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  4-year PhD Studentship: Impact of the microbial biodiversity and micro-ecological processes on the transmission and persistency of diseases in dairy farms: a multidisciplinary, adaptive research approach

   Bristol Veterinary School

   Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Soil provides the basic structure for the development of the ecosystem where humans and animals live. Soil microbiota, including different pathogenic and non-pathogenic microorganisms, are responsible for the health and maintenance of the ecosystem, creating the greatest biodiversity in the world. The interactions of the microorganisms harboured in the soil are complex. In most undisturbed ecosystems, these organisms are regulated by complex ecological mechanisms such as relationships, competition and predator–prey systems. Most soilborne/dwelling microorganisms do not pose a risk to human health, but, some of the microorganisms that cause human disease can be naturally present in the soil/environment or be excreted by animals such cattle and harbored in the soil. Furthermore, many of them have vectors that live in or spend part of their life cycle in soil. However, there is a lack of understanding about the role played directly or indirectly by those vectors in the maintenance and persistence of certain diseases and pathogens as well as the impact of the agricultural land management on the soil health, biodiversity and pathogen survival, particularly considering different key evolving factors as land use and degradation, changing climate and pandemic development.

Aims and objectives

This project aims to

1) Study the microbial population in soils and cow feces from different dairy farming systems, 2) assess and monitor the presence of pathogenic bacteria in soils and cow feces from different dairy farming systems, 3) assess the presence and viability of pathogenic bacteria in earthworms, 4) assess the presence and viability of pathogenic bacteria in amoebae, 5) identify possible natural or anthropogenic factors that may influence the presence and persistency in the soil and vectors (amoebae and earthworms) of pathogenic microorganisms. 6) evaluate the presence and diffusion of antimicrobial resistance in relation to the farming system.


The project is structured as

Identification of the farms and literature research

Dairy farms with different farming systems will be selected for this study and interviewed to evaluate critical points in their management system that may influence ecological biodiversity within the farm.


Samples of the same soils and same cow faeces will be taken over a period of several weeks. Furthermore, earthworms from the farm will be also collected as well as samples for culturing amoebae.

Sample analysis

The samples will be submitted to physicochemical analysis, molecular analysis and sequencing for a quali-quantitative study of the microorganisms present with a particular focus on pathogenic bacteria. When identified, pathogens will be cultured to evaluate their viability. Earthworms and cultured amoebae will be subjected to in situ hybridization for an in-depth analysis of the vector-pathogen interactions. Earthworms will be also subjected to histological examination.

Antimicrobial resistance analysis will be finally performed on the pathogenic bacteria identified along with disinfectant susceptibility of pathogenic bacteria and amoebae isolated under different farming management conditions.

Supervisors: Benedetta Amato (primary supervisor), Daniel Enriquez Hidalgo , Gary Barker,Christopher Williamson, Penny Johnes

Funding available

This project is open for Bristol PGR scholarship applications (closing date 1st December 2023)

The Bristol PGR scholarship funds tuition fees, the costs of carrying out your research and a maintenance stipend (at the minimum UKRI rate) for the duration of a PhD (four years).

How to apply for this project

This project will be based in Bristol Veterinary School in the Faculty of Health Sciences at the University of Bristol. Use this information to search for the relevant programme in our online application system.

Please visit the Faculty of Health Sciences website for details of how to apply, the information you must include in your application, and for information about our online Application Workshop to help you submit a competitive application.

Agriculture (1) Biological Sciences (4) Environmental Sciences (13) Veterinary Sciences (35)

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