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

Abstract

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.

The Mangrove Microbiome of the Malay Peninsula

“…In both species, leaves and fruiting bodies, or above ground structures have a similar diversity, of the living parts the pneumatophore has the most diverse microbial community. Similar to other studies the highest diversity of microbes is seen in sediment samples [39, 40, 58, 59]. Our ordinations further support these observations with fruit and leaves having similar microbial communities and therefore clustering together, while pneumatophores and sediment samples form well-defined and clearly differentiated clusters.…”

“…Consistent with other work examining microbial community structure in a variety of host taxa, we show that microbial community structure does exist around the Malay Peninsula [39, 40, 54, 55, 78, 79], and this structure is driven primarily by plant part sampled, location sampled, and host identity. It is likely that these differences are driven by local environmental conditions, with locations closer together tending to have more similar environmental conditions in comparison to those that are more geographical distant.…”

“…Despite this recognised importance, the dynamics, distribution, and community composition of microbes in mangrove ecosystemsremains vague [10, 11, 38]. This paucity is particularly acute in Southeast Asian coastal regions, but see [39, 40] for relevant work examining seagrass ecosystems.…”

Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria

“…Rather, it appears that dispersal across Wallace's Line is limited. But, it should be noted that environmental conditions have been shown to influence seagrass associated microbiota in Southeast Asia [66][67][68]. Samples collected west of the line were made on the Sunda Shelf, where average water depths are approximately 70 m [69], whereas the region east of this line is dominated by deep water that can exceed 7000 m [70].…”

The ecology of potentially pathogenicVibriospp. in a seagrass meadow ecosystem

“…On the other hand, sequence variants classified as Vibrio spp. were also specifically detected in association with different seagrasses (Hassenrück et al 2015, Bengtsson et al 2017, Ugarelli et al 2018, Sun et al 2020, Tarquinio et al 2021, Yan et al 2021. Moreover, marine biofilms have in general been identified as reservoirs of pathogenic Vibrio (Shikuma & Hadfield 2010, Lutz et al 2013, raising the possibility that also seagrass surfaces may harbor Vibrio strains capable of causing infections in humans and marine wildlife.…”