Impact of Agricultural Practices on Antifungal Resistance in Soil Ecosystems 

Summary: This project aims to advance understanding of how different farming practices (e.g., pesticide application, crop rotation, organic farming) influence the development and spread of antifungal resistance in soils. 

Background: Antifungal resistance is an emerging global concern, traditionally associated with clinical settings but increasingly recognised as a significant environmental issue (Fisher et al., 2018). Soil ecosystems, particularly those influenced by agricultural activity, are critical reservoirs for microbial life and potential hotspots for resistance evolution (Pagaling et al., 2023). The widespread use of fungicides in agriculture alongside other practices such as crop rotation, monoculture, and organic farming can exert selective pressures on soil microbiota, potentially driving the emergence and dissemination of antifungal-resistant organisms. 

Despite growing awareness, the environmental dimensions of antifungal resistance remain underexplored. Understanding how different agricultural practices contribute to resistance dynamics in soil is essential for developing sustainable farming strategies and mitigating risks to both environmental and human health. This project addresses a critical knowledge gap by investigating the ecological and molecular mechanisms underpinning antifungal resistance in agricultural soils. 

The primary aim of this project is to evaluate the impact of diverse agricultural practices on the development and spread of antifungal resistance in soil ecosystems. The research will focus on: 

• Characterising soil microbial communities under different farming regimes. 

• Identifying resistance genes/mutations and their prevalence across agricultural landscapes. 

• Assessing the influence of specific practices (e.g., pesticide application, crop rotation, organic amendments) on resistance selection. 

• Exploring microbial interactions that facilitate resistance spread. 

This interdisciplinary project will integrate microbiology, molecular ecology, environmental genomics, and agricultural science to build a comprehensive understanding of resistance ecology in soils. During the PhD the student will have the opportunity to employ a combination of field sampling, laboratory experiments, and bioinformatics analyses. Studies could include complementing soil sampling across farms with varied agricultural practices with  DNA/RNA extraction and metagenomic sequencing and Quantitative PCR to characterise microbial communities or detect resistance genes, or isolation and characterisation of fungi from the environment. Data analysis will be supported by statistical modelling to correlate farming practices with resistance patterns. Opportunities for collaboration with agricultural stakeholders and environmental agencies will enhance the real-world relevance of the findings. 

Collaborative opportunity: Jointly supervised between Fera and UoLeeds this project offers a rich and supportive research environment with opportunities to contribute to a growing field with direct implications for sustainable agriculture and public health. The candidate will engage with interdisciplinary teams across microbiology, agronomy, and environmental science and have the opportunity to present findings at international conferences and publish in high-impact journals. The student will be encouraged to shape the direction of the project based on emerging data and personal research interests, fostering independence and innovation. 

We welcome applications from candidates with backgrounds in microbiology, environmental science, molecular biology, or related disciplines. Experience with laboratory techniques, bioinformatics, or fieldwork is advantageous but not essential. Most importantly, we seek a motivated and curious researcher eager to tackle complex ecological questions with real-world impact.