Publications

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2020                                                                                                                                                                

 

L. Ezzat, Lamy, T., Maher, R. L., Munsterman, K., Landfield, K., Schmeltzer, E. R., Clements, C., Vega-Thurber, R., and Burkepile, D. E., “Parrotfish predation drives distinct microbial communities in reef-building corals”, Animal Microbiome, vol. 2, 2020.

D. C. Claar, J. M. McDevitt‐Irwin, M. Garren, R. L. Vega Thurber, R. D. Gates, J. K. Baum, "Increased diversity and concordant shifts in community structure of coral‐associated Symbiodiniaceae and bacteria subjected to chronic human disturbance", Molecular Ecology, Volume 29, Issue 13, 2020.

J. M. Flores, “Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans”, Bulletin of the American Meteorological Society, 2020.

2019                                                                                                                                                                

 

M. M. Rice and Maher, R. L., “Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral”, PeerJ, vol. 7, 2019.

S. M. Rosales and Thurber, R. Vega, “Draft Genome Sequence of Phocine Herpesvirus 1 Isolated from the Brain of a Harbor Seal.”, Microbiol Resour Announc, vol. 8, no. 14, 2019.

G. G and Tara Pacific Consortium, “Expanding Tara Oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-18)”, Frontiers in Marine Science, 2019.

L. G. E. Wilkins, Leray, M., O'Dea, A., Yuen, B., Peixoto, R. S., Pereira, T. J., Bik, H. M., Coil, D. A., J Duffy, E., Herre, E. Allen, Lessios, H. A., Lucey, N. M., Mejia, L. C., Rasher, D. B., Sharp, K. H., Sogin, E. M., Thacker, R. W., Thurber, R. Vega, Wcislo, W. T., Wilbanks, E. G., and Eisen, J. A., “Host-associated microbiomes drive structure and function of marine ecosystems.”, PLoS Biol, vol. 17, no. 11, p. e3000533, 2019.

D. E. Burkepile and Thurber, R. L. Vega, “The Long Arm of Species Loss: How Will Defaunation Disrupt Ecosystems Down to the Microbial Scale?”, BioScience, vol. 69, pp. 443-454, 2019.

I. A. Morelan, Gaulke, C. K., Sharpton, T. J., Thurber, R. Vega, and Denver, D. R., “Microbiome Variation in an Intertidal Sea Anemone Across Latitudes and Symbiotic States”, Frontiers in Marine Science, vol. 6, 2019.

S. Roux, “Minimum Information about an Uncultivated Virus Genome (MIUViG)”, Nature Biotechnology, vol. 37, pp. 29-37, 2019.

R. L. Maher, Rice, M. M., McMinds, R., Burkepile, D. E., and Vega-Thurber, R., “Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome”, Scientific Reports, 2019.

J. G. Klinges, Rosales, S. M., McMinds, R., Shaver, E. C., Shantz, A. A., Peters, E., Eitel, M., Wörheide, G., Sharp, K. H., Burkepile, D. E., Silliman, B. R., and Thurber, R. Vega, “Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov”, The ISME Journal, vol. 13, pp. 2938–2953, 2019.

L. Ezzat, Lamy, T., Maher, R. L., Munsterman, K., Landfield, K., Schmeltzer, E. R., Gaulke, C., Burkepile, D. E., and Thurber, R. Vega, “Surgeonfish feces increase microbial opportunism in reef-building corals”, Marine Ecological Progress Series, 2019.

S. Planes, Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Bourdin, G., Bowler, C., Douville, E., J Flores, M., Forcioli, D., Furla, P., Galand, P. E., Ghiglione, J. - F., Gilson, E., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Troublé, R., de Vargas, C., Vega-Thurber, R., Voolstra, C. R., Wincker, P., and Zoccola, D., “The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.”, PLoS Biol, vol. 17, no. 9, p. e3000483, 2019.

J. M. McDevitt-Irwin, Garren, M., McMinds, R., Vega-Thurber, R., and Baum, J. K., “Variable interaction outcomes of local disturbance and El Niño-induced heat stress on coral microbiome alpha & beta diversity.”, Coral Reefs, vol. 38, pp. 331-345, 2019.

 

 

2018                                                                                                                                                                

J. F. Pollock and McMinds, R., “Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny”, Nature Communications, vol. 9, 2018.

