Strategies to manage soil-borne fungi and mitigate sugarcane yield decline : Final report 2013/101

Abstract

Culture–dependent and culture-independent analyses of sugarcane rhizosphere fungal and oomycete communities were conducted across two cropping seasons at two sites. Agronomic treatments included replant continuous cane, cane-legume rotations and longer-term (LT) ratoon cane. A native forest soil was included as a comparison with cane cropping. Relative abundances of fungal taxa were used to define impacts of agronomic treatments on the structure of the fungal microbiome. Fungal communities of LT ratoon cane were significantly different (P<0.003) from replant continuous cane and cane-legume rotations. Forest soil communities were highly differentiated (P<0.001) from the adjacent sugarcane cropping treatments and had the greatest (P<0.001) diversity and taxonomic eveness. The majority of differences among sugarcane fungal rhizosphere soil communities were attributed to 33 taxa, their abundance differing (0.001<P<0.05) among cropping treatments. These included numerous soil and root-associated saprophytes, potentially pathogen antagonistic Trichoderma, Epicoccum, Humicola, Bullera and Clonostachys spp., plant pathogenic Fusarium spp. and functionally diverse Helotiales, Hypocreales, Myriangiales and Pleosporales comprising mycorrhizal, mycoparasitic and plant pathogenic species. Culture-dependent root endophytic fungal communites were dominated by saprophytic Chaetomium, Mortierella and Penicillum, pathogen antagonistic Trichoderma and plant pathogenic Fusarium spp. Oomycete communities were dominated by plant pathogenic Pythium spinosum. Pachymetra chaunorhiza was not isolated from roots or rhizosphere soils. Saprophytic and plant pathogenic taxa were more abundant (P<0.001) in replant continuous cane and cane-legume rotations. Trichoderma and Epicoccum spp. were more abundant under LT ratoon cane (P<0.001) and produced metabolites that inhibited root pathogens in vitro, implying a mechanism for rhizosphere selection and disease suppression by these taxa.