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1. Harnessing island–ocean connections to maximize marine benefits of island conservation

Author: Sandin, Stuart A, Becker, Penny A, Becker, Ceiba, Brown, Kate, Erazo, Natalia G, Figuerola, Cielo, Fisher, Robert N, Friedlander, Alan M, Fukami, Tadashi, Graham, Nicholas AJ, Gruner, Daniel S, Holmes, Nick D, Holthuijzen, Wieteke A, Jones, Holly P, Rios, Mariela, Samaniego, Araceli, Sechrest, Wes, Semmens, Brice X, Thornton, Hazel E, Thurber, Rebecca Vega, Wails, Christy N, Wolf, Coral A, and Zgliczynski, Brian J
Subjects: Life on Land, Life Below Water, Animals, Humans, Ecosystem, Conservation of Natural Resources, Biodiversity, Introduced Species, Climate Change, Mammals, invasive mammals, island management, land–sea linkage
Abstract: Islands support unique plants, animals, and human societies found nowhere else on the Earth. Local and global stressors threaten the persistence of island ecosystems, with invasive species being among the most damaging, yet solvable, stressors. While the threat of invasive terrestrial mammals on island flora and fauna is well recognized, recent studies have begun to illustrate their extended and destructive impacts on adjacent marine environments. Eradication of invasive mammals and restoration of native biota are promising tools to address both island and ocean management goals. The magnitude of the marine benefits of island restoration, however, is unlikely to be consistent across the globe. We propose a list of six environmental characteristics most likely to affect the strength of land-sea linkages: precipitation, elevation, vegetation cover, soil hydrology, oceanographic productivity, and wave energy. Global databases allow for the calculation of comparable metrics describing each environmental character across islands. Such metrics can be used today to evaluate relative potential for coupled land-sea conservation efforts and, with sustained investment in monitoring on land and sea, can be used in the future to refine science-based planning tools for integrated land-sea management. As conservation practitioners work to address the effects of climate change, ocean stressors, and biodiversity crises, it is essential that we maximize returns from our management investments. Linking efforts on land, including eradication of island invasive mammals, with marine restoration and protection should offer multiplied benefits to achieve concurrent global conservation goals.
Published: 2022

2. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Author: Reddy, Maggie M., Goossens, Corentine, Zhou, Yuxiang, Chaib, Slimane, Raviglione, Delphine, Nicolè, Florence, Hume, Benjamin C. C., Forcioli, Didier, Agostini, Sylvain, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Voolstra, Christian R., Allemand, Denis, Planes, Serge, Thomas, Olivier P., and Banaigs, Bernard
Published: 2023
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3. Different environmental response strategies in sympatric corals from Pacific Islands

Author: Porro, Barbara, Zamoum, Thamilla, Forcioli, Didier, Gilson, Eric, Poquet, Adrien, Di Franco, Eugenio, Barnay-Verdier, Stéphanie, Lombard, Fabien, Voolstra, Christian R., Hume, Benjamin C. C., Galand, Pierre E., Moulin, Clémentine, Boissin, Emilie, Bourdin, Guillaume, Iwankow, Guillaume, Poulain, Julie, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Planes, Serge, Allemand, Denis, Röttinger, Eric, and Furla, Paola
Published: 2023
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4. Engaging the tropical majority to make ocean governance and science more equitable and effective

Author: Spalding, Ana K., Grorud-Colvert, Kirsten, Allison, Edward H., Amon, Diva J., Collin, Rachel, de Vos, Asha, Friedlander, Alan M., Johnson, Steven Mana’oakamai, Mayorga, Juan, Paris, Claire B., Scott, Cinda, Suman, Daniel O., Cisneros-Montemayor, Andrés M., Estradivari, Giron-Nava, Alfredo, Gurney, Georgina G., Harris, Jean M., Hicks, Christina, Mangubhai, Sangeeta, Micheli, Fiorenza, Naggea, Josheena, Obura, David, Palacios-Abrantes, Juliano, Pouponneau, Angelique, and Thurber, Rebecca Vega
Published: 2023
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5. Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution

Author: Leray, Matthieu, Wilkins, Laetitia GE, Apprill, Amy, Bik, Holly M, Clever, Friederike, Connolly, Sean R, De León, Marina E, Duffy, J Emmett, Ezzat, Leïla, Gignoux-Wolfsohn, Sarah, Herre, Edward Allen, Kaye, Jonathan Z, Kline, David I, Kueneman, Jordan G, McCormick, Melissa K, McMillan, W Owen, O’Dea, Aaron, Pereira, Tiago J, Petersen, Jillian M, Petticord, Daniel F, Torchin, Mark E, Thurber, Rebecca Vega, Videvall, Elin, Wcislo, William T, Yuen, Benedict, and Eisen, Jonathan A
Subjects: Microbiology, Biological Sciences, Ecology, Genetics, Life Below Water, Acclimatization, Animals, Aquatic Organisms, Biological Evolution, Ecosystem, Humans, Microbiota, Symbiosis, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract: Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host's physiological capacities; however, the identity and functional role(s) of key members of the microbiome ("core microbiome") in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems' capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts' plastic and adaptive responses to environmental change requires (i) recognizing that individual host-microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.
Published: 2021

6. Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral

Author: Rice, Mallory M, Maher, Rebecca L, Thurber, Rebecca Vega, and Burkepile, Deron E
Subjects: Environmental Sciences, Biological Sciences, Ecology, Environmental Management, Life Below Water, Climate Action, Corallivory, Seawater warming, Nitrate, Ammonium, Coral microbiome, Nutrient loading, Medical and Health Sciences
Abstract: Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals' response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.
Published: 2019

7. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A
Subjects: Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
Published: 2019

8. Host-associated microbiomes drive structure and function of marine ecosystems

Author: Wilkins, Laetitia GE, Leray, Matthieu, O’Dea, Aaron, Yuen, Benedict, Peixoto, Raquel, Pereira, Tiago J, Bik, Holly M, Coil, David A, Duffy, J Emmett, Herre, Edward Allen, Lessios, Harilaos, Lucey, Noelle M, Mejia, Luis C, Rasher, Douglas B, Sharp, Koty, Sogin, Emilia M, Thacker, Robert W, Thurber, Rebecca Vega, Wcislo, William T, Wilbanks, Elizabeth G, and Eisen, Jonathan A
Subjects: Microbiology, Biological Sciences, Ecology, Life Below Water, Animals, Aquatic Organisms, Bacteria, Ecosystem, Host Microbial Interactions, Humans, Microbiota, Symbiosis, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract: The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.
Published: 2019

9. The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally

Author: Baker, Lydia J., Reich, Hannah G., Kitchen, Sheila A., Grace Klinges, J., Koch, Hanna R., Baums, Iliana B., Muller, Erinn M., and Thurber, Rebecca Vega
Published: 2022
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10. Horizon scanning the application of probiotics for wildlife

Author: Garcias-Bonet, Neus, Roik, Anna, Tierney, Braden, Garcia, Francisca C., Villela, Helena D.M., Dungan, Ashley M., Quigley, Kate, Sweet, Michael, Berg, Gabriele, Gram, Lone, Bourne, David G., Ushijima, Blake, Sogin, Maggie, Hoj, Lone, Duarte, Gustavo, Hirt, Heribert, Smalla, Kornelia, Rosado, Alexandre S., Carvalho, Susana, Thurber, Rebecca Vega, Ziegler, Maren, Mason, Christopher E., van Oppen, Madeleine J.H., Voolstra, Christian R., Peixoto, Raquel S., Garcias-Bonet, Neus, Roik, Anna, Tierney, Braden, Garcia, Francisca C., Villela, Helena D.M., Dungan, Ashley M., Quigley, Kate, Sweet, Michael, Berg, Gabriele, Gram, Lone, Bourne, David G., Ushijima, Blake, Sogin, Maggie, Hoj, Lone, Duarte, Gustavo, Hirt, Heribert, Smalla, Kornelia, Rosado, Alexandre S., Carvalho, Susana, Thurber, Rebecca Vega, Ziegler, Maren, Mason, Christopher E., van Oppen, Madeleine J.H., Voolstra, Christian R., and Peixoto, Raquel S.
Abstract: The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called “probiotics for wildlife” is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
Published: 2024

11. Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales

Author: Zaneveld, Jesse R, Burkepile, Deron E, Shantz, Andrew A, Pritchard, Catharine E, McMinds, Ryan, Payet, Jerome P, Welsh, Rory, Correa, Adrienne M. S, Lemoine, Nathan P, Rosales, Stephanie, Fuchs, Corinne, Maynard, Jeffrey A, and Thurber, Rebecca Vega
Published: 2016

12. Bacterial predation in a marine host-associated microbiome

Author: Welsh, Rory M, Zaneveld, Jesse R, Rosales, Stephanie M, Payet, Jérôme P, Burkepile, Deron E, and Thurber, Rebecca Vega
Subjects: Genetics, Emerging Infectious Diseases, Infectious Diseases, Human Genome, Infection, Life Below Water, Animals, Anthozoa, Biota, Coral Reefs, Microbial Interactions, Microbiota, Proteobacteria, Vibrio, Environmental Sciences, Biological Sciences, Technology, Microbiology
Abstract: In many ecological communities, predation has a key role in regulating community structure or function. Although predation has been extensively explored in animals and microbial eukaryotes, predation by bacteria is less well understood. Here we show that predatory bacteria of the genus Halobacteriovorax are prevalent and active predators on the surface of several genera of reef-building corals. Across a library of 198 16S rRNA samples spanning three coral genera, 79% were positive for carriage of Halobacteriovorax. Cultured Halobacteriovorax from Porites asteroides corals tested positive for predation on the putative coral pathogens Vibrio corallyticus and Vibrio harveyii. Co-occurrence network analysis showed that Halobacteriovorax's interactions with other bacteria are influenced by temperature and inorganic nutrient concentration, and further suggested that this bacterial predator's abundance may be driven by prey availability. Thus, animal microbiomes can harbor active bacterial predators, which may regulate microbiome structure and protect the host by consuming potential pathogens.
Published: 2016

13. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Author: Voolstra, Christian R., primary, Hume, Benjamin C. C., additional, Armstrong, Eric J., additional, Mitushasi, Guinther, additional, Porro, Barbara, additional, Oury, Nicolas, additional, Agostini, Sylvain, additional, Boissin, Emilie, additional, Poulain, Julie, additional, Carradec, Quentin, additional, Paz-García, David A., additional, Zoccola, Didier, additional, Magalon, Hélène, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Planes, Serge, additional, Allemand, Denis, additional, and Forcioli, Didier, additional
Published: 2023
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14. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Author: Rouan, Alice, primary, Pousse, Melanie, additional, Djerbi, Nadir, additional, Porro, Barbara, additional, Bourdin, Guillaume, additional, Carradec, Quentin, additional, Hume, Benjamin CC., additional, Poulain, Julie, additional, Lê-Hoang, Julie, additional, Armstrong, Eric, additional, Agostini, Sylvain, additional, Salazar, Guillem, additional, Ruscheweyh, Hans-Joachim, additional, Aury, Jean-Marc, additional, Paz-García, David A., additional, McMinds, Ryan, additional, Giraud-Panis, Marie-Josèphe, additional, Deshuraud, Romane, additional, Ottaviani, Alexandre, additional, Morini, Lycia Die, additional, Leone, Camille, additional, Wurzer, Lia, additional, Tran, Jessica, additional, Zoccola, Didier, additional, Pey, Alexis, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, de Vargas, Colomban, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Douville, Eric, additional, Flores, Michel, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Planes, Serge, additional, Allemand, Denis, additional, Pesant, Stephane, additional, Galand, Pierre E., additional, Wincker, Patrick, additional, Sunagawa, Shinichi, additional, Röttinger, Eric, additional, Furla, Paola, additional, Voolstra, Christian R., additional, Forcioli, Didier, additional, Lombard, Fabien, additional, and Gilson, Eric, additional
Published: 2023
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15. Pervasive tandem duplications and convergent evolution shape coral genomes

Author: Noel, Benjamin, primary, Denoeud, France, additional, Rouan, Alice, additional, Buitrago-López, Carol, additional, Capasso, Laura, additional, Poulain, Julie, additional, Boissin, Emilie, additional, Pousse, Mélanie, additional, Da Silva, Corinne, additional, Couloux, Arnaud, additional, Armstrong, Eric, additional, Carradec, Quentin, additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Lê-Hoang, Julie, additional, Tambutté, Sylvie, additional, Barbe, Valérie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, J. Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Allemand, Denis, additional, Planes, Serge, additional, Gilson, Eric, additional, Zoccola, Didier, additional, Wincker, Patrick, additional, Voolstra, Christian R., additional, and Aury, Jean-Marc, additional
Published: 2023
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16. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean

Author: Armstrong, Eric J., primary, Lê-Hoang, Julie, additional, Carradec, Quentin, additional, Aury, Jean-Marc, additional, Noel, Benjamin, additional, Hume, Benjamin C. C., additional, Voolstra, Christian R., additional, Poulain, Julie, additional, Belser, Caroline, additional, Paz-García, David A., additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Da Silva, Corinne, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Zoccola, Didier, additional, Planes, Serge, additional, Allemand, Denis, additional, and Wincker, Patrick, additional
Published: 2023
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17. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, primary, Bourdin, Guillaume, additional, Pesant, Stéphane, additional, Agostini, Sylvain, additional, Baudena, Alberto, additional, Boissin, Emilie, additional, Cassar, Nicolas, additional, Clampitt, Megan, additional, Conan, Pascal, additional, Da Silva, Ophélie, additional, Dimier, Céline, additional, Douville, Eric, additional, Elineau, Amanda, additional, Fin, Jonathan, additional, Flores, J. Michel, additional, Ghiglione, Jean-François, additional, Hume, Benjamin C. C., additional, Jalabert, Laetitia, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, McMinds, Ryan, additional, Mériguet, Zoé, additional, Metzl, Nicolas, additional, Paz-García, David A., additional, Pedrotti, Maria Luiza, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Ras, Joséphine, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Rouan, Alice, additional, Röttinger, Eric, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Moulin, Clémentine, additional, Iwankow, Guillaume, additional, Banaigs, Bernard, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Sullivan, Matthew B., additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Boss, Emmanuel, additional, and Gorsky, Gaby, additional
Published: 2023
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18. Diversity of the Pacific Ocean coral reef microbiome