L. Wang, “Corals and Their Microbiomes Are Differentially Affected by Exposure to Elevated Nutrients and a Natural Thermal Anomaly”, Frontiers in Marine Science, vol. 5, 2018.

 

2017                                                                                                                                                                

R. M. Welsh, Rosales, S. M., Zaneveld, J. R., Payet, J. P., McMinds, R., Hubbs, S. L., and Vega-Thurber, R. L., “Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators.”, PeerJ, vol. 5, 2017.

E. C. Shaver, Shantz, A. A., McMinds, R., Burkepile, D. E., Vega-Thurber, R. L., and Silliman, B. R., “Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral”, Ecology, 2017.

G. Torda, Donelson, J. M., Aranda, M., Barshis, D. J., Bay, L., Berumen, M. L., Bourne, D. G., Cantin, N., Foret, S., Matz, M., Miller, D. J., Moya, A., Putnam, H. M., Ravasi, T., van Oppen, M. J. H., Vega-Thurber, R. L., Vidal-Dupiol, J., Voolstra, C. R., Watson, S. - A., Whitelaw, E., Willis, B. L., and Munday, P. L., “Rapid adaptive responses to climate change in corals”, Nature Climate Change, vol. 7, no. 9, pp. 627 - 636, 2017.

J. M. McDevitt-Irwin, Baum, J. K., Garren, M., and Vega-Thurber, R. L., “Responses of Coral-Associated Bacterial Communities to Local and Global Stressors”, Frontiers in Marine Science, 2017.

J. R. Zaneveld, McMinds, R., and Vega-Thurber, R. L., “Stress and stability: applying the Anna Karenina principle to animal microbiomes”, Nature Microbiology, vol. 2, p. 17121, 2017.

R. L. Vega-Thurber, Payet, J. P., Thurber, A. R., and Correa, A. M. S., “Virus-host interactions and their roles in coral reef health and disease”, Nature Reviews Microbiology, 2017.

2016                                                                                                                                                                

S. M. Rosales and Vega-Thurber, R. L., “Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection”, PeerJ, vol. 4, p. e2819, 2016.

C. A. Burge, 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. L., “Complementary approaches to diagnosing marine diseases: a union of the modern and the classic”, Philosophical Transactions of the Royal Society of London B: Biological Sciences, vol. 371, 2016.

J. R. R. Zaneveld, Burkepile, D. E., Shantz, A. A., Pritchard, C. E., McMinds, R., Payet, J. P., Welsh, R., Correa, A. M. S., Lemoine, N. P., Rosales, S., Fuchs, C., Maynard, J. A., and Vega-Thurber, R. L., “Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales”, Nature Communications, vol. 7, p. 11833, 2016.

J. R. Pawlik, Burkepile, D. E., and Vega-Thurber, R. L., “A vicious circle? Altered carbon and nutrient cycling may explain the low resilience of Caribbean coral reefs”, BioScience, vol. 66, pp. 470–476, 2016.

A. M. S. Correa, Ainsworth, T. D., Rosales, S. M., Thurber, A. R., Butler, C. R., and Vega-Thurber, R. L., “Viral outbreak in corals associated with an in situ bleaching event: atypical herpes-like viruses and a new megavirus infecting Symbiodinium”, Frontiers in Microbiology, vol. 7, 2016.

 

2015                                                                                                                                                                

R. M. Welsh, Zaneveld, J. R., Rosales, S. M., Payet, J. P., Burkepile, D. E., and Vega-Thurber, R. L., “Bacterial predation in a marine host-associated microbiome”, The ISME Journal, 2015.

S. M. Rosales and Vega-Thurber, R. L., “Brain meta-transcriptomics from harbor seals to infer the role of the microbiome and virome in a stranding event”, PloS one, vol. 10, 2015.

A. S. Bourque, Vega-Thurber, R. L., and Fourqurean, J. W., “Microbial community structure and dynamics in restored subtropical seagrass sediments”, Aquatic Microbial Ecology, vol. 74, no. 1, 2015.

S. Joseph Bryson, Thurber, A. R., Correa, A., Orphan, V. J., and Vega-Thurber, R. L., “A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments”, Environmental Microbiology, 2015.

