http://lod.bco-dmo.org/id/dataset/954262
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
2025-02-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020
2025-04-08
publication
2025-04-08
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-15
publication
https://doi.org/10.26008/1912/bco-dmo.954262.1
Tom C. Adam
University of California-Santa Barbara
principalInvestigator
Deron Burkepile
University of California-Santa Barbara
principalInvestigator
Thomas J. Sharpton
Oregon State University
principalInvestigator
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Hannah E. Epstein
Oregon State University
principalInvestigator
Emily R. Schmeltzer
Oregon State University
principalInvestigator
Kelly E. Speare
University of California-Santa Barbara
principalInvestigator
Alex Dmitry Vompe
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: Vompe, A. D., Epstein, H. E., Speare, K. E., Schmeltzer, E. R., Adam, T. C., Burkepile, D., Sharpton, T. J., Vega Thurber, R. (2025) Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.954262.1 [access date]
RECHARGE 2018 - 2020 Microbiome Data Dataset Description: Methods and Sampling: <p>Relevant Materials and Methods from Vompe et al. (2023):</p>
<h3><strong>Site and in&nbsp;situ experiment</strong></h3>
<p>Our experimental study site is located on the northern forereef in Mo'orea, French Polynesia (S17° 28.386′ W149° 49.059′). Mo'orea is a tropical, volcanic high island in the Central South Pacific Ocean. A shallow, ~1 km wide lagoon and barrier reef surround the island. The forereef gradually slopes downwards toward the open ocean and is composed of coral spur and sand groove formations. At the inception of our experiment in August 2018, this reef was dominated by scleractinian corals with low abundance of fleshy macroalgae. Coral cover was 56.0 ± 1.0% (mean ± SE) and macroalgae cover was 0.8 ± 0.2% (mean ± SE).</p>
<p>At this site, we have an ongoing in&nbsp;situ experiment investigating tipping points of coral benthic and microbial ecology in response to nutrient enrichment and herbivore reduction, as in Adam et&nbsp;al.&nbsp;(2022). Briefly, our experimental platform is a factorial design at 10 m depth on the forereef, consisting of four herbivore exclosures (~1 m2&nbsp;each) placed over eight natural 30-m2&nbsp;reef plots. The plots are exposed to two levels of nutrient enrichment (four plots ambient/four plots enriched) and four levels of herbivory (exclosures with different size holes of 2.5 cm × 2.5 cm, 5.0 cm × 5.0 cm, 7.5 cm × 7.5 cm, or open top, with one exclosure of each herbivory condition at each plot). Nutrient enrichment was achieved in the plots via PVC tubes with Osmocote® (19-6-12, N-P-K) slow-release garden fertilizer. These tubes were wrapped in plastic mesh to contain the fertilizer. The nutrient enrichment tubes were replaced every 12–16 weeks, except for two periods during the COVID-19 pandemic when travel to Mo'orea was not possible. See&nbsp;Supplementary Methods (Vompe et al. 2023) for a full description of the experimental setup.</p>
<h3><strong>Coral sampling for microbiome analysis</strong></h3>
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">To investigate how the microbiomes of different coral species respond to environmental stress, samples of&nbsp;</span><em>Acropora retusa</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">,&nbsp;</span><em>Porites lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex, and&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. were collected over 2 years (July 2018–August 2020), 3× a year, in March, July or August, and November. Corals in the&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex will be referred to as&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;below for brevity. However, we acknowledge there may be cryptic diversity in our samples (Brown et&nbsp;al.,&nbsp;2021). A nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis distances between&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;sample microbiomes from July 2018 suggests that the possible presence of cryptic members of the&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex in our dataset was unlikely to affect&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;microbiome variation, as there are no obvious sample microbiome composition clusters. The taxonomic name&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. is used for this study because&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species have high cryptic diversity (Johnston et&nbsp;al.,&nbsp;2022), which makes it difficult to visually delineate among species. We selected&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. specimens that had consistent phenotypes similar to those now defined as&nbsp;</span><em>Pocillopora meandrina</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;or Haplotype 8a as described in Figure&nbsp;1 of Johnston et&nbsp;al.&nbsp;(2022). Different coral species, even genotypes, tend to have distinct microbiomes (Bourne et&nbsp;al.,&nbsp;2016; Dunphy et&nbsp;al.,&nbsp;2019; Rosales et&nbsp;al.,&nbsp;2019). A NMDS ordination of Bray–Curtis distances between&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. sample microbiomes from July 2018 suggests that the possible presence of cryptic&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species in our dataset was unlikely to affect&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. microbiome variation, as there are no obvious sample microbiome composition clusters.</span></p>
