Local hydrology and seasonality outweigh the influence of Phragmites australis on coastal bacterial communities across two Baltic Sea bays

Background Aquatic macrophytes shape microbial habitats in shallow coastal systems, yet the relative influence of plant-driven effects versus local hydrology and seasonal environmental variation remains poorly resolved. We investigated how Phragmites australis influences sediment, water, and phyllosphere bacterial communities in two shallow Baltic Sea bays, Haapsalu and Pärnu, that are approximately 83 km from each other. Results Bacterial communities clustered strongly by substrate (sediment, water, and phyllosphere). Sediments exhibited higher 𝛼-diversity and stronger site specificity than water or phyllosphere habitats, with bulk sediments harboring greater richness than Phragmites -associated sediments. Seasonal 𝛼-diversity peaked in summer–autumn and reached minima in spring across sediments, whereas water communities showed weaker seasonality. β-diversity analyses revealed that sediments maintained lower seasonal turnover (i.e., more temporally stable) and site-specific communities compared to water and phyllosphere habitats, which showed rapid compositional shifts and higher seasonal dissimilarity. Pärnu Bay, which experiences stronger riverine influence, exhibits larger temporal shifts in both 𝛼- and β-diversity than Haapsalu Bay. Taxonomic differences between bays included the dominance of Cyanobium in Haapsalu Bay and Synechococcus in Pärnu Bay, most likely driven by site-specific hydrology and nutrient regimes. After accounting for environmental gradients, P. australis had only modest, context-dependent effects on the bacterial community composition. Conclusions Local hydrology and seasonal variation, particularly riverine inputs and salinity dynamics, exert stronger control over coastal bacterial community composition in top-layer sediment and water than the presence of P. australis . While sediments act as relatively stable, site-specific reservoirs, water, and phyllosphere communities were more labile and seasonally dynamic. These findings underscore the importance of site-specific assessments in shallow coastal studies and caution against generalizing results across bays.