Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

Version 1, which has been archived under DOI number 10.26008/1912/bco-dmo.845039.1, was supported by NSF awards OCE-1635913 and OCE-1635798 as part of the project "Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling". Version 2 is a continuation or extension of the data in version 1. It was supported by NSF award OCE-1933165 as part of the project "RAPID: Ecosystem impact of a coral bleaching event: The role of coral exudates in shifting oligotrophic biogeochemistry and reef microbiomes."

Coral, water and sediment were sampled at 21 sites around the island of Mo'orea, French Polynesia in 2017, 2018, 2019, and 2020. 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.

Coral: Individual corals from three species (Acropora hyacinthus, Porites lobata, and Pocillopora sp.) were tagged and repeatedly sampled twice a year in the rainy and dry seasons at depths between 1 and 10 meters water depth. Note that Pocillopora are a species complex on the Island of Mo'orea and while all individuals appeared to be Pocillopora meandrina, different species of this genus are morphologically indistinguishable at the size of these corals. Sampling was done free-diving or on SCUBA, with individual corals sampled using bone cutters (or chisels for P. lobata) 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. 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 Celsius) until processing.

Sediment: 2 milliliters (mL) 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 Celsius) until processing.

Water: 500 mL of seawater was collected and kept chilled until it was filtered onto a 0.1 micron filter, then put into Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees Celsius) until processing.

Sample processing:
Initial processing included bead beating of all samples prior to them being frozen at -80 degrees Celsius 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. 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. 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. In certain cases, there were repeated sequencing runs for individual samples. That is indicated with different numbers.

Accession numbers of DNA sequences generated as part of this project are archived and available in the National Center for Biotechnology Information (NCBI) Short Read Archive under BioProject Identifier PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406).

Data processing:
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.

Version History:
Version 1
Version 1 date: 2021-03-14.
Version 1 was supported by NSF awards OCE-1635913 and OCE-1635798 as part of the project "Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling".
BCO-DMO processing description for version 1:
The original data submitted in CSV file "AroundIsland_Metadata_final.csv" was modified during processing:
- Adjusted field/parameter names to comply with database requirements
- Added a conventional header with dataset name, PI names, version date, and BioProject
- Added separate columns for Latitude and Longitude and converted to decimal degrees
- Split column "collection_date" to show separate "Month" and Year" columns

Version 2
Version 2 date: 2023-07-27.
Version 2 is a continuation or extension of the data in version 1. It was supported by NSF award OCE-1933165 as part of the project "RAPID: Ecosystem impact of a coral bleaching event: The role of coral exudates in shifting oligotrophic biogeochemistry and reef microbiomes."
BCO-DMO processing description for version 2:
- imported original file named "UpdateCoralMicrobiome.txt" into the BCO-DMO system;
- converted year and month columns into a single date field with format YYYY-MM;
- renamed fields to comply with BCO-DMO naming conventions;
- separated latitude and longitude into separate columns;
- concatenated the version 1 data with the data in "UpdateCoralMicrobiome.txt";
- named the final data file "845039_v2_coral_microbes.csv".

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.

NSF Award Abstract:
Shallow tropical reefs are biodiversity hotspots. Their ecosystem services make them key areas of economic, ecological, and cultural importance. Yet coral reefs are under significant threat due to both local and global stressors which can lead to coral bleaching, disease, and eventually coral death. When corals bleach, they release materials such as dead tissue, mucus, bacteria, and viruses that may affect the entire ecosystem. This project uses a wide-spread bleaching event at a Long Term Ecological Research site in French Polynesia to explore how these released materials impact the reef ecosystem The water chemistry and microbes associated with the corals and surrounding water are examined. This research aims to better understand how corals interact with their environment and how this interaction changes when corals are stressed. Throughout this project two female graduate students are being trained and interactive programs are used to communicate results to elementary, high school, and undergraduate students in Oregon. A 20-minute documentary for web release focusing on the reef scale impact of coral bleaching is in preparation together with film students.

Coral exudates include particulate and dissolved material (sloughed tissue, mucus, bacteria, viruses) that together add limiting nutrients and carbon compounds to the reef, fueling auto- and heterotrophic bacterial production. In recent experiments, coral-bleaching derived exudates were observed to themselves cause rapid bleaching, and often mortality, of previously healthy corals. Importantly, these negative impacts of coral exudate exposure were far greater than thermal stress. These experiments provided insight into a novel mechanism in which bleaching corals can adversely affect the health of adjacent corals. This project leverages these data and an extensive and ongoing bleaching event on the island of Mo?orea to quantify the cascading effects of coral exudates on reef ecosystems. It is hypothesized that during widespread bleaching: (1) DOC is significantly elevated across the reefscape; (2) coral holobiont components become enriched in the pelagic microbiome; (3) the water column microbial community shifts in function to increased heterotrophy and pathogenicity; and (4) coral holobionts diverge from their previous stable state leading to coral reef dysbiosis and/or disease and mortality. Sampling throughout the course of an ongoing bleaching event in Mo?orea is used to quantify the effects of this bleaching event on DOM dynamics and reef health. Mo'orea is situated in the MCR Long Term Ecological Research (MCR LTER) site. The rare reef-scale bleaching event at this well-studied location provides the unusual opportunity to quantify the impact of coral exudates on reef health and to better understand the temporal and spatial impacts of an island-wide bleaching event in an oligotrophic ecosystem. Measurement of the amount of organic matter released per unit area of coral on an island where the reef ecosystem is well parameterized over time and space allows development of a model of the impact of bleaching events on the island carbon budget.

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.