In the UK, 70% of solid waste from wastewater treatment processes is recycled to land as agricultural fertiliser. As wastewater treatment works collect viruses shed in faeces and urine of the population in their catchment areas, these biosolids could potentially contaminate agricultural land with various human, plant and animal pathogens. Biosolids also represent a valuable source of nutrients for sustainable food production, however the impact of their use on the soil virus community, and the ability of biosolids-associated viruses to persist, has yet to be explored at a community scale.

The aims of this thesis were to assess the impact of biosolids amendment on the soil virus community, assess the persistence of biosolids-associated viruses over different timescales, and to develop techniques that expand the characterisation of terrestrial virus communities. This thesis reviews our current knowledge of terrestrial viral ecology, the techniques used to investigate viruses in the environment and the production and use of wastewater derived biosolids (Chapter 1), before examining the long-term impact of biosolids amendment on the soil virus community over 25 years and comparing this with soils that had historically been amended with biosolids 19 years previously (Chapter 2). The study found no difference in overall virus community diversity, and a 100-fold reduction in the relative abundance of biosolids-associated viruses between long-term and historically amended soils. To build on this understanding, the impact of a single amendment of biosolids on the soil viral community was assessed under controlled conditions (Chapter 3). This revealed that at the point of amendment, biosolids import substantial quantities of viruses into the soil virus community, causing a reduction in overall diversity but after one year, biosolids-associated viruses had reduced eight-fold in their relative abundance.

Neither experiment detected any human pathogens. However, many pathogenic viruses are RNA based, and no studies of soil RNA viruses existed at the start of this research. To fill this knowledge gap, a feasibility study on the application of viromics to studying soil RNA viruses was carried out on an altitudinal productivity gradient of grassland soils (Chapter 4). This study identified 3,462 novel soil RNA viruses and demonstrated that RNA virus communities contain viruses of a wide range of host organisms, whereas soil DNA viral ecology studies are often dominated by viruses of bacteria.

The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic highlighted the im- pact that viruses continue to have on public health. To meet this emerging threat, a study was conducted on the use of wastewater based epidemiology to monitor the prevalence and diversity of SARS-CoV-2 within wastewater treatment plant catchments (Chapter 5). Quantities of SARS-CoV-2 RNA in influent wastewater correlated with local clinical cases and deaths from COVID-19, and the genetic diversity of SARS-CoV-2 in wastewater mirrors that observed in clinical testing. This work also formed the basis for national surveillance programmes within the UK.

This body of work clearly demonstrates how viral ecology can develop our understanding of the diversity of soil ecosystems and the potential roles that viruses can play in their function via their influence on host organisms. It has also demonstrated how viral ecology can be used to assess the impact of land-management on soil virus communities, and monitor the spread of viral pathogens. Future work will continue to build on this understanding by examining how active virus infections integrate into microbial and macrobiological soil community dynamics, and expand our knowledge of non-DNA bacteriophage viruses in these environments. Finally, the knowledge gained will also aid in improving global soil health, food security and reducing the burden on society of COVID-19 and future pandemic diseases.