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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.

Mineral fertilisers in agriculture are key to meeting the food requirements of the predicted 9.8 billion population by 2050. But raw resources of these are finite and their use is beset with problems such cost, access and environmental issues. Furthermore, increases in soil degradation makes it more difficult to meet food demands. This work considers polyhalite, 'POLY4' (K2Ca2Mg(SO4)4.2(H2O)) as a new UK potassium fertiliser resource with the proposal that the base cations it contains, could have additional beneficial effects on soil physical structure. A series of experiments were undertaken to study the effects of POLY4 on soil structural and stability properties and on nutrient behaviour. Initially, small-scale laboratory experiments were used to determine strength and stiffness changes in a wide range of soils after POLY4 addition. Strong responses were found in three of the soil types, with one demonstrating a 156% increase in soil tensile strength. Two soils were selected - Insch series, a sandy loam, and Pow Series, a silt loam, to undergo additional testing after exposure to simulated weathering stresses. Whilst most soil physical properties demonstrated limited evidence of changes from POLY4 or gypsum addition, there were differences in pH and shifts in the availability of the cations between the two treatments. When barley plants were grown, the drying and nutrient uptake from roots had a greater impact than K fertiliser source. Insch soil released soil K+ with application of potash fertiliser. Overall POLY4 did not confer any extra advantage on soil or plant properties over MOP or gypsum use as alternative K, Ca and S sources. POLY4, therefore could provide a suitable alternative K fertiliser. It has the potential to contribute to improving food security, whilst having a similar impact on soil properties to that of current mineral fertiliser options.

Potentially toxic elements (PTEs) are present in agricultural land due to diffuse and point source emissions. Because of their persistency, large quantities of PTEs have been accumulated in the soils. In the context of hazard assessment, traditionally, the PTEs have been assessed by measuring chemical concentrations or evaluating physical parameters. This fails to determine the availability of the PTEs to target biota. An assessment of the bioavailability of PTEs in environmental samples is of significant importance. In recent years, genetically engineered whole cell microbial biosensors have been applied as a tool in the assessment of the bioavailability of PTEs. The biosensors were comprehensively characterised and the bioassay procedure was optimised prior to deployment in soils. The overall objective of this study was to integrate the biosensor responses with chemical analysis and to evaluate the bioavailability and toxicity of PTEs from amended soil samples. To date, the application of microbial biosensors has relied solely on the extraction of soil waters and the subsequent exposure to test organisms. Bioavailability and toxicity of copper (Cu) and zinc (Zn) in soil waters extracted from artificially amended soils was studied in Chapters 5 and 6, respectively. Prior to application of the bioassay, the speciation of the Cu and Zn in soil waters was assessed. Both free ion concentrations of Cu and Zn dominated the bioavailable Cu and Zn fractions and represented the most toxic form in soil waters. After extraction of soil waters from the soil solid phase, the physico-chemical equilibrium may change and alter the PTEs speciation. The soil solid phase of this complex environment was likely to contain most of the labile and bioavailable fractions of PTEs. A novel yet representative solid phase contact assay provided an in situ procedure which allowed a direct contact between the microbial biosensors (test organisms) and the fraction of PTEs both sorbed to the soil solid phase and those dissolved in soil waters. To deploy the solid phase systems in amended soils, the bioavailability and toxicity of soil amended with Cu and Zn was measured. The bioavailable Cu and Zn concentrations predicted by the induced biosensors were, on average, one to ten orders of magnitude higher than those in soil waters (p < 0.05). The toxicity of Cu and Zn measured in the soil solid phase was, on average, one to two orders of magnitude higher than those in soil waters (p < 0.05). In the Cu study, the DGT (diffusive gradient in thin films) reflected the labile Cu concentration and accounted for 86% of the Cu in soil waters. This confirmed that Cu concentrations in soil waters were buffered from the resupply from the soil solid phase. Microbial biosensors provide a useful tool for assessing the PTEs bioavailability and toxicity in artificially amended soils. The data complemented the chemical analysis. This technology could be applied to historically contaminated soils and / or soils contaminated with a suite range of contaminant (e.g. organic compounds) by the deployment of the soil solid phase systems.