Author: Galand, Pierre E., primary, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Hochart, Corentin, additional, Henry, Nicolas, additional, Hume, Benjamin C. C., additional, Oliveira, Pedro H., additional, Perdereau, Aude, additional, Labadie, Karine, additional, Belser, Caroline, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Armstrong, Eric J., additional, Paz-García, David A., additional, Ziegler, Maren, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Voolstra, Christian R., additional, Thurber, Rebecca Vega, additional, Sunagawa, Shinichi, additional, Wincker, Patrick, additional, Allemand, Denis, additional, and Planes, Serge, additional
Published: 2023
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19. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author: Hochart, Corentin, primary, Paoli, Lucas, additional, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Ziegler, Maren, additional, Porro, Barbara, additional, Armstrong, Eric J., additional, Hume, Benjamin C. C., additional, Aury, Jean-Marc, additional, Pogoreutz, Claudia, additional, Paz-García, David A., additional, Nugues, Maggy M., additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Thurber, Rebecca Vega, additional, Voolstra, Christian R., additional, Sunagawa, Shinichi, additional, and Galand, Pierre E., additional
Published: 2023
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20. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, Gorsky, Gaby, Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, and Gorsky, Gaby
Abstract: The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
Published: 2023
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21. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Author: Pollock, F. Joseph, McMinds, Ryan, Smith, Styles, Bourne, David G., Willis, Bette L., Medina, Mónica, Thurber, Rebecca Vega, and Zaneveld, Jesse R.
Published: 2018
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22. A communal catalogue reveals Earths multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Subjects: Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]
Published: 2017
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23. Harnessing the microbiome to prevent global biodiversity loss

Author: Peixoto, Raquel S., Voolstra, Christian R., Sweet, Michael, Duarte, Carlos M., Carvalho, Susana, Villela, Helena, Lunshof, Jeantine E., Gram, Lone, Woodhams, Douglas C., Walter, Jens, Roik, Anna, Hentschel, Ute, Thurber, Rebecca Vega, Daisley, Brendan, Ushijima, Blake, Daffonchio, Daniele, Costa, Rodrigo, Keller-Costa, Tina, Bowman, Jeff S., Rosado, Alexandre S., Reid, Gregor, Mason, Christopher E., Walke, Jenifer B., Thomas, Torsten, Berg, Gabriele, Peixoto, Raquel S., Voolstra, Christian R., Sweet, Michael, Duarte, Carlos M., Carvalho, Susana, Villela, Helena, Lunshof, Jeantine E., Gram, Lone, Woodhams, Douglas C., Walter, Jens, Roik, Anna, Hentschel, Ute, Thurber, Rebecca Vega, Daisley, Brendan, Ushijima, Blake, Daffonchio, Daniele, Costa, Rodrigo, Keller-Costa, Tina, Bowman, Jeff S., Rosado, Alexandre S., Reid, Gregor, Mason, Christopher E., Walke, Jenifer B., Thomas, Torsten, and Berg, Gabriele
Abstract: Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
Published: 2022
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24. Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals

Author: Messyasz, Adriana, primary, Maher, Rebecca L., additional, Meiling, Sonora S., additional, and Thurber, Rebecca Vega, additional
Published: 2021
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25. Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration.

Author: Thurber, Rebecca Vega, Schmeltzer, Emily R., Grottoli, Andréa G., van Woesik, Robert, Toonen, Robert J., Warner, Mark, Dobson, Kerri L., McLachlan, Rowan H., Barott, Katie, Barshis, Daniel J., Baumann, Justin, Chapron, Leila, Combosch, David J., Correa, Adrienne M. S., DeCarlo, Thomas M., Hagedorn, Mary, Hédouin, Laetitia, Hoadley, Kenneth, Felis, Thomas, and Ferrier-Pagès, Christine
Subjects: CORAL bleaching, CORAL declines, BACTERIAL communities, LIQUID nitrogen
Abstract: Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundationsponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at -80 °C to -20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses. [ABSTRACT FROM AUTHOR]
Published: 2022
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26. The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally

Author: Baker, Lydia J., primary, Reich, Hannah G., additional, Kitchen, Sheila A., additional, Grace Klinges, J., additional, Koch, Hanna R., additional, Baums, Iliana B., additional, Muller, Erinn M., additional, and Thurber, Rebecca Vega, additional
Published: 2021
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27. Viruses manipulate the marine environment

Author: Rohwer, Forest and Thurber, Rebecca Vega
Subjects: Marine ecology -- Research -- Environmental aspects -- Genetic aspects, Adaptation (Biology) -- Research -- Environmental aspects -- Genetic aspects, Biological diversity conservation -- Management -- Research -- Genetic aspects -- Environmental aspects, Virus-vector relationships -- Research -- Genetic aspects, Biogeochemistry -- Environmental aspects -- Research -- Genetic aspects, Viruses -- Genetic aspects -- Natural history -- Environmental aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Company business management, Management, Research, Genetic aspects, Natural history, Environmental aspects
Abstract: Marine viruses affect Bacteria, Archaea and eukaryotic organisms and are major components of the marine food web. Most studies have focused on their role as predators and parasites, but many of the interactions between marine viruses and their hosts are much more complicated. A series of recent studies has shown that viruses have the ability to manipulate the life histories and evolution of their hosts in remarkable ways, challenging our understanding of this almost invisible world., Marine virology has traditionally focused on two areas: viruses as pathogens of aquatic organisms, and phage-driven dynamics of the marine microbial food web. Both of these influence global biogeochemistry and [...]
Published: 2009

28. Functional metagenomic profiling of nine biomes

Author: Dinsdale, Elizabeth A., Edwards, Robert A., Hall, Dana, Angly, Florent, Breitbart, Mya, Brulc, Jennifer M., Furlan, Mike, Desnues, Christelle, Haynes, Matthew, Li, Linlin, McDaniel, Lauren, Moran, Mary Ann, Nelson, Karen E., Nilsson, Christina, Olson, Robert, Paul, John, Brito, Beltran Rodriguez, Ruan, Yijun, Swan, Brandon K., Stevens, Rick, Valentine, David L., Thurber, Rebecca Vega, Wegley, Linda, White, Bryan A., and Rohwer, Forest
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Microbial activities shape the biogeochemistry of the planet (1,2) and macroorganism health (3). Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for [...]
Published: 2008

