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bioRxiv · 10.64898/2026.03.31.715732

Urbanisation Reshapes Freshwater Microbiomes: A Systematic Review of Ecological Patterns and Functional Shifts

Thakur, K.·Jain, R.·CHAKMA, H.·Panda, S.·Sudhir, A.·Mukherjee, A.
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Abstract

Rapid urbanisation has profoundly shaped microbial diversity across different ecosystems. Freshwater microbiomes are particularly affected by urbanisation activities, such as eutrophication, pollution, runoff, and sewage. This is of significant concern as marginalised communities often depend on waterbodies for their livelihood. Freshwater bodies play a crucial role in maintaining both human and ecological health at population level. Currently, we lack a systematic understanding of the global impacts of urbanisation on freshwater microbiomes in relation to human health, ecosystem functioning, and sustainability. We identified 90 eligible papers from the last 25 years after screening based on the inclusion exclusion criteria. We extracted data that examined changes in the functional traits such as antimicrobial resistance (AMR), nutrient cycling of the microbiome in urban waterbodies and several other factors. Data were extracted by a thematic analysis followed by a narrative synthesis on specific functional traits. This systematic review presents a comprehensive analysis on the changes and challenges brought about by urbanisation on freshwater bodies. Our results indicate that urbanisation leads to reduced bacterial diversity of urban waterbodies, with a striking increase in reporting of Proteobacteria, Cyanobacteria and Coliform bacteria. These insights will help inform public health strategies and sustainable urban planning. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/715732v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1198ae7org.highwire.dtl.DTLVardef@1ee7db3org.highwire.dtl.DTLVardef@7e959corg.highwire.dtl.DTLVardef@90653b_HPS_FORMAT_FIGEXP M_FIG C_FIG Waterbodies in urban areas function as convergence platforms for anthropogenic and environmental microbiomes. Runoffs, wastewater and effluents contain antimicrobial resistance genes and other pathogens that survive in water due to inadequate treatment. Disposal, use, and overflow of wastewater cause restructuration of microbial communities, proliferation of opportunistic microorganisms, and spread of antimicrobial resistance in aquatic ecosystems.

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Thakur, K., Jain, R., CHAKMA, H., Panda, S., Sudhir, A., Mukherjee, A.. 2026-04-01. Urbanisation Reshapes Freshwater Microbiomes: A Systematic Review of Ecological Patterns and Functional Shifts. https://doi.org/10.64898/2026.03.31.715732

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