<p>All colonies of each coral species appeared healthy when initially selected for microbiome sampling. Live tissue on these focal colonies was repeatedly sampled throughout the study regardless of subsequent visual phenotype, as long as live tissue remained. Live tissue was sampled at haphazardly chosen locations on the colonies at each time point. For&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp., haphazardly chosen live branch tips were sampled. For&nbsp;<em>P. lobata</em>, live tissue was sampled from haphazardly chosen locations around the center of the colony. Coral samples were collected in July 2018, November 2018, March 2019, August 2019, November 2019, March 2020, and August 2020, covering a 28-month period. Additional coral colonies were sampled in November 2018, March 2019, and August 2019 to increase sample sizes and to account for initial focal colony mortality. Colonies of each species were also added to the dataset in March 2020 and August 2020 to restore sample size due to colony mortality. Bleaching and mortality data for coral colonies added to the microbiome sampling effort after the start of the experiment were collected retroactively. This was possible because these corals were already present in the exclosures and data could be collected from our photomosaic time series from before they were added to the microbiome sampling effort.</p>
<p>During each sampling event, coral fragments &lt;1 cm3&nbsp;were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Corals were sampled between 08:00 and 14:00 h to help minimize diel microbiome variation. Fragments were immediately placed in sterile 207 mL Whirl-Paks. This volume of sample is sufficient to produce accurate microbiome data without significantly damaging the focal colony (Zaneveld et&nbsp;al.,&nbsp;2016). Upon surfacing, Whirl-paks were placed on ice and transported to shore (~15 min) then transferred to Qiagen DNeasy PowerSoil lysis matrix tubes, containing a guanidinium thiocyanate preservative, using 95% ethanol flame-sterilized forceps. Tubes were stored at −40°C prior to transport on Techni Ice to Oregon State University where they were stored at −80°C until further processing.</p>
<h3><strong>Microbiome analyses</strong></h3>
<p>The V4 region of the 16S rRNA gene was amplified using 515F and 806RB primers from total DNA, then barcoded, purified, and sequenced (Apprill et&nbsp;al.,&nbsp;2015; Parada et&nbsp;al.,&nbsp;2016). Microbiome sequence library generation, sequence processing, and quality control were done as in Williams et&nbsp;al.&nbsp;(2022) with some modifications. See the&nbsp;Supplementary Methods&nbsp;(Vompe et al. 2023) for full protocols and conditions.&nbsp;All microbiome analyses were performed in R v4.2.2, using functions from base R and “tidyverse” (Wickham et&nbsp;al.,&nbsp;2019), as well as functions from a suite of packages developed for microbiome analyses, including “phyloseq” (McMurdie &amp; Holmes,&nbsp;2013), “vegan” (Oksanen et&nbsp;al.,&nbsp;2022), and Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in the “ANCOMBC” package (Lin &amp; Peddada,&nbsp;2020; Vompe et&nbsp;al.,&nbsp;2023).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023701 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023701
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023424 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023424
completed
Tom C. Adam
University of California-Santa Barbara
805-893-7625
UCSB Marine Science Institute Bldg 520 Rm 4002 FI 4L
Santa Barbara
CA
93106
United States
thomascadam@gmail.com
pointOfContact
Deron Burkepile
University of California-Santa Barbara
805-893-3067
Department of Ecology, Evolution, and Marine Biology
Santa Barbara
CA
93106
USA
dburkepile@ucsb.edu
pointOfContact
Thomas J. Sharpton
Oregon State University
thomas.sharpton@oregonstate.edu
pointOfContact
Rebecca Vega Thurber
Oregon State University
rvegathurber@gmail.com
pointOfContact
Hannah E. Epstein
Oregon State University
hannah.epstein@essex.ac.uk
pointOfContact
Emily R. Schmeltzer
Oregon State University
eschmeltzer@usgs.gov
pointOfContact
Kelly E. Speare
University of California-Santa Barbara
kellyspeare@gmail.com
pointOfContact
Alex Dmitry Vompe
Oregon State University