29. Biodiversity and biogeography of phages in modern stromatolites and thrombolites

Author: Desnues, Christelle, Rodriguez-Brito, Beltran, Rayhawk, Steve, Kelley, Scott, Tran, Tuong, Haynes, Matthew, Liu, Hong, Furlan, Mike, Wegley, Linda, Chau, Betty, Ruan, Yijun, Hall, Dana, Angly, Florent E., Edwards, Robert A., Li, Linlin, Thurber, Rebecca Vega, Reid, R. Pamela, Siefert, Janet, Souza, Valeria, Valentine, David L., Swan, Brandon K., Breitbart, Mya, and Rohwer, Forest
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been [...]
Published: 2008

30. Coral-associated viral assemblages from the central Red Sea align with host species and contribute to the holobiont genetic diversity

Author: Cárdenas, Anny, Ye, Jin, Ziegler, Maren, Payet, Jérôme P., McMinds, Ryan, Thurber, Rebecca Vega, and Voolstra, Christian R.
Subjects: ddc:570, fungi, technology, industry, and agriculture, population characteristics, virus, coral, Metagenomics, metatranscriptomics, metaorganism, holobiont, Red Sea, biochemical phenomena, metabolism, and nutrition, geographic locations
Abstract: Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatransciptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, other biological traits such as coral life history strategies correlated with patterns of viral community composition. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect fungal associates, Myoviridae and Siphoviridae that presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, and Hepadnaviridae and Retroviridae that might affect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common in viral sequences, corroborating a contribution of viruses to the holobiont’s genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns. published
Published: 2020

31. Mystery solved: Disease detectives identify the cause of a mass die-off in the sea.

Author: Thurber, Rebecca Vega and Hay, Mark
Abstract: The article focuses on identifying the cause of a mass die-off in the sea, specifically the common sea urchin Diadema antillarum in the Caribbean. Topics include die-offs that led to significant changes in the ecosystem, including the decline of corals and the proliferation of macroalgae; scientists have now identified the culprit as an infectious single-celled protist called a scuticociliate with the importance of studying and managing marine diseases to protect fragile ecosystems.
Published: 2023
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32. Apoptosis in early development of the sea urchin, Strongylocentrotus purpuratus

Author: Thurber, Rebecca Vega and Epel, David
Subjects: Apoptosis, Biological sciences
Abstract: Byline: Rebecca Vega Thurber, David Epel Keywords: Apoptosis; Development; Sea urchin; Embryo; Blastula; Programmed cell death; Necrosis Abstract: Apoptosis provides metazoans remarkable developmental flexibility by (1) eliminating damaged undifferentiated cells early in development and then (2) sculpting, patterning, and restructuring tissues during successive stages thereafter. We show here that apoptotic programmed cell death is infrequent and not obligatory during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus. During the first 30 h of urchin development, fewer than 20% of embryos exhibit any cell death. Cell death during the cleavage stages consists of necrotic or pathological cell death, while cell death during the blastula and gastrula stages is random and predominantly caspase-mediated apoptosis. Apoptosis remains infrequent during the late blastula stage followed by a gradual increase in frequency during gastrulation. Even after prolonged exposure during the cleavage period to chemical stress, apoptosis occurs in less than 50% of embryos and always around the pre-hatching stage. Embryonic suppression of apoptosis through caspase inhibition leads to functionally normal larvae that can survive to metamorphosis, but in the presence of inducers of apoptosis, caspase inhibition leads to deformed larvae and reduced survival. Remarkably, however, pharmacological induction of apoptosis, while reducing overall survival, also significantly accelerates development of the survivors such that metamorphosis occurs up to a week before controls. Author Affiliation: Stanford University, Hopkins Marine Station, 120 Oceanview Blvd. Pacific Grove, CA 93950, USA Article History: Received 30 July 2006; Revised 23 October 2006; Accepted 13 November 2006
Published: 2007

33. Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning.

Author: David, Maude M., Tataru, Christine, Pope, Quintin, Baker, Lydia J., English, Mary K., Epstein, Hannah E., Hammer, Austin, Kent, Michael, Sieler Jr, Michael J., Mueller, Ryan S., Sharpton, Thomas J., Tomas, Fiona, Thurber, Rebecca Vega, and Fern, Xiaoli Z.
Published: 2022
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34. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean

