Analysis of microbial community in Japanese vineyard soils by culture-independent molecular approach

Keiko Fujita, Seiichi Furuya, Minako Kohno, Shunji Suzuki, Tsutomu Takayanagi
Institute of Enology and Viticulture, University of Yamanashi, Kofu, Yamanashi, Japan

Abstract: Soil microbes play an important role in the management of soil environment. They form various microbial communities in response to environmental factors, including soil texture and chemical components. Because of this, it is difficult to determine the microbial community structure of soil. In vineyard soils, the overall microbial community structure has yet to be unraveled. To understand the microbial community in vineyard soil, we surveyed comprehensively microbial communities in Japanese vineyard soils by using a culture-independent molecular approach. We identified 681 fungal clone sequences and 1076 bacterial clone sequences in soil samples collected from nine independent Japanese vineyards, and the results suggested that Ascomycota is the dominant group in the fungal community, whereas Proteobacterium and Acidobacterium are the dominant groups in the bacterial community. DNA was directly extracted from the soil samples, and the fungal internal transcribed spacer 1 (ITS 1) region or the bacterial 16S ribosomal DNA (rDNA) region was amplified by polymerase chain reaction. The recovered fungal clones were sorted into 225 operational taxonomic units and the majority of the clone sequences were assigned to Ascomycota. Meanwhile, the recovered bacterial clones were sorted into 17 phyla, and the abundant phyla were Proteobacterium and Acidobacterium. These results differed from the reported fungal and bacterial community structures in forest and agricultural soils. Moreover, we preliminarily generated a catalog of Japanese vineyard soils. The microbial community structures in the vineyard soils were extremely complex, suggesting that the microbial community structure in each vineyard soil has individual characteristics. Our study comprehensively showed for the first time fungal and bacterial community structures in Japanese vineyard soils, and is most likely to provide a clue to understand the nature of Japanese vineyard soils.

Keywords: Japanese vineyard, soil microbe, microbial community structure, 16S rDNA