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Manure and slurry are valuable resources that may enhance many soil properties. However, organic amendments can pose a significant health risk to both humans and livestock if not managed correctly due to pathogenic loads that may be carried within them. Therefore it is crucial to identify the factors that affect pathogen survival in soil, in order to gain maximum benefit from such resources, whilst minimising the threat to public and animal welfare. This research aimed to elucidate the impact of microbial community structure on pathogen decline following entry of such organisms into the soil. It was hypothesised that pathogen survival would be significantly influenced by both diversity and phenotypic configuration of the microbial community. This was experimentally investigated within three distinctly different biological contexts. Firstly, it was shown that the survival of Escherichia coli 0157 was significantly affected by the presence of an intact microbial community. Microcosms consisting of sterile and non-sterile sand and clay soils were inoculated with E. coli and destructively sampled over time. The pathogen remained stable at 4°C, irrespective of biological status. However at 18°C, the pathogen grew in sterile soil and declined in non-sterile soil. This result was attributed to microbial antagonism in non-sterile soil, which only became apparent at 18°C, due to increased metabolic activity of the native community. The next experiment was designed to investigate the impact of microbial diversity and community configuration on the survival of a suite of model pathogens. A gradient of community complexity was created by inoculation of gamma-irradiated soil mesocosms with a serial-dilution of a suspension of a field soil. Soils were incubated to allow biomass equilibration and the establishment of distinct community phenotypes. Sub-samples were then inoculated with Listeria, Salmonella and E. coli strains and survival was monitored over 160 days. Death rates were calculated and plotted as a function of dilution, which represented diversity, and of principal component (PC) scores from PLFA profiles, which represented the phenotypic community context. There was some evidence of a diversity effect as weak negative linear correlations were observed between death rate and dilution for S. Dublin and environmentally-persistent E. coli. However, a much stronger correlation was observed between death rate and certain PC scores for these organisms. No effect of diversity or phenotype was detected on either L. monocytogenes or E. coli 0157. These results suggest that pathogen survival was affected by diversity, but the phenotypic community context was apparently much more influential. Additionally, such community effects were specific to pathogen type. Pathogen survival was also investigated in the context of highly-contrasting communities within a range of naturally-derived field soils. PLFA analysis was used to determine phenotypic community structure and soils were also characterized for a range of physico-chemical properties. They were inoculated with Listeria, Salmonella and E. coli strains as above. Pathogen survival was monitored over 110 days and death rates were calculated. Physicochemical and biotic data, including PC scores derived from PLFA profiles, were used in stepwise regression analysis to determine the predominant factor influencing pathogen-specific death rates. PC scores were identified as the most significant factor in pathogen decay for all organisms tested, with the exception of an environmentally-persistent E. coli isolate. Overall, these results demonstrate the importance of soil biological quality, specifically the configuration of the microbial community, in pathogen suppression, and provide a possible means to assess the inherent potential of soils to regulate pathogen survival. This may lead to the identification of management strategies which will ultimately accelerate pathogen decay, and therefore improve the safety of agricultural practice.

