Linking metabolomics and metagenomics to resolve plant-microbial interactions involved in soil aggregation and carbon storage

植物-微生物-土壤相互作用的四年博士学位：保持健康和肥沃的土壤对全球粮食安全至关重要。植物-微生物的相互作用在土壤大团聚体(直径500微米的土屑)的形成中起主要作用，这些团聚体储存碳、养分和水分，是大多数优质耕地土壤的基本成分。传统的集约耕作降低了大团聚体的丰度，增加了作物产量受到干旱和洪水限制以及土壤被侵蚀的风险(Blankinship等人，2016，Geoderma)。作物及其相关的土壤微生物种群在支持土壤聚集的程度上有所不同，其中最好的是含有草和三叶草混合物的短期草地(LEY)。虽然已知土壤聚集涉及植物根、土壤微生物和有机分子之间的相互作用，但其机制仍然知之甚少，限制了我们通过有针对性的作物育种和土地管理的变化来恢复这些退化但关键的耕地结构的能力。目标：使用2015年在继续进行常规管理的重复耕地中种植的草三叶草，这名研究生将结合使用对土壤微生物群落的元基因组分析与不同大小土壤团聚体中新陈代谢指纹和总有机碳的测量。这些研究将寻求同时解决与根相关的微生物群落和代谢物之间的相互依赖关系，这些微生物群落和代谢物与耕地相比，增加了大团聚体的形成和土壤碳储量。我们的概念验证研究显示，与未耕作的农田边缘相比，耕地土壤团聚体中的代谢物存在重要差异，我们的LEY改善了土壤聚集性，并使土壤储水量增加了10%。新颖性和及时性：该项目寻求解决植物-微生物群落及其代谢物驱动土壤聚集性的相互作用和影响的机制基础，以及LEY在这些过程和结果上与耕地的不同之处。该项目受益于使用新的便携式质谱计，能够在土壤采样后立即快速分析代谢物，并辅之以一系列专业的质谱分析设施，包括稳定同位素(13C，15N)和使用超性能会聚色谱(Upc2)的高通量脂肪分析。此外，约克大学的下一代Illumina MiSeq和纳米孔(Minion)测序设施，以及赫尔加森博士实验室开发的用于分析的生物信息学管道，也与这些设施相辅相成。该项目结合了从不同大小的土壤团聚体的规模到土地管理和田间轮作变化的影响的这些最先进的“组学”技术的应用，以获得对Leys如何改善土壤质量的机械理解。学生实习将包括一个3个月的专业实习安排，远离实验室

Four year PhD on plant-microbe-soil interactions: Maintaining healthy and productive soils is essential for global food security. Plant-microbial interactions play a major role in the formation of soil macroaggregates (>500 um diameter soil crumbs) that store carbon, nutrients and water and are essential components of most high quality arable soils. Conventional intensive arable cropping has decreased the abundance of macroaggregates, increasing the risks of crop yields being limited by drought and flooding, and soil being eroded (Blankinship et al.,2016, Geoderma). Crops and their associated soil microbial populations differ in the extent to which they support soil aggregation, amongst the best being short-term grassland (leys) containing a mixture of grass and clover. Although soil aggregation is known to involve interactions between plant roots, soil microorganisms, and organic molecules, the mechanisms remain poorly understood, constraining our abilities to restore these degraded but critical components of arable soil structure through targeted crop-breeding and changes to land management.Objectives: Using grass-clover ley plots planted in 2015 in replicated arable fields that continue to be conventionally managed, the research student will combine the use of metagenomic analyses of soil microbial communities with metabolomic 'fingerprinting' and total organic carbon measurements in soil aggregates of different sizes. These studies will seek to simultaneously resolve the co-dependence of root-associated microbial communities and metabolites increasing macroaggregate formation and soil carbon storage in leys compared to arable fields. Our proof-of concept studies reveal important differences in metabolites in soil aggregates from arable land compared to unploughed field margins, and our leys improve soil aggregation, and increase soil water storage by 10%.Novelty and Timeliness: The project seeks to resolve the mechanistic basis of plant-microbial community and interactions and effects of their metabolites driving soil aggregation and how leys differ from arable land in these processes and outcomes. The project benefits from access to a new portable mass-spectrometer, enabling rapid analysis of metabolites immediately on soil sampling, complemented by a wide range of specialist mass-spectrometry facilities including stable isotope (13C, 15N) and high throughput lipid analysis using Ultra Performance Convergence Chromatography (UPC2). These are complemented by the high-throughput next generation Illumina MiSeq and nanopore (MinION) sequencing facilities at the University of York, together with bioinformatics pipelines for analysis developed in Dr Helgason's lab. The project couples the application of these state-of-the-art 'omics' technologies from the scale of different sized soil aggregates through to the effects of changes in land management and crop rotations at field-scales to gain mechanistic understanding of how leys improve soil quality. The studentship will include a 3 month Professional Internship Placement away from the lab