Ecological assessments of Pseudomonas communities in pastoral soils: implications for disease suppression and sustainable production in agricultural grasslands

Grasslands are an important source of biodiversity, providing a range of essential ecosystem services such as ensuring water quality and soil carbon storage. An increasing proportion of grasslands are being used to support grazing livestock, with agricultural grasslands covering over 25% of the Earth’s ice-free land surface. Despite the increasing economic value of pasture-derived exports, and the recognised importance of soil-borne disease to pasture productivity, there has been little fundamental or applied research effort aimed at understanding or controlling the diverse and dynamic soil-borne pathogen complexes that develop under pasture. Soil-borne plant pathogens can be suppressed through the general activity of the total soil microbiota acting in competition with the pathogenic microbiota, or by increases in the abundance and activity of specific microbes or microbial consortia that are antagonistic against selected pathogens. Management of the diverse soil microbial communities towards a disease suppressive microbiome is an emerging approach to plant disease control in agricultural systems. In comparison to arable systems however, disease suppression under pastoral agriculture remains vastly understudied. As such, the overarching aim of this thesis was to “identify farm management practices that provide opportunities by which the indigenous microbial communities of pastoral soils may be ‘engineered’ towards an enhanced state of general disease suppression”. Soil microbial community properties known to be associated with disease suppression were examined across 50 pastoral fields. The composition and abundance of the disease-suppressive community was assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). Land use intensification was identified as the primary driver of the compositions of both Pseudomonas communities and disease suppressive functional genes. Furthermore, using a multivariate statistical approach, it was possible to associate main changes in the soil Pseudomonas populations, and functional gene abundance, with measures of soil organic matter quality, C:P ratio (nutrient stoichiometry), and aromaticity of the dissolved organic matter content (carbon recalcitrance). These associations between soil organic matter quality and soil disease suppressive communities were challenged and validated using a structured experimental design. Soils collected from a long-term grassland field trial were used to investigate the impact of 20 years of plant residue management on soil suppressiveness. A novel, pasture-relevant plant pathogen bioassay, Rhizoctonia solani AG2-1 induced damping-off (wirestem) of kale (Brassica oleracea), was used to detect natural variation in soil disease suppression and link this with changes in soil biology and chemistry. Frequent inputs of plant material into soil altered the chemical, physical, and microbiological parameters of the pasture. Notably, Pseudomonas community composition (species richness and diversity), soil organic matter content, and carbon recalcitrance were associated with enhanced suppression of damping-off disease. Subsequent microcosm experiments, simulating on-farm management of carbon availability, assessed the importance of soil, plant, and proximity to the plant root, in shaping microbial communities in pastoral soils. While the ‘parent’ soil (within which crops were planted or residues added) was identified as the primary driver of both bacterial and Pseudomonas communities, the composition of the Pseudomonas community, particularly species diversity indices, was more sensitive to plant species-specific effects than the total bacterial community. Collectively, the research conducted in this PhD programme has demonstrated how edaphic, environmental, and farm-management factors can alter key phylogenetic and functional traits of the resident soil community. Importantly, pastoral management decisions that affect soil organic matter content, particularly carbon quality, were identified here as key opportunities to manage the indigenous microbial communities of pastoral soils to favour development of a suppressive microbiome.