vompealex@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
Date_MonthYear
Coral_Code
Herbivory
Nutrients
Plot
Tag
Batch
Run
AssayType
AvgSpotLen
Bases
BioProject
BioSample
BioSampleModel
Bytes
CenterName
Collection_Date
Consent
DATASTORE_filetype
DATASTORE_provider
DATASTORE_region
env_broad_scale
env_local_scale
env_medium
Experiment
geo_loc_name_country
geo_loc_name_country_continent
geo_loc_name
Host
Instrument
Latitude
Longitude
LibraryName
LibraryLayout
LibrarySelection
LibrarySource
Organism
Platform
ReleaseDate
create_date
version
SRA_Study
unique_sample_identifier
Illumina MiSeq System
bone cutters
Eppendorf Benchtop Centrifuge 5430
Thermo Fisher Scientific Owl A3-1 Large-Gel Electrophoresis System
Invitrogen Qubit 4 Fluorometer
Vortex
Thermocycler
theme
None, User defined
sample identification
date
taxon
treatment
Site_ID
sample description
experiment id
NCBI SRA run accession (SRR)
seq_descrip
NCBI BioProject accession
NCBI BioSample accession
file_size
No BCO-DMO term
NCBI SRA experiment accession (SRX)
region
species scientific name (binomial)
instrument
latitude
longitude
ISO_DateTime_UTC
NCBI SRA study accession (SRP)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
bone cutter
Centrifuge
Electrophoresis Chamber
Qubit fluorometer
Shaker
Thermal Cycler
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: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature
https://osprey.bco-dmo.org/project/850105
Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature
<p><em>NSF Award Abstract:</em><br />
Coral reefs are some of the most diverse, yet most imperiled, ecosystems on the planet. Global change has driven the decline of corals worldwide with many reefs now lacking corals and being overrun by macroalgae. This research examines the impacts of several factors of thermal stress, overfishing of important herbivorous fishes, and nutrient pollution on the health of corals and their ability to recover after large coral-killing disturbances. Importantly, the investigators address the impacts of global change on the coral microbiome, the microbes that associate with corals and impact coral health. The overarching hypothesis is that factors such as overfishing and nutrient pollution impact coral health via impacts to their microbes. This 6-year experiment on the coral reefs of Mo’orea, French Polynesia examines what levels of herbivory, mostly by parrotfishes and surgeonfishes, are needed to provide resistance and resilience of corals and their microbiomes when reefs are exposed to elevated nutrients and ocean temperatures. Notably, the team tests how local stressors (overfishing, nutrient pollution) potentially interact with global stressors (climate change and rising ocean temperatures) to impact coral reef health. This research may yield insight into how to manage local factors (reducing fishing, mitigating nutrient pollution) to help corals survive the global stress of climate change. The field experiment provides a realistic platform to test questions about how local management of fisheries can alter reef health and provides data about the recoverability of reefs should new water quality management be put into place. This interdisciplinary work trains a new generation of both marine ecologists and microbiologists, including one postdoctoral researcher, two graduate students, as well as numerous undergraduates. The main international outreach effort is to map the microbiome of the island of Mo’orea. Mo’orea is approximately 130 square-kilometers in area and has five major watersheds that transport sediment and nutrients to the nearshore coral reef ecosystems. Thus poor stewardship of these watersheds likely contributes to the local phase shifts currently occurring in several areas of the lagoon. Therefore the team has engaged the local community to help collect microbiome samples from 50 terrestrial, 50 stream, 25 coastal sites, and 25 offshore sites around the island. The sampling effort is generating an island-wide map of the microbial communities associated with the soils, streams, and coastal waters that can be linked to adjacent coral reef health - The Moorea Microbiome! As part of this outreach effort, the team also collaborates with filmmakers to make a trilingual (English, French, and Tahitian) film about the project to serve as local engagement and teaching tool to help educate school groups and different stakeholders about both the seen and unseen connections between land and sea on their island.</p>
