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Two long-term field trials in South Australia were used to detect and characterise changes in soil biological properties that were a consequence of different agricultural management. The properties examined were total bacteria, fungi, and actinomycetes; total pseudomonads; cellulolytic bacteria and fungi; mycorrhizal fungi; plant root pathogens (Gaeumannomyces graminis var. tritici, Rhizoctonia solani, Pythium irregulare); bacterial-feeding protozoa; soil mesofauna (collembola and acari); earthworms; microbial biomass; C and N mineralisation; in situ CO2 respiration; cellulose decomposition; and soil enzyme activity (peptidase, phosphatase, sulfatase). The sensitivity of these biological properties was assessed to tillage (no-tillage v. conventional cultivation), stubble management (stubble retained v. stubble harvested), crop rotation (continuous wheat v. wheat-sown pasture), and N fertilisation (nil v. 80 kg N/ha applied during the crop phase). Tillage, stubble management, crop rotation, and N fertilisation significantly (P<0.01) affected C mineralisation and microbial biomass. Tillage with stubble management significantly affected root pathogenic fungi, protozoa, collembola, earthworms, and cellulose decomposition. Crop rotation affected mycorrhizal fungi, protozoa, and soil peptidase activity, and N fertiliser had a significant effect on mycorrhizal fungi, protozoa, and cellulose decomposition. As these biological properties are responsive to agricultural management, they may have potential as bioindicators. Total bacteria, fungi, and actinomycetes, cellulosedecomposing bacteria and fungi, soil phosphatase and sulfatase activity, and N mineralisation were less affected by these treatments and may therefore have limited potential as bioindicators.

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

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