Pootakham, W. et al. Dynamics of coral-associated microbiomes during a thermal bleaching event. Microbiologyopen 7, e00604 (2018).
Krediet, C. J., Ritchie, K. B., Paul Valerie, J. & Max, T. Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases. Proc. R. Soc. B Biol. Sci. 280, 20122328 (2013).
Ziegler, M., Seneca, F. O., Yum, L. K., Palumbi, S. R. & Voolstra, C. R. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat. Commun. 8, 14213 (2017).
Rädecker, N., Pogoreutz, C., Voolstra, C. R., Wiedenmann, J. & Wild, C. Nitrogen cycling in corals: The key to understanding holobiont functioning?. Trends Microbiol. 23, 490–497 (2015).
Ritchie, K. B. & Smith, G. W. Microbial communities of coral surface mucopolysaccharide layers. In Coral Health and Disease (eds Rosenberg, E. & Loya, Y.) 259–264 (Springer, Berlin Heidelberg, 2004).
Holm, J. B. & Heidelberg, K. B. Microbiomes of Muricea californica and M. fruticosa: Comparative analyses of two co-occurring eastern pacific octocorals. Front. Microbiol. 7, 917 (2016).
Sweet, M. J., Brown, B. E., Dunne, R. P., Singleton, I. & Bulling, M. Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera. Coral Reefs 36, 815–828 (2017).
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 (2016).
Archer, S. D. J. et al. Air mass source determines airborne microbial diversity at the ocean–atmosphere interface of the Great Barrier Reef marine ecosystem. ISME J. https://doi.org/10.1038/s41396-019-0555-0 (2019).
Wainwright, B. J., Afiq-Rosli, L., Zahn, G. L. & Huang, D. Characterisation of coral-associated bacterial communities in an urbanised marine environment shows strong divergence over small geographic scales. Coral Reefs https://doi.org/10.1007/s00338-019-01837-1 (2019).
Chu, N. D. & Vollmer, S. V. Caribbean corals house shared and host-specific microbial symbionts over time and space. Environ. Microbiol. Rep. 8, 493–500 (2016).
Wainwright, B. J., Bauman, A. G., Zahn, G. L., Todd, P. A. & Huang, D. Characterization of fungal biodiversity and communities associated with the reef macroalga Sargassum ilicifolium reveals fungal community differentiation according to geographic locality and algal structure. Mar. Biodivers. https://doi.org/10.1007/s12526-019-00992-6 (2019).
Wainwright, B. J., Zahn, G. L., Arlyza, I. S. & Amend, A. S. Seagrass-associated fungal communities follow Wallace’s line, but host genotype does not structure fungal community. J. Biogeogr. 45, 762–770 (2018).
Hernandez-Agreda, A., Leggat, W., Bongaerts, P., Herrera, C. & Ainsworth, T. D. Rethinking the coral microbiome: Simplicity exists within a diverse microbial biosphere. mBio 9, e00812 (2018).
Williams, A. D., Brown, B. E., Putchim, L. & Sweet, M. J. Age-related shifts in bacterial diversity in a reef coral. PLoS ONE 10, e0144902 (2015).
Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 4921 (2018).
Epstein, H. E., Torda, G., Munday, P. L. & van Oppen, M. J. H. Parental and early life stage environments drive establishment of bacterial and dinoflagellate communities in a common coral. ISME J. 13, 1635–1638 (2019).
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
van Dongen, W. F. et al. Age-related differences in the cloacal microbiota of a wild bird species. BMC Ecol. 13, 11 (2013).
Huang, D. et al. Extraordinary diversity of reef corals in the South China Sea. Mar. Biodivers. 45, 157–168 (2015).
Toda, T. et al. Community structures of coral reefs around Peninsular Malaysia. J. Oceanogr. 63, 113–123 (2007).
Tanzil, J. T. I. et al. Regional decline in growth rates of massive Porites corals in Southeast Asia. Glob. Change Biol. 19, 3011–3023 (2013).
Tanzil, J. T. I. et al. Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia. Limnol. Oceanogr. 61, 2003–2026 (2016).
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 (2017).
Øvreås, L., Daae, F. L., Torsvik, V. & Rodríguez-Valera, F. Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb. Ecol. 46, 291–301 (2003).
Baker, B. J. & Banfield, J. F. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44, 139–152 (2003).
Li, S.-J. et al. Microbial communities evolve faster in extreme environments. Sci. Rep. 4, 6205 (2014).
Peter, J. et al. A microbial signature of psychological distress in irritable bowel syndrome. Psychosom. Med. 80, 698–709 (2018).
Karl, J. P. et al. Effects of psychological, environmental and physical stressors on the gut microbiota. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.02013 (2018).
