Bourne DG, Morrow KM, Webster NS. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu Rev Microbiol. 2016;70:317–40.
Google Scholar
Ainsworth TD, Thurber RV, Gates RD. The future of coral reefs: a microbial perspective. Trends Ecol Evol. 2010;25:233–40.
Google Scholar
Huettel M, Wild C, Gonelli S. Mucus trap in coral reefs: formation and temporal evolution of particle aggregates caused by coral mucus. Mar Ecol Prog Ser. 2006;307:69–84.
Google Scholar
Coffroth M. Mucous sheet formation on poritid corals: an evaluation of coral mucus as a nutrient source on reefs. Mar Biol. 1990;105:39–49.
Google Scholar
Brown BE, Bythell JC. Perspectives on mucus secretion in reef corals. Mar Ecol Prog Ser. 2005;296:291–309.
Google Scholar
Sweet M, Croquer A, Bythell J. Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs. 2011;30:39–52.
Google Scholar
Yancey PH. Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J Exp Biol. 2005;208:2819–30.
Google Scholar
Burg MB, Ferraris JD. Intracellular organic osmolytes: function and regulation. J Biol Chem. 2008;283:7309–13.
Google Scholar
Singh LR, Dar TA, editors. Cellular osmolytes: from chaperoning protein folding to clinical perspectives. 1st ed. Singapore: Springer Nature Singapore Pte Ltd.; 2017.
Yancey PH, Heppenstall M, Ly S, Andrell RM, Gates RD, Carter VL, et al. Betaines and dimethylsulfoniopropionate as major osmolytes in cnidaria with endosymbiotic dinoflagellates. Physiol Biochem Zool. 2010;83:167–73.
Google Scholar
Mayfield AB, Gates RD. Osmoregulation in anthozoan—dinoflagellate symbiosis. Compar Biochem Physiol A. 2007;147:1–10.
Google Scholar
Rublee PA, Lasker HR, Gottfried M, Roman MR. Production and bacterial colonization of mucus from the soft coral Briarium asbestinum. Bull Mar Sci. 1980;30:888–93.
Wild C, Woyt H, Huettel M. Influence of coral mucus on nutrient fluxes in carbonate sands. Mar Ecol Prog Ser. 2005;287:87–98.
Google Scholar
Coles SL, Strathmann R. Observations on coral mucus “flocs” and their potential trophic significance. Limnol Oceanogr. 1973;18:673–8.
Google Scholar
Pernice M, Raina J-B, Rädecker N, Cárdenas A, Pogoreutz C, Voolstra CR. Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME J. 2020;14:325–34.
Google Scholar
Falini G, Fermani S, Goffredo S. Coral biomineralization: a focus on intra-skeletal organic matrix and calcification. Semin Cell Dev Biol. 2015;46:17–26.
Google Scholar
Constantz B, Weiner S. Acidic macromolecules associated with the mineral phase of scleractinian coral skeletons. J Exp Zool. 1988;248:253–8.
Google Scholar
Muscatine L, Goiran C, Land L, Jaubert J, Cuif JP, Allemand D. Stable isotopes (delta C-13 and delta N-15) of organic matrix from coral skeleton. Proc Natl Acad Sci USA. 2005;102:1525–30.
Google Scholar
Sorek M, Díaz-Almeyda EM, Medina M, Levy O. Circadian clocks in symbiotic corals: the duet between Symbiodinium algae and their coral host. Mar Genom. 2014;14:47–57.
Google Scholar
Agostini S, Suzuki Y, Higuchi T, Casareto B, Yoshinaga K, Nakano Y, et al. Biological and chemical characteristics of the coral gastric cavity. Coral Reefs. 2012;31:147–56.
Google Scholar
Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007;5:355–62.
Google Scholar
Ritchie KB. Bacterial symbionts of corals and Symbiodinium. In: Rosenberg E, Gophna U editors. Beneficial microorganisms in multicellular life forms. 1st ed. Berlin Heidelberg: Springer-Verlag Berlin Heidelberg; 2012. pp 139–50.
Apprill A, Weber LG, Santoro AE. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems. 2016;1:e00143–00116.
Google Scholar
Pollock FJ, McMinds R, Smith S, Bourne DG, Willis BL, Medina M, et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat Commun. 2018;9:1–13.
Google Scholar
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, et al. Population genomics of early events in the ecological differentiation of bacteria. Science. 2012;336:48–51.
Google Scholar
Youngblut ND, Wirth JS, Henriksen JR, Smith M, Simon H, Metcalf WW, et al. Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME J. 2015;9:2191–205.
Google Scholar
Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ, et al. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. ISME J. 2016;10:2468–77.
Google Scholar
Chase AB, Arevalo P, Brodie EL, Polz MF, Karaoz U, Martiny JB. Maintenance of sympatric and allopatric populations in free-living terrestrial bacteria. Mbio. 2019;10:e02361–02319.
