Understanding risks and optimising anaerobic digestion to minimise pathogen and antimicrobial resistance genes entering the environment

Organic wastes from municipal and farm wastes can be used in anaerobic digestors to produce biogas and liquid fertilizer, but there are risks to transmit pathogens and antimicrobial resistance genes to land, then to the food chain, and finally to human/livestock. This project aims to minimise pathogen and antimicrobial resistance genes entering the environment from anaerobic digestion, as well as maximize biogas production.

Start date
1 September 2021
3 years
Application deadline
Funding source
Funding information

£15,285 per year in 2020-21 plus a Research Training and Support budget to cover costs such as conferences, workshops and equipment.


Anaerobic digestion (AD) utilises organic materials to produce biogas while also producing nutrient-rich digestate ideal for land application as fertiliser. However, there may be a risk to human/livestock health through transmission of pathogens to land and uptake into the food chain. This is compounded by concerns over antibiotic-resistant bacteria (ARBs) entering the environment. Resistance genes (ARGs) can be transferred widely within the bioreactor and soil microbiome, including to and from pathogens. Pathogens of concern include Clostridia, which can proliferate during digestion and resist pasteurisation. The key challenge is to optimise AD processes to minimise risks associated with land application without compromising biogas generation. Furthermore, there is little clarity on how feedstocks might be ranked in terms of their pathogen/ARG content, nor the fate of pathogens/ARGs once applied to land. This understanding is critical because process optimisation and post-digestion sanitisation that do not require the energy inputs of high temperature pasteurisation (which is also not practical in some circumstances e.g. small-scale systems, developing countries) could make energy generation through AD more sustainable and more widely viable.

The project aims to:

1) evaluate pathogen/ARG content of common AD feedstocks:

- literature review, sample and enumerate a suite of pathogens/ARGs in feedstocks from a range of digesters.

2) understand the role of feedstock type and process conditions on pathogen/ARG persistence:

- operate laboratory-scale digesters to manipulate process conditions.

3) compare persistence of pathogens/ARG in traditional organic waste-amended soils vs. digestate-amended soils:

- establish field experiments in grass/crop plots (applied digestate, livestock manure/slurry and an inorganic fertilise, untreated control plots). Plots will be sampled over a year and pathogens/ARGs, soil nutrients/physico-chemical characteristics and soil microbiome analyses will be undertaken.


Related links
Antimicrobial resistance SCENARIO

The proposal provides structural guidance and relevant support to ensure students can succeed and generate novel data to present at institutional, national and international level conferences and high-quality journal papers. The student will have access to expertise on environmental engineering (Surrey), facilities to establish mesocosm scale anaerobic digesters (Hutton) access to a state-of-the-art microbiology laboratory with expertise in the pathogen-related microbiology of AD (Avery) and to expertise in environmental risk assessment (Hough). The supervisory team has existing links with AD operators at different scales and utilising different feedstocks, therefore access to sampling locations is readily available.

Students at the James Hutton Institute have access to statistics courses through BiOSS and are part of a lively and vibrant graduate school which hosts an annual symposium and a number of other events and courses. The student will have the opportunity to learn molecular microbiology, field sampling skills, environmental microbiology and risk assessment skills.

The James Hutton Institute has strong links with Scottish Water (e.g. Deerdykes AD) farm scale AD operators (e.g. Gask Farm, Turriff) and our intention is to arrange for the student to spend time with these organisations as part of their training. Conversations have been initiated with potential partners to this effect.


Avery et al. (2014) Biomass Bioenergy 70, 112-24.

Xu et al. (2019) Bioresour. Technol. 282, 179-88.

Pulvirenti et al. (2015) Biomass Bioenergy 81, 479-82.

Eligibility criteria

Applicants are expected to hold a first or upper-second class degree in a relevant discipline (or equivalent overseas qualification), or a lower second plus a good Masters degree (distinction normally required).

This studentship is available for UK, EU and overseas students.

IELTS Academic: 6.5 or above (or equivalent) with 6.0 in each individual category.

In light of current challenges students face, we are accepting the following for courses that start in February 2021: IELTS Indicator, TOEFL iBT Special Home Edition, and the Duolingo English Test. In the case of Duolingo, we accept a score of 90 as the equivalent of IELTS 5.5, 100 as the equivalent of 6.0, 110 as the equivalent of 6.5, and 120 as the equivalent of 7.0.

These equivalencies apply for both the overall and component scores e.g. for a programme requiring 6.5 overall with 5.5 in each component and 6.0 in Writing, we would look for Duolingo results of 110 overall with 90 in each of the following components (Comprehension, Conversation, Production) and 100 in Literacy.


How to apply

All applications to SCENARIO are made via the University of Reading, whether the projects you are interested in are based at Reading, Surrey, Centre for Ecology and Hydrology, British Geological Survey or Institute of Zoology.

Choose the PhD projects that interest you most (maximum of 4) and rank your choices in order of interest. Your application is only sent to supervisors for projects where you express an interest, so listing more increases your chances of success. If in doubt, choose 4. There will be limited possibilities to express interest for other projects later in the Admissions process.

Each project description indicates the name and institution of the lead supervisor and has a reference number. You are welcome and encouraged to email the lead supervisors of projects to ask them any questions you may have or to discuss the project.

Main interview day: 10 February 2021

It is likely that our interview day will be an online event but that decision will be made nearer the time based on governmental Coronavirus guidelines.

Application deadline

Contact details

Bing Guo
02 AA 03
Telephone: +44 (0)1483 686617
E-mail: b.guo@surrey.ac.uk

Centre for Environmental Health and Engineering

Department of Civil and Environmental Engineering

We are a multidisciplinary research centre with international expertise which undertakes research activities and services that address today’s environmental and public health global challenges. Projects cover the entire water, wastewater, pollution cycle and encompass topics such as:

  • Water resources surveillance
  • Modelling and management
  • Advanced water and wastewater treatment
  • Resource recovery
  • Pollution control and waste management
  • Water quality and public health
  • Risk assessment and management.

Studentships at Surrey

We have a wide range of studentship opportunities available.