Novel bacterial lineages assembled from wastewater-impacted river metagenomes unveil ecosystem functions and risk of antibiotic resistance spread in the community

The Mahananda River, coursing through Siliguri, India, is subject to intense anthropogenic stressors, including urban wastewater, industrial effluents, and agrochemical runoff, necessitating a high-resolution microbial assessment. Leveraging whole-metagenome sequencing, we analyzed midstream water samples (APMG02 and APMG03) and reconstructed 25 metagenome-assembled genomes (MAGs), of which 14 met stringent quality criteria. We identified four novel bacterial species, Candidatus Aquabacterium mahanandaense APR203, Candidatus Sulfurospirillum siliguriense APR208, Candidatus Fluviibacter nbuensis APR306, and Candidatus Paludibacter darjeelingensis APR314, which exhibited critical genomic signatures associated with hydrocarbon degradation, heavy metal detoxification, quorum sensing, and stress response, underscoring microbial plasticity in response to pollutant influx. Detecting pathogenicity-associated factors, antimicrobial resistance determinants, and mobile genetic elements raise critical public health concerns. Comparative global river-water microbiome analyses delineate a distinct anthropogenically sculpted microbial consortium in the Mahananda River, emphasizing the profound ecological ramifications of unchecked contamination. This study underscores the transformative potential of metagenomics in deciphering riverine microbiome dynamics and pollutant resilience.