Author: Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-francois, Gilson, Eric, Lombard, Fabien, Moulin, Clementine, Pesant, Stephane, Poulain, Julie, Reynaud, Stephanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Trouble, Romain, De Vargas, Colomban, Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, Planes, S., Allemand, D., Agostini, S., Armstrong, E., Audrain, S., Aury, J-m, Banaig, B., Barbe, V, Belser, C., Beraud, E., Boissin, E., Bonnival, E., Boss, E., Bourdin, G., Bourgois, E., Bowler, C., Carradec, Q., Cassar, N., Cohen, N. R., Conan, P., Cronin, D. R., Da Silva, O., De Vargas, C., Djerbi, N., Dolan, J. R., Herta, Dominguez G., Du J, Filee, J., Flores, J. M., Forcioli, D., Friedrich, R., Furla, P., Galand, P. E., Ghiglione, J-f, Gilson, E., Gorsky, G., Guinther, M., Haentjens, N., Henry, N., Hertau, M., Hochart, C., Hume, B. C. C., Iwankow, G., John, S. G., Karp-boss, L., Kelly, R. L., Kitano, Y., Klinges, G., Koren, I, Labadie, K., Lancelot, J., Lang-yona, N., Le-hoang, J., Lemee, R., Lin, Y., Lombard, F., Marie, D., Mcmind, R., Miguel-gordo, M., Trainic, M., Monmarche, D., Moulin, C., Mucherie, Y., Noel, B., Ottaviani, A., Paoli, L., Pedrotti, M-l, Pesant, S., Pogoreutz, C., Poulain, J., Pujo-pay, M., Reverdin, G., Reynaud, S., Romac, S., Rothig, T., Rottinger, E., Rouan, A., Ruscheweyh, H-j, Salazar, G., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Trouble, R., Vardi, A., Vega-thunder, R., Voolstra, C. R., Wincker, P., Zahed, A., Zamoum, T., Ziegler, M., Zoccola, D., Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre Scientifique de Monaco (CSM), Tara Expéditions, Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, University of Maine, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Ohio State University [Columbus] (OSU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), University of Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Department of Earth Sciences [USC Los Angeles], University of Southern California (USC), Martin Ryan Institute, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Derby [United Kingdom], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-17-CE02-0020,CORALGENE,Complexité génomique de l'holobionte ' corail ' à l'échelle du Pacifique(2017), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Justus-Liebig-Universität Gießen (JLU), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0301 basic medicine, Topography, Coral reefs, Effects of global warming on oceans, Coral, Biodiversity, Marine and Aquatic Sciences, Ecosystem services, 0302 clinical medicine, Community Page, Oceans, Biology (General), Islands, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography.geographical_feature_category, Ecology, Microbiota, General Neuroscience, Eukaryota, Coral reef, Anthozoa, Plankton, Holobiont, Corals, Expeditions, General Agricultural and Biological Sciences, Marine ecosystems, QH301-705.5, Climate change, Marine Biology, Biology, Ecosystems, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, ddc:570, Animals, Metabolomics, Marine ecosystem, 14. Life underwater, Symbiosis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Landforms, geography, Pacific Ocean, General Immunology and Microbiology, ACL, Ecology and Environmental Sciences, Organisms, Biology and Life Sciences, Geomorphology, Bodies of Water, 15. Life on land, Invertebrates, 030104 developmental biology, 13. Climate action, Earth Sciences, Reefs, Metagenomics, Reef ecosystems, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery
Abstract: Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing 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. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., This Community Page article presents the Tara Pacific expedition, which aims to shed light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs, and providing a reference of the biological state of modern reef systems.
Published: 2019

35. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., and Eloe-Fadrosh, Emiley A.
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
Published: 2019

36. Evaluation of the Effects of Library Preparation Procedure and Sample Characteristics on the Accuracy of Metagenomic Profiles.

Author: Gaulke, Christopher A., Schmeltzer, Emily R., Dasenko, Mark, Tyler, Brett M., Thurber, Rebecca Vega, and Sharpton, Thomas J.
Published: 2021
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37. A review of coral bleaching specimen collection, preservation, and laboratory processing methods.

Author: McLachlan, Rowan H., Dobson, Kerri L., Schmeltzer, Emily R., Thurber, Rebecca Vega, and Grottoli, Andréa G.
Subjects: CORAL bleaching, SCLERACTINIA, CORAL reefs & islands, CORAL declines, ACROPORA
Abstract: Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen’s investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen’s utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect. [ABSTRACT FROM AUTHOR]
Published: 2021
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38. The coral symbiont CandidatusAquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally

