Publications


Wilson, J. M., Erazo, N., Connors, E., Chamberlain, E. J., Clements, S. M., Carter, M. L., Smith, J. E., & Bowman, J. S. (2022). Substantial microbial community shifts in response to an exceptional harmful algal bloom in coastal Southern California. Elementa: Science of the Anthropocene, 10(1), 00088. https://doi.org/10.1525/elementa.2021.00088
Donham, E. M., Hamilton, S. L., Aiello, I., Price, N. N., & Smith, J. E. (2022). Consequences of warming and acidification for the temperate articulated coralline alga, Calliarthron tuberculosum (Florideophyceae, Rhodophyta). Journal of Phycology, jpy.13272. https://doi.org/10.1111/jpy.13272
Khen, A., Johnson, M. D., Fox, M. D., Clements, S. M., Carter, A. L., & Smith, J. E. (2022). Decadal stability of coral reef benthic communities on Palmyra Atoll, central Pacific, through two bleaching events. Coral Reefs. https://doi.org/10.1007/s00338-022-02271-6
Sandin, S. A., Alcantar, E., Clark, R., De Leon, R., Dilrosun, F., Edwards, C. B., Estep, A. J., Eynaud, Y., French, B. J., Fox, M. D., Grenda, D., Hamilton, S. L., Kramp, H., Marhaver, K. L., Miller, S. D., Roach, T. N. F., Seferina, G., Silveira, C. B., Smith, J. E., … Vermeij, M. J. A. (2022). Benthic assemblages are more predictable than fish assemblages at an island scale. Coral Reefs. https://doi.org/10.1007/s00338-022-02272-5
Johnson, M. D., Price, N. N., & Smith, J. E. (2022). Calcification accretion units (CAUs): A standardized approach for quantifying recruitment and calcium carbonate accretion in marine habitats. Methods in Ecology and Evolution, 11. https://doi.org/10.1111/2041-210x.13867
Leliaert, F., Kelly, E. L. A., Janouskovec, J., Fox, M. D., Johnson, M. D., Redfern, F. M., Eria, T., Haas, A. F., Sala, E., Sandin, S. A., & Smith, J. E. (2022). Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean. Journal of Phycology, 15. https://doi.org/10.1111/jpy.13230
Fox, M. D., Cohen, A. L., Rotjan, R. D., Mangubhai, S., Sandin, S. A., Smith, J. E., Thorrold, S. R., Dissly, L., Mollica, N. R., & Obura, D. (2021). Increasing coral reef resilience through successive marine heatwaves. Geophysical Research Letters, 48(17), 11. https://doi.org/10.1029/2021gl094128
Martin, N., Bernat, T., Dinasquet, J., Stofko, A., Damon, A., Deheyn, D. D., Azam, F., Smith, J. E., Davey, M. P., Smith, A. G., Vignolini, S., & Wangpraseurt, D. (2021). Synthetic algal-bacteria consortia for space-efficient microalgal growth in a simple hydrogel system. Journal of Applied Phycology. https://doi.org/10.1007/s10811-021-02528-7
Donham, E. M., Hamilton, S. L., Price, N. N., Kram, S., Kelly, E., Johnson, M. D., Neu, A. T., & Smith, J. (2021). Experimental assessment of the impacts of ocean acidification and urchin grazing on benthic kelp forest assemblages. Journal of Experimental Marine Biology and Ecology, 540, 11. https://doi.org/10.1016/j.jembe.2021.151548
Fox, M. D., Nelson, C. E., Oliver, T. A., Quinlan, Z. A., Remple, K., Glanz, J., Smith, J. E., & Putnam, H. M. (2021). Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life-history traits. Functional Ecology. https://doi.org/10.1111/1365-2435.13780
Tran, L. A. T., Bafort, Q., Steen, F., Garreta, A. G., D’Hondt, S., Miller, K. A., Vranken, S., Zuljevic, A., Smith, J. E., & De Clerck, O. (2020). Dictyota cyanoloma (Dictyotales, Phaeophyceae), a Newly Introduced Brown Algal Species in California(1). Journal of Phycology. https://doi.org/10.1111/jpy.13100