The perceived benefits of food grown under organic (low-input) management practices include lower levels of potentially harmful pesticides and an increased awareness of environmental protection. It is also believed that such crops are inherently more tolerant to biotic stresses, although there is little evidence to support this. The aims of this thesis are to investigate differential effects of conventional and organic management practices on soil microbial community structure and consequences for plant growth using Arabidopsis thaliana, as the model plant species. Soil used in the study was from ‘Palace Leas hay plots long term field trial’ where Plot 2 is fertilised using farmyard manure (FYM) and Plot 13 is fertilised using inorganic fertilisers. Changes in community structure of the two different fertiliser amendments were measured over time using T-RFLP. The laboratory addition of inorganic fertiliser had a significant effect on the bacterial community (p=0.047); however, neither initial field treatment nor time had any effect (p=0.263, p=0.842, respectively). The fungal community showed no significant effect from field treatment, laboratory amendment or time (p=0.342, p=0.131, p=0.219). A. thaliana plants grown in conventionally fertilised soil (Plot 13) grew slower and were smaller than those grown in FYM amended soil (Plot 2). After 28 days, rosette area was 552.1cm2 and 418.4cm2 for plants grown with FYM and mineral amendment, respectively (p=0.01). Dry weights of the rosette were 92.6mg and 72.8mg for FYM and conventionally grown plants respectively (p=0.044). Levels of boron (org=0.73ppm, conv=0.31ppm at 30 days), calcium (org=177.7ppm, conv=124.9ppm, at 30 days), potassium (org=331.0ppm, conv=161.5ppm at 30 days) and magnesium (org=29.5ppm, conv=18.3ppm at 30 days) were all significantly higher in FYM grown plants. The ratios of K:Ca and K:Mg in plants grown on FYM amended soil were higher than for those grown on mineral fertiliser amended soil, indicating that the latter plants were under increased stress. Analysis of the leaf proteome demonstrated that nitrilase 1, 14-3-3 like protein GF14, Heat Shock Cognate 70kDa Protein 1, and glutathione-S-transferases PM24 and ERD13 were up-regulated in conventionally grown plants, whilst lipoxygenase and Annexin D6 were downregulated. Again, this indicates that A.thaliana is under increased stress when grown in conventionally treated soil. Glucosinolates and volatiles, produced as part of the plant’s inducible defence system, were investigated by HPLC/MS. There were both qualitative and quantitative differences in glucosinolate profiles. Plants grown on FYM amended soils had higher levels of the alkyl glucoside gluconaprin, whilst those on the conventionally treated soil contained glucoraphanin and glucoerucin. Subsequent aphid infestation resulted in a small (7% and 8% for conventionally and FYM grown plants, respectively) increase in the indole glucosides. Those grown on the conventionally amended soil produced 26 different volatile chemicals compared to 18 from the FYM amended soil (Plot 2); average levels of volatiles released where higher from the former than the latter. The results indicate that there was little effect of amendment practice on direct defence mechanisms in A. thaliana, although indirect defence was altered by amendment practice. The interactions between fertiliser amendment, soil microbial community, and plant and aphid herbivores were investigated using Structural Equation Modelling. The only significant relationship was a positive correlation between organic FYM amendment and rate of plant growth (p=0.004), indicating that the use of FYM as an additional amendment increased plant growth. The effect of the rate of plant growth on the rate of aphid reproduction was almost significant and negative (p=0.067), indicating that the rate of plant growth negatively impacted the rate of aphid reproduction.

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Understanding soil structure, in particular the void spaces through which water, gases and solutes flow and in which organisms exist, is vital to a sustainable future on earth. The investigation of the structural behaviour of soil under different influences is fundamental to understanding and protecting the soil. This study has investigated the impact of bacteria on the biophysics of water retention and flow, aiming to elucidate the effect of three key components produced by the model organism, Pseudomonas fluorescens SBW25. Cellulose is an extracellular polysaccharide involved in the formation of the matrix of the bacterial biofilm, lipopolysaccharide is a cell membrane component required for bacterial attachment, and viscosin is a biosurfactant released from the bacteria. Four isogenic strains mutated so as to heighten or suppress production of one of these key components were used in addition to the wild-type strain. Labfield sandy loam soil was sieved and packed into replicate experimental cores which were incubated with different bacterial treatments. Following sterilisation, the gravimetric water content (u g g-1) of the soil was determined at equilibrated matric potentials from -1 cm to -100 cm during two wet-dry cycles. Sorptivity (S, mm s-1/2) of the soil, indicative of water repellency, was determined using a mini-infiltrometer setup and has been reported as the rate of infiltration of water into the soil. Bacteria have been shown to increase water repellency of soil, decrease the total water content at saturation and increase the water retaining ability of the soil as it drains (p < 0.05). Three-dimensional analysis of core scale structure was carried out using micro X-ray computed tomography (µXCT) and of aggregate scale structure using synchrotron-µXCT. Volumetric analyses of the 3D structures has shown decreased pore connectivity and destabilisation of aggregates in soil systems treated with bacteria deficient in the production of a key extracellular component, cellulose, LPS or viscosin (p < 0.05). Analyses of cracking patterns in two types of sandy loam soil, Labfield and Bullionfield has highlighted the importance of taking into account the soil type and its composition when studying soils, as even within soil classification groups different behaviours are observed. This study has provided clear evidence of the ability of bacteria and their extracellular components to impact upon (i) the hydrodynamics of water retention and flow in soil and (ii) the structural organisation, aggregation and stabilisation of soil.