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

可持续的耕地耕作方式依赖于与微生物的有益相互作用，通过促进植物生长、减轻环境压力和增强对病原体的防御来提高作物产量。根环境，称为根际，是植物和微生物之间强烈生物活动和相互作用的区域。植物通过光合作用产生的碳至少有一半被输送到地下，其中大部分以根系分泌物的形式释放到土壤环境中，根系分泌物会招募和刺激有益微生物。这些微生物包括那些动员磷、固定大气氮和产生植物激素的微生物，所有这些对植物健康都至关重要。人们对形成根际土壤微生物群落的因素了解甚少。我们假设微生物的病毒（称为噬菌体）在控制植物病原体和塑造健康的植物微生物组方面起着关键作用。其他环境中的噬菌体已被证明通过杀死微生物、影响特定种群的活动或传递关键的分解代谢基因来塑造群落。噬菌体在植物环境中的活性和作用尚未得到广泛研究，是一个令人兴奋的研究领域。在这个项目中，我们将探索植物在患病和健康状态下微生物组中噬菌体的多样性和活性。我们将重点关注特定微生物的噬菌体，包括植物病原体，以及根际共生微生物（细菌，古细菌）。经典的微生物学方法和生物信息学方法将用于研究微生物与噬菌体之间的相互作用。微生物和噬菌体将在实验室培养和研究，高通量测序和稳定同位素探测将用于表征自然系统中的噬菌体。这一研究将为植物病原菌的生物防治提供新的方法，并有助于更好地了解病毒在植物健康和可持续农业中的作用。

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.