A distinct microbial community is established in a given environment as a consequence of the community evolution of individual component microorganisms. According to the "Community Theory", microorganisms proliferate not as individual species but as a community in response to changes in the environment, evolving into a biological network that is most suitable for their survival and/or further growth. During this process, individual microorganisms interact and communicate with each other by sharing their limited genetic information in order to exploit available resources. Consequently, a functional community comprising many different species is formed. Such microbial communities are comparable to multi-cellular organisms in many ways, but often too complex to be characterized. Nutrient enrichment is one approach to the study of the functions of these inextricably linked biological networks. For soil microbial communities, amendment with organic matter can be employed to apply selective environmental advantages in order to transfer microbial communities to newly evolved biological consortia with distinctive functions. Many studies have reported that the incorporation of composts or green manures rendered soils suppressive to various soilborne pathogens. Among the pathogens that are controlled effectively are Pythium, Phytophthora, and Rhizoctonia. Soil enrichment with organic matter may be the most fundamental and sustainable approach to the biological control of soilborne diseases.

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To understand the ecological role of cyanophage and its effect on nutrients cycling in the coastal marine environment, it is critical to understand cyanophage infectivity and the interactions that occur between the phage and its host, marine cyanobacterial picoplankton (Synechococcus sp.). We previously isolated a new virulent cyanophage (strain S-KM1), and here have investigated its seasonal infectivity of cyanophage, phycoerythrin-rich Synechococcus sp. (strain KFM001) in Kagoshima Bay. We found that the phage titers ranged from undetectable to 7.5×10³/ml in autumn, and began to increase about one week after the onset of the Synechococcus autumn bloom. During the autumn months, the phage numbers oscillated in a fashion that mirrored levels of host abundance, showing a lag of about one week. We calculated that from 0.0055% to 2.1% of the host population per day was lysed by the phage during a Synechococcus bloom in autumn. This suggests that lytic phages have a noticeable effect on regulating the densities of marine Synechococcus populations.

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When module 1 of the microcystin synthetase gene was isolated from two strains, Microcystis aeruginosa NIES298 and M. viridis NIES102 with different types of module 3, the sequence identity was very high. Twenty toxic strains and 18 non-toxic strains of Microcystis were subjected to PCR amplification with primers (M1F3-M1R3) designed from completely conserved regions of module 1. The specific PCR products were amplified from toxic strains and no amplified products were observed in the non-toxic strains. Prior to the development of the competitive PCR, template DNA was isolated from the Microcystis cultures using four isolation methods focused on removing polysaccharide. The potassium xanthogenate-sodium dodecyl sulfate procedure gave a high extraction yield and purity and was used for the preparation of template for competitive PCR. By competitive PCR with M1F3-M1R3, cultured cells of toxic Microcystis were quantitatively detected at 10³−10⁵ cells/mL. In environmental water samples from Lake Mikata and Lake Suigetsu, plots of the toxin concentration versus density of toxic cells measured by the competitive PCR showed a positive correlation (r²=0.98), which suggested that competitive PCR with M1F3-M1R3 is useful for the quantitative detection of toxic Microcystis cells in complex environmental samples.

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The distribution of antibiotic-resistant bacteria in Lake Biwa sediment with depth from a relatively shallow (0−1 cm) to a relatively deep (9−10 cm) layer was investigated. More colonies formed on 100-fold diluted nutrient broth (DNB) agar medium than nutrient broth (NB) medium. The colony number and its difference between the two media decreased with depth. The resistance to antibiotics, ampicillin, chloramphenicol, erythromycin, rifampicin, streptomycin, sulfamethoxazole and tetracycline, was examined. The ratio of antibiotic-resistant strains increased with the depth of sediment. The isolates obtained from the deepest layer using antibiotic-free DNB medium included significantly more strains which were resistant to higher concentrations and many more kinds of antibiotics. In contrast, the isolates from the antibiotic-containing medium showed no such features. According to the 16S rDNA sequence, the isolates from the shallowest layer belonged to the Actinobacteria phylum and the Alpha-, Beta- and Gamma-proteobacteria. The isolates from the deepest layer, however, belonged to the Firmicutes phylum and the Alphaproteobacteria with some exceptions. Many of the multi-resistant isolates were similar to the genus Ralstonia, Afipia, or Bacillus cereus, known for the biodegradation of xenobiotics or pathogenicities mediated via plasmids.

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Microbial contamination of groundwater by bacteria as a result of human activities has gained considerable attention because of public health concerns. The objective of this study was to examine the vertical transport and accumulation of bacteria during infiltration of water into an Andosol derived from volcanic ash with variable surface charge as well as a high organic matter content, which may enhance the adsorption of bacteria by soil particles. First, 70−720 ml of Burkholderia cepacia suspension containing 10⁷ cells ml⁻¹ was supplied to the upper surface of repacked soil columns (Kannondai Andosol and Sawara Gray Lowland soil for comparison), 5.0 cm in diameter and 17.5 to 100 cm long, at a negative pressure head of −5 cm using a disk permeameter. After terminating the infiltration, the columns were rapidly sectioned and profiles of the number of B. cepacia were determined using a selective medium containing tetracycline (10 mg l⁻¹), ampicillin (100 mg l⁻¹) and cycloheximide (300 mg l⁻¹). The distance traveled by B. cepacia in the Kannondai Andosol was found to be smaller than that of water derived from the infiltrated suspension, with B. cepacia heavily accumulated at a 0−5 cm depth of the soil in all columns. In contrast, B. cepacia moved deeper in the Sawara soil, and the travel distance increased with the volume of the suspension infiltrated. The observed difference in the bacterial transport could be due to the differences in the surface electrical properties and organic matter content, or alternatively, the pore size distribution of the two soils.

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The mechanism of dominance by Microcystis spp. (Cyanophyceae) was examined with special reference to the concentration of dissolved inorganic carbon (DIC), in in situ experiments using lake water. Lake water collected from mesotrophic Lake Biwa was enriched with nitrogen and phosphorus nutrients prior to the experiments, and use of a NaHCO₃-Na₂CO₃ buffer was successful in allowing a change of DIC concentrations for phytoplankton without lowering the pH. The experiments consisted of a control (no DIC addition) and a treatment. There were no significant differences in levels or patterns of change in pH values, nutrient (nitrogen and phosphorus) or chlorophyll concentrations between the two systems. Microcystis became dominant in the control system, while Scenedesmus sp. dominated in the DIC system. This suggested that the low DIC concentration in surrounding water favored dominance by Microcystis although this cyanobacterium needed some other carbon sources in order to proliferate. The buoyancy regulation of Microcystis may be the strategy by which it floats up to the surface layer, where there is abundant CO₂, and dominates when the DIC concentration in the water column is low.

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Toxic effects of dichloromethane and trichloroethylene on the growth of three planktonic green algae, Chlorella vulgaris NIES227, Selenastrum capricornutum NIES35, and Volvulina steinii NIES545, were examined. The two organic solvents at concentrations of up to a hundred-fold the Japanese national effluent standards did not affect the growth of the former two algae, but at just a tenth of the concentration of the standards were fatal to the latter. Even water with a relatively low concentration of pollutants, which meets the effluent standards for human health, is not necessarily harmless to the natural ecosystem.

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