Author: Baker, Lydia J, Reich, Hannah G, Kitchen, Sheila A, Klinges, J Grace, Koch, Hanna R, Baums, Iliana B, Muller, Erinn M, and Thurber, Rebecca Vega
Abstract: The symbiont “CandidatusAquarickettsia rohweri” infects a diversity of aquatic hosts. In the threatened Caribbean coral, Acropora cervicornis, Aquarickettsiaproliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality of coral. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsiainfecting threatened corals, Ac. cervicornis, and Ac. palmataand their hybrid (“Ac. prolifera”). Aquarickettsiawas found in all acroporids, with coral host and geographic location impacting the infection magnitude. Phylogenomic and genome-wide single-nucleotide variant analysis of Aquarickettsiafound phylogenetic clustering by geographic region, not by coral taxon. Analysis of Aquarickettsiafixation indices suggests multiple sequential infections of the same coral colony are unlikely. Furthermore, relative to other Rickettsiales species, Aquarickettsiais undergoing positive selection, with Florida populations experiencing greater positive selection relative to other Caribbean locations. This may be due in part to Aquarickettsiaproliferating in response to greater nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsiawas not found to significantly codiversify with either the coral animal or the coral’s algal symbiont (Symbiodinium“fitti”). Quantitative PCR analysis showed that gametes, larvae, recruits, and juveniles from susceptible, captive-reared coral genets were not infected with Aquarickettsia. Thus, horizontal transmission of Aquarickettsiavia coral mucocytes or an unidentified host is more likely. The prevalence of Aquarickettsiain Ac. cervicornisand its high abundance in the Florida coral population suggests that coral disease mitigation efforts focus on preventing early infection via horizontal transmission.
Published: 2022
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39. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Roux, Simon, primary, Adriaenssens, Evelien M, additional, Dutilh, Bas E, additional, Koonin, Eugene V, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Kuhn, Jens H, additional, Lavigne, Rob, additional, Brister, J Rodney, additional, Varsani, Arvind, additional, Amid, Clara, additional, Aziz, Ramy K, additional, Bordenstein, Seth R, additional, Bork, Peer, additional, Breitbart, Mya, additional, Cochrane, Guy R, additional, Daly, Rebecca A, additional, Desnues, Christelle, additional, Duhaime, Melissa B, additional, Emerson, Joanne B, additional, Enault, François, additional, Fuhrman, Jed A, additional, Hingamp, Pascal, additional, Hugenholtz, Philip, additional, Hurwitz, Bonnie L, additional, Ivanova, Natalia N, additional, Labonté, Jessica M, additional, Lee, Kyung-Bum, additional, Malmstrom, Rex R, additional, Martinez-Garcia, Manuel, additional, Mizrachi, Ilene Karsch, additional, Ogata, Hiroyuki, additional, Páez-Espino, David, additional, Petit, Marie-Agnès, additional, Putonti, Catherine, additional, Rattei, Thomas, additional, Reyes, Alejandro, additional, Rodriguez-Valera, Francisco, additional, Rosario, Karyna, additional, Schriml, Lynn, additional, Schulz, Frederik, additional, Steward, Grieg F, additional, Sullivan, Matthew B, additional, Sunagawa, Shinichi, additional, Suttle, Curtis A, additional, Temperton, Ben, additional, Tringe, Susannah G, additional, Thurber, Rebecca Vega, additional, Webster, Nicole S, additional, Whiteson, Katrine L, additional, Wilhelm, Steven W, additional, Wommack, K Eric, additional, Woyke, Tanja, additional, Wrighton, Kelly C, additional, Yilmaz, Pelin, additional, Yoshida, Takashi, additional, Young, Mark J, additional, Yutin, Natalya, additional, Allen, Lisa Zeigler, additional, Kyrpides, Nikos C, additional, and Eloe-Fadrosh, Emiley A, additional
Published: 2018
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40. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-fadrosh, Emiley A, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-fadrosh, Emiley A
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
Published: 2018

41. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-fadrosh, Emiley A, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-fadrosh, Emiley A
Published: 2018

42. A communal catalogue reveals Earth's multiscale microbial diversity

Author: Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
Published: 2017

43. The coral symbiont CandidatusAquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally

Author: Baker, Lydia J., Reich, Hannah G., Kitchen, Sheila A., Grace Klinges, J., Koch, Hanna R., Baums, Iliana B., Muller, Erinn M., and Thurber, Rebecca Vega
Abstract: The symbiont “CandidatusAquarickettsia rohweri” infects a diversity of aquatic hosts. In the threatened Caribbean coral, Acropora cervicornis, Aquarickettsiaproliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality of coral. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsiainfecting threatened corals, Ac. cervicornis, and Ac. palmataand their hybrid (“Ac. prolifera”). Aquarickettsiawas found in all acroporids, with coral host and geographic location impacting the infection magnitude. Phylogenomic and genome-wide single-nucleotide variant analysis of Aquarickettsiafound phylogenetic clustering by geographic region, not by coral taxon. Analysis of Aquarickettsiafixation indices suggests multiple sequential infections of the same coral colony are unlikely. Furthermore, relative to other Rickettsiales species, Aquarickettsiais undergoing positive selection, with Florida populations experiencing greater positive selection relative to other Caribbean locations. This may be due in part to Aquarickettsiaproliferating in response to greater nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsiawas not found to significantly codiversify with either the coral animal or the coral’s algal symbiont (Symbiodinium“fitti”). Quantitative PCR analysis showed that gametes, larvae, recruits, and juveniles from susceptible, captive-reared coral genets were not infected with Aquarickettsia. Thus, horizontal transmission of Aquarickettsiavia coral mucocytes or an unidentified host is more likely. The prevalence of Aquarickettsiain Ac. cervicornisand its high abundance in the Florida coral population suggests that coral disease mitigation efforts focus on preventing early infection via horizontal transmission.
Published: 2021
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44. Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral.

