Management factors affecting size and structure of soil Fusarium communities under irrigated maize in Australia

Fungi in the genus Fusarium are ubiquitous in agricultural soils and have a wide range of ecological roles. We conducted a series of field trials, glasshouse trials, and soil microcosm experiments to assess the effects of stubble and N management, crop type, incorporation of residue originating from different plants and seed-applied fungicides on soil Fusarium. A community level approach was used based on PCR-DGGE and a semi-quantitative nested qPCR approach. Soil Fusarium communities were found to be primarily affected by plant residue inputs. In a field trial, incorporation of maize residue into soil significantly increased the relative abundance of Fusarium Ef1α gene copies (P < 0.001) and increased the diversity of Fusarium genotypes present in the field when compared to stubble burned treatments. In particular, the important mycotoxin-producing Fusarium verticillioides was present where stubble had been retained and absent where stubble was burnt. Fusarium oxysporum was common in soil regardless of stubble management. In the field trial, the application of mineral N fertiliser (329 kg N ha−1 year−1) had no effect on abundance or diversity of soil Fusarium (P > 0.05). Glasshouse trials tested the effects of fungicides and crop rotation on the diversity and abundance of soil Fusarium spp. Using soil repeatedly cropped with maize (5 years), the subsequent growth of neither canola, wheat nor maize significantly altered the relative abundance of Fusarium in soil (P < 0.05), but growth of adzuki bean resulted in a significant decrease (P < 0.05). Furthermore, the growth of different plants had no effect on the species of Fusarium present in the soil. However, in a microcosm experiment, the return of residues of these plants to soil (at equivalent dry weights) resulted in increases to the size and change to the composition of the Fusarium community (P = 0.001). Treatment of maize seed with the fungicides metalaxyl-M, tolclofos-methyl, or fludioxonil increased plant growth and the relative abundance of Fusarium Ef1α genes in DNA extracted from the bulk soil. This may have occurred by suppressing soil microorganisms competing with Fusarium for plant residues. Fungicide addition also effected a short-term change to the Fusarium community structure. This work clearly demonstrates the effects of crop residue quantity and quality (origin) on soil Fusarium communities, indicating its importance for integrated management of Fusarium in production systems.