Dr. Rebecca Vega Thurber, Associate Professor
Research Interests: Environmental virology and microbiology; metagenomics and marine disease ecology. My lab investigates how bacteria, viruses, and other microorganisms interact with and regulate marine ecosystems. Currently our projects focus on tropical reef and deep-sea ecosystems. Our lab is funded primarily by the National Science Foundation.
Courses Taught: MB 420/520 Microbial genomes, biogeochemistry and diversity; MB 599 Microbial systems with Theo Dreher; MB 310 Bacterial molecular genetics
My lab’s research uses interdisciplinary and high technology approaches to address questions about how viruses and microbes function in and affect the environment. Using a combination of empirical experimentation, field work, metagenomics, microscopy and molecular biology, my research provides important insight into a variety of fields including: virology, microbiology, coral reef ecology, animal physiology, and the evolution of symbioses.
Viral Disease Ecology of Tropical Reefs: Using microscopy and metagenomic techniques, we study how viruses are important in regulating many aspects of marine biology and oceanography. A majority of our studies focus on the isolation, identification, and evaluation of eukaryotic viruses associated with important marine species. Coral reefs are hotspots of biodiversity but are increasingly threatened by factors such as climate change, pollution, and overfishing. One effect of these combined stressors is that corals are more frequently suffering from diseases of unknown origin. By isolating the viruses from healthy and sick corals, we can begin to understand which viruses may contribute to disease and decline of these precious habitats. Currently we have several projects on the types of viruses associated with Caribbean, Hawaiian, and Indo-Pacific coral diseases and bleaching events. We also are evaluating the types and effects of viruses on the development, fecundity, and health state of several species corals from across the globe.
Marine Phage Dynamics and Genomics: In addition to eukaryotic viruses, we study the ecology of marine phages, the viruses that infect bacteria and archaea. Our lab investigates the types, roles, and abundances of phages in the sea. To do this we use next generation sequencing and bioinformatics to sequence, assemble, and annotate phage genomes that we have isolated from a habitat. Once annotated, we can infer various things about the phages, including their potential hosts and the effects on their host’s physiology and ecology. Currently we are focusing our work on the phages associated with methane seeps off the Coast of Oregon and California.
Roles of Marine Bacteria on the Degradation of Coastal Habitats: Microscopic marine Bacteria, Archaea and Eukaryotes play pivotal roles in the oceans. On coral reefs, microbes are responsible for continued remineralization of important nutrients and are also symbiotic members of corals themselves. As temperatures, nutrient concentrations, and top down pressures change, so does the structure and function of the microbial component of those environments. Such alterations maybe have negative effects on the community of benthic or aquatic animals and plants. A major focus in my lab is to understand how shifts in environmental parameters drive changes (structural and functional) in the microbial community and how these changes then cascade down to the function of that habitat. To do this, we perform on site (in the Florida Keys) experimental manipulations (herbivore abundance and inorganic nutrient concentrations) of reef habitats and then monitor the communities of microbes associated with corals and macroalgae.
Influence of Predatory Bacteria on Marine Microbial Ecology: The top down regulation of marine microbial communities is thought to be driven mostly by either phage lysis or consumption by eukaryotic predators. Bacteriovorax species are a unique group of predatory bacteria whose role in marine food web dynamics is often overlooked or ignored. We monitor the natural dynamics of these organisms in marine systems to better understand their biology and ecology. However we also use them as a model system to ask questions about predator-prey dynamics on surfaces in the ocean. To do this we cultivate several strains of Bacteriovorax and prey marine bacteria to conduct in lab experiments that mimic natural conditions in the environment.
Pollock, J.F., McMinds, R., Welsh, R., Smith, S., Bourne, D.G., Willis, B.L., Medina, M., Vega-Thurber, R., and Zaneveld, J.R. 2018. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny (in press, Nature Commun.)
Roux, S., Adriaenssens, E.M., et al. 2018. Minimum information about uncultivated virus genomes (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses (in press, Nature Biotechnol.)
Wang, L., Shantz, A.A., Payet, J., Sharpton, T.J., Foster, A., Burkepile, D.E., and Vega-Thurber, R. 2018. Corals and their microbiomes are differentially affected by exposure to elevated nutrients and a natural thermal anomaly. Frontiers of Mar. Sci. 5:101.
Thurber, R.V., Payet, J.P., Thurber, A.R. and Correa, A.M.S. 2017. Virus-host interactions and their roles in coral-reef health and disease. Nature Rev. Microbiol. 15(4):205-216.
Zaneveld, J.R., McMinds, R., and Vega-Thurber, R. 2017. Stress and stability: Applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2:17121.