Author: Rice, Mallory M., Maher, Rebecca L., Thurber, Rebecca Vega, and Burkepile, Deron E.
Subjects: CORALS, CORAL reef ecology, OCEAN acidification, SPECIFIC gravity, OCEAN temperature, CORAL declines, AMMONIUM nitrate, FACTORIAL experiment designs
Abstract: Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment. [ABSTRACT FROM AUTHOR]
Published: 2019
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45. Bacterial predation in a marine host-associated microbiome

Author: Welsh, Rory M, primary, Zaneveld, Jesse R, additional, Rosales, Stephanie M, additional, Payet, Jérôme P, additional, Burkepile, Deron E, additional, and Thurber, Rebecca Vega, additional
Published: 2015
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46. Potential role of viruses in white plague coral disease

Author: Soffer, Nitzan, primary, Brandt, Marilyn E, additional, Correa, Adrienne MS, additional, Smith, Tyler B, additional, and Thurber, Rebecca Vega, additional
Published: 2013
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47. Viral and microbial community dynamics in four aquatic environments

Author: Rodriguez-Brito, Beltran, primary, Li, LinLin, additional, Wegley, Linda, additional, Furlan, Mike, additional, Angly, Florent, additional, Breitbart, Mya, additional, Buchanan, John, additional, Desnues, Christelle, additional, Dinsdale, Elizabeth, additional, Edwards, Robert, additional, Felts, Ben, additional, Haynes, Matthew, additional, Liu, Hong, additional, Lipson, David, additional, Mahaffy, Joseph, additional, Martin-Cuadrado, Anna Belen, additional, Mira, Alex, additional, Nulton, Jim, additional, Pašić, Lejla, additional, Rayhawk, Steve, additional, Rodriguez-Mueller, Jennifer, additional, Rodriguez-Valera, Francisco, additional, Salamon, Peter, additional, Srinagesh, Shailaja, additional, Thingstad, Tron Frede, additional, Tran, Tuong, additional, Thurber, Rebecca Vega, additional, Willner, Dana, additional, Youle, Merry, additional, and Rohwer, Forest, additional
Published: 2010
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48. Erratum: Functional metagenomic profiling of nine biomes

Author: Dinsdale, Elizabeth A., primary, Edwards, Robert A., additional, Hall, Dana, additional, Angly, Florent, additional, Breitbart, Mya, additional, Brulc, Jennifer M., additional, Furlan, Mike, additional, Desnues, Christelle, additional, Haynes, Matthew, additional, Li, Linlin, additional, McDaniel, Lauren, additional, Moran, Mary Ann, additional, Nelson, Karen E., additional, Nilsson, Christina, additional, Olson, Robert, additional, Paul, John, additional, Brito, Beltran Rodriguez, additional, Ruan, Yijun, additional, Swan, Brandon K., additional, Stevens, Rick, additional, Valentine, David L., additional, Thurber, Rebecca Vega, additional, Wegley, Linda, additional, White, Bryan A., additional, and Rohwer, Forest, additional
Published: 2008
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49. Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Author: Dinsdale, Elizabeth A., primary, Pantos, Olga, additional, Smriga, Steven, additional, Edwards, Robert A., additional, Angly, Florent, additional, Wegley, Linda, additional, Hatay, Mark, additional, Hall, Dana, additional, Brown, Elysa, additional, Haynes, Matthew, additional, Krause, Lutz, additional, Sala, Enric, additional, Sandin, Stuart A., additional, Thurber, Rebecca Vega, additional, Willis, Bette L., additional, Azam, Farooq, additional, Knowlton, Nancy, additional, and Rohwer, Forest, additional
Published: 2008
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50. Potential role of viruses in white plague coral disease.

Author: Soffer, Nitzan, Brandt, Marilyn E, Correa, Adrienne MS, Smith, Tyler B, and Thurber, Rebecca Vega
Subjects: CORAL diseases, PLAGUE, DNA viruses, ETIOLOGY of diseases, TRANSMISSION electron microscopy, HERPESVIRUSES, SYMBIODINIUM
Abstract: White plague (WP)-like diseases of tropical corals are implicated in reef decline worldwide, although their etiological cause is generally unknown. Studies thus far have focused on bacterial or eukaryotic pathogens as the source of these diseases; no studies have examined the role of viruses. Using a combination of transmission electron microscopy (TEM) and 454 pyrosequencing, we compared 24 viral metagenomes generated from Montastraea annularis corals showing signs of WP-like disease and/or bleaching, control conspecific corals, and adjacent seawater. TEM was used for visual inspection of diseased coral tissue. No bacteria were visually identified within diseased coral tissues, but viral particles and sequence similarities to eukaryotic circular Rep-encoding single-stranded DNA viruses and their associated satellites (SCSDVs) were abundant in WP diseased tissues. In contrast, sequence similarities to SCSDVs were not found in any healthy coral tissues, suggesting SCSDVs might have a role in WP disease. Furthermore, Herpesviridae gene signatures dominated healthy tissues, corroborating reports that herpes-like viruses infect all corals. Nucleocytoplasmic large DNA virus (NCLDV) sequences, similar to those recently identified in cultures of Symbiodinium (the algal symbionts of corals), were most common in bleached corals. This finding further implicates that these NCLDV viruses may have a role in bleaching, as suggested in previous studies. This study determined that a specific group of viruses is associated with diseased Caribbean corals and highlights the potential for viral disease in regional coral reef decline. [ABSTRACT FROM AUTHOR]
Published: 2014
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