The functional gene composition and metabolic potential of coral-associated microbial communities.

Joy D Van Nostrand,Hongyan Sun,Chongqing Wen,Junde Dong,Zhou Shi,Yanying Zhang,Juan Ling,Qingyun Yan,Qingsong Yang,Jizhong Zhou

doi:10.1038/srep16191

Abstract

The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems.

Highlights

Determining the functional role of complex and dynamic coral-associated microbial communities is challenging due to our inability to culture the vast majority (~99%) of microorganisms[1,17]
Coral reefs often reside in oligotrophic waters and it has been suggested that the coral-associated microbes supply nutrients for the coral animal
Results from this study showed that 288 to 348 functional genes were detected from individual coral samples related to key biogeochemical cycling processes, including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism

Summary

Introduction

Determining the functional role of complex and dynamic coral-associated microbial communities is challenging due to our inability to culture the vast majority (~99%) of microorganisms[1,17]. Rapid development of high-throughput metagenomic technologies enabled scientists to discover the potential functional roles of the coral holobiont members. The metagenomic study by Wegley et al (2007)[18] provides a metabolic snapshot of microbes associated with the reef-building coral Porites astreoides. Aiming to obtain insights into the associations between microorganisms and corals, four coral species Galaxea astreata (GA), Porites lutea (PL), Porites andrewsi (PA) and Pavona decussata (PD) were collected from the Luhuitou fringing reef, South China Sea. High throughput 16S rRNA Illumina sequencing and GeoChip 5.0 were employed to test (1) whether the functional potential of coral-associated microbes play a more important role than taxonomic composition within a coral species and (2) whether microbial functional potential is driven by local environmental factors, given the important role of microbes in driving biogeochemical cycles. In contrast to microbial taxonomic composition, environmental factors accounted for the variations of microbial functional potentials

Methods

Results

Conclusion