Viruses in the rhizosphere: the role of phages in the soil and plant root environment

Sustainable arable farming practices rely on beneficial interactions with microorganisms that improve crop production by improving plant growth, alleviating environmental stress, and increasing defense against pathogens. The root environment, called the rhizosphere, in particular is a zone of intense biological activity and interaction between plants and microorganisms. At least half the carbon a plant produces by photosynthesis is transported belowground, much of which is released to the soil environment as root exudates that recruit and stimulate beneficial microbes. These microbes include those that mobilise phosphorus, fix atmospheric nitrogen, and produce phytohormones, all of which is crucial for plant health. The factors that shape the community of microorganisms in the rhizosphere soil are poorly understood. We hypothesize that viruses of microorganisms (called phages) play a critical role in controlling phytopathogens and shaping a healthy plant microbiome. Phages in other environments have been shown to shape communities by killing microbes, influencing the activity of specific populations, or delivering key catabolic genes. The activity and roles of phages in the plant environment has not been extensively studied and is an exciting area of research. In this project we will explore the diversity and activity of phages in the microbiome of plants in both diseased and healthy states. We will focus on the phages of specific microbes, including plant pathogens, as well as commensal microbes (bacteria, archaea) in the rhizosphere. Both classic microbiology methods and bioinformatic approaches will be used to study the interaction between microbes and phages. Microbes and phage will be cultivated and studied in the laboratory and high-throughput sequencing and stable-isotope probing will be used to characterise phages in natural systems. This research could lead to novel methods of biocontrol against plant pathogens and a better understanding of the role of the virome in plant health and sustainable agriculture.