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Biological soil disinfestations (BSDs) were developed separately in Japan and in The Netherlands as an alternative to chemical fumigations. In Japan, it was developed based on the knowledge of irrigated paddy rice and upland crop rotation system that was rather tolerant of soil-borne disease development. The methods consist of application of easily decomposable organic matter, irrigation, and covering the soil surface with plastic film, thereby inducing anaerobic (reductive) soil conditions and suppressing many soil-borne pests including fungi, bacteria, nematodes, and weeds. The methods are widely used by organic farmers in the area where residences and agricultural fields are intermingled. To note one advantage of these methods, maintenance of soil suppressiveness to Fusarium wilt of tomato was suggested, while soil treated with chloropicrin became conducive to the disease. Suppression of soil-borne fungal pathogens by BSDs might be attributed to anaerobicity and high temperature, organic acids generated, and metal ions released into soil water. Contributions of respective factors to suppression of respective pathogens might be diverse. Presumably, these factors might vary on the fungal community structure in BSD-treated soil. These factors also work in paddy fields. Therefore, the BSDs developed in Japan are probably a method to raise the efficacy of paddy-upland rotation through intensive organic matter application and through maintenance of a strongly anaerobic (reductive) soil condition.

Biological soil disinfestation (BSD) is one of the methods for soil disinfestation recently developed and consists of organic amendment, irrigation, and covering the soil surface with plastic film. BSD trials with artificially infested soils effectively killed Fusarium oxysporum f. sp. lycopersici and Ralstonia solanacearum. F. oxysporum f. sp. lycopersici was not detected 9 days after treatment. Application of BSD to R. solanacearum-infested soil decreased disease severity 4 weeks after transplantation. Reduction in soil pH and Eh was observed in the BSD-treated soil. HPLC analysis revealed the accumulation of acetic acid and butyric acid in the soil and the disinfestation effect of BSD was almost reproduced by mixing these organic acids with the infested soil. Volatile compound(s) evolved in the BSD-treated soil was also suggested to contribute to disinfestation. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) analysis revealed the increase in the abundance of several bacteria in the BSD-treated soil, and two of them had 100% similarity with potential organic acid producers, Clostridium sp. and Enterobacter sp.

Verticillium dahliae infecting tomato can be differentiated into races 1 and 2 based on differential pathogenicity on tomato cultivars carrying resistance gene Ve1. Although no commercial cultivars resistant to race 2 are available, race 2‐resistant rootstock cultivars Aibou and Ganbarune‐Karis have been bred in Japan. Nevertheless, the resistance of these rootstocks appears to be unstable in commercial tomato fields. Pathogenicity assays conducted under controlled conditions revealed that these rootstock cultivars are resistant to some isolates of race 2; this resistance is controlled by a single dominant locus, denoted by V2, based on segregation of resistance in F2 populations from selfed rootstock cultivars. However, some other isolates of race 2 can overcome this resistance. Therefore it is proposed that the current race 2 of V. dahliae should be divided into two races, i.e. ‘race 2’ (nonpathogenic on Aibou) and ‘race 3’ (pathogenic on Aibou). The distribution of these races was surveyed in 70 commercial tomato fields in Hida, Gifu Prefecture, Japan. Race 3 was found in 45 fields, indicating that race 3 had already spread throughout the region. On the other hand, 25 fields had only race 2, and thus race 2‐resistant rootstocks would be effective for disease management in these fields. Races 2 and 3 could not be identified by genomic Southern hybridization probed with a telomere sequence, nor with previously reported race‐specific PCR assays. Elucidation of race‐determining mechanisms and development of methods for quick race identification should be made in future studies.

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