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

可持续的可耕地农业实践依赖于与微生物的有益相互作用，通过改善植物生长，缓解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，特别是植物和微生物之间强烈的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，招募和刺激有益的微生物。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，所有这些都对植物健康至关重要。根际土壤中微生物群落的形成因素知之甚少。我们假设微生物病毒（称为病毒）在控制植物病原体和塑造健康的植物微生物组中起着关键作用。其他环境中的噬菌体已被证明通过杀死微生物，影响特定群体的活动或传递关键的分解代谢基因来塑造社区。在植物环境中的活性和作用，并没有得到广泛的研究，是一个令人兴奋的研究领域。在这个项目中，我们将探索在患病和健康状态下植物微生物组中微生物的多样性和活性。我们将专注于特定微生物的研究，包括植物病原体，以及根际微生物（细菌，古细菌）。经典的微生物学方法和生物信息学方法将被用来研究微生物和微生物之间的相互作用。微生物和噬菌体将在实验室中培养和研究，高通量测序和稳定同位素探测将用于自然系统中的微生物。这项研究可能会导致对植物病原体的生物防治的新方法，并更好地了解病毒组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.