Current research foci include:
1. Investigating the phylogenetic, genomic, and biogeographic characteristics of novel bacterial and eukaryotic symbionts of corals to survey the prevalence, ecology, and evolution of new taxa.
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2. Utilizing experimental manipulations to understand how shifts in environmental parameters drive changes (structural and functional) in the microbial community of coral reefs and how these changes cascade down to the remineralization of important nutrients in the reef, the community composition of benthic or aquatic animals and plants, and the general function of the habitat.
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3. Using microscopy and meta'omics to study how phage and eukaryotic viruses regulate aspects of marine biology and oceanography, particularly to understand which viruses may contribute to disease or decline in these habitats.
Current projects
Research
2024 -
Biocode 2.0
The Mo'orea Coral Reef Holobiont Sequencing Project
This project aims to advance scientific understanding of the unseen biodiversity of reefs. Using both archived and newly collected type specimens along with environmental samples, this project will conduct genome skimming and holobiont meta ‘omics (eukaryotes, bacteria, archaea, and viruses) to characterize the diversity of one of the most intensively studied coral reef systems in the world. This is a large collaborative project between multiple partners, including community members of Moorea, UC Berkeley, Ethnocode, Local Contexts, and the Smithsonian.
Selection of the ‘host’ species (target holobionts) and the sampling strategy will be co-designed with local community members around species that are ecologically, culturally, and economically important to the people of Moorea. This collaboration will also ensure agency, trust, transparency, and accessibility throughout the process. We are currently in the process of selecting our first species and Rio Kashimoto has plans to collect Porites spp. corals in April 2025. Elliott Cameron is also working on this project.
2023 -
Around the Island (ATI): eDNA for Reefs
Oceankind eDNA Project for Reef Restoration on Mo'orea Island
Funded by Oceankind, this project collaborates with Coral Gardeners, Conservation Metrics, and the Burkepile Lab at the University of California, Santa Barbara to use environmental DNA (eDNA) to assess biodiversity and guide coral restoration and conservation efforts on Moorea Island, French Polynesia. Annually, samples are collected from approximately 200 locations around the island to analyze different genetic markers from microorganisms to vertebrates. We seek to identify ecological patterns and priority areas for restoration, mapping biodiversity at different trophic levels and evaluating how environmental factors, including nutrient pollution and water quality, influence the ecological structure and the presence of essential keystone species for reef health. Our goal is to establish eDNA as a scalable tool for marine conservation, integrating ecological surveys and predictive models to improve restoration and conservation strategies.
2022 -
Unveiling the Viral Diversity of Amazonian Mosquitoes
The Amazon Basin Mosquito Virome Project is a large-scale viral surveillance effort focused on characterizing RNA viruses associated with mosquito populations in the Juruá River region of the western Amazon Basin. This project is part of an ongoing collaboration between the Vega Thurber Lab, The Levi Lab at Oregon State University, and Instituto Juruá from Brazil. Field collections span multiple ecologically distinct sites, where mosquito pools are preserved for high-throughput sequencing and metagenomic analysis. Current graduate student Eddie Fuques is leading the bioinformatic analysis of the RNA sequencing data, assembling and characterizing viral genomes to investigate their genetic diversity, evolutionary relationships, and potential ecological roles. Through this work, we aim to better understand the composition and dynamics of mosquito-associated viruses in one of the most biodiverse and understudied regions on Earth.
2021 -
Understanding the Rules of Life (RoL)
Predictors of microbiome sensitivity & resilience
In collaboration with several labs at Oregon State University, this project aims to identify system-agnostic microbiome metrics (SAMMs) that indicate microbiome resilience and sensitivity to ecological perturbations. Using metagenomic approaches and 16S rRNA gene analysis, we are studying how the microbiome of Acropora cervicornis responds to antibiotic, thermal, and pathogenic stressors. The same methods will be applied to seagrass and zebrafish. Coupled with deep-learning, this will help us predict microbiome responses across systems and stressors. Our goal is to understand universal microbiome functions and identify metrics of species susceptibility or resilience, enhancing current microbiome research. Lab members include Sunni Patton, Denise Silva, and Eddie Fuques.