Welsh, R.M., Rosales, S.M., Zaneveld, J.R., Payet, J.P., McMinda, R., Hubbs, S.L. and Vega Thurber, R.L. 2017. Alien vs predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators. PeerJ. PMID: 28584701.
Shaver, E.C., Shantz, A.A., McMinds, R., Burkepile, D.E., Vega Thurber, R.L., and Silliman, B.R. 2017. Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral. Ecology. 98(3):830-839. doi: 10.1002/ecy.1709.
Pawlik, J.R., Burkepile, D.E. and Vega Thruber, R.L. 2016. A vicious circle? Altered carbon and nutrient cycling may explain the low resilience of Caribbean coral reefs. BioSci. 66:470-476.
Zaneveld, J.R.R., Burkepile, D.E., Shantz, A.A., Pritchard, C.E., McMinds, R., Payet, J.P., Welsh,R., Correa, A.M.S., Lemonine, N.P., Rosales, Fuchs, C., Maynard, J., and Vega Thurber, R.L. 2015. Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales. Nature Commun. 7:11833.
Rosales, S.M., and Vega Thurber, R.L. 2016. Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection. PeerJ. 4:e2819. doi: 10.7717/peerj.2819. PMID:28028481
Correa, A.M., Ainsworth, T.D., Rosales, S.M., Thurber, A.R., Butler, C.R., and Vega Thurber, R.L. 2016. Viral Outbreak in Corals Associated with an In Situ Bleaching Event: Atypical Herpes-Like Viruses and a New Megavirus Infecting Symbiodinium. Front Microbiol. 7:127. doi: 10.3389/fmicb.2016.00127. PMID:26941712
Burge, C.A., Friedman, C.S., Getchell, R., House, M., Lafferty, K.D., Mydlarz, L.D., Prager, K.C., Sutherland, K.P., Renault, T., Kiryu, I, and Vega-Thurber, R. 2016. Complementary approaches to diagnosing marine diseases: a union of the modern and the classic. Philos Trans R Soc Lond B Biol Sci. 371(1689). pii: 20150207. doi: 10.1098/rstb.2015.0207. Review.
Bryson, S.J., Thurber, A.R., Correa, A.M., Orphan, V.J., and Vega Thurber, R. 2015. A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments.
Environ Microbiol. 17(10):3708-21. doi: 10.1111/1462-2920.12758.
Rosales, S.M. and Vega-Thurber, R. 2015. Correction: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event.
Rosales, S.M. and Vega-Thurber, R. 2015. Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLoS One. 10(12):e0143944.
Borque, A.S., Vega-Thurber, R., Fourqurean, J.W. 2015. Microbial community structure and dynamics in restored subtropical seagrass sediments. Aquatic Microbial Ecol. 74(1).
Welsh, R.M., Rosales, S.M., Zaneveld, J.R.R., Payet, J.P., McMinds, R., Hubbs, S.L., Thurber, R.V.L. 2015. Alien vs Predator: Pathogens open niche space for opportunists, unless controlled by predators. PeerJ PrePrints.
Wear, S.L., Vega-Thurber, R. 2015. Sewage pollution: Mitigation is key for coral reef stewardship. Annals of the New York Acad. of Sci.
Welsh, R.M., Zaneveld, J.R., Rosales, S.M., Payet, J.P., Burkepile, D.E., and Vega-Thurber, R. 2015. Bacterial predation in a marine host-associated microbiome. The ISME Journal.
Bryson, S.J., Thurber, A.R., Correa, A.M., Orphan, V.J. and Vega-Thurber, R. (2015). A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments. Environ. Microbiol. 17(10):3708-21.
Payet, J.P., McMinds, R., Burkepile, D.E., and Vega-Thurber, R.L. (2014). Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean. Front Microbiol. 5:493.
Soffer, N., Zaneveld, J., Vega-Thurber, R. (2015). Phage-bacteria network analysis and its implication for the understanding of coral disease. Environ. Microbiol. PMID: 25039472.
Vega Thurber, R.L., Burkepile, D.E., Fuchs, C., Shantz, A.A., McMinds, R., Zaneveld, J.R. (2013). Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching. Glob Chang Biol 2014 Feb; 20(2):544-54. doi: 10.1111/gcb.12450. Epub 2013 Nov. 26; PMID: 24277207.
Langille, M.G., Zaneveld, J., Caporaso, J.G., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker Gene sequences. Nature Biotechnology, 31(9):814-821.
Soffer, N., Brandt, M.E., Correa, A.M., Smith, T.B., Vega Thurber, R. (2013). Potential role of viruses in white plague coral disease. ISME J. doi:10.1038/ismej.2013.137.
