Oliver, A., Podell, S., Wegley Kelly, L., Sparagon, W. J., Plominsky, A. M., Nelson, R. S., Laurens, L. M. L., Augyte, S., Sims, N. A., Nelson, C. E., & Allen, E. E. (2024). Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. MBio, e00496-24. https://doi.org/10.1128/mbio.00496-24

Yus, J., Nixon, E. N., Li, J., Noriega Gimenez, J., Bennett, M.-J., Flores, D., Marhaver, K. L., Wegley Kelly, L., Espinosa-Marzal, R. M., & Wagoner Johnson, A. J. (2024). Composite substrates for coral larval settlement and reef restoration based on natural hydraulic lime and inorganic strontium and magnesium compounds. Ecological Engineering, 202, 107236. https://doi.org/10.1016/j.ecoleng.2024.107236

Quinlan, Z. A., Bennett, M.-J., Arts, M. G. I., Levenstein, M., Flores, D., Tholen, H. M., Tichy, L., Juarez, G., Haas, A. F., Chamberland, V. F., Latijnhouwers, K. R. W., Vermeij, M. J. A., Johnson, A. W., Marhaver, K. L., & Kelly, L. W. (2023). Coral larval settlement induction using tissue-associated and exuded coralline algae metabolites and the identification of putative chemical cues. Proceedings of the Royal Society B: Biological Sciences, 290(2009), 20231476. https://doi.org/10.1098/rspb.2023.1476

Mannochio-Russo, H., Swift, S. O. I., Nakayama, K. K., Wall, C. B., Gentry, E. C., Panitchpakdi, M., Caraballo-Rodriguez, A. M., Aron, A. T., Petras, D., Dorrestein, K., Dorrestein, T. K., Williams, T. M., Nalley, E. M., Altman-Kurosaki, N. T., Martinelli, M., Kuwabara, J. Y., Darcy, J. L., Bolzani, V. S., Wegley Kelly, L., … Nelson, C. E. (2023). Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses. Communications Biology, 6(1), 896. https://doi.org/10.1038/s42003-023-05230-1

Candy, A. S., Taylor Parkins, S. K., Van Duyl, F. C., Mueller, B., Arts, M. G. I., Barnes, W., Carstensen, M., Scholten, Y. J. H., El-Khaled, Y. C., Wild, C., Wegley Kelly, L., Nelson, C. E., Sandin, S. A., Vermeij, M. J. A., Rohwer, F. L., Picioreanu, C., Stocchi, P., & Haas, A. F. (2023). Small-scale oxygen distribution patterns in a coral reef. Frontiers in Marine Science, 10, 1135686. https://doi.org/10.3389/fmars.2023.1135686

Silveira, C. B., Luque, A., Haas, A. F., Roach, T. N. F., George, E. E., Knowles, B., Little, M., Sullivan, C. J., Varona, N. S., Wegley Kelly, L., Brainard, R., Rohwer, F., & Bailey, B. (2023). Viral predation pressure on coral reefs. BMC Biology, 21(1), 77. https://doi.org/10.1186/s12915-023-01571-9

Nelson, C. E., Wegley Kelly, L., & Haas, A. F. (2023). Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience. Annual Review of Marine Science, 15(1), 431–460. https://doi.org/10.1146/annurev-marine-042121-080917

Quinlan, Z. A., Koester, I., Aron, A. T., Petras, D., Aluwihare, L. I., Dorrestein, P. C., Nelson, C. E., & Wegley Kelly, L. (2022). ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction. Metabolites, 12(12), 1275. https://doi.org/10.3390/metabo12121275

Levenstein, M. A., Gysbers, D. J., Marhaver, K. L., Kattom, S., Tichy, L., Quinlan, Z., Tholen, H. M., Wegley Kelly, L., Vermeij, M. J. A., Wagoner Johnson, A. J., & Juarez, G. (2022). Millimeter-scale topography facilitates coral larval settlement in wave-driven oscillatory flow. PLOS ONE, 17(9), e0274088. https://doi.org/10.1371/journal.pone.0274088