N. Soffer, Zaneveld, J., and Vega-Thurber, R. L., “Phage–bacteria network analysis and its implication for the understanding of coral disease”, Environmental Microbiology, vol. 17, pp. 1203–1218, 2015.

S. L. Wear and Vega-Thurber, R. L., “Sewage pollution: mitigation is key for coral reef stewardship”, Annals of the New York Academy of Sciences, 2015.

 

2014                                                                                                                                                                

R. L. Vega-Thurber, Burkepile, D. E., Fuchs, C., Shantz, A. A., McMinds, R., and Zaneveld, J. R., “Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching”, Global Change Biology, vol. 20, pp. 544–554, 2014.

J. R. R. Zaneveld and Vega-Thurber, R. L., “Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses”, Frontiers in Microbiology, vol. 5, p. 431, 2014.

N. Soffer, Brandt, M. E., Correa, A. M. S., Smith, T. B., and Vega-Thurber, R. L., “Potential role of viruses in white plague coral disease”, The ISME Journal, vol. 8, pp. 271–283, 2014.

M. L. Cuvelier, Blake, E., Mulheron, R., McCarthy, P. J., Blackwelder, P., Vega-Thurber, R. L., and Lopez, J. V., “Two distinct microbial communities revealed in the sponge Cinachyrella”, Frontiers in Microbiology, vol. 5, 2014.

J. P. Payet, McMinds, R., Burkepile, D. E., and Vega-Thurber, R. L., “Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean”, Frontiers in Microbiology, vol. 5, p. 493, 2014.

2013                                                                                                                                                                

M. E. Brandt, Smith, T. B., Correa, A. M. S., and Vega-Thurber, R. L., “Disturbance driven colony fragmentation as a driver of a coral disease outbreak”, PloS one, vol. 8, no. 2, p. e57164, 2013.

M. G. I. Langille, Zaneveld, J., J Caporaso, G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega-Thurber, R. L., Knight, R., Beiko, R. G., and Huttenhower, C., “Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences”, Nature Biotechnology, vol. 31, no. 9, pp. 814-21, 2013.

A. M. S. Correa, Welsh, R. M., and Thurber, R. L. Vega, “Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals”, The ISME Journal, vol. 7, no. 1, pp. 13-27, 2013.

2012                                                                                                                                                                

R. Vega Thurber, Burkepile, D. E., Correa, A. M. S., Thurber, A. R., Shantz, A. A., Welsh, R., Pritchard, C., and Rosales, S., “Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides”, PloS one, vol. 7, no. 9, p. e44246, 2012.

2011                                                                                                                                                                

 

R. Vega Thurber, “Methods in Viral Metagenomics”, in Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, 2011, pp. 15–24.

R. L. Vega Thurber and Correa, A. M. S., “Viruses of reef-building scleractinian corals”, Journal of Experimental Marine Biology and Ecology, vol. 408, pp. 102-113, 2011.

2010                                                                                                                                                                

 

T. D. Ainsworth, Thurber, R. Vega, and Gates, R. D., “The future of coral reefs: a microbial perspective”, Trends in Ecology & Evolution, vol. 25, pp. 233–240, 2010.

B. Rodriguez-Brito, Li, L., Wegley, L., Furlan, M., Angly, F. E., Breitbart, M., Buchanan, J., Desnues, C., Dinsdale, E. A., Edwards, R. A., Felts, B., Haynes, M., Liu, H., Lipson, D., Mahaffy, J., Martin-Cuadrado, A. Belen, Mira, A., Nulton, J., Pasić, L., Rayhawk, S., Rodriguez-Mueller, J., Rodriguez-Valera, F., Salamon, P., Srinagesh, S., Thingstad, T. Frede, Tran, T., Thurber, R. Vega, Willner, D., Youle, M., and Rohwer, F. L., “Viral and microbial community dynamics in four aquatic environments”, The ISME Journal, vol. 4, pp. 739–751, 2010.

2009                                                                                                                                                                

R. Vega Thurber, “Current insights into phage biodiversity and biogeography”, Current Opinion in Microbiology, vol. 12, pp. 582–587, 2009.

