PhD: Antibiotic resistance genes in chalk streams

University of Southampton

Southampton, UK 🇬🇧

Dr Marc Dumont; Dr Kelvin Peh; Dr Robert Holland


Our river systems face multiple threats. Summer 2022’s drought, followed by rain and discharge of sewage from overflows, and the widespread problem of plastic pollution, highlight the challenges that we face in managing our water resources under climate change. Chalk streams are among the rarest of freshwater habitats globally and are critical for biodiversity as well as having substantial cultural value1, yet their microbial communities are poorly characterized. Of particular concern are microbes with genes encoding antimicrobial resistance that could contribute to treatment-resistant infections. For example, agricultural run-off of nutrients and pesticides, or pharmaceutical compounds escaping from sewage works, or the contamination with plastic waste2 could all be leading to the enrichment of antibiotic-resistant bacterial populations. We hypothesise that antibiotic resistance genes (ARGs) accumulate at specific sites, such as downstream of wastewater treatment works, or specifically within biofilms on plastics or microplastics. The objective of this project is to assess bacterial communities in different locations in chalk rivers and identify factors that lead to the selection of antibiotic-resistant bacteria.


The aim is to investigate the microbial community functions on biofilms and water in the Rivers Test and Itchen, iconic Hampshire chalk systems with SSSI status that provide key ecosystem services. Various locations will be examined, such as near sites of recreation, agricultural use, and below wastewater treatment plants. Microbial biogeochemical processes such as CO2 fluxes, nitrification, methanogenesis and methane oxidation will be measured in the laboratory to assess wider microbial functions. Bacterial communities will be examined by cultivation, 16S rRNA amplicon sequencing and quantitative polymerase chain reaction assays. Metagenomic sequencing of selected samples will be performed to evaluate the genomes of the microbial communities to better infer microbial functions.

As an analogue to the “plastisphere”, pre-sterilised coupons of different material (e.g. PPE, HDPE, plus controls, e.g., steel) will be incubated on the river bed, for example upstream and downstream of the Chickenhall Lane Sewage Works in Eastleigh. Bacterial communities will be characterised by sequencing and ARGs identified and enumerated within metagenomes (e.g. ResFinder). In addition, bacteria will be isolated and studied under controlled laboratory conditions to identify potential drivers of antimicrobial resistance, such as low concentrations of antibiotics or heavy metals at concentrations typical in UK rivers.


University of Southampton, Highfield Campus


The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the School of Biological Sciences. Specific training will include:

A bioinformatics training course at the NERC Environmental Omics Facility (NEOF) to learn the analysis pipelines for metagenomic sequencing. Additional training in bioinformatics will be received for the analysis of 16S rRNA amplicon sequencing data. These analyses will be performed using the University of Southampton Iridis high-performance computer for which the student will receive specific support and training. The project includes both classic microbiology methods (cultivation of bacteria) and cultivation independent approaches (e.g., quantitative PCR, sequencing), providing training in a range of research skills.

Eligibility & Funding Details: 

Please see for details.

Background Reading: 

1. Rangeley-Wilson (2021). CaBA Chalk Stream Restoration Strategy.…

2. Guo et al. (2020). Antibiotic resistance genes in biofilms on plastic wastes in an estuarine environment. Sci Total Environ 745, 140916.

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IHE Delft MSc in Water and Sustainable Development