Environmental influence on seagrass condition and host-associated microbiomes across an urbanised temperate estuary

Seagrasses are key habitat-forming species that support essential ecosystem services, yet their condition is influenced by multiple stressors operating across varying spatial scales. Poor water quality is a major anthropogenic stressor affecting seagrass health, but its effects on seagrass condition and associated microbial communities remain poorly understood. We examined how the condition of the seagrasses Zostera muelleri and Heterozostera nigricaulis and their below-ground bacterial community structure (bulk sediment and rhizosphere) were influenced by large-scale abiotic factors (e.g. salinity) and localised changes in water quality (e.g., proximity to stormwater outfalls) along the Derwent estuary, Tasmania. Seagrass total biomass and leaf length were reduced closer to stormwater outfalls. Several putative "core" bacterial taxa (e.g. Desulforhopalus and Thiodiazotropha) were abundant in the seagrass rhizosphere, whereas other taxa (e.g. Saccharicrinis, Lacinutrix, Vallitalea) were associated with degraded seagrass meadows, characterised by lower biomass and higher epiphyte cover. Among large-scale abiotic factors, only salinity was negatively related with leaf length and below-ground bacterial community structure. Our findings highlight the stronger influence of localised changes in water quality on seagrass condition and below-ground microbial communities compared to larger-scale abiotic factors, and provide evidence for the role of both potentially beneficial and detrimental bacteria. This study establishes baseline knowledge of multiple stressors affecting Tasmanian seagrasses and their microbiomes in a highly urbanised temperate estuary, with implications for stress thresholds that influence seagrass health, distribution and restoration potential.