Metagenomic analysis of the microbial community associated with the coral Porites astreoides

Abstract

The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific; coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide diversity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

“…The diversity of microbial communities associated with corals and sponges is known to be influenced by host interactions (Wegley et al, 2007;Kimes et al, 2010;Raina et al, 2010;Fan et al, 2012), the production of antimicrobial compounds (Ritchie, 2006;Shnit-Orland and Kushmaro, 2009) and environmental conditions (Hong et al, 2009;Ceh et al, 2011). Recent studies, however, indicate that other members of the coral holobiont (in particular Symbiodinium dinoflagellates) also influence microbial community structure through release of complex carbon-containing exudates including dimethylsulfoniopropionate (DMSP; Ikeda and Miyachi, 1995;Raina et al, 2009Raina et al, , 2010.…”

Potential role of viruses in white plague coral disease

“…Active infection of Symbiodinium by members of the Phycodnaviridae was indirectly demonstrated based on the identification of phycodnavirus-like complementary DNAs in cultures of two different clades of Symbiodinium . Finally, sequence similarities to and viral-like particles reminiscent of nano-, circo-and geminiviruses, all of which are eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses and their associated satellites (collectively referred to 'SCSDVs' in this paper) also have been found in corals (Davy and Patten, 2007;Wegley et al, 2007;Marhaver et al, 2008;Patten et al, 2008;Vega Thurber et al, 2008;Littman et al, 2011;Rosario et al, 2012).…”

“…As only the WP Diseased and seawater viromes, but not the bleached and healthy viromes, contained high amounts of these viral types, it is evident that the changes detected in the relative abundance of similarities to these viral types are not the result of MDA. Finally, a previous comparative study on stressed Pacific coral species (not infected with WP) also used MDA but detected SCSDV sequences only in 2 viromes out of 6 (Vega Thurber et al, 2008), while another study on another Pacific coral species using MDA amplification identified o5% nano/ circo viruses with no similarities to satellite DNAs or geminiviruses (Wegley et al, 2007).…”

“…Studies have characterized the viruses associated with bleached and healthy corals, corals exposed to different environmental stressors, and within the algal symbionts (Symbiodinium spp.) of corals (Wilson et al, 2004;Wegley et al, 2007;Marhaver et al, 2008;Vega Thurber et al, 2008;Correa et al, 2013). Based on these works, four major groups of viruses are predicted to infect corals and their associated microbes: bacteriophages, enveloped herpes-like viruses, nucleocytoplasmic large DNA viruses (NCLDVs, including members of the Phycodnaviridae, Mimiviridae and Iridoviridae), and small circular single-stranded DNA (ssDNA) viruses (for a review, see Vega Thurber and Correa, 2011).…”

Investigating the Driving Mechanisms Behind Differences in Bleaching and Disease Susceptibility Between Two Scleractinian Corals, Pseudodiploria Strigosa and Diploria Labyrinthiformis

“…Corals harbor many essential microorganisms including viruses, bacteria, archaea, fungi, and the symbiotic algae Symbiodinium, which all play roles in maintaining the health of the coral holobiont Wegley et al 2007). …”