Levenstein, M. A., Marhaver, K. L., Quinlan, Z. A., Tholen, H. M., Tichy, L., Yus, J., Lightcap, I., Kelly, L. W., Juarez, G., Vermeij, M. J. A., & Johnson, A. J. W. (2022). Composite substrates reveal inorganic material cues for coral larval settlement. Acs Sustainable Chemistry & Engineering, 10(12), 3960–3971. https://doi.org/10.1021/acssuschemeng.1c08313

Remple, K. L., Silbiger, N. J., Quinlan, Z. A., Fox, M. D., Kelly, L. W., Donahue, M. J., & Nelson, C. E. (2021). Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. Npj Biofilms and Microbiomes, 7(1), 11. https://doi.org/10.1038/s41522-021-00252-1

Kelly, L. W., Nelson, C. E., Aluwihare, L. I., Arts, M. G. I., Dorrestein, P. C., Koester, I., Matsuda, S. B., Petras, D., Quinlan, Z. A., & Haas, A. F. (2021). Molecular commerce on coral reefs: Using metabolomics to reveal biochemical exchanges underlying holobiont biology and the ecology of coastal ecosystems. Frontiers in Marine Science, 8, 11. https://doi.org/10.3389/fmars.2021.630799

Roach, T. N. F., Little, M., Arts, M. G. I., Huckeba, J., Haas, A. F., George, E. E., Quinn, R. A., Cobian-Guemes, A. G., Naliboff, D. S., Silveria, C. B., Vermeij, M. J. A., Kelly, L. W., Dorrestein, P. C., & Rohwer, F. (2021). A multiomic analysis of in situ coral-turf algal interactions. Proceedings of the National Academy of Sciences of the United States of America, 117(24), 13588–13595. https://doi.org/10.1073/pnas.1915455117

Little, M., George, E. E., Arts, M. G. I., Shivak, J., Benler, S., Huckeba, J., Quinlan, Z. A., Boscaro, V., Mueller, B., Guemes, A. G. C., Rojas, M. I., White, B., Petras, D., Silveira, C. B., Haas, A. F., Kelly, L. W., Vermeij, M. J. A., Quinn, R. A., Keeling, P. J., … Roach, T. N. F. (2021). Three-dimensional molecular cartography of the Caribbean reef-building coral Orbicella faveolata. Frontiers in Marine Science, 8. https://doi.org/ARTN 627724 10.3389/fmars.2021.627724

Kelly, L. W., Nelson, C. E., Haas, A. F., Naliboff, D. S., Calhoun, S., Carlson, C. A., Edwards, R. A., Fox, M. D., Hatay, M., Johnson, M. D., Kelly, E. L. A., Lim, Y. W., Macherla, S., Quinlan, Z. A., Silva, G. G. Z., Vermeij, M. J. A., Zgliczynski, B., Sandin, S. A., Smith, J. E., & Rohwer, F. (2019). Diel population and functional synchrony of microbial communities on coral reefs. Nature Communications, 10. https://doi.org/10.1038/s41467-019-09419-z

James, A. K., Kelly, L. W., Nelson, C. E., Wilbanks, E. G., & Carlson, C. A. (2019). Elevated pCO(2) alters marine heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton organic matter. Environmental Microbiology, 21(2), 541–556. https://doi.org/10.1111/1462-2920.14484

Quinlan, Z. A., Remple, K., Fox, M. D., Silbiger, N. J., Oliver, T. A., Putnam, H. M., Kelly, L. W., Carlson, C. A., Donahue, M. J., & Nelson, C. E. (2018). Fluorescent organic exudates of corals and algae in tropical reefs are compositionally distinct and increase with nutrient enrichment. Limnology and Oceanography Letters, 3(4), 331–340. https://doi.org/10.1002/lol2.10074

