Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377. https://doi.org/10.1038/nature21707 (2017).
LaJeunesse, T. C. et al. Systematic revision of symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580. https://doi.org/10.1016/j.cub.2018.07.008 (2018).
Bourne, D. G., Morrow, K. M. & Webster, N. S. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu. Rev. Microbiol. 70, 317–340. https://doi.org/10.1146/annurev-micro-102215-095440 (2016).
Peixoto, R. S., Rosado, P. M., Leite, D. C. D., Rosado, A. S. & Bourne, D. G. Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience. Front. Microbiol. https://doi.org/10.3389/Fmicb.2017.00341 (2017).
Reshef, L., Koren, O., Loya, Y., Zilber-Rosenberg, I. & Rosenberg, E. The coral probiotic hypothesis. Environ. Microbiol. 8, 2068–2073. https://doi.org/10.1111/j.1462-2920.2006.01148.x (2006).
Lesser, M. P. et al. Nitrogen fixation by symbiotic cyanobacteria provides a source of nitrogen for the scleractinian coral Montastraea cavernosa. Mar. Ecol. Prog. Ser. 346, 143–152. https://doi.org/10.3354/meps07008 (2007).
Ben-Haim, Y. et al. Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. Int. J. System. Evol. Microbiol. 53, 309–315. https://doi.org/10.1099/ijs.0.02402-0 (2003).
Johnston, E. C. et al. A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci. Rep. https://doi.org/10.1038/S41598-017-06085-3 (2017).
Shearer, T. L., Van Oppen, M. J., Romano, S. L. & Worheide, G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11, 2475–2487 (2002).
Hellberg, M. E. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol. Biol. 6, 24. https://doi.org/10.1186/1471-2148-6-24 (2006).
Wares, J. P. Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals. PeerJ 2, e564. https://doi.org/10.7717/peerj.564 (2014).
Arrigoni, R. et al. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol. Ecol. Resour. 17, 1054–1071. https://doi.org/10.1111/1755-0998.12640 (2017).
Suzuki, G. & Nomura, K. Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers. Zool. Sci. 30, 626–632. https://doi.org/10.2108/zsj.30.626 (2013).
Gelin, P., Postaire, B., Fauvelot, C. & Magalon, H. Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Mol. Phylogenet. Evol. 109, 430–446. https://doi.org/10.1016/j.ympev.2017.01.018 (2017).
LaJeunesse, T. C. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the its region: In search of a “species” level marker. J. Phycol. 37, 866–880. https://doi.org/10.1046/j.1529-8817.2001.01031.x (2001).
Hume, B. C. C. et al. An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region. PeerJ 6, e4816. https://doi.org/10.7717/peerj.4816 (2018).
Hume, B. C. C. et al. SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. Mol. Ecol. Resour. 19, 1063–1080. https://doi.org/10.1111/1755-0998.13004 (2019).
Arif, C. et al. Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Mol. Ecol. 23, 4418–4433. https://doi.org/10.1111/mec.12869 (2014).
Smith, E. G., Ketchum, R. N. & Burt, J. A. Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach. Isme J. 11, 1500–1503. https://doi.org/10.1038/ismej.2016.206 (2017).
Ziegler, M. et al. Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula. J. Biogeogr. 44, 674–686. https://doi.org/10.1111/jbi.12913 (2017).
Mouchka, M. E., Hewson, I. & Harvell, C. D. Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts. Integr. Comp. Biol. 50, 662–674. https://doi.org/10.1093/icb/icq061 (2010).
Hernandez-Agreda, A., Leggat, W., Bongaerts, P. & Ainsworth, T. D. The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. mBio https://doi.org/10.1128/mBio.00560-16 (2016).
Neave, M. J., Apprill, A., Ferrier-Pages, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324. https://doi.org/10.1007/s00253-016-7777-0 (2016).
Hernandez-Agreda, A., Gates, R. D. & Ainsworth, T. D. Defining the Core Microbiome in Corals’ Microbial Soup. Trends Microbiol. 25, 125–140. https://doi.org/10.1016/j.tim.2016.11.003 (2017).
Roder, C., Bayer, T., Aranda, M., Kruse, M. & Voolstra, C. R. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences. Mol. Ecol. 24, 3501–3511. https://doi.org/10.1111/mec.13251 (2015).
Pogoreutz, C. et al. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol. Evol. 8, 2240–2252. https://doi.org/10.1002/ece3.3830 (2018).
Neave, M. J. et al. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. Isme J. 11, 186–200. https://doi.org/10.1038/ismej.2016.95 (2017).
Menegon, M. et al. On site DNA barcoding by nanopore sequencing. PLoS ONE 12, e0184741. https://doi.org/10.1371/journal.pone.0184741 (2017).
Parker, J., Helmstetter, A. J., Devey, D., Wilkinson, T. & Papadopulos, A. S. T. Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci. Rep. 7, 8345. https://doi.org/10.1038/s41598-017-08461-5 (2017).
Pomerantz, A. et al. Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building. Gigascience https://doi.org/10.1093/gigascience/giy033 (2018).
Santos, A., van Aerle, R., Barrientos, L. & Martinez-Urtaza, J. Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Comput. Struct. Biotechnol. J. 18, 296–305. https://doi.org/10.1016/j.csbj.2020.01.005 (2020).