<p>On the island of Mo’orea, French Polynesia, coral communities have exhibited strikingly different trajectories, with some reefs recovering from disturbances and others undergoing protracted coral decline, accompanied by an increase in macroalgae. This diversity in coral community dynamics makes Mo’orea an excellent model system for testing why some reefs are resilient and return to abundant coral while others are not and undergo persistent phase shifts to macroalgal dominance. This 6-year experiment will measure the dynamics of benthic communities, coral demography, and the coral microbiome across seasonal change in ocean temperature, allowing the team to (1) link changes in coral microbiomes (e.g., a rise in pathogenic bacteria) to the trajectories of coral decline or recovery and (2) link nutrients, herbivory, and temperature to phase shifts in both benthic communities and coral microbiomes. Importantly, the team is testing the resistance of phase shifts of benthic communities and coral microbiomes by measuring their changes after removing the nutrient enrichment treatment at the end of year 3 and tracking recovery of the system for 3 more years. Thus, this project begins to answer whether reef and microbial community phase shifts can be easily reversed once they occur. Many studies have focused on the factors that disassemble coral reef communities, but this is the first to examine how reef communities can be reassembled from the microbiome upwards.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
RECHARGE
largerWorkCitation
project
eng; USA
biota
oceans
-149.81765
-149.81765
-17.4731
-17.4731
2018-07-01
2020-08-31
Mo’orea, French Polynesia
0
BCO-DMO catalogue of parameters from Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020
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/958209.rdf
Name: Sample
Units: unitless
Description: <p>Unique sample name, containing the Illumina MiSeq lane, placeholder sample number, the Nextera barcode sequences, and the unique sample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958210.rdf
Name: Date_MonthYear
Units: unitless
Description: <p>Collection date given as the month and year</p>
http://lod.bco-dmo.org/id/dataset-parameter/958211.rdf
Name: Coral_Code
Units: unitless
Description: <p>Code for the host coral species sampled (Aret = Acropora retusa, Plob = Porites lobata, Poc = Pocillopora)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958212.rdf
Name: Herbivory
Units: unitless
Description: <p>Consumer pressure level generated by the experimental exclosures (1x1, 2x2, 3x3, open)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958213.rdf
Name: Nutrients
Units: unitless
Description: <p>Enrichment condition in the exclosures (Nutrient or Ambient)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958214.rdf
Name: Plot
Units: unitless
Description: <p>Unique plot containing a set of coral exclosures (A1, A2, B3, B4, C1, C3, D2, or D4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958215.rdf
Name: Tag
Units: unitless
Description: <p>Unique colony identifier (numeric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958216.rdf
Name: Batch
Units: unitless
Description: <p>Identifier of Illumina MiSeq run (R1, R2, or R3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958217.rdf
Name: Run
Units: unitless
Description: <p>NCBI SRA SRR identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/958218.rdf
Name: AssayType
Units: unitless
Description: <p>Type of DNA sequencing performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/958219.rdf
Name: AvgSpotLen
Units: unitless
Description: <p>Total across paired reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/958220.rdf
Name: Bases
Units: unitless
Description: <p>Number of bases in the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/958221.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI SRA BioProject containing the sequences from these samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/958222.rdf
Name: BioSample
Units: unitless
Description: <p>SAMN identifier for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/958223.rdf
Name: BioSampleModel
Units: unitless
Description: <p>Type of metagenomic survey</p>
http://lod.bco-dmo.org/id/dataset-parameter/958224.rdf
Name: Bytes
Units: bytes
Description: <p>Total size of the sequencing data files</p>
http://lod.bco-dmo.org/id/dataset-parameter/958225.rdf
Name: CenterName
Units: unitless
Description: <p>Institution where sequencing was conducted</p>
http://lod.bco-dmo.org/id/dataset-parameter/958226.rdf
Name: Collection_Date
Units: unitless
Description: <p>Collection date given as [year]-[month]</p>
http://lod.bco-dmo.org/id/dataset-parameter/958227.rdf
Name: Consent
Units: unitless
Description: <p>Availability of the data</p>
http://lod.bco-dmo.org/id/dataset-parameter/958228.rdf
Name: DATASTORE_filetype
Units: unitless
Description: <p>Available file types for downloading the raw sequencing data</p>
http://lod.bco-dmo.org/id/dataset-parameter/958229.rdf
Name: DATASTORE_provider
Units: unitless
Description: <p>Organizations linked to this repository</p>
http://lod.bco-dmo.org/id/dataset-parameter/958230.rdf
Name: DATASTORE_region
Units: unitless
Description: <p>Data storage region</p>
http://lod.bco-dmo.org/id/dataset-parameter/958231.rdf
