Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea

Abstract

Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.

Keywords: 16S rRNA; Bacterial diversity; Coral; Metagenome; Next generation sequencing; Pathogenicity.

Figure 1. Appearance of coral specimens in healthy and infected stages; (A) black band disease, (B) white band disease, (C) white plaque disease, (D) yellow blotch disease.

Figure 2. Comparison of Shannon’s diversity indexes (A) and number of shared/unique OTUs (B) between healthy and infected conditions in each coral species.

Coral species marked with asterisk represented significant difference (White’s non-parametric t-test) between healthy and infected corals.

Figure 3. Relative abundance of bacterial distribution profiles at class level within the coral metagenomic samples obtained from healthy and diseased coral specimens.

Bacterial taxa labelled with coral species; Aa, Af, Cs, and Is indicated significantly difference (White’s non-parametric t-test) between healthy and infected corals.

Figure 4. Taxonomic classification of bacterial diversity at the genus level.

Major bacterial genera were selected and shown as (A) a heat map based on the coral species and their health status and (B –E) difference in mean proportions healthy and infected corals.

Figure 5. Weighted UniFrac PCoA plot showing the differences between bacterial communities based on (A) the coral health status and (B) coral species.

Figure 6. Jackknifed UPGMA tree of all coral samples based on weighted UniFrac distance matrix.

The jackknifed bootstrapped tree was illustrated with internal nodes colored; red for 75–100% support, yellow for 50–75%, green for 25–50%, and blue for < 25% support.