Abstract: Modern microbiology has been developed based upon cultivation of organisms in pure culture. Cultivation of organisms on solidified media brought about a revolution in microbiology in 1890’s but it did not take long to find a clear limitation of this strategy, which is often referred to as “great plate count anomaly”, a disparity between total cell counts and culturable cells counts on plates in environmental samples. Recent massive DNA sequencing technology allows to construct genomes of yet-to-be cultured organisms in silico, thus microbiologists can circumvent time-consuming and laborious isolation works. Nonetheless, what genome sequencing tells us is always speculative, and it never shows us the entity and the way of living in a vital way without having pure culture and cultivation-dependent studies. Here I overview the limitation of culturing organisms and issues behind it. I am also emphasizing that gelling agents and the way of medium preparation are crucial factors affecting the culturability of microorganisms.
The application of slaked lime is expected to increase soil pH. In this study, we examined the effect of slaked lime on clubroot of broccoli and its influence on the plant growth. We also investigated the chemical properties of the soil and micronutrient contents in the plant. Application of 400–500 kg/10 a to gray lowland soil, which is the major soil type in the Kagawa Prefecture, resulted in maintaining a stable yield of broccoli, and in suppressing clubroot development without showing micronutrient deficiencies. We found that the slaked lime application by combining Amisulbrom wettable powder treatment in nursery boxes was practically effective on controlling the disease in the severely infested field. However, micronutrient contents in broccoli tended to decrease due to the increase of insoluble forms of micronutrients, suggesting that micronutrient deficiencies may occur after applying slaked lime in fields.
The proteolytic bacterial communities were investigated with a clone library analysis that targeted the neutral metalloprotease gene (npr). Soil samples were collected from the vegetable fields with different cultivation methods in Tsukuba city, Ibaraki, Japan. The deduced Npr protein sequences from the retrieved npr that indicated 100% similarities to those of B. megaterium and B. butanolivorans were detected in all soil samples, and thus these two genera of Bacillus appeared to exist widely in the fields investigated in this study. On the other hand, the deduced Npr protein sequences that closely related to those of the uncultured bacteria were also detected, suggesting co-existence of unknown proteolytic bacteria. Both the proteolytic bacterial community structure and soil chemical properties tended to differ among the farmers rather than the cultivation methods or sampling seasons according to the principal component analysis. However, none of the soil chemical properties evaluated in this study were strongly related to the proteolytic bacterial community structure in the canonical corresponding analysis.
Since 1970s, there has been a series of studies focusing on suppression of soilborne pests under reductive conditions. Anaerobic soil disinfestation (ASD) was developed in 1999 from such studies. In these years, ASD has been used in a wide range of production systems, especially in USA and Japan, though these two countries have different kinds of needs or demands. Recent findings have suggested that ASD has advantages in both crop yield and maintenance of soil
health (in terms of soil suppressiveness), in comparison with soil fumigation. Future works need to improve the efficacy
of the technique under relatively low temperature conditions and to expand its applicability to soilless potting mixes.
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