Name: env_broad_scale
Units: unitless
Description: <p>General description of the sampling environment</p>
http://lod.bco-dmo.org/id/dataset-parameter/958232.rdf
Name: env_local_scale
Units: unitless
Description: <p>Specific description of the sampling environment at the local scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/958233.rdf
Name: env_medium
Units: unitless
Description: <p>Medium from which DNA was isolated (Coral Tissue or PCR water)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958234.rdf
Name: Experiment
Units: unitless
Description: <p>NCBI SRA SRX identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/958235.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Region where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/958236.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Continent where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/958237.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Specific name of sampling environment</p>
http://lod.bco-dmo.org/id/dataset-parameter/958238.rdf
Name: Host
Units: unitless
Description: <p>Most accurate possible host taxonomy</p>
http://lod.bco-dmo.org/id/dataset-parameter/958239.rdf
Name: Instrument
Units: unitless
Description: <p>Instrument for DNA sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/958240.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of collection, South is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/958241.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of collection, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/958242.rdf
Name: LibraryName
Units: unitless
Description: <p>Equivalent to 'Sample'</p>
http://lod.bco-dmo.org/id/dataset-parameter/958243.rdf
Name: LibraryLayout
Units: unitless
Description: <p>Type of amplicon sequencing performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/958244.rdf
Name: LibrarySelection
Units: unitless
Description: <p>Selection to perform amplicon sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/958245.rdf
Name: LibrarySource
Units: unitless
Description: <p>DNA source type</p>
http://lod.bco-dmo.org/id/dataset-parameter/958246.rdf
Name: Organism
Units: unitless
Description: <p>Organism type (coral reef metagenome or indoor metagenome)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958247.rdf
Name: Platform
Units: unitless
Description: <p>Platform for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/958248.rdf
Name: ReleaseDate
Units: unitless
Description: <p>Public release date for the raw sequencing data</p>
http://lod.bco-dmo.org/id/dataset-parameter/958249.rdf
Name: create_date
Units: unitless
Description: <p>Date the dataset was initially uploaded to the NCBI SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/958250.rdf
Name: version
Units: unitless
Description: <p>Version of the public dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/958251.rdf
Name: SRA_Study
Units: unitless
Description: <p>SRA study Identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/958252.rdf
Name: unique_sample_identifier
Units: unitless
Description: <p>A unique number identifying each sample</p>
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.
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510616
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/defcbd25-e22d-46ef-8eb3-22ff733b767b/content
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https://doi.org/10.26008/1912/bco-dmo.954262.1
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dataset
<p>Relevant Materials and Methods from Vompe et al. (2023):</p>
<h3><strong>Site and in&nbsp;situ experiment</strong></h3>
<p>Our experimental study site is located on the northern forereef in Mo'orea, French Polynesia (S17° 28.386′ W149° 49.059′). Mo'orea is a tropical, volcanic high island in the Central South Pacific Ocean. A shallow, ~1 km wide lagoon and barrier reef surround the island. The forereef gradually slopes downwards toward the open ocean and is composed of coral spur and sand groove formations. At the inception of our experiment in August 2018, this reef was dominated by scleractinian corals with low abundance of fleshy macroalgae. Coral cover was 56.0 ± 1.0% (mean ± SE) and macroalgae cover was 0.8 ± 0.2% (mean ± SE).</p>
<p>At this site, we have an ongoing in&nbsp;situ experiment investigating tipping points of coral benthic and microbial ecology in response to nutrient enrichment and herbivore reduction, as in Adam et&nbsp;al.&nbsp;(2022). Briefly, our experimental platform is a factorial design at 10 m depth on the forereef, consisting of four herbivore exclosures (~1 m2&nbsp;each) placed over eight natural 30-m2&nbsp;reef plots. The plots are exposed to two levels of nutrient enrichment (four plots ambient/four plots enriched) and four levels of herbivory (exclosures with different size holes of 2.5 cm × 2.5 cm, 5.0 cm × 5.0 cm, 7.5 cm × 7.5 cm, or open top, with one exclosure of each herbivory condition at each plot). Nutrient enrichment was achieved in the plots via PVC tubes with Osmocote® (19-6-12, N-P-K) slow-release garden fertilizer. These tubes were wrapped in plastic mesh to contain the fertilizer. The nutrient enrichment tubes were replaced every 12–16 weeks, except for two periods during the COVID-19 pandemic when travel to Mo'orea was not possible. See&nbsp;Supplementary Methods (Vompe et al. 2023) for a full description of the experimental setup.</p>
