The microbiome of the seagrass Halophila ovalis: community structuring from plant parts to regional scales

Seagrass meadows are critical marine ecosystems. They are significant carbon sinks and play numerous important roles in coastal areas. They help to prevent shoreline erosion and serve as nursery grounds for many marine species. Like their terrestrial counterparts, seagrasses form symbiotic relationships with diverse communities of bacteria that help to promote and maintain host fitness. In this study, we sampled the seagrass Halophila ovalis throughout Singapore and Peninsular Malaysia to characterise the associated bacterial communities and distributions in this acknowledged seagrass biodiversity hotspot. Three different parts of the seagrass (leaves, roots and rhizomes) were collected, and a sediment sample was collected in close proximity to each host. We used high-throughput 16S rRNA amplicon sequencing to examine the bacterial communities associated with each plant part and location. Our analyses indicated that bacterial assemblages associated with H. ovalis were distinct among locations, and different plant parts harboured divergent bacterial communities. We uncovered a significant distance-decay relationship, suggesting that dispersal limitations could explain the observed bacterial community structuring. We further identified bacterial indicator amplicon sequence variants (ASVs) that were associated with degraded or healthy seagrass meadows. The identification of indicator ASVs that are indicative of anthropogenically stressed seagrass, or a declining environment, could be used to implement proactive seagrass conservation and management schemes. This study addresses a current scientific gap within the characterisation of seagrass microbiomes, specifically of those from Southeast Asia, a region of acute seagrass losses, and provides a solid foundation for future seagrass research in the region.