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

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 µm 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.