Metagenomic analysis of stressed coral holobionts. Environ Microbiol

Department of Biology, San Diego State University, San Diego, CA, USA.
Environmental Microbiology (Impact Factor: 6.2). 05/2009; 11(8):2148-63. DOI: 10.1111/j.1462-2920.2009.01935.x
Source: PubMed

ABSTRACT The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic samples were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.

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Available from: Rebecca Vega Thurber, Jul 11, 2014
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    • "Coral nubbins were thawed slowly on ice and removed from the RNA - later solution using sterile forceps and kimwipes to remove excess solution ( Vega Thurber et al . , 2009 ) . Replicate nubbins from the same donor colony ( A , B , or C ) were pooled and placed into sterile 150 mL conical flasks containing 15 mL sterile - autoclaved calcium and magnesium free seawater plus 10 mM EDTA ( CMFSWE ) . The surfaces of the nubbins were airbrushed using 80 psi with a sterile 1 mL barrier tip ( fresh tip for each n"
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    Frontiers in Microbiology 05/2015; 6:432. DOI:10.3389/fmicb.2015.00432 · 3.99 Impact Factor
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    • "Bacteriovorax are predatory bacteria whose presence in host organisms is thought to shape the natural microbial community through trophic interactions (Thurber et al. 2009; Chen et al. 2012). Particularly, Bacteriovorax are known to prey on Gram-negative bacteria such as members of the genus Vibrio. "
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    Molecular Ecology 02/2015; 24(5). DOI:10.1111/mec.13097 · 6.49 Impact Factor
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    • "Most of the metagenomic studies have been carried out with human or water related environments (Venter et al., 2004; Daniel, 2005; Ghai et al., 2011, 2012; Yu and Zhang, 2012; Lipson et al., 2013; Mizuno et al., 2013). There are only few studies of the microbiota associated to animals and even less to wild animals (Vega Thurber et al., 2009; Swanson et al., 2011; Marcobal and Sonnenburg, 2012; Parfrey and Knight, 2012; Ross et al., 2012, 2013; Schwartz et al., 2012; Singh et al., 2012; Wong and Rawls, 2012; Bodewes et al., 2014). In this study, we analyzed the viral content of the epidermal mucosa of the eel to test the hypothesis that it concentrates phages present in water, which in turn, control bacterial populations, including those of pathogenic species. "
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    ABSTRACT: In this work, we used the eel (Anguilla anguilla) as an animal model to test the hypothesis of Barr et al. about the putative role of the epidermal mucosa as a phage enrichment layer. To this end, we analyzed the microbial content of the skin mucus of wild and farmed eels by using a metagenomic approach. We found a great abundance of replicating phage genomes (concatemers) in all the samples. They were assembled in four complete genomes of three Myovirus and one Podovirus. We also found evidences that ΦKZ and Podovirus phages could be part of the resident microbiota associated to the eel mucosal surface and persist on them over the time. Moreover, the viral abundance estimated by epiflorescent counts and by metagenomic recruitment from eel mucosa was higher than that of the surrounding water. Taken together, our results support the hypothesis that claims a possible role of phages in the animal mucus as agents controlling bacterial populations, including pathogenic species, providing a kind of innate immunity.
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