<h3><strong>Coral sampling for microbiome analysis</strong></h3>
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">To investigate how the microbiomes of different coral species respond to environmental stress, samples of&nbsp;</span><em>Acropora retusa</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">,&nbsp;</span><em>Porites lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex, and&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. were collected over 2 years (July 2018–August 2020), 3× a year, in March, July or August, and November. Corals in the&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex will be referred to as&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;below for brevity. However, we acknowledge there may be cryptic diversity in our samples (Brown et&nbsp;al.,&nbsp;2021). A nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis distances between&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;sample microbiomes from July 2018 suggests that the possible presence of cryptic members of the&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species complex in our dataset was unlikely to affect&nbsp;</span><em>P. lobata</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;microbiome variation, as there are no obvious sample microbiome composition clusters. The taxonomic name&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. is used for this study because&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species have high cryptic diversity (Johnston et&nbsp;al.,&nbsp;2022), which makes it difficult to visually delineate among species. We selected&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. specimens that had consistent phenotypes similar to those now defined as&nbsp;</span><em>Pocillopora meandrina</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;or Haplotype 8a as described in Figure&nbsp;1 of Johnston et&nbsp;al.&nbsp;(2022). Different coral species, even genotypes, tend to have distinct microbiomes (Bourne et&nbsp;al.,&nbsp;2016; Dunphy et&nbsp;al.,&nbsp;2019; Rosales et&nbsp;al.,&nbsp;2019). A NMDS ordination of Bray–Curtis distances between&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. sample microbiomes from July 2018 suggests that the possible presence of cryptic&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;species in our dataset was unlikely to affect&nbsp;</span><em>Pocillopora</em><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">&nbsp;spp. microbiome variation, as there are no obvious sample microbiome composition clusters.</span></p>
<p>All colonies of each coral species appeared healthy when initially selected for microbiome sampling. Live tissue on these focal colonies was repeatedly sampled throughout the study regardless of subsequent visual phenotype, as long as live tissue remained. Live tissue was sampled at haphazardly chosen locations on the colonies at each time point. For&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp., haphazardly chosen live branch tips were sampled. For&nbsp;<em>P. lobata</em>, live tissue was sampled from haphazardly chosen locations around the center of the colony. Coral samples were collected in July 2018, November 2018, March 2019, August 2019, November 2019, March 2020, and August 2020, covering a 28-month period. Additional coral colonies were sampled in November 2018, March 2019, and August 2019 to increase sample sizes and to account for initial focal colony mortality. Colonies of each species were also added to the dataset in March 2020 and August 2020 to restore sample size due to colony mortality. Bleaching and mortality data for coral colonies added to the microbiome sampling effort after the start of the experiment were collected retroactively. This was possible because these corals were already present in the exclosures and data could be collected from our photomosaic time series from before they were added to the microbiome sampling effort.</p>