Google Scholar
Huggett MJ, Apprill A. Coral microbiome database: integration of sequences reveals high diversity and relatedness of coral-associated microbes. Environ Microbiol Rep. 2019;11:372–85.
Google Scholar
Apprill A, Marlow HQ, Martindale MQ, Rappe MS. The onset of microbial associations in the coral Pocillopora meandrina. ISME J. 2009;3:685–99.
Google Scholar
Epstein HE, Torda G, Munday PL, van Oppen MJH. Parental and early life stage environments drive establishment of bacterial and dinoflagellate communities in a common coral. ISME J. 2019;13:1635–8.
Google Scholar
Freire I, Gutner-Hoch E, Muras A, Benayahu Y, Otero A. The effect of bacteria on planula-larvae settlement and metamorphosis in the octocoral Rhytisma fulvum fulvum. PLoS ONE. 2019;14:e0223214.
Google Scholar
Miura N, Motone K, Takagi T, Aburaya S, Watanabe S, Aoki W, et al. Ruegeria sp. strains isolated from the reef-building coral Galaxea fascicularis inhibit growth of the temperature-dependent pathogen Vibrio coralliilyticus. Mar Biotechnol. 2019;21:1–8.
Google Scholar
Apprill A, Hughen K, Mincer T. Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals. Environ Microbiol. 2013;15:2063–72.
Google Scholar
Sekar R, Kaczmarsky LT, Richardson LL. Microbial community composition of black band disease on the coral host Siderastrea siderea from three regions of the wider Caribbean. Mar Ecol Prog Ser. 2008;362:85–98.
Google Scholar
Casey JM, Connolly SR, Ainsworth TD. Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens. Sci Rep. 2015;5:11903–11903.
Google Scholar
Tsang RHL, Ang PO. Resistance to temperature stress and Drupella corallivory may promote the dominance of Platygyra acuta in the marginal coral communities in Hong Kong. Mar Environ Res. 2019;144:20–27.
Google Scholar
Tam TW, Ang PO Jr. Repeated physical disturbances and the stability of sub‐tropical coral communities in Hong Kong, China. Aquat Conserv. 2008;18:1005–24.
Google Scholar
Ang Jr PO, Choi LS, Choi MM, Cornish A, Fung HL, Lee MW et al. Hong Kong. In: Centre JWR editors. Status of coral reefs of the East Asian Seas region: 2004. Tokyo: Ministry of the Environment; 2005. pp 121–52.
Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev. 2014;78:573–87.
Google Scholar
Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The family Rhodobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F editors. The Prokaryotes: alphaproteobacteria and Betaproteobacteria. 4th ed. Berlin Heidelberg: Springer-Verlag Berlin Heidelberg; 2014. pp 439–512.
Johannes RE, Wiebe WJ. Method for determination of coral tissue biomass and composition. Limnol Oceanogr. 1970;15:822–4.
Google Scholar
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:1–14.
Google Scholar
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
Google Scholar
Achtman M, Wagner M. Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol. 2008;6:431–40.
Google Scholar
Feil EJ, Spratt BG. Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol. 2001;55:561–90.
Google Scholar
Wang X, Zhang Y, Ren M, Xia T, Chu X, Liu C, et al. Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. ISME J. 2020;14:3106–19.
Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012;8:e1002453.
Google Scholar
Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol. 2015;11:e1004041.
Google Scholar
Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10:564–7.
Google Scholar
Sun Y, Luo H. Homologous recombination in core genomes facilitates marine bacterial adaptation. Appl Environ Microbiol. 2018;84:e02545–02517.
Google Scholar
Librado P, Vieira FG, Rozas J. BadiRate: estimating family turnover rates by likelihood-based methods. Bioinformatics. 2011;28:279–81.
Google Scholar
Slatkin M, Maddison WP. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 1989;123:603–13.
Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:1–8.
Google Scholar
Lohr KE, Khattri RB, Guingab-Cagmat J, Camp EF, Merritt ME, Garrett TJ, et al. Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral. Sci Rep. 2019;9:1–11.
Google Scholar
Hill R, Li C, Jones A, Gunn J, Frade P. Abundant betaines in reef-building corals and ecological indicators of a photoprotective role. Coral Reefs. 2010;29:869–80.
Google Scholar
Gowrishankar J. Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli. J Bacteriol. 1989;171:1923–31.
Google Scholar
Chandravanshi M, Gogoi P, Kanaujia SP. Computational characterization of TTHA0379: A potential glycerophosphocholine binding protein of Ugp ATP-binding cassette transporter. Gene. 2016;592:260–8.
Google Scholar
Ziegler C, Bremer E, Krämer R. The BCCT family of carriers: from physiology to crystal structure. Mol Microbiol. 2010;78:13–34.
Google Scholar
Geiger O, López-Lara IM, Sohlenkamp C. Phosphatidylcholine biosynthesis and function in bacteria. Biochim Biophys Acta Mol Cell Biol Lipids. 2013;1831:503–13.
