Sudhir, A. | Search bioRxiv

bioRxiv2026

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

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.

genomics↗

bioRxiv2025

The effect of above-ground vegetation on soil microbiome in urban green spaces: A systematic evidence map

Soil microbiome in urban areas is continuously shaped by urbanization and associated processes like native plant species removal, type of vegetation (native and exotic), soil physicochemical properties and anthropogenic activities, and the introduction of invasive plants, etc. Subsequently, above-ground vegetation is shaped by the soil microbiome. However, such information is hardly included while selecting plant species for greening efforts or plantations within green spaces. This could be due to a lack of studies connecting above-ground vegetation and soil microbial communities. In particular, the number of studies investigating soil microbiota and its effects on aboveground vegetation are gaining traction only recently. Existing studies vary in research questions, methodologies, urban green spaces explored, microbial community aspects, and soil characteristics examined. In this study, we are conducting a systematic evidence mapping to consolidate this research and identify global trends and gaps. We focus on the effect of above-ground vegetation on the soil microbiome in urban green spaces. Using an exhaustive search string, we retrieved 598 papers in total from two databases (Web of Science and SCOPUS) and one search engine (Google Scholar). By focusing on these relationships, we provide insights for planning and maintaining urban green spaces. This evidence mapping contributes to the scientific understanding of urban green spaces and offers practical guidance for rapidly urbanizing countries, emphasizing the integration of soil microbial communities in designing and restoring urban green spaces across different geographical locations.

ecology↗