Berntson, E. A., Bayer, F. M., McArthur, A. G. & France, S. C. Phylogenetic relationships within the Octocorallia (Cnidaria:Anthozoa) based on nuclear 18S rRNA sequences. Mar. Biol. 138, 235–246. https://doi.org/10.1007/s002270000457 (2001).
Pootakham, W. et al. High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Sci. Rep. 7, 2774. https://doi.org/10.1038/s41598-017-03139-4 (2017).
Hume, B. et al. Corals from the Persian/Arabian Gulf as models for thermotolerant reef-builders: prevalence of clade C3 Symbiodinium, host fluorescence and ex situ temperature tolerance. Mar. Pollut. Bull. 72, 313–322. https://doi.org/10.1016/j.marpolbul.2012.11.032 (2013).
Hume, B. C. et al. Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf. Sci. Rep. 5, 8562. https://doi.org/10.1038/srep08562 (2015).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100. https://doi.org/10.1093/bioinformatics/bty191 (2018).
Noonan, S. H. C., Fabricius, K. E. & Humphrey, C. Symbiodinium community composition in scleractinian corals is not affected by life-long exposure to elevated carbon dioxide. PLoS ONE https://doi.org/10.1371/journal.pone.0063985 (2013).
Bayer, T. et al. Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps10197 (2013).
Glasl, B., Herndl, G. J. & Frade, P. R. The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. Isme J. 10, 2280–2292. https://doi.org/10.1038/ismej.2016.9 (2016).
Morrow, K. M. et al. Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges. Isme J. 9, 894–908. https://doi.org/10.1038/ismej.2014.188 (2015).
Morrow, K. M., Bromhall, K., Motti, C. A., Munn, C. B. & Bourne, D. G. Allelochemicals produced by brown macroalgae of the lobophora genus are active against coral larvae and associated bacteria, supporting pathogenic shifts to vibrio dominance. Appl. Environ. Microb. https://doi.org/10.1128/AEM.02391-16 (2017).
Neave, M. J., Michell, C. T., Apprill, A. & Voolstra, C. R. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci. Rep. 7, 40579. https://doi.org/10.1038/srep40579 (2017).
Cardenas, A. et al. Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton. Isme J. 12, 59–76. https://doi.org/10.1038/ismej.2017.142 (2018).
Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. https://doi.org/10.1038/S41467-018-07275-X (2018).
Cardenas, A., Rodriguez, L. M., Pizarro, V., Cadavid, L. F. & Arevalo-Ferro, C. Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease. Isme J. 6, 502–512. https://doi.org/10.1038/ismej.2011.123 (2012).
Gajigan, A. P., Diaz, L. A. & Conaco, C. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature. Microbiologyopen https://doi.org/10.1002/mbo3.478 (2017).
Shnit-Orland, M., Sivan, A. & Kushmaro, A. Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral. Int. J. System. Evol. Microbiol. 60, 2293–2297. https://doi.org/10.1099/ijs.0.015768-0 (2010).
Ziegler, M. et al. Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea. Mar. Pollut. Bull. 105, 629–640. https://doi.org/10.1016/j.marpolbul.2015.12.045 (2016).
Paramasivam, N. et al. Bacterial Consortium of Millepora dichotoma exhibiting unusual multifocal lesion event in the gulf of Eilat Red Sea. Microb Ecol 65, 50–59. https://doi.org/10.1007/s00248-012-0097-8 (2013).
Paramasivam, N., Ben-Dov, E., Arotsker, L. & Kushmaro, A. Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma. Int. J. Syst. Evol. Microbiol. 63, 1880–1884. https://doi.org/10.1099/ijs.0.043976-0 (2013).
Spring, S., Lunsdorf, H., Fuchs, B. M. & Tindall, B. J. The photosynthetic apparatus and its regulation in the aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp nov. PLoS ONE https://doi.org/10.1371/journal.pone.0004866 (2009).
Roder, C. et al. Bacterial profiling of White Plague Disease in a comparative coral species framework. Isme J. 8, 31–39. https://doi.org/10.1038/ismej.2013.127 (2014).
Sekar, R., Mills, D. K., Remily, E. R., Voss, J. D. & Richardson, L. L. Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl. Environ. Microbiol. 72, 5963–5973. https://doi.org/10.1128/AEM.00843-06 (2006).
Blackall, L. L., Wilson, B. & van Oppen, M. J. Coral-the world’s most diverse symbiotic ecosystem. Mol. Ecol. 24, 5330–5347. https://doi.org/10.1111/mec.13400 (2015).
LaJeunesse, T. C. “Species” radiations of symbiotic Dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition (vol 22, pg 570, 2005). Mol. Biol. Evol. 22, 1158–1158. https://doi.org/10.1093/molbev/msi042 (2005).
Hume, B. C. et al. Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change. Proc. Natl. Acad. Sci. USA 113, 4416–4421. https://doi.org/10.1073/pnas.1601910113 (2016).
Thornhill, D. J., Lewis, A. M., Wham, D. C. & LaJeunesse, T. C. Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts. Evolution 68, 352–367. https://doi.org/10.1111/evo.12270 (2014).
Source: Ecology - nature.com