Nakajima, R., Haas, A. F., Silveira, C. B., Kelly, E. L. A., Smith, J. E., Sandin, S., Kelly, L. W., Rohwer, F., Nakatomi, N., & Kurihara, H. (2018). Release of dissolved and particulate organic matter by the soft coral Lobophytum and subsequent microbial degradation. Journal of Experimental Marine Biology and Ecology, 504, 53–60. https://doi.org/10.1016/j.jembe.2018.02.008

Linda Wegley Kelly, Andreas F. Haas, & Craig E. Nelson. (2018). Ecosystem microbiology of coral reefs: Linking genomic, metabolomic, and biogeochemical Dynamics from animal symbioses to reefscape processes. MSystems, 3(2), e00162-17. https://doi.org/doi:10.1128/mSystems.00162-17

Petras, D., Koester, I., Da Silva, R., Stephens, B. M., Haas, A. F., Nelson, C. E., Kelly, L. W., Aluwihare, L. I., & Dorrestein, P. C. (2017). High-resolution liquid chromatography tandem mass spectrometry enables large scale molecular characterization of dissolved organic matter. Frontiers in Marine Science, 4(405). https://doi.org/10.3389/fmars.2017.00405

Knowles, B., Bailey, B., Boling, L., Breitbart, M., Cobian-Guemes, A., del Campo, J., Edwards, R., Felts, B., Grasis, J., Haas, A. F., Katira, P., Kelly, L. W., Luque, A., Nulton, J., Paul, L., Peters, G., Robinett, N., Sandin, S., Segall, A., … Rohwer, F. (2017). Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature Microbiology, 2(7). https://doi.org/10.1038/nmicrobiol.2017.64

Roach, T. N. F., Abieri, M. L., George, E. E., Knowles, B., Naliboff, D. S., Smurthwaite, C. A., Kelly, L. W., Haas, A. F., & Rohwer, F. L. (2017). Microbial bioenergetics of coral-algal interactions. PeerJ, 5, e3423. https://doi.org/10.7717/peerj.3423

Quistad, S. D., Lim, Y. W., Silva, G. G. Z., Nelson, C. E., Haas, A. F., Kelly, L. W., Edwards, R. A., & Rohwer, F. L. (2016). Using viromes to predict novel immune proteins in non-model organisms. Proceedings of the Royal Society B: Biological Sciences, 283(1837), 20161200. https://doi.org/10.1098/rspb.2016.1200

Haas, A. F., Fairoz, M. F. M., Kelly, L. W., Nelson, C. E., Dinsdale, E. A., Edwards, R. A., Giles, S., Hatay, M., Hisakawa, N., Knowles, B., Lim, Y. W., Maughan, H., Pantos, O., Roach, T. N. F., Sanchez, S. E., Silveira, C. B., Sandin, S., Smith, J. E., & Rohwer, F. (2016). Global microbialization of coral reefs. Nature Microbiology, 1(6). https://doi.org/10.1038/nmicrobiol.2016.42

Knowles, B., Silveira, C. B., Bailey, B. A., Barott, K., Cantu, V. A., Cobian-Guemes, A. G., Coutinho, F. H., Dinsdale, E. A., Felts, B., Furby, K. A., George, E. E., Green, K. T., Gregoracci, G. B., Haas, A. F., Haggerty, J. M., Hester, E. R., Hisakawa, N., Kelly, L. W., Lim, Y. W., … Rohwer, F. (2016). Lytic to temperate switching of viral communities. Nature, 531(7595), 466-+. https://doi.org/10.1038/nature17193

Haas, A. F., Knowles, B., Lim, Y. W., McDole Somera, T., Kelly, L. W., Hatay, M., & Rohwer, F. (2014). Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology. J Vis Exp, 93, e52131. https://doi.org/10.3791/52131