Kaplanis, N. J., Harris, J. L., & Smith, J. E. (2020). A cross-genus comparison of grazing pressure by two native marine herbivores on native, non-native naturalized, and non-native invasiveSargassummacroalgae. Helgoland Marine Research, 74(1). https://doi.org/10.1186/s10152-020-00541-w
Thapa, H. R., Lin, Z. J., Yi, D. Q., Smith, J. E., Schmidt, E. W., & Agarwal, V. (2020). Genetic and biochemical reconstitution of bromoform biosynthesis in asparagopsis lends insights into seaweed reactive oxygen species enzymology. Acs Chemical Biology, 15(6), 1662–1670. https://doi.org/10.1021/acschembio.0c00299
Kaplanis, N. J., Edwards, C. B., Eynaud, Y., & Smith, J. E. (2020). Future sea-level rise drives rocky intertidal habitat loss and benthic community change. PeerJ, 8. https://doi.org/10.7717/peerj.9186
Johnson, M. D., Fox, M. D., Kelly, E. L. A., Zgliczynski, B. J., Sandin, S. A., & Smith, J. E. (2020). Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific. PLOS ONE, 15(2), e0228448. https://doi.org/10.1371/journal.pone.0228448
Kelly, E. L. A., Cannon, A. L., & Smith, J. E. (2020). Environmental impacts and implications of tropical carrageenophyte seaweed farming. Conservation Biology. https://doi.org/10.1111/cobi.13462
Carter, A. L., Edwards, C. B., Fox, M. D., Amir, C. G., Eynaud, Y., Johnson, M. D., Lewis, L. S., Sandin, S. A., & Smith, J. E. (2019). Changes in benthic community composition associated with the outbreak of the corallimorph, Rhodactis howesii, at Palmyra Atoll. Coral Reefs, 38(6), 1267–1279. https://doi.org/10.1007/s00338-019-01841-5
Cyronak, T., Takeshita, Y., Courtney, T. A., DeCarlo, E. H., Eyre, B. D., Kline, D. I., Martz, T., Page, H., Price, N. N., Smith, J., Stoltenberg, L., Tresguerres, M., & Andersson, A. J. (2019). Diel temperature and pH variability scale with depth across diverse coral reef habitats. Limnology and Oceanography Letters. https://doi.org/10.1002/lol2.10129
Pedersen, N. E., Edwards, C. B., Eynaud, Y., Gleason, A. C. R., Smith, J. E., & Sandin, S. A. (2019). The influence of habitat and adults on the spatial distribution of juvenile corals. Ecography. https://doi.org/10.1111/ecog.04520
Darling, E. S., McClanahan, T. R., Maina, J., Gurney, G. G., Graham, N. A. J., Januchowski-Hartley, F., Cinner, J. E., Mora, C., Hicks, C. C., Maire, E., Puotinen, M., Skirving, W. J., Adjeroud, M., Ahmadia, G., Arthur, R., Bauman, A. G., Beger, M., Berumen, M. L., Bigot, L., … Mouillot, D. (2019). Social-environmental drivers inform strategic management of coral reefs in the Anthropocene. Nature Ecology & Evolution, 3(9), 1341–1350. https://doi.org/10.1038/s41559-019-0953-8
Fox, M. D., Carter, A. L., Edwards, C. B., Takeshita, Y., Johnson, M. D., Petrovic, V., Amir, C. G., Sala, E., Sandin, S. A., & Smith, J. E. (2019). Limited coral mortality following acute thermal stress and widespread bleaching on Palmyra Atoll, central Pacific. Coral Reefs, 38(4), 701–712. https://doi.org/10.1007/s00338-019-01796-7
Lewis, L. S., & Smith, J. E. (2019). Functional diversity among herbivorous sea urchins on a coral reef: grazing rate, dietary preference, and metabolism. Marine Ecology Progress Series, 625, 71–87. https://doi.org/10.3354/meps13038
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
Fox, M. D., Williams, G. J., Johnson, M. D., Radice, V. Z., Zgliczynski, B. J., Kelly, E. L. A., Rohwer, F. L., Sandin, S. A., & Smith, J. E. (2018). Gradients in primary production predict trophic strategies of mixotrophic corals across spatial scales. Current Biology, 28(21), 3355-+. https://doi.org/10.1016/j.cub.2018.08.057
