Nowell RW, Green S, Laue BE, Sharp PM. The extent of genome flux and its role in the differentiation of bacterial lineages. Genome Biol Evol. 2014;6:1514–29.
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304.
Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.
Albalat R, Cañestro C. Evolution by gene loss. Nat Rev Genet. 2016;17:379–91.
Jacq C, Miller JR, Brownlee GG. A pseudogene structure in 5S DNA of Xenopus laevis. Cell. 1977;12:109–20.
Li W-H, Gojobori T, Nei M. Pseudogenes as a paradigm of neutral evolution. Nature. 1981;292:237–9.
Ohta T. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst. 1992;23:263–86.
Bolotin E, Hershberg R. Gene loss dominates as a source of genetic variation within clonal pathogenic bacterial species. Genome Biol Evol. 2015;7:2173–87.
Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S. Bacterial adaptation through loss of function. PLoS Genet. 2013;9:e1003617.
Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun. 2018;9:1–9.
Sokurenko EV, Hasty DL, Dykhuizen DE. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol. 1999;7:191–5.
Ortega AP, Villagra NA, Urrutia IM, Valenzuela LM, Talamilla-Espinoza A, Hidalgo AA, et al. Lose to win: marT pseudogenization in Salmonella enterica serovar Typhi contributed to the surV-dependent survival to H2O2, and inside human macrophage-like cells. Infect Genet Evol. 2016;45:111–21.
Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Curr Opin Microbiol. 2015;23:102–9.
Johnson LJ. Pseudogene rescue: an adaptive mechanism of codon reassignment. J Evol Biol. 2010;23:1623–30.
Librado P, Vieira FG, Rozas J. BadiRate: estimating family turnover rates by likelihood-based methods. Bioinformatics. 2012;28:279–81.
David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature. 2011;469:93–96.
Avni E, Montoya D, Lopez D, Modlin R, Pellegrini M, Snir S. A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes—the Mycobacterium leprae case. PLoS One. 2017;13:e0204322.
Ochman H. The nature and dynamics of bacterial genomes. Science. 2006;311:1730–3.
Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio. 2012;3:e00252–12.
Giovannoni SJ, Cameron Thrash J, Temperton B. Implications of streamlining theory for microbial ecology. ISME J. 2014;8:1553–65.
Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol. 2005;71:5665–77.
Luo H, Moran MA. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends Microbiol. 2015;23:577–84.
Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev. 2014;78:573–87.
Tujula NA, Crocetti GR, Burke C, Thomas T, Holmström C, Kjelleberg S. Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga. ISME J. 2010;4:301–11.
Littman RA, Willis BL, Pfeffer C, Bourne DG. Diversities of coral-associated bacteria differ with location, but not species, for three acroporid corals on the Great Barrier Reef. FEMS Microbiol Ecol. 2009;68:152–63.
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.
Sweet MJ, Croquer A, Bythell JC. Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs. 2011;30:39–52.
Crossland CJ, Barnes DJ, Borowitzka MA. Diurnal lipid and mucus production in the staghorn coral Acropora acuminata. Mar Biol. 1980;60:81–90.
Shashar N, Stambler N. Endolithic algae within corals—life in an extreme environment. J Exp Mar Biol Ecol. 1992;163:277–86.
Highsmith RC. Lime-boring algae in hermatypic coral skeletons. J Exp Mar Biol Ecol. 1981;55:267–81.
Kühl M, Holst G, Larkum AWD, Ralph PJ. Imaging of oxygen dynamics within the endolithic algal community of the massive coral Porites lobata. J Phycol. 2008;44:541–50.
Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, et al. Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics. 2011;12:324.
Lachnit T, Fischer M, Künzel S, Baines JF, Harder T. Compounds associated with algal surfaces mediate epiphytic colonization of the marine macroalga Fucus vesiculosus. FEMS Microbiol Ecol. 2013;84:411–20.
Singh RP, Reddy CRK. Seaweed–microbial interactions: key functions of seaweed-associated bacteria. FEMS Microbiol Ecol. 2014;88:213–30.
Khailov KM, Burlakova ZP. Release of dissolved organic matter by marine seaweeds and distribution of their total organic production to inshore communities. Limnol Oceanogr. 1969;14:521–7.
