The effect of crop rotation on the structure of the fungal community colonising rice straw residues in paddy rice cultured soil in the Mekong Delta of Vietnam

Abstract

In this study, we compared a rice monoculture and alternating crop rotation on fungal population . The studied crop rotation systems were rice-rice-rice (CRS1), rice-rice-baby corn (CRS2), rice-rice-mungbean (CRS3) and baby corn-rice-mungbean (CRS4). A fungal primer pair (ITS1–ITS2) was used to amplify internal transcribed spacer (ITS) sequences from total DNA extracts from rice straw residues. Amplified DNA was analyzed by DGGE. Individual bands from DGGE gels were cloned and sequenced. DGGE gels representing the fungal communities of the continuous rice and the rotation site were compared and related to fungal identified from the field.The results demonstrate that the colonizing rice straw residues fungal communities were affected differently depending on crop rotation. Significant differences between the fungal communities from rice straw residues of rice in monoculture and alternating crop rotation of mungbean and baby corn were found. Cloning and sequencing of bands from the DGGE gels revealed the presence of Ascomycota and Basidiomycota that are common in agricultural soils. It was shown that the colonizing rice straw residues of crop rotation seemed to select the phylum Ascomycetes, while different members of the phylum Ascomycota and Basidiomycota were detected in the of colonizing rice straw residues rice monoculture.