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Soil suppressiveness to Fusarium root rot of soybean had been observed in a black soil field after a long-term fertilization with nitrogen (N) and phosphorus (P) fertilizer combined with pig manure as organic amendment (NPM), rather than that with only nitrogen and phosphorus fertilizer (NP) or no fertilizer (NF). To determine the microbial role on this suppressiveness, fungal and bacterial community characteristics in NPM, NP and NF treatments were investigated by qPCR and DGGE. Compared with the similar bacterial community characteristics among 3 treatments, fungal community, especially Fusarium population size and community composition in NPM treatment were different with those of NP and NF groups. Based on the isolation and pathogenicity test, patho-genic F. oxysporum, F. graminearum, F. verticillioide and F. lateritium absolutely dominated Fusarium community in NF and NP groups. Nonpathogenic F. avenaceum, F. equiseti, F. culmorum, F. redolens, F. solani and F. tricinctum dominated Fusarium community in NPM group. Isolation rate of pathogenic Fusarium in NPM reduced from 100%to 38%in NF. These results suggested that the dominance of soil non-pathogenic Fusarium population induced by organic amendment might play an important role on suppressing Fusarium root rot in the tested field.