d’Auriac, I. G., Quinn, R. A., Maughan, H., Nothias, L. F., Little, M., Kapono, C. A., Cobian, A., Reyes, B. T., Green, K., Quistad, S. D., Leray, M., Smith, J. E., Dorrestein, P. C., Rohwer, F., Deheyn, D. D., & Hartmann, A. C. (2018). Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism. Proceedings of the Royal Society B-Biological Sciences, 285(2884). https://doi.org/10.1098/rspb.2018.1307
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
Williams, G. J., Sandin, S. A., Zgliczynski, B. J., Fox, M. D., Gove, J. M., Rogers, J. S., Furby, K. A., Hartmann, A. C., Caldwell, Z. R., Price, N. N., & Smith, J. E. (2018). Biophysical drivers of coral trophic depth zonation. Marine Biology, 165(4). https://doi.org/10.1007/s00227-018-3314-2
Ruttenberg, B., Caselle, J. E., Estep, A. J., Johnson, A. E., Marhaver, K. L., Richter, L. J., Sandin, S. A., Vermeij, M. J. A., Smith, J. E., Grenda, D., & Cannon, A. (2018). Ecological assessment of the marine ecosystems of Barbuda, West Indies: Using rapid scientific assessment to inform ocean zoning and fisheries management. PLOS ONE, 13(1). https://doi.org/10.1371/journal.pone.0189355
Lewis, L. S., Smith, J. E., & Eynaud, Y. (2018). Comparative metabolic ecology of tropical herbivorous echinoids on a coral reef. PLOS ONE, 13(1). https://doi.org/10.1371/journal.pone.0190470
Edwards, C. B., Eynaud, Y., Williams, G. J., Pedersen, N. E., Zgliczynski, B. J., Gleason, A. C. R., Smith, J. E., & Sandin, S. A. (2017). Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef. Coral Reefs, 36(4), 1291–1305. https://doi.org/10.1007/s00338-017-1624-3
Johnson, M. D., Comeau, S., Lantz, C. A., & Smith, J. E. (2017). Complex and interactive effects of ocean acidification and temperature on epilithic and endolithic coral-reef turf algal assemblages. Coral Reefs, 36(4), 1059–1070. https://doi.org/10.1007/s00338-017-1597-2
Kersten, R. D., Lee, S., Fujita, D., Pluskal, T., Kram, S., Smith, J. E., Iwai, T., Noel, J. P., Fujita, M., & Weng, J. K. (2017). A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis. Journal of the American Chemical Society, 139(46), 16838–16844. https://doi.org/10.1021/jacs.7b09452
Kelly, E. L. A., Eynaud, Y., Williams, I. D., Sparks, R. T., Dailer, M. L., Sandin, S. A., & Smith, J. E. (2017). A budget of algal production and consumption by herbivorous fish in an herbivore fisheries management area, Maui, Hawaii. Ecosphere, 8(8). https://doi.org/10.1002/ecs2.1899
Nakajima, R., Yamazaki, H., Lewis, L. S., Khen, A., Smith, J. E., Nakatomi, N., & Kurihara, H. (2017). Planktonic trophic structure in a coral reef ecosystem - Grazing versus microbial food webs and the production of mesozooplankton. Progress in Oceanography, 156, 104–120. https://doi.org/10.1016/j.pocean.2017.06.007
Furby, K. A., Smith, J. E., & Sandin, S. A. (2017). Porites superfusa mortality and recovery from a bleaching event at Palmyra Atoll USA. PeerJ, 5. https://doi.org/10.7717/peerj.3204
McLaughlin, K., Dickson, A., Weisberg, S. B., Coale, K., Elrod, V., Hunter, C., Johnson, K. S., Kram, S., Kudela, R., Martz, T., Negrey, K., Passow, U., Shaughnessy, F., Smith, J. E., Tadesse, D., Washburn, L., & Weis, K. R. (2017). An evaluation of ISFET sensors for coastal pH monitoring applications. Regional Studies in Marine Science, 12, 11–18. https://doi.org/10.1016/j.rsma.2017.02.008
Kelly, E. L. A., Eynaud, Y., Clements, S. M., Gleason, M., Sparks, R. T., Williams, I. D., & Smith, J. E. (2016). Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes. Oecologia, 182(4), 1151–1163. https://doi.org/10.1007/s00442-016-3724-0
