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We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from\n                    <jats:italic>Myroides<\/jats:italic>\n                    dominance toward a more diverse assemblage enriched in pollution\u2010tolerant and opportunistic genera, notably\n                    <jats:italic>Comamonas, Brevundimonas, Tissierella<\/jats:italic>\n                    , and\n                    <jats:italic>Aeromonas<\/jats:italic>\n                    . Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as\n                    <jats:italic>merA<\/jats:italic>\n                    . Concurrent increases in multidrug efflux pump genes suggested potential co\u2010selection driven by metal and chemical stressors. These findings indicate that dry\u2010season pollutant concentration reshapes both microbial communities and resistance profiles through non\u2010antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate\u2010stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.\n                  <\/jats:p>","DOI":"10.1002\/mbo3.70359","type":"journal-article","created":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T20:43:01Z","timestamp":1782938581000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-0307-3243","authenticated-orcid":false,"given":"Muhammad Ehteshamul","family":"Haque","sequence":"first","affiliation":[{"name":"Department of Microbiology University of Dhaka  Dhaka Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3039-9337","authenticated-orcid":false,"given":"Md. Shaminur","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Microbiology Jashore University of Science and Technology  Jashore Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8563-3661","authenticated-orcid":false,"given":"Munawar","family":"Sultana","sequence":"additional","affiliation":[{"name":"Department of Microbiology University of Dhaka  Dhaka Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9915-3311","authenticated-orcid":false,"given":"Anowara","family":"Begum","sequence":"additional","affiliation":[{"name":"Department of Microbiology University of Dhaka  Dhaka Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,1]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10123-024-00607-6"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11356-025-37227-0"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1086\/510603"},{"key":"e_1_2_12_5_1","unstructured":"Andrews S.2010.FastQC: A Quality Control Tool for High Throughput Sequence Data."},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.154890"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.65088"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.556136"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11356-022-24637-7"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0239594"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1890\/1540-9295(2003)001[0376:ASSIE2].0.CO;2"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/0169-5347(94)90088-4"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1043"},{"key":"e_1_2_12_15_1","unstructured":"Bushnell B.2014.BBMap: A Fast Accurate Splice\u2010Aware Aligner. 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