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


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.


Available from: Rebecca Vega Thurber, Jul 11, 2014
    • "In most of the marine environment, Proteobacteria dominate the bacterial diversity (Amaral-Zettler et al., 2010). This is true for many tropical coral species (Frias-Lopez et al., 2002; Bourne and Munn, 2005; Thurber et al., 2009) as well as cold-water scleractinians and octocorals (Penn et al., 2006; Yakimov et al., 2006; Neulinger et al., 2008; Hansson et al., 2009; Galkiewicz et al., 2011; Van Bleijswijk et al., 2015). In this study a similar pattern was observed. "
    [Show abstract] [Hide abstract] ABSTRACT: Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.
    No preview · Article · Apr 2016 · Frontiers in Microbiology
    • "Coral reefs are very rich and diverse ecosystems, though due to both local and global anthropogenic disturbances, they are in a state of gradual decline (Pandolfi et al., 2003). Local impacts such as coastal pollution (Brodie et al., 2012) and overfishing (De'ath et al., 2012) affect both the reef macrobiota (Fabricius, 2005; Sandin et al., 2008) and the microorganisms in their associated microbiomes (Dinsdale et al., 2008; Thurber et al., 2009; Webster et al., 2011). Microorganisms not only underpin the marine food web and system function (Azam et al., 1983; Fenchel, 2008), but also form intimate relationships with corals that are essential for their health (Rohwer et al., 2002; Lesser et al., 2004; Lema, Willis & Bourne, 2012). "
    [Show abstract] [Hide abstract] ABSTRACT: Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems.
    No preview · Article · Mar 2016 · PeerJ
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    • "In addition, the small size and fast reproduction rate of microorganisms make them very efficient at cycling nutrients, metabolizing foreign compounds in marine ecosystems and colonizing new ecological niches (Thurber et al., 2009). "
    [Show abstract] [Hide abstract] ABSTRACT: The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus ), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.
    Full-text · Article · Jan 2016 · PeerJ
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