2017 -
Mo'orea Virus Project (MVP)
The Mo’orea Virus Project is a collaboration with the Correa Lab at Rice University and the Thurber Lab at Oregon State University. Many members of the Vega Thurber Lab have participated in this multi-year time series in Mo’orea, French Polynesia. Lab and field experiments continue to be conducted at the Moorea Coral Reef LTER to characterize the spatiotemporal dynamics of viruses within three dominant reef-building coral species (Acropora hyacinthus, Pocillopora verrucosa, and Porites lobata) that differ in their susceptibility to abiotic stress. Marker colonies from these species have been sampled for four years across three unique reef environments (fore, back, and fringing reef).
2017 -
RECHARGE
RECHARGE is a six-year time series in Mo'orea exploring the interacting effects of herbivory, nutrient enrichment, and seasonal temperature variation on coral reef ecosystems and their associated microbes. A collaboration with the Burkepile Lab at University of California Santa Barbara, this project assesses cascading effects of exclusion of reef herbivores from coral plots in tandem with exposure to inorganic nutrients on reef health and recovery to disruption. We examine reef ecosystem health using metrics ranging from the micro to macro scales, including microbial community structure, fish and algal abundance, and coral recruitment and growth. Lab members involved in this project include Alex Vompe, Hannah Epstein, Grace Klinges, and Emily Schmeltzer.
2017 -
Rickettsiales in Caribbean Acropora (RICA)
Despite connections between overall microbial community composition and coral health, assessing the roles of individual microbial community members has proved difficult. We identified a novel Rickettsiales genus, Aquarickettsia, members of which are capable of both ATP and amino acid parasitism of their hosts. This parasite is strongly associated with disease susceptibility in Acropora cervicornis and responds positively to nutrient-rich conditions. To better understand the role of this parasite in host health, we employ diverse techniques including qPCR, FISH, metagenomics, RNA-Seq of both the parasite and host, and nanoSIMS. Lab members involved in this project include Grace Klinges, Lydia Baker, and Becca Maher.
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2017 -
Coral-Viral Community Shifts During Bleaching and Coral Giant Viruses
This work investigates viral metagenomes (viromes) from both bleached and non-bleached corals. These coral phenotypes were found during a bleaching event, where one bleached colony was directly adjacent to another non-bleached colony. We conducted viral community analysis during this paradoxical bleaching pattern and found that bleached corals had a higher relative percent abundance of eukaryotic virus-like sequences, and non-bleached corals had a higher relative percent abundance of bacteriophage-like sequences. Adriana Messyasz assembled the first coral-associated dsDNA eukaryotic giant virus, which we believe is distantly related to other marine Nucleocytoplasmic large DNA viruses (NCLDVs) and may play a role in coral bleaching.
2014 -
The Global Coral Microbiome Project (GCMP)
Investigating interactions and coevolution among bacteria and corals across the globe. Bacteria perform a plethora of beneficial functions for their coral hosts, but the majority are unknown and uncharacterized. This project aims to identify microbial functions that have been selected by corals over their evolutionary history, and will begin to do so by characterizing the microbial communities of a wide geographic and taxonomic range of corals which have never been sampled. This project is headed by Dr. Rebecca Vega Thurber, postdoc Jesse Zaneveld, Ph.D. student Ryan McMinds, and collaborators at Penn State University Monica Medina and Joe Pollock. GCMP and those involved in the project were featured in the 2018 Oregon State University-produced documentary “Saving Atlantis.”
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To learn more: The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean
2016 - 2018 (expedition) 2018 - (analysis)
Tara Pacific
A large collaborative project with the Tara Foundation, in which our role is to assess the biogeography of microbes (particularly viruses) in the water and in association with corals across the Pacific. The Tara Pacific Expedition (2016-2018) embarked on an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates in order to characterize local and global reef biodiversity and chemical gradients. Current and former lab members Dr. Rebecca Vega Thurber, Grace Klinges, Kalia Bistolas, Ryan McMinds, and Jerome Payet have all participated in the project, including field work on Tara and downstream analysis of samples.
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To learn more:
2019-
Tetiaroa: Impacts of Rat Eradication on Reef Health
This cross-disciplinary collaboration with the Tetiaroa Society and the Graham Lab at Lancaster University capitalizes on a planned rat eradication occurring on the island of Tetiaroa, French Polynesia, to examine the impacts of rat removal and the eventual return of a healthy seabird population on adjacent reef and island health. By integrating experimental manipulations of nutrients and monitoring of islands and reefs pre and post eradication, we aim to identify: (1) how rat removal impacts island and reef associated microbes, (2) how changes in microbial communities impact biogeochemical cycling, and (3) how changes in biogeochemical cycling impact coral health and resilience to heat stress.