Two Amazon freshwater sponges, Drulia brownii and Tubella paulula, share a resilient microbiome strongly shaped by seasonality and urbanization

Sponges are among the earliest-diverging metazoans, and their evolutionary success has been strongly linked to their symbiosis with microorganisms. While marine sponge-microbiome associations have been extensively characterized, freshwater sponges remain comparatively understudied, particularly in tropical systems such as the Amazon, where sponges undergo seasonal flood pulses and urbanization-derived disturbance. Here we characterized the microbiomes of two freshwater sponge species, Drulia brownii and Tubella paulula, from two contrasting sites in the Tapajos River (Amazon basin), a non-urbanized and an urbanized site, at two time points, the rainy and dry seasons. The whole metagenome was sequenced using a long-read shotgun approach, and metabarcoding was employed to characterize the gemmule microbiome. The analyses revealed that microbiome composition was primarily influenced by season, with urbanization exerting a secondary but significant effect. In non-urbanized rainy-season sponges, the microbiome was dominated by Pseudomonadales and Bacillales, whereas urbanized sponges showed more diverse profiles enriched with Burkholderiales, a possible symbiont. During the dry season, communities converged across sites, with Burkholderiales becoming the dominant taxon, including in gemmules. The 23 high-quality MAGs recovered revealed symbiosis-related genes, broad biosynthetic repertoires, and a distinctive carbohydrate-active enzyme profile. Functional analyses suggest that Pseudomonadales and Burkholderiales may play complementary roles across seasons, and Bacillales may be associated with organic matter turnover. These results show that Amazonian freshwater sponges harbor stress-sensitive but resilient microbiomes, with seasonality driving major compositional shifts and urbanization accelerating convergence toward Burkholderiales-dominated consortia, and highlight the central role of bacterial symbionts in nutrient acquisition, photoprotection, and chemical defense.