Spatial Patterns and Overlap of Sedimentary and Rhizosphere Microbiomes of the Seagrass Zostera capensis

Seagrasses are important nature-based solutions for climate change mitigation and adaptation due to their carbon stocks and ecosystem service co-benefits. Characterising microbial communities in seagrass sediments and rhizospheres is essential for understanding their roles in biogeochemical cycling, seagrass health, and potential contributions to ecosystem functioning. However, the extent to which seagrass microbiomes are shared at different spatial scales is not well understood. We utilised 16S rRNA metabarcoding to characterise prokaryotic communities in the sediments of the seagrass Zostera capensis at three estuaries spanning the environmental gradient of South Africa. In addition, we characterised the rhizosphere microbiome (rhizobiome) to better understand rhizosphere and sediment community dynamics. Overall, after accounting for community in adjacent seawater, we found that Z. capensis sediment and rhizosphere microbiomes largely overlap, sharing 34 genera but also harbour core genera. The sediment microbiome and rhizobiome showed significant spatial variability, suggesting that both local-scale and broader estuary-specific factors shape site-level microbial signatures. Further, predictive functional analysis showed that the rhizobiome was enriched for nutrient cycling pathways potentially beneficial to Z. capensis. Our findings support the exploration of sediment and rhizosphere microbial communities for monitoring ecosystem health and assessing impacts from threats such as pollution and climate change.