Host senescence and urbanized conditions drive bacterial communities of the freshwater sponge Spongilla lacustris

Abstract Freshwater sponge holobionts remain poorly characterized despite their ecological importance and exposure to strong anthropogenic pressures. Here, we investigated spatio-temporal dynamics of the bacterial microbiome within the freshwater sponge Spongilla lacustris across three sites with contrasting nutrient levels in the urban and peri-urban canal systems of Leiden (The Netherlands). Sponge and freshwater samples were collected every two weeks from October to December 2021, covering major stages of the adult sponge life cycle, including gemmulation, bleaching, and senescence. Using 16S rRNA gene metabarcoding, major differences in the sponge microbiome diversity were observed through a temporal dynamic, being associated with host physiological changes. Senescent and bleached sponges were characterized by an increased β-diversity dispersion, consistent with a potential dysbiosis process following the Anna Karenina Principle. A wide range of biomarker taxa were associated with this bleached stage and may correspond to opportunistic microbial scavengers degrading organic matter released during host decomposition. To a lesser extent, spatial patterns were also observed: ammonium- and phosphate-enriched sites harbored a limited number of discriminant taxa, characterised primarily as denitrifiers and methanotrophs, suggesting nutrient-driven functional structuring. Together, these results indicate that S. lacustris microbiomes are primarily shaped by host senescence, while environmental eutrophication influences specific taxa, providing new insights into freshwater sponge holobiont ecology under urbanized conditions. Graphical abstract