Wai TC, Ng JSS, Leung KMY, Dudgeon D, Williams GA. The source and fate of organic matter and the significance of detrital pathways in a tropical coastal ecosystem. Limnol Oceanogr. 2008;53:1479–92.
Braeckman U, Pasotti F, Vázquez S, Zacher K, Hoffmann R, Elvert M, et al. Degradation of macroalgal detritus in shallow coastal Antarctic sediments. Limnol Oceanogr. 2019;64:1423–41.
Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S, et al. Ecological genomics of marine roseobacters. Appl Environ Microbiol. 2007;73:4559–69.
Sonnenschein EC, Nielsen KF, D’Alvise P, Porsby CH, Melchiorsen J, Heilmann J, et al. Global occurrence and heterogeneity of the Roseobacter clade species Ruegeria mobilis. ISME J. 2017;11:569–83.
Slightom RN, Buchan A. Surface colonization by marine roseobacters: integrating genotype and phenotype. Appl Environ Microbiol. 2009;75:6027–37.
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.
Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, et al. Genome characteristics of a generalist marine bacterial lineage. ISME J. 2010;4:784–98.
Brinkhoff T, Giebel H-A, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol. 2008;189:531–9.
Luo H, Löytynoja A, Moran MA. Genome content of uncultivated marine Roseobacters in the surface ocean. Environ Microbiol. 2012;14:41–51.
Lerat E, Ochman H. Ψ-Φ: Exploring the outer limits of bacterial pseudogenes. Genome Res. 2004;14:2273–8.
Lerat E, Ochman H. Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Res. 2005;33:3125–32.
Kuo C-H, Ochman H. The extinction dynamics of bacterial pseudogenes. PLoS Genet. 2010;6:e1001050.
Umezaki I. Ecological studies of Sargassum hemiphyllum C. AGARDH in Obama Bay, Japan Sea. Nippon Suisan Gakkaishi. 1984;50:1677–83.
Tam TW, Ang PO. Repeated physical disturbances and the stability of sub-tropical coral communities in Hong Kong. China Aquat Conserv Mar Freshw Ecosyst. 2008;18:1005–24.
Cheang CC, Chu KH, Ang PO. Phylogeography of the marine macroalga Sargassum hemiphyllum (Phaeophyceae, Heterokontophyta) in northwestern Pacific. Mol Ecol. 2010;19:2933–48.
Raghunathan C, Venkataraman K. Diversity and distribution of corals and their associated fauna of Rani Jhansi Marine National Park, Andaman and Nicobar Islands. In: Venkataraman K, Raghunathan C, Sivaperuman C, (eds). Ecology of Faunal Communities on the Andaman and Nicobar Islands. Berlin, Heidelberg: Springer; 2012. p. 177–208.
Ang PO. Phenology of Sargassum spp. in Tung Ping Chau Marine Park, Hong Kong SAR, China. J Appl Phycol. 2006;18:629–36.
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.
Passel MWJ, van, Marri PR, Ochman H. The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput Biol. 2008;4:e1000059.
Ochman H. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 2002;18:335–7.
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238.
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.
Schliep KP. Phangorn: phylogenetic analysis in R. Bioinformatics. 2011;27:592–3.
Liu Y, Harrison PM, Kunin V, Gerstein M. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 2004;5:R64.
Halldal P. Photosynthetic capacities and photosynthetic action spectra of endozoic algae of the massive coral Favia. Biol Bull. 1968;134:411–24.
Shibata K, Haxo FT. Light transmission and spectral distribution through epi- and endozoic algal layers in the brain coral, Favia. Biol Bull. 1969;136:461–8.
Park JT, Uehara T. How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan). Microbiol Mol Biol Rev. 2008;72:211–27.
Mauck J, Chan L, Glaser L. Turnover of the cell wall of gram-positive bacteria. J Biol Chem. 1971;246:1820–7.
Goodell E. Recycling of murein by Escherichia coli. J Bacteriol. 1985;163:305–10.
Uehara T, Suefuji K, Jaeger T, Mayer C, Park JT. MurQ etherase is required by Escherichia coli in order to metabolize Anhydro-N-Acetylmuramic acid obtained either from the environment or from its own cell wall. J Bacteriol. 2006;188:1660–2.
Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol. 2017;52:503–42.