Lim, Y. W., Cuevas, D. A., Silva, G. G. Z., Aguinaldo, K., Dinsdale, E. A., Haas, A. F., Hatay, M., Sanchez, S. E., Wegley-Kelly, L., Dutilh, B. E., Harkins, T. T., Lee, C. C., Tom, W., Sandin, S. A., Smith, J. E., Zgliczynski, B., Vermeij, M. J. A., Rohwer, F., & Edwards, R. A. (2014). Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ, 2. https://doi.org/10.7717/peerj.520

Kelly, L. W., Williams, G. J., Barott, K. L., Carlson, C. A., Dinsdale, E. A., Edwards, R. A., Haas, A. F., Haynes, M., Lim, Y. W., McDole, T., Nelson, C. E., Sala, E., Sandin, S. A., Smith, J. E., Vermeij, M. J. A., Youle, M., & Rohwer, F. (2014). Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences of the United States of America, 111(28), 10227–10232. https://doi.org/10.1073/pnas.1403319111

Haas, A. F., Nelson, C. E., Rohwer, F., Wegley-Kelly, L., Quistad, S. D., Carlson, C. A., Leichter, J. J., Hatay, M., & Smith, J. E. (2013). Influence of coral and algal exudates on microbially mediated reef metabolism. PeerJ, 1, e108. https://doi.org/10.7717/peerj.108

Nelson, C. E., Goldberg, S. J., Kelly, L. W., Haas, A. F., Smith, J. E., Rohwer, F., & Carlson, C. A. (2013). Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. Isme Journal, 7(5), 962–979. https://doi.org/10.1038/ismej.2012.161

Kelly, L. W., Barott, K. L., Dinsdale, E., Friedlander, A. M., Nosrat, B., Obura, D., Sala, E., Sandin, S. A., Smith, J. E., Vermeij, M. J. A., Williams, G. J., Willner, D., & Rohwer, F. (2012). Black reefs: iron-induced phase shifts on coral reefs. Isme Journal, 6(3), 638–649. https://doi.org/10.1038/ismej.2011.114

Haas, A. F., Nelson, C. E., Wegley Kelly, L., Carlson, C. A., Rohwer, F., Leichter, J. J., Wyatt, A., & Smith, J. E. (2011). Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PLOS ONE, 6(11), e27973. https://doi.org/10.1371/journal.pone.0027973

Rodriguez-Brito, B., Li, L. L., Wegley, L., Furlan, M., Angly, F., Breitbart, M., Buchanan, J., Desnues, C., Dinsdale, E., Edwards, R., Felts, B., Haynes, M., Liu, H., Lipson, D., Mahaffy, J., Martin-Cuadrado, A. B., Mira, A., Nulton, J., Pasic, L., … Rohwer, F. (2010). Viral and microbial community dynamics in four aquatic environments. Isme Journal, 4(6), 739–751. https://doi.org/10.1038/ismej.2010.1

Angly, F. E., Willner, D., Prieto-Davo, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., Haynes, M., Henn, M. R., Hu, Y. F., Kirchman, D. L., McDole, T., McPherson, J. D., Meyer, F., … Rohwer, F. (2009). The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. Plos Computational Biology, 5(12). https://doi.org/ARTN e1000593 10.1371/journal.pcbi.1000593

Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L., & Rohwer, F. (2009). Laboratory procedures to generate viral metagenomes. Nature Protocols, 4(4), 470–483. https://doi.org/10.1038/nprot.2009.10

Vega Thurber, R., Willner-Hall, D., Rodriguez-Mueller, B., Desnues, C., Edwards, R. A., Angly, F., Dinsdale, E., Kelly, L., & Rohwer, F. (2009). Metagenomic analysis of stressed coral holobionts. Environmental Microbiology, 11(8), 2148–2163. https://doi.org/10.1111/j.1462-2920.2009.01935.x

Thurber, R. L. V., Barott, K. L., Hall, D., Liu, H., Rodriguez-Mueller, B., Desnues, C., Edwards, R. A., Haynes, M., Angly, F. E., Wegley, L., & Rohwer, F. L. (2008). Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proceedings of the National Academy of Sciences of the United States of America, 105(47), 18413–18418. https://doi.org/10.1073/pnas.0808985105

Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L. L., McDaniel, L., Moran, M. A., Nelson, K. E., Nilsson, C., Olson, R., Paul, J., Brito, B. R., Ruan, Y. J., Swan, B. K., … Rohwer, F. (2008). Functional metagenomic profiling of nine biomes. Nature, 452(7187), 629-U8. https://doi.org/10.1038/nature06810

Desnues, C., Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Furlan, M., Wegley, L., Chau, B., Ruan, Y. J., Hall, D., Angly, F. E., Edwards, R. A., Li, L. L., Thurber, R. V., Reid, R. P., Siefert, J., Souza, V., … Rohwer, F. (2008). Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature, 452(7185), 340-U5. https://doi.org/10.1038/nature06735

Dinsdale, E. A., Pantos, O., Smriga, S., Edwards, R. A., Angly, F., Wegley, L., Hatay, M., Hall, D., Brown, E., Haynes, M., Krause, L., Sala, E., Sandin, S. A., Thurber, R. V., Willis, B. L., Azam, F., Knowlton, N., & Rohwer, F. (2008). Microbial ecology of four coral atolls in the northern Line Islands. PLOS ONE, 3(2). https://doi.org/10.1371/journal.pone.0001584

Wegley, L., Edwards, R., Rodriguez-Brito, B., Liu, H., & Rohwer, F. (2007). Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental Microbiology, 9(11), 2707–2719. https://doi.org/10.1111/j.1462-2920.2007.01383.x

Beman, J. M., Roberts, K. J., Wegley, L., Rohwer, F., & Francis, C. A. (2007). Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Applied and Environmental Microbiology, 73(17), 5642–5647. https://doi.org/10.1128/Aem.00461-07

Wegley, L., Mosier-Boss, P., Lieberman, S., Andrews, J., Graff-Baker, A., & Rohwer, F. (2006). Rapid estimation of microbial numbers in water using bulk fluorescence. Environmental Microbiology, 8(10), 1775–1782. https://doi.org/10.1111/j.1462-2920.2006.01062.x

Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D. M., Saar, M. O., Alexander, S., Alexander, E. C., & Rohwer, F. (2006). Using pyrosequencing to shed light on deep mine microbial ecology. Bmc Genomics, 7. https://doi.org/Artn 57 10.1186/1471-2164-7-57

Casas, V., Kline, D. I., Wegley, L., Yu, Y. N., Breitbart, M., & Rohwer, F. (2004). Widespread association of a Rickettsiales-like bacterium with reef-building corals. Environmental Microbiology, 6(11), 1137–1148. https://doi.org/10.1111/j.1462-2920.2004.00647.x

Sano, E., Carlson, S., Wegley, L., & Rohwer, F. (2004). Movement of viruses between biomes. Applied and Environmental Microbiology, 70(10), 5842–5846. https://doi.org/10.1128/Aem.70.10.5842-5846.2004

Breitbart, M., Wegley, L., Leeds, S., Schoenfeld, T., & Rohwer, F. (2004). Phage community dynamics in hot springs. Applied and Environmental Microbiology, 70(3), 1633–1640. https://doi.org/10.1128/Aem.70.3.1633-1640.2004

Wegley, L., Yu, Y. N., Breitbart, M., Casas, V., Kline, D. I., & Rohwer, F. (2004). Coral-associated Archaea. Marine Ecology-Progress Series, 273, 89–96. https://doi.org/10.3354/meps273089

Mosier-Boss, P. A., Lieberman, S. H., Andrews, J. M., Rohwer, F. L., Wegley, L. E., & Breitbart, M. (2003). Use of fluorescently labeled phage in the detection and identification of bacterial species. Applied Spectroscopy, 57(9), 1138–1144. https://doi.org/Doi 10.1366/00037020360696008