Takeshita, Y., McGillis, W., Briggs, E. M., Carter, A. L., Donham, E. M., Martz, T. R., Price, N. N., & Smith, J. E. (2016). Assessment of net community production and calcification of a coral reef using a boundary layer approach. Journal of Geophysical Research-Oceans, 121(8), 5655–5671. https://doi.org/10.1002/2016jc011886
Mullen, A. D., Treibitz, T., Roberts, P. L. D., Kelly, E. L. A., Horwitz, R., Smith, J. E., & Jaffe, J. S. (2016). Underwater microscopy for in situ studies of benthic ecosystems. Nature Communications, 7. https://doi.org/10.1038/ncomms12093
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
Kaplanis, N. J., Harris, J. L., & Smith, J. E. (2016). Distribution patterns of the non-native seaweeds Sargassum horneri (Turner) C. Agardh and Undaria pinnatifida (Harvey) Suringar on the San Diego and Pacific coast of North America. Aquatic Invasions, 11(2), 111–124. https://doi.org/10.3391/ai.2016.11.2.01
Quinn, R. A., Vermeij, M. J. A., Hartmann, A. C., d’Auriac, I. G., Benler, S., Haas, A., Quistad, S. D., Lim, Y. W., Little, M., Sandin, S., Smith, J. E., Dorrestein, P. C., & Rohwer, F. (2016). Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proceedings of the Royal Society B-Biological Sciences, 283(1829). https://doi.org/10.1098/rspb.2016.0469
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
Smith, J. E., Brainard, R., Carter, A., Grillo, S., Edwards, C., Harris, J., Lewis, L., Obura, D., Rohwer, F., Sala, E., Vroom, P. S., & Sandin, S. (2016). Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific. Proceedings of the Royal Society B-Biological Sciences, 283(1822). https://doi.org/10.1098/rspb.2015.1985
Vargas-Angel, B., Richards, C. L., Vroom, P. S., Price, N. N., Schils, T., Young, C. W., Smith, J., Johnson, M. D., & Brainard, R. E. (2015). Baseline assessment of net calcium carbonate accretion rates on US Pacific reefs. PLOS ONE, 10(12). https://doi.org/10.1371/journal.pone.0142196
Haas, A. F., Guibert, M., Foerschner, A., Co, T., Calhoun, S., George, E., Hatay, M., Dinsdale, E., Sandin, S. A., Smith, J. E., Vermeij, M. J. A., Felts, B., Dustan, P., Salamon, P., & Rohwer, F. (2015). Can we measure beauty? Computational evaluation of coral reef aesthetics. PeerJ, 3. https://doi.org/10.7717/peerj.1390
Takeshita, Y., Frieder, C. A., Martz, T. R., Ballard, J. R., Feely, R. A., Kram, S., Nam, S., Navarro, M. O., Price, N. N., & Smith, J. E. (2015). Including high-frequency variability in coastal ocean acidification projections. Biogeosciences, 12(19), 5853–5870. https://doi.org/10.5194/bg-12-5853-2015
Beijbom, O., Edmunds, P. J., Roelfsema, C., Smith, J., Kline, D. I., Neal, B. P., Dunlap, M. J., Moriarty, V., Fan, T. Y., Tan, C. J., Chan, S., Treibitz, T., Gamst, A., Mitchell, B. G., & Kriegman, D. (2015). Towards automated annotation of benthic survey images: Variability of human experts and operational modes of automation. PLOS ONE, 10(7). https://doi.org/10.1371/journal.pone.0130312
Harris, J. L., Lewis, L. S., & Smith, J. E. (2015). Quantifying scales of spatial variability in algal turf assemblages on coral reefs. Marine Ecology Progress Series, 532, 41–57. https://doi.org/10.3354/meps11344
Bracken, M. E. S., Hillebrand, H., Borer, E. T., Seabloom, E. W., Cebrian, J., Cleland, E. E., Elser, J. J., Gruner, D. S., Harpole, W. S., Ngai, J. T., & Smith, J. E. (2015). Signatures of nutrient limitation and co-limitation: responses of autotroph internal nutrient concentrations to nitrogen and phosphorus additions. Oikos, 124(2), 113–121. https://doi.org/10.1111/oik.01215