Soil is the universal substrate which underpins agricultural productivity, providing plants and soil organisms with water and nutrient resources, as well as a plethora of additional anthropogenic ecosystem services. However, the sustained intensity at which we are using soil resources and the increasing frequency and intensity of extreme weather events is leading to a serious decline in soil quality, often defined as ‘the capacity of the soil to function’, and associated ecosystem function and service delivery. Better understanding and monitoring soil quality is key to slowing and reversing this decline. Soil biology (and related biochemistry) has often been underutilised as an indicator of soil quality; however, it is one of the most reactive and sensitive indicators. This thesis explores novel methods of profiling the small organic molecules (i.e., metabolites) in the soil; produced by the biological community during the catabolism of substrates and anabolism of cellular metabolites. It examines methods of profiling both primary (i.e., compounds involved directly in the growth, development and reproduction of organisms) and secondary (i.e., compounds performing additional functions)
metabolites in relation to soil quality and carbon (C) cycling. Specifically, I applied untargeted primary and secondary metabolomic methods to ‘real world’ field conditions and laboratory mesocosm experiments, assessing their applicability and aiming to further understand the complex biochemical interactions within the soil under a range of conditions, combining this data with a suite of physicochemical measurements to make conclusions about changes in soil quality and function. Here, I showed that, under field drought conditions, the primary metabolome shows similar trends to previous laboratory-based research, with significant increases in drought ‘biomarker’ compounds and storage lipids during drought, followed by a significant, rapid decrease in those compounds under post-drought conditions. Overall, soil functionality showed a high resilience to drought. Additionally, I showed that pure microplastic (MP) addition has little impact on the biological functioning of soil over a field season, even at unrealistically high loading rates. From the biological, physical and chemical indicators measured, few significant effects relative to no MP application were observed. However, it was concluded that while in the short-to-medium term MPs are recalcitrant and inert, pure plastic loading is unrealistic, and further research should be undertaken on the effect of plastic additives on soil health. Further, I mechanistically disentangled the effect of nutrient addition (C:N:P) on the soil microbial metabolite profile and C use efficiency. Demonstrating that; nitrogen (N) addition had the greatest impact on the ability of the soil microbial community to utilise excess C substrates, while phosphorus (P) addition led to significant increases in the synthesis of fatty acids. I concluded that inorganic nutrient enrichment of soils is likely to have substantial implications for labile and recalcitrant C cycling and microbial resource partitioning within the soil system. Additionally, I explored soil-derived secondary metabolites as an indicator of soil quality, by applying a headspace-solid phase microextraction (HS-SPME) method to profile the volatile organic compounds (VOCs) under a variety of induced ‘soil qualities’. I identified compounds associated with the differences between treatments, showing that substrate availability and quality are key in the production and emission of VOCs. Also, I evaluated a novel HS-SPME-trap-enrichment method to improve compound recovery and sensitivity, comparing it with other HS-VOC extraction methods. I concluded that
metabolomic and volatilomic methods provide another sensitive tool in the kit for the characterisation and elucidation of soil biochemistry and chemical ecology, to aid the understanding of the complex small molecule interactions taking place within soils. The ultimate aim being the integration of metabolomics with other ‘omics platforms, with an emphasis on providing a greater functional understanding of key soil processes and the development of new soil health metrics.