Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis

Abstract

Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the roles of endolithic anaerobic micro-organisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated <i>Prosthecochloris</i> (CAP), a genus of anaerobic green sulphur bacteria, was dominant in the skeleton of the coral <i>Isopora palifera</i>. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living <i>Prosthecochloris</i>. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new high-quality CAP genomes - <i>Candidatus</i> Prosthecochloris isoporae and <i>Candidatus</i> Prosthecochloris sp. N1 - from the coral <i>I. palifera</i> endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other <i>Prosthecochloris</i> and harbour several CAP-unique genes. Interestingly, different CAP species harbour various pigment synthesis and sulphur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel high-quality genome of sulfate-reducing bacterium (SRB)- <i>Candidatus</i> Halodesulfovibrio lyudaonia - was also recovered from the same culture. The fact that CAP and various SRB co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of <i>Ca</i>. P. sp. N1, <i>Ca</i>. P. isoporae and <i>Ca</i>. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.