Of the organic matter in soils typically < 1% by weight is dissolved in the soil solution (dissolved organic matter; DOM). DOM is a continuum of molecules of various sizes and chemical structures which has largely been operationally defined as the fraction of total organic carbon in an aqueous solution that passes through a 0.45 µm filter. Although only representing a relatively small proportion, it represents the most mobile part of soil organic carbon and is probably enriched with highly labile compounds. DOM acts as a source of nutrients for both soil and aquatic micro-organisms, influences the fate and transport of organic and inorganic contaminants, presents a potential water treatment problem and may indicate the mobilisation rate of key terrestrial carbon stores. The objective of this research was to ascertain some of the biologically relevant characteristics of soil DOM and specifically to determine: (1) the influence of method and time of extraction of DOM from the soil on its biochemical composition and concentration; (2) the dynamics of DOM biodegradation; and, (3) the effects of repeated applications of trace amounts of DOM on the rate of soil carbon mineralization. To examine the influence of method and time of extraction on the composition and concentration of DOM, soil solution was collected from a raised peat bog in Central Scotland using water extraction, field suction lysimetry, and centrifugation techniques on a bimonthly basis over the period of a year (Aug 2003 – Jun 2004). Samples were analysed for dissolved organic carbon (DOC), dissolved organic nitrogen (DON), protein, carbohydrate and amino acid content. For all of the sampled months except June the biochemical composition of DOC varied with extraction method, suggesting the biological, chemical and/or physical influences on DOC production and loss are different within the differently sized soil pores. Water-extractable DOC generally contained the greatest proportion of carbohydrate, protein and/or amino acid of the three extraction methods. Time of extraction had a significant effect on the composition of water- and suction-extracted DOC: the total % carbohydrate + protein + amino acid C was significantly higher in Oct than Dec, Feb and Jun for water-extracted DOC and significantly greater in Dec than Aug, Apr and Jun for suction-extracted DOC. There was no significant change in the total % carbohydrate + protein + amino acid C of centrifuge-extracted DOC during the sampled year. Time of extraction also had a significant effect on the % protein + amino acid N in water- and centrifuge-extracted DON: Oct levels were significantly higher than Feb for water-extracted DON and significantly higher in Aug and Apr for centrifuge-extracted DON. Concentrations of total DOC and total DON were also found to be dependent on time of extraction. DOC concentrations showed a similar pattern of variation over the year for all methods of extraction, with concentrations relatively constant for most of the year, rising in April to reach a peak in Jun. DON concentrations in water- and centrifuge-extracted DON peaked later, in Aug. There were no significant seasonal changes in the concentration of suction-extracted DON. A lack of correlation between DOC and DON concentrations suggested that DOC and DON production and/or loss are under different controls. Laboratory-based incubation experiments were carried out to examine the dynamics of DOC biodegradation. Over a 70 day incubation period at 20oC, the DOM from two types of peat (raised and blanket) and four samples of a mineral soil (calcaric gleysol), each previously exposed to a different management strategy, were found to be comprised of a rapidly degradable pools (half-life: 3 – 8 days) and a more stable pool (half-life: 0.4 to 6 years). For all soil types/treatments, excepting raised peat, the total net loss of DOC from the culture medium was greater than could be accounted for by the process of mineralization alone. A comparison between net loss of DOC and loss of DOC to CO2 and microbial biomass determined by direct microscopy suggested that at least some of the differences between DOC mineralised and net DOC loss were due to microbial assimilation and release. Changes in the microbial biomass during the decomposition process showed proliferation followed by decline over 15 days. The protein and carbohydrate fractions showed a complex pattern of both degradation and production throughout the incubation. The effects of repeated applications of trace amounts of litter-derived DOC on the rate of carbon mineralization over a 35 day period were investigated in a laboratory based incubation experiment. The addition of trace amounts of litter-derived DOC every 7 and 10.5 days appeared to ‘trigger’ microbial activity causing an increase in CO2 mineralisation such that extra C mineralised exceeded DOC additions by more than 2 fold. Acceleration in the rate of extra C mineralised 7 days after the second addition suggested that either the microbial production of enzymes responsible for biodegradation and/or an increase in microbial biomass, are only initiated once a critical concentration of a specific substrate or substrates has been achieved. The addition of ‘DOC + nutrients’ every 3.5 days had no effect on the total rate of mineralization. To date DOC has tended to be operationally defined according to its chemical and physical properties. An understanding of the composition, production and loss of DOC from a biological perspective is essential if we are to be able to predict the effects of environmental change on the rate of mineralization of soil organic matter. This research has shown that the pools of DOC extracted, using three different methods commonly used in current research, are biochemically distinct and respond differently to the seasons. This suggests some degree of compartmentalisation of biological processes within the soil matrix. The observed similarities between the characteristics of the decomposition dynamics of both peatland and agricultural DOC suggests that either there is little difference in substrate quality between the two systems or that the microbial community have adapted in each case to maximise their utilisation of the available substrate. The dependency of the concentration and biochemical composition of DOC on the seasons requires further work to ascertain which biotic and/or abiotic factors are exerting control. Published research has focussed on factors such as temperature, wet/dry cycles, and freeze/thawing. The effect of the frequency of doses of trace amounts of DOC on increasing the rate of soil organic C mineralization, evident from this research, suggests that the interval between periods of rainfall may be relevant. It also emphasises how it can be useful to use knowledge of a biological process as the starting point in determining which factors may be exerting control on DOC production and loss.