Guest, J. R. et al. 27 years of benthic and coral community dynamics on turbid, highly urbanised reefs off Singapore. Sci. Rep. 6, 36260 (2016).
Wong, J. S. Y. et al. Comparing patterns of taxonomic, functional and phylogenetic diversity in reef coral communities. Coral Reefs 37, 737–750 (2018).
Chow, G. S. E., Chan, Y. K. S., Jain, S. S. & Huang, D. Light limitation selects for depth generalists in urbanised reef coral communities. Mar. Environ. Res. 147, 101–112 (2019).
Calvani, R. et al. Of microbes and minds: A narrative review on the second brain aging. Front. Med. (Lausanne) https://doi.org/10.3389/fmed.2018.00053 (2018).
Nagpal, R. et al. Gut microbiome and aging: Physiological and mechanistic insights. Nutr Healthy Aging 4, 267–285 (2018).
Choi, J., Hur, T.-Y. & Hong, Y. Influence of altered gut microbiota composition on aging and aging-related diseases. J. Lifestyle Med. 8, 1–7 (2018).
Soong, K., Chen, C. A. & Chang, J.-C. A very large poritid colony at Green Island, Taiwan. Coral Reefs 18, 42–42 (1999).
Goodkin, N. et al. Coral communities of Hong Kong: Long-lived corals in a marginal reef environment. Mar. Ecol. Prog. Ser. 426, 185–196 (2011).
Bythell, J. C., Brown, B. E. & Kirkwood, T. B. L. Do reef corals age?. Biol. Rev. 93, 1192–1202 (2018).
Lee, N. L. Y., Huang, D., Quek, Z. B. R., Lee, J. N. & Wainwright, B. J. Mangrove-associated fungal communities are differentiated by geographic location and host structure. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.02456 (2019).
Wainwright, B. J. et al. Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration. Ecol. Evol. 9, 11288–11297 (2019).
Röthig, T., Ochsenkühn, M. A., Roik, A., van der Merwe, R. & Voolstra, C. R. Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome. Mol. Ecol. 25, 1308–1323 (2016).
Sin, T. M. et al. The urban marine environment of Singapore. Region. Stud. Mar. Sci. 8, 331–339 (2016).
Chénard, C. et al. Temporal and spatial dynamics of bacteria, Archaea and protists in equatorial coastal waters. Sci. Rep. 9, 1–13 (2019).
Ford, A. K. et al. Reefs under Siege—The rise, putative drivers, and consequences of benthic cyanobacterial mats. Front. Mar. Sci. https://doi.org/10.3389/fmars.2018.00018 (2018).
Charpy, L., Casareto, B. E., Langlade, M. J. & Suzuki, Y. Cyanobacteria in coral reef ecosystems: A review. J. Mar. Biol. 2012, 1–9 (2012).
Huang, D., Tun, K., Chou, L. M. & Todd, P. A. An inventory of zooxanthellate scleractinian corals in Singapore, including 33 new records. Raffles Bull. Zool. Suppl. 22, 69 (2009).
Todd, P. A. et al. Towards an urban marine ecology: Characterizing the drivers, patterns and processes of marine ecosystems in coastal cities. Oikos https://doi.org/10.1111/oik.05946 (2019).
Rubin, B. E. R. et al. Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS ONE 8, e70460 (2013).
Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R. & Fierer, N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples: Influence of short-term storage conditions on microbiota. FEMS Microbiol. Lett. 307, 80–86 (2010).
Carruthers, L. V. et al. The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ 7, e8133 (2019).
Veron, J. Corals of the World (Australian Institute of Marine Science, Townsville, 2000).
Forsman, Z., Wellington, G. M., Fox, G. E. & Toonen, R. J. Clues to unraveling the coral species problem: Distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ 3, e751 (2015).
Forsman, Z. H., Barshis, D. J., Hunter, C. L. & Toonen, R. J. Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites. BMC Evol. Biol. 9, 45 (2009).
Terraneo, T. I. et al. Environmental latitudinal gradients and host-specificity shape Symbiodiniaceae distribution in Red Sea Porites corals. J. Biogeogr. https://doi.org/10.1111/jbi.13672 (2019).
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS 108, 4516–4522 (2011).
Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. & Dangl, J. L. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10, 999–1002 (2013).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).
Cole, J. R. et al. The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35, D169–D172 (2007).
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Oksanen, J. et al. vegan: Community Ecology Package (2019).
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Martin, B. D., Witten, D. & Willis, A. D. Modeling microbial abundances and dysbiosis with beta-binomial regression. Ann. Appl. Stat. 14, 94–115 (2020).
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