High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

Wirulda Pootakham,Wuttichai Mhuantong,Lalita Putchim,Nalinee Thongtham,Thippawan Yoocha,Sithichoke Tangphatsornruang,Chutima Sonthirod,Chaiwat Naktang

doi:10.1038/s41598-017-03139-4

Abstract

Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.

Highlights

Coral reefs are among the most productive and biologically diverse marine ecosystems, harbouring approximately 30% of the known aquatic species and supporting the productivity of ~25% of marine fisheries[1]
Due to the high cost and low-throughput nature of the approach, the number of 16S rRNA sequences used in Sanger-based bacterial profiling studies was often lower than 200 sequences per sample, which was hardly sufficient to capture the complete diversity of the population[13,14,15]
Our objective here is twofold; first to demonstrate the feasibility and practicality of utilising Pacific Biosciences (PacBio) circular consensus sequencing (CCS) technology in microbial community studies, and second to investigate the diversity and structure of bacterial communities associated with P. lutea

Summary

Introduction

Coral reefs are among the most productive and biologically diverse marine ecosystems, harbouring approximately 30% of the known aquatic species and supporting the productivity of ~25% of marine fisheries[1]. Despite the fact that PacBio platform can provide full-length 16S rRNA sequence data at a fraction of the cost of Sanger sequencing, it is still not as cost-effective as the short-read Illumina or Ion Torrent technologies This may be one of the reasons why PacBio system has not widely been adopted in microbial community surveys[25, 26]. Our objective here is twofold; first to demonstrate the feasibility and practicality of utilising PacBio CCS technology in microbial community studies, and second to investigate the diversity and structure of bacterial communities associated with P. lutea This is the first 16S rRNA gene-based community survey of marine environmental samples that takes full advantage of the PacBio SMRT sequencing system to capture full-length 16S rRNA sequences. With tens of thousands of full-length 16S reads obtained from each sample, we thoroughly examined the core microbiome harboured by P. lutea and compared the diversity and composition of bacterial communities associated with corals from the Gulf of Thailand and Andaman Sea

Objectives

Methods

Results