<p>During each sampling event, coral fragments &lt;1 cm3&nbsp;were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Corals were sampled between 08:00 and 14:00 h to help minimize diel microbiome variation. Fragments were immediately placed in sterile 207 mL Whirl-Paks. This volume of sample is sufficient to produce accurate microbiome data without significantly damaging the focal colony (Zaneveld et&nbsp;al.,&nbsp;2016). Upon surfacing, Whirl-paks were placed on ice and transported to shore (~15 min) then transferred to Qiagen DNeasy PowerSoil lysis matrix tubes, containing a guanidinium thiocyanate preservative, using 95% ethanol flame-sterilized forceps. Tubes were stored at −40°C prior to transport on Techni Ice to Oregon State University where they were stored at −80°C until further processing.</p>
<h3><strong>Microbiome analyses</strong></h3>
<p>The V4 region of the 16S rRNA gene was amplified using 515F and 806RB primers from total DNA, then barcoded, purified, and sequenced (Apprill et&nbsp;al.,&nbsp;2015; Parada et&nbsp;al.,&nbsp;2016). Microbiome sequence library generation, sequence processing, and quality control were done as in Williams et&nbsp;al.&nbsp;(2022) with some modifications. See the&nbsp;Supplementary Methods&nbsp;(Vompe et al. 2023) for full protocols and conditions.&nbsp;All microbiome analyses were performed in R v4.2.2, using functions from base R and “tidyverse” (Wickham et&nbsp;al.,&nbsp;2019), as well as functions from a suite of packages developed for microbiome analyses, including “phyloseq” (McMurdie &amp; Holmes,&nbsp;2013), “vegan” (Oksanen et&nbsp;al.,&nbsp;2022), and Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in the “ANCOMBC” package (Lin &amp; Peddada,&nbsp;2020; Vompe et&nbsp;al.,&nbsp;2023).</p>
Specified by the Principal Investigator(s)
- Import "complete sample data.xlsx" into BCO-DMO system
- Split lat_lon field into Latitude and Longitude, with negative values for S and W
- Remove original lat_lon field
- Export file "954262_v1_microbiome_accession_info.csv"
Taxonomic names checked using the World Register of Marine Species Taxa Match tool on 2025-04-15. All names matched a known name exactly.
Specified by BCO-DMO Data Managers
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 System
Illumina MiSeq System
PI Supplied Instrument Name: Illumina MiSeq System PI Supplied Instrument Description:The V4 region of the 16S rRNA gene was amplified using 515F and 806RB primers from total DNA, then barcoded, purified, and sequenced (Apprill et al., 2015; Parada et al., 2016). Microbiome sequence library generation, sequence processing, and quality control were done as in Williams et al. (2022) with some modifications. 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.
bone cutters
bone cutters
PI Supplied Instrument Name: bone cutters PI Supplied Instrument Description:During each sampling event, coral fragments less than 1 cm3 were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Instrument Name: bone cutter Instrument Short Name: Instrument Description: A bone cutter is a surgical instrument used to cut bones or coral fragments.
Eppendorf Benchtop Centrifuge 5430
Eppendorf Benchtop Centrifuge 5430
PI Supplied Instrument Name: Eppendorf Benchtop Centrifuge 5430 Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Thermo Fisher Scientific Owl A3-1 Large-Gel Electrophoresis System
Thermo Fisher Scientific Owl A3-1 Large-Gel Electrophoresis System
PI Supplied Instrument Name: Thermo Fisher Scientific Owl A3-1 Large-Gel Electrophoresis System PI Supplied Instrument Description:Thermo Fisher Scientific Owl A3-1 Large-Gel Electrophoresis System. A Gel Transilluminator was also used. Instrument Name: Electrophoresis Chamber Instrument Short Name: Instrument Description: General term for an apparatus used in clinical and research laboratories to separate charged colloidal particles (or molecules) of varying size through a medium by applying an electric field.
Invitrogen Qubit 4 Fluorometer
Invitrogen Qubit 4 Fluorometer
PI Supplied Instrument Name: Invitrogen Qubit 4 Fluorometer PI Supplied Instrument Description:Invitrogen Qubit 4 Fluorometer Instrument Name: Qubit fluorometer Instrument Short Name: Instrument Description: Benchtop fluorometer. The Invitrogen Qubit Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality.
Manufactured by Invitrogen, Carlsbad, CA, USA (Invitrogen is one of several brands under the Thermo Fisher Scientific corporation.)
Vortex
Vortex
PI Supplied Instrument Name: Vortex PI Supplied Instrument Description:Used with Qiagen Bead Beater Vortex Attachment Instrument Name: Shaker Instrument Short Name: Instrument Description: A Shaker is a piece of lab equipment used to mix, blend, or to agitate substances in tube(s) or flask(s) by shaking them, which is mainly used in the fields of chemistry and biology. A shaker contains an oscillating board which is used to place the flasks, beakers, test tubes, etc.
Thermocycler
Thermocycler
PI Supplied Instrument Name: Thermocycler PI Supplied Instrument Description:The V4 region of the 16S rRNA gene was amplified using 515F and 806RB primers from total DNA, then barcoded, purified, and sequenced (Apprill et al., 2015; Parada et al., 2016). Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)