Spatially structured bacterial assemblages in Eastern Ghats aquatic ecosystems highlight the ecological significance of rare taxa

Aquatic bacterial communities play a vital role in ecosystem functioning, yet their large-scale biogeographic patterns remain poorly understood in ecologically diverse and understudied regions like the Eastern Ghats of India. Despite growing global interest in microbial ecology, this region, with its mosaic of waterbodies influenced by varying hydrology, abiotic factors and human activities remains underrepresented in bacterial diversity studies. To address this, we sampled 40 sites across 23 aquatic ecosystems in the Eastern Ghats. Environmental DNA (eDNA) was extracted from filtered water samples, the V4 region of 16S rRNA was PCR-amplified and sequenced using Illumina NovaSeq 6000, generating ∼1 million paired-end reads per sample. Our results revealed geographically distinct bacterial communities with limited OTU overlap, indicating localized assemblages. Cyanobacteriota and Pseudomonadota were the dominant phyla. The genus Vulcanococcus was widely distributed, suggesting its role in community stability, while the presence of bloom-forming genera like Planktothrix and Microcystis at specific sites highlighted eutrophication and risk of blooms. Differences in alpha and beta diversity were mainly driven by regionally rare taxa, which, although sparsely distributed, contributed significantly to community composition. In contrast, taxa with higher relative abundance showed less diversity but were consistently present across sites. Functional predictions revealed distinct ecological roles: rare taxa were associated with stress response and xenobiotic degradation, whereas abundant taxa were linked to core metabolic and signalling pathways. The findings also underscore habitat specialization and spatial structuring of bacterial communities. This study is the first comprehensive insight into the bacterial biogeography of the Eastern Ghats. • First biogeography study of aquatic bacterial communities in Eastern Ghats, India. • Bacterial communities varied with ecology, human impact, and protection level. • Rare taxa drive diversity and aid in functions like xenobiotic degradation. • Abundant taxa are less diverse, supporting core metabolism and signalling. • Bacterial landscape was shaped by habitat specialists.