Urban wastewater microbiomes reveal distinct taxonomic and functional variation across seasons and locations in Aizawl, Mizoram.

Wastewater microbiomes provide valuable information on environmental processes and community health while supporting wastewater-based epidemiology. This study investigated relationships among wastewater source, seasonality and SARS-CoV-2 occurrence on microbial community dynamics in Aizawl, Mizoram, India, using full length 16S rRNA nanopore sequencing. Thirty wastewater samples collected from four domestic sewage sites and one sewage treatment plant influent across autumn, winter, summer and summer monsoon seasons were analyzed together with SARS-CoV-2 detection by RT qPCR. Taxonomic profiling revealed a core microbiome dominated by Bacillota, Pseudomonadota, Bacteroidota and Actinomycetota. Seasonal variation influenced community composition, with summer and monsoon samples showing increased abundances of Pseudomonadota and Bacteroidota, whereas autumn and winter samples were enriched in Bacillota. STP influent receiving mixed urban and industrial inputs exhibited greater taxonomic richness than predominantly domestic wastewater, whereas predominantly domestic wastewater showed higher community evenness. SARS-CoV-2-positive samples showed increased abundances of enteric and opportunistic bacterial genera, including Escherichia, Klebsiella and Acinetobacter, and displayed distinct community clustering patterns. LEfSe analysis identified microbial biomarkers associated with wastewater source, season and viral status, including Aliarcobacter, Segatella copri and Escherichia coli. Co-occurrence network analysis revealed a highly interconnected microbial community comprising 46 nodes and 383 significant associations, with Segatella and Streptococcus acting as major hub taxa. Functional prediction indicated the predominance of chemoheterotrophy, fermentation and nitrogen transformation pathways. These findings demonstrate that wastewater microbial communities exhibit distinct patterns across seasons, wastewater source types and SARS-CoV-2 detection status while maintaining a stable functional framework, highlighting their value for environmental surveillance.