not acceptable and only forward reads were used and uploaded to the Sequence Read Archive (SRA). 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. All data associated with this submission has been made available through the NCBI Short Read Archive under BioProject PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406). The accompanying data files list the accessions numbers and sampling information. Sample ID/ Library ID details: B = blank C = control V = exudate VB = exudate blank N = nutrient T = temperature ACR = Acropora POC = Pocillopora "Vd-12_water_Experiment_d" means Exudate, replicate d, 12 hours into treatment, water experiment, replicate d "ACR-Cb-0-20_b2" means Acropora, Control, replicate b, zero time (0 hours into treatment), sequential sample number 20, replicate b2 "POC-Cc-0-44_c3" means Pocillopora, Control, replicate c, 0 hours into treatment, sample number 44, replicate c3
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protocol: HTTP
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description: Institution web page
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name: Oregon State University website
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extent:
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beginPosition: 2018-08-01
endPosition: 2021-08-31
supplementalInformation: (missing)
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distributionInfo: (MD_Distribution)
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distributorContact: (CI_ResponsibleParty)
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electronicMailAddress: NCEI.Info@noaa.gov
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fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
orderingInstructions: Contact NCEI for other distribution options and instructions.
distributorFormat: (MD_Format)
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protocol: FTP
applicationProfile: Any FTP client
name: FTP
description: These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
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name: NCEI Accession 0291557 v1.1
description: published 2024-04-21T16:12:06Z
function: (CI_OnLineFunctionCode) download
role: (inapplicable)
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
