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

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.

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

“…We identified three dominant bacterial families across all factors (species, site, and coral condition), suggesting a putatively important potential role in coral health and function due to their widespread prevalence and high abundance. Bacterial community stability was largely attributed to the abundance of Hahellaceae (comprising Endozoicomonas —ranging between 10% and 44% for all coral species; Supporting Information Table ), congruent with recent work (Bayer et al, ; Neave, Apprill, Ferrier‐Pagès, & Voolstra, ; Neave, Rachmawati, et al, ; Pogoreutz et al, ; Pootakham et al, ). While the function of Endozoicomonas has not yet been defined, their genomes are significantly enriched in genes for carbohydrate transport and recycling as well as for protein and amino acid provision (Neave, Michell, Apprill, & Voolstra, ) and phenotypic assays confirm a high metabolic versatility in vitro (Yang et al, ).…”

Quorum Sensing Interference and Structural Variation of Quorum Sensing Mimics in Australian Soft Coral

“…Many of the recovered genera have also previously been isolated from coral mucus samples including Alteromonas, Bacillus, Endozoicomonas, Erythrobacter, Micrococcus, Pseudoalteromonas, Shewanella, and Vibrio (Lampert et al, 2006;Nithyanand and Pandian, 2009;Pootakham et al, 2017). The isolates were dominated by gammaproteobacteria belonging to the family Vibrionaceae, a result that is consistent with previous observations in scleractinian corals (Kvennefors et al, 2010(Kvennefors et al, , 2012.…”

Air mass source determines airborne microbial diversity at the ocean–atmosphere interface of the Great Barrier Reef marine ecosystem

“…Relative abundance of bacterial taxa between air and coral sequence libraries for all taxa with >0.05% mean relative abundance. a) direct ASV matches between our study by source and the Pootakham et al coral microbiome [20], b) direct ASV matches that are classified at genus level between our study and the Pootakham et al coral microbiome [20] c) shared ASVs (by ≥97% sequence identity) between our study and the Wainwright et al coral microbiome [21]. .…”

“…We first searched for relevant recent published studies and constrained our search as follows: The first 20 matches by relevance from the search parameters ["16S" "coral"] and ["16S" "reef"] from 2015 to 2019 with Google Scholar were employed to determine if there was any publicly available next-generation sequencing data that encompassed the compatible 16S rRNA gene region. Based on these criteria, we identified a single publication [20] which allowed for direct ASV analysis. Another dataset with limited overlap was also assessed based on similarity searches of representative sequences to determine shared taxa [21].…”

“…PacBio SMRT sequencing of 16S rRNA gene amplicons from corals of Gulf of Thailand and Andaman Sea was conducted by Pootakham et al, (2017) [20]. The raw reads were retrieved from NCBI Short Read Archive (accession SRR5149735) via NCBI SRA toolkit (https://github.com/ncbi/sra-tools/wiki).…”