Jiang H, Kong R, Xu X. The N-acetylmuramic acid 6-phosphate etherase gene promotes growth and cell differentiation of cyanobacteria under light-limiting conditions. J Bacteriol. 2010;192:2239–45.
Ferrer LM, Szmant AM. Nutrient regeneration by the endolithic community in coral skeletons. In: Proceedings of the 6th International Coral Reef Symposium 1988. pp 1–4.
Risk MJ, Muller HR. Porewater in coral heads: evidence for nutrient regeneration. Limnol Oceanogr. 1983;28:1004–8.
Yu LJ, Wu JR, Zheng ZZ, Lin CC, Zhan XB. Changes in gene transcription and protein expression involved in the response of Agrobacterium sp. ATCC 31749 to nitrogen availability during curdlan production. Appl Biochem Microbiol. 2011;47:487–93.
Wada S, Aoki M, Mikami A, Komatsu T, Tsuchiya Y, Sato T, et al. Bioavailability of macroalgal dissolved organic matter in seawater. Mar Ecol Prog Ser. 2008;370:33–44.
Essenberg MK, Cooper RA. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur J Biochem. 1975;55:323–32.
Nelson CE, Goldberg SJ, Wegley Kelly L, Haas AF, Smith JE, Rohwer F, et al. Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. ISME J. 2013;7:962–79.
Mulligan C, Fischer M, Thomas GH. Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea. FEMS Microbiol Rev. 2011;35:68–86.
Beyenbach KW, Wieczorek H. The V-type H+ ATPase: molecular structure and function, physiological roles and regulation. J Exp Biol. 2006;209:577–89.
Guadayol Ò, Silbiger NJ, Donahue MJ, Thomas FIM. Patterns in temporal variability of temperature, oxygen and pH along an environmental gradient in a coral reef. PLoS One. 2014;9:e85213.
Bodenmiller DM, Spiro S. The yjeB(nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator. J Bacteriol. 2006;188:874–81.
Gilberthorpe NJ, Lee ME, Stevanin TM, Read RC, Poole RK. NsrR: a key regulator circumventing Salmonella enterica serovar Typhimurium oxidative and nitrosative stress in vitro and in IFN-γ-stimulated J774.2 macrophages. Microbiology. 2007;153:1756–71.
da Fonseca RR, Johnson WE, O’Brien SJ, Vasconcelos V, Antunes A. Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases. BMC Evol Biol. 2010;10:281.
Green ER, Mecsas J. Bacterial secretion systems—an overview. Microbiol Spectr. 2016;4:1–32.
Ansari MI, Schiwon K, Malik A, Grohmann E. Biofilm formation by environmental bacteria. In: Malik A, Grohmann E (eds). Environmental protection strategies for sustainable development. 2012. Springer Netherlands, Dordrecht, pp 341–77.
Meron D, Efrony R, Johnson WR, Schaefer AL, Morris PJ, Rosenberg E, et al. Role of flagella in virulence of the coral pathogen Vibrio coralliilyticus. Appl Environ Microbiol. 2009;75:5704–7.
Attmannspacher U, Scharf BE, Harshey RM. FliL is essential for swarming: motor rotation in absence of FliL fractures the flagellar rod in swarmer cells of Salmonella enterica. Mol Microbiol. 2008;68:328–41.
Fernando SC, Wang J, Sparling K, Garcia GD, Francini-Filho RB, de Moura RL, et al. Microbiota of the major south atlantic reef building coral Mussismilia. Micro Ecol. 2015;69:267–80.
Pollock FJ, McMinds R, Smith S, Bourne DG, Willis BL, Medina M, et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat Commun. 2018;9:4921.
Marcelino VR, van Oppen MJ, Verbruggen H. Highly structured prokaryote communities exist within the skeleton of coral colonies. ISME J. 2018;12:300–3.
Hill C. Virulence or niche factors: what’s in a name? J Bacteriol. 2012;194:5725–7.
Egan S, Harder T, Burke C, Steinberg P, Kjelleberg S, Thomas T. The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol Rev. 2013;37:462–76.
Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2018;50:138–50.
Koren O, Rosenberg E. Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol. 2006;72:5254–9.
Wang X, Grus WE, Zhang J. Gene losses during human origins. PLoS Biol. 2006;4:e52.
Source: Ecology - nature.com