Google Scholar
Lidbury I, Kimberley G, Scanlan DJ, Murrell JC, Chen Y. Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Environ Microbiol. 2015;17:5048–62.
Google Scholar
Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, et al. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME J. 2012;6:2229–44.
Google Scholar
Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, DuGar B, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472:57–63.
Google Scholar
Jones M, Talfournier F, Bobrov A, Grossmann JG, Vekshin N, Sutcliffe MJ, et al. Electron transfer and conformational change in complexes of trimethylamine dehydrogenase and electron transferring flavoprotein. J Biol Chem. 2002;277:8457–65.
Google Scholar
Chen Y. Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environ Microbiol. 2012;14:2308–22.
Google Scholar
Schäfer H, McDonald IR, Nightingale PD, Murrell JC. Evidence for the presence of a CmuA methyltransferase pathway in novel marine methyl halide‐oxidizing bacteria. Environ Microbiol. 2005;7:839–52.
Google Scholar
McNicholas PM, Chiang RC, Gunsalus RP. Anaerobic regulation of the Escherichia coli dmsABC operon requires the molybdate‐responsive regulator ModE. Mol Microbiol. 1998;27:197–208.
Google Scholar
Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, et al. Structural and biochemical identification of a novel bacterial oxidoreductase. J Biol Chem. 2004;279:50391–50400.
Google Scholar
Hillyer KE, Dias DA, Lutz A, Wilkinson SP, Roessner U, Davy SK. Metabolite profiling of symbiont and host during thermal stress and bleaching in the coral Acropora aspera. Coral Reefs. 2017;36:105–18.
Google Scholar
Rösgen J. Molecular basis of osmolyte effects on protein and metabolites. Methods Enzymol. 2007;428:459–86.
Google Scholar
Cunliffe M. Correlating carbon monoxide oxidation with cox genes in the abundant marine Roseobacter clade. ISME J. 2011;5:685–91.
Google Scholar
Bartling P, Vollmers J, Petersen J. The first world swimming championships of Roseobacters—phylogenomic insights into an exceptional motility phenotype. Syst Appl Microbiol. 2018;41:544–54.
Google Scholar
Michael V, Frank O, Bartling P, Scheuner C, Goker M, Brinkmann H, et al. Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters. ISME J. 2016;10:2498–513.
Google Scholar
Armitage JP. Behavioural responses of bacteria to light and oxygen. Arch Microbiol. 1997;168:249–61.
Google Scholar
Jorgensen NOG. Uptake of urea by estuarine bacteria. Aquat Micro Ecol. 2006;42:227–42.
Google Scholar
Pernice M, Raina J-B, Rädecker N, Cárdenas A, Pogoreutz C, Voolstra CR. Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME J. 2019: 1–10.
Krajewska B, Ureases I. Functional, catalytic and kinetic properties: a review. J Mol Catal B Enzym. 2009;59:9–21.
Google Scholar
Cheng L, Cord-Ruwisch R. In situ soil cementation with ureolytic bacteria by surface percolation. Ecol Eng. 2012;42:64–72.
Google Scholar
Cho BC, Park MG, Shim JH, Azam F. Significance of bacteria in urea dynamics in coastal surface waters. Mar Ecol Prog Ser. 1996;142:19–26.
Google Scholar
Jin D, Zhao SG, Zheng N, Beckers Y, Wang JQ. Urea metabolism and regulation by rumen bacterial urease in ruminants—a review. Ann Anim Sci. 2018;18:303–18.
Google Scholar
Collier JL, Baker KM, Bell SL. Diversity of urea-degrading microorganisms in open-ocean and estuarine planktonic communities. Environ Microbiol. 2009;11:3118–31.
Google Scholar
Biscéré T, Ferrier-Pagès C, Grover R, Gilbert A, Rottier C, Wright A, et al. Enhancement of coral calcification via the interplay of nickel and urease. Aquat Toxicol. 2018;200:247–56.
Google Scholar
Crossland C, Barnes D. The role of metabolic nitrogen in coral calcification. Mar Biol. 1974;28:325–32.
Google Scholar
Goodkin NF, Switzer AD, Mccorry D, Devantier L, True J, Hughen KA, et al. Coral communities of Hong Kong: long-lived corals in a marginal reef environment. Mar Ecol Prog Ser. 2011;426:185–96.
Google Scholar
Bernasconi R, Stat M, Koenders A, Paparini A, Bunce M, Huggett MJ. Establishment of coral-bacteria symbioses reveal changes in the core bacterial community with host ontogeny. Front Mirobiol. 2019;10:1529.
Google Scholar
Chu X, Li S, Wang S, Luo D, Luo H. Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage. ISME J. 2020;15:489–502.
Google Scholar
Gardner SN, Slezak T, Hall BG. kSNP3. 0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics. 2015;31:2877–8.
Google Scholar
Krzywinski M, Schein JE, Birol I, Connors JM, Gascoyne RD, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Google Scholar
Source: Ecology - nature.com