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

Anaerobic digestion (AD) utilises organic materials to produce energy via biogas while also producing nutrient-rich digestate ideal for land application as fertiliser. However, there may be a risk to human (and livestock) health through transmission of pathogens to land and uptake into the food chain, direct environmental contact or run-off into water courses. 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 application of AD to land. Lack of data has precluded evaluation of risk from pathogens entering the environment through AD and information on manipulating AD to reduce pathogens and resistance genes without compromising gas generation are scarce. Furthermore, there is little clarity on how feedstocks might be ranked in terms of their pathogen or ARG content, nor how that feeds through into 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
2) understand the role of feedstock type and process conditions on pathogen/ARG persistence
3) compare persistence of pathogens/ARG in traditional organic waste-amended soils vs. digestate-amended soils.

The aims will be addressed through a series of experimental and literature-based steps:
1. Pathogen/ARG content of feedstocks
The student will undertake a literature review including a synthesis of data on pathogen/ARG presence and concentrations in different feedstocks for AD. This will be supplemented with experimental work in which the student will sample and enumerate a suite of pathogens/ARGs in feedstocks from a range of digesters with which the supervisors have existing links.
2. Role of feedstock and process conditions on pathogen/ARG persistence during AD
The student will establish laboratory scale digesters through which to undertake experiments to manipulate process conditions (e.g. loading rates/retention time, water content, temperature) within industry-relevant operating envelopes as identified during the literature review and through discussion with site operators during (1) above. These will exploit the opportunity to control feedstocks and conditions carefully to define optimal envelopes of operation for both gas production and purity, pathogen/ARG reduction and production of an agriculturally useful digestate. This will be supplemented by sampling digestate corresponding to feedstock samples in (1) above, with process conditions recorded.
3. Pathogen/ARG persistence in amended soils
The student will establish field experiments in which digestate will be applied to experimental grass/crop plots in a factorial experiment also incorporating livestock manure/slurry and an inorganic fertiliser as treatments, alongside untreated control plots. Plots will be sampled over the period of a year and pathogens/ARGs, soil nutrients/physico-chemical characteristics and soil microbiome analyses will be undertaken.
Throughout, PCR/multiplex PCR and culture will be used for sample screening for pathogens/ARGs followed by q-PCR for quantification.