Comparative analysis of environmental variability and fungal community structure in soils between organic and conventional commercial farms of cherry tomato in Japan

Soil environmental variability and fungal community structures were analyzed to evaluate differences in soils managed under organic (ORG) and conventional (CNV) systems of farming in Fukushima and Yamagata prefectures in Japan. The soils were collected from 8 ORG and 13 CNV farms in 2005, and 6 ORG and 13 CNV farms in 2006. Principal component analysis (PCA) of 26 environmental variables demonstrated that plots of ORG and CNV were separated; however, the differences were unclear. Environmental variability and scores of principal components indicated more MgO, available phosphorous, NO3-N, and K2O in ORG than in CNV, and more silt, Mn, and Mg/K in CNV than in ORG. The differences were considered distinguishing for these farming systems. The fungal DGGE profiles and characteristic band intensities could not be used to distinguish between ORG and CNV. However, the PCA of band profiles slightly differentiated the plots of each system for both 2005 and 2006, as was the case for environmental variability. Furthermore, analysis of the PCA scores revealed several characteristic bands in DGGE profiles. A sequence analysis of the characteristic bands indicated the genus Mortierella sp. and close relatives of Cheatomium globosum to be characteristic fungi in CNV, although definitive characteristic fungi were not found in ORG. Since these results were obtained from soils differing in the type and amount of fertilizer, the application of pesticide, and management system, they are considered to reflect the general difference between ORG and CNV soils.