Brandt, M.E., Smith, T.B., Correa, A.M., Vega Thurber, R. (2013). Disturbance driven colony fragmentation as a driver of a coral disease outreak. PLOS one, 8(2):e57164.
Correa, A.S., Welsh, R.M., & Vega Thurber, R. (2013). Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals. ISME J doi:10.1038/ismej.2012.75
Vega Thurber, R., Burkepile, D.E., Correa, A.M., Thurber, A.R., Shantz, A.A., Welsh, R., Pritchard C., Rosales, S. (2012). Macroalgae decrease growth and alter microbial community structure of the reef-building coral Porites astreoides. PLoS One 7(9):e44246. doi:10.1371/journal.pone.0044246. Epub 2012 Sep 5; PMID: 22957055.
Vega Thurber R. et al. (2012). Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides. PLoS One http://dx.plos.org/10.1371/journal.pone.0044246.
Vega Thurber R. & Correa A. (2011). Viruses of Tropical Stony Corals. Journal of Experimental Marine Biology and Ecology 408:102-113.
Vega Thurber, R. (2011). Methods in Viral Metagenomics. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats” Wiley/Blackwell, editor Frans J. de Bruijin (book chapter)
Rodriguez-Brito B., et al. (2010). Viral and Microbial Community Dynamics in Four Aquatic Environments. ISME Journal 4:739-751
Ainsworth, T., Vega Thurber, R., & Gates, R. (2010). The Future of Coral Reefs: a Microbial Perspective. Trends in Ecology and Evolution 25:223-240
Angly, F. et al. (2009). The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. PLoS Comput Biol 5(12): e1000593. doi:10.1371/journal.pcbi.1000593
Vega Thurber, R. (2009). Current Insights into Phage Biodiversity & Biogeography. Current Opinion in Microbiology 12: 582-587
Rohwer, F. & Vega Thurber, R. (2009). Viruses Manipulate the Marine Environment. Nature 459:207-212
Vega Thurber, R. et al. (2009). Experimental Methods to Generate Viral Metagenomes. Nature Protocols 4: 470-483 March 19 oi:10.1038/nprot.2009.10
Vega Thurber, R. et al. (2009). Metagenomic Analysis of Stressed Coral Holobionts. Environmental Microbiology 11: 2148–2163
Willner-Hall, D., Vega Thurber, R., and Rohwer, F. (2009). Metagenomic Signatures of 86 Microbial and Viral Metagenomes. Environmental Microbiology 11: 1752-1766
Vermeji, M.J.L., Smith, J.E., Smith, C.M., Vega Thurber, R., and Sandin, S.A. (2009). Survival and Settlement Success of Coral Planulae: Independent and Synergistic Effects of Macroalgae and Microbes. Oecologia 159:325–336
Vega Thurber, R. et al. (2008). Metagenomic Analysis Indicated that Stressors Induce Production of Herpes-like Viruses in the Coral Porites compressa. PNAS USA 105: 18413-1841
Dinsdale, E. et al. (2008b). Functional metagenomic profiling of nine biomes. Nature 452: 629-632
Dinsdale, E. et al. (2008a). Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS One 3(2): e1584. doi:10.1371/journal.pone.0001584
Desnues, C.M. et al. (2008). Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343
Vega Thurber, R. & Epel, D. (2007). Apoptosis in Early Development of the Sea Urchin, Strongylocentrotus purpuratus. Developmental Biology 303: 336-346
Epel, D., Cole, B., Hamdoun, A., and Vega Thurber, R. (2006). The Sea Urchin Embryo as a Model for Studying Efflux Transporters: Roles and Energy Cost. Marine Environmental Research 62: S1-D4
Smital, T. et al. (2004). Emerging contaminants: pesticides, PPCPs, microbial degradation products and natural substances as inhibitors of the multixenobiotic defense in aquatic organisms. Mutation Research 552: 101-117
Vega, R.L. and Epel, D. (2004). Stress-Induced Apoptosis in Sea Urchin Embryogenesis. Marine Environmental Research 58: 799-802
Epel, D. and Vega, R. L. (2002). The floating world: Problems and adaptations to ultraviolet radiation. AAAS Annual Meeting and Science Innovation Exposition 168: p.A23
Grey Literature. Couch CS, Barnett, C, Vega Thurber R. Examining the Role of Environment and Viruses in Growth Anomalies of Porites lobata on the Island of Hawaii (2012). NOAA Coral Reef Conservation Program. PI Drew Harvell #NA09NMF4630121
Biography in Popular Press: Rebecca Vega Thurber: The coral doctor (2009) The Scientist 23 (8): 50; http://www.thescientist.com/2009/08/1/50/1/