DNA from non-viable bacteria biases diversity estimates in the coralsAcropora loripesandPocillopora acuta

Abstract

AbstractBackgroundNucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.ResultsBy combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes,A. millepora,A. kenti,Platygyra daedalea,Pocillopora acuta, andPorites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue forA. loripesonly. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, >30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples forA. loripesandP. acutaindicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.ConclusionsOur study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.