F. E. Angly, Willner, D., Prieto-Davó, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., Haynes, M., Henn, M. R., Hu, Y., Kirchman, D. L., McDole, T., McPherson, J. D., Meyer, F., R Miller, M., Mundt, E., Naviaux, R. K., Rodriguez-Mueller, B., Stevens, R., Wegley, L., Zhang, L., Zhu, B., and Rohwer, F., “The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes”, PLoS computational biology, vol. 5, no. 12, p. e1000593, 2009.

R. V. Thurber, Haynes, M., Breitbart, M., Wegley, L., and Rohwer, F., “Laboratory procedures to generate viral metagenomes”, Nature Protocols, vol. 4, pp. 470–483, 2009.

R. Vega Thurber, Willner-Hall, D., Rodriguez-Mueller, B., Desnues, C., Edwards, R. A., Angly, F., Dinsdale, E., Kelly, L., and Rohwer, F., “Metagenomic analysis of stressed coral holobionts”, Environmental microbiology, vol. 11, no. 8, pp. 2148-63, 2009.

D. Willner, Thurber, R. Vega, and Rohwer, F., “Metagenomic signatures of 86 microbial and viral metagenomes”, Environmental Microbiology, vol. 11, pp. 1752–1766, 2009.

M. J. A. Vermeij, Smith, J. E., Smith, C. M., R Thurber, V., and Sandin, S. A., “Survival and settlement success of coral planulae: independent and synergistic effects of macroalgae and microbes”, Oecologia, vol. 159, no. 2, pp. 325-36, 2009.

F. L. Rohwer and Thurber, R. Vega, “Viruses manipulate the marine environment”, Nature, vol. 459, pp. 207–212, 2009.

 

2008                                                                                                                                                                

 

C. Desnues, Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Furlan, M., Wegley, L., Chau, B., Ruan, Y., Hall, D., Angly, F. E., Edwards, R. A., Li, L., Thurber, R. Vega, R Reid, P., Siefert, J., Souza, V., Valentine, D. L., Swan, B. K., Breitbart, M., and Rohwer, F., “Biodiversity and biogeography of phages in modern stromatolites and thrombolites”, Nature, vol. 452, pp. 340–343, 2008.

E. A. Dinsdale, Edwards, R. A., Hall, D., Angly, F. E., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., McDaniel, L., Moran, M. Ann, Nelson, K. E., Nilsson, C., Olson, R., Paul, J., Brito, B. Rodriguez, Ruan, Y., Swan, B. K., Stevens, R., Valentine, D. L., Thurber, R. Vega, Wegley, L., White, B. A., and Rohwer, F. L., “Functional metagenomic profiling of nine biomes”, Nature, vol. 452, pp. 629–632, 2008.

R. L. Vega Thurber, Barott, K. L., Hall, D., Liu, H., Rodriguez-Mueller, B., Desnues, C., Edwards, R. A., Haynes, M., Angly, F. E., Wegley, L., and Rohwer, F. L., “Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa”, Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 47, pp. 18413-8, 2008.

E. A. Dinsdale, Pantos, O., Smriga, S., Edwards, R. A., Angly, F. E., Wegley, L., Hatay, M., Hall, D., Brown, E., Haynes, M., Krause, L., Sala, E., Sandin, S. A., Thurber, R. Vega, Willis, B. L., Azam, F., Knowlton, N., and Rohwer, F. L., “Microbial ecology of four coral atolls in the Northern Line Islands”, PLoS ONE, vol. 3, p. e1584, 2008.

 

2007                                                                                                                                                                

 

R. Vega Thurber and Epel, D., “Apoptosis in early development of the sea urchin, Strongylocentrotus purpuratus”, Developmental Biology, vol. 303, no. 1, pp. 336-46, 2007.

D. Epel, Cole, B., Hamdoun, A. M., and Thurber, R. Vega, “The sea urchin embryo as a model for studying efflux transporters: roles and energy cost”, Marine Environmental Research, vol. 62 Suppl, pp. S1–4, 2006.

T. Smital, Luckenbach, T., Sauerborn, R., Hamdoun, A. M., Thurber, R. Vega, and Epel, D., “Emerging contaminants–pesticides, PPCPs, microbial degradation products and natural substances as inhibitors of multixenobiotic defense in aquatic organisms”, Mutation Research, vol. 552, pp. 101–117, 2004.

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