Repeated fed-batch composting (FBC) processes, which are modifications of traditional composting technology, have in recent years attracted attention not only in their biotechnological aspects but also from ecological viewpoints. FBC processes differ from the conventional batch system in that the biodegradation of solid organic waste proceeds without definitive thermal stages including the thermophilic phase under self-heating conditions. Mesophilic FBC processes for treating household biowaste are also characterized by low moisture contents, alkaline pH and the presence of high population densities of microorganisms under steady state conditions. Kinetic and microbiological studies of the FBC process have increasingly been conducted using commercially available composters as well as laboratory-and bench-scale reactors. Information from recent studies on FBC processes has provided new insight into our understanding of compost microbiology. This article reviews current knowledge of the FBC process with a special emphasis on microbial diversity, succession and activity in garbage composters. The potential application of FBC technology for bioremediation purpose is also discussed.

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Bacterial flora of a biofilm formed on the submerged stems of reeds (Phragmites australis) was studied in comparison with the flora in the water surrounding the reeds and on the aerial stems of the reeds. Most of the isolates from the above three samples were Gram-negative (90%) and rod-shaped (87%) with a distinct difference in glucose metabolism: largely oxidative (aerial stem surface), less oxidative (biofilm) and not at all (water). Most of the isolates (90%) belonged to the α, β, and γ-Proteobacteria, with Sphingomonadaceae a common group. Isolates from the aerial stem were phylogenetically different from those of the biofilm and water. The biofilm and water samples consisted of a phylogenetically common and a different group. The biofilm was characterized by 1) a seasonal change in thickness with a maximum in spring and a minimum in winter, 2) the existence of plastic-degrading strains phylogenetically close to Roseateles depolymerans, and 3) strong denitrifying activity even under aerobic conditions in a thicker biofilm formed in spring.

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A laboratory-scale solid-phase denitrification process for nitrogen removal was constructed by acclimating sewage activated sludge with poly(ε-caprolactone) (PCL) as the sole substrate under denitrifying conditions. The sludge thus acclimated exhibited a nitrogen removal rate of 6-7 mg NO₃-N g^-1 h^-1 with PCL as the sole source of reducing power. The microbial community and the distribution of denitrifying bacteria in this process were studied by rRNA-targeted fluorescence in situ hybridization, quinone profiling and standard cultivation methods. The culture-independent molecular and biomarker approaches demonstrated that members of the class Alphaproteobacteria predominated and those of Betaproteobacteria were the second most abundant group of bacteria in the process. The plate counts of denitrifying bacteria with a non-selective agar medium accounted for 6% of the total count and 10% of the direct viable count on average. The most probable number (MPN) obtained with PCL-containing medium under denitrifying conditions was one order of magnitude lower than the plate count. Most of the denitrifying isolates from the MPN enrichment tubes and 10% of the predominant denitrifying bacteria isolated by the plate-counting method were capable of degrading PCL. 16S rRNA gene sequence comparisons showed that the greater majority of the predominant denitrifiers were members of the genera Comamonas, Diaphorobacter and Paracoccus. All of the PCL-degrading denitrifying strains isolated were assigned to a previously unknown species of the genus Comamonas. The results of this study suggest that, apart from their PCL-degrading capacity, members of Alphaproteobacteria and Betaproteobacteria are mainly responsible for nitrogen removal in the PCL-acclimated denitrification process.

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Nine fungi belonging to the Phoma sp. and one non-sporulating fungus from zoysiagrass rhizospheres were tested for their ability to promote the growth of cucumber plants (cv. Aodai kyuri, Jibai, Ochiai fushinari, and Shogoin fushinari) at 4 weeks after planting in a growth chamber. The fungal isolates were introduced individually into natural soil in barley kernels (2%, w/w). The result indicated that plant dry biomass rather than plant length was increased by all the fungal isolates and the increase was cultivar-specific. Isolates GS8-1, GS8-2 and GS8-3 which had a consistent growth-promoting effect on both the height and dry biomass of all cultivars and GU21-2, which had less of an effect on growth and yield, were further tested for their ability to promote growth of a popular cv. Jibai until 10 weeks in the greenhouse and field. All isolates significantly increased plant length and plant dry biomass at 6 and 10 weeks after planting, and the number of leaves and cucumbers produced at 10 weeks in the greenhouse. In the field, these isolates were also effective in promoting growth and increasing yield at 6 and 10 weeks. The number and fresh biomass of marketable cucumbers produced at 6 weeks was significantly high in comparison to that of untreated controls. At 10 weeks after planting, the number of marketable cucumbers was significantly increased by isolates GS8-3 and GU21-2, while the fresh biomass of marketable cucumbers was significantly increased by all four isolates. GS8-1, GS8-2 and GS8-3 were isolated from roots of cucumber (cv. Jibai) even at 10 weeks after planting in both the greenhouse and field experiments. GU21-2 was not isolated from cucumber roots. It is suggested that the increased absorption of mineral nutrient by plants following the colonization and degradation of barley kernels by fungal isolates and the association of fungal isolates with roots might lead to enhanced plant growth and increased yield.

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Environmental factors and rates of terminal electron-accepting (TEA) activities, such as methane production, sulfate reduction, and metal reduction, in estuarine sediment at the mouth of the Orikasa river (Yamada-cho, Iwate, Japan) were investigated over a period of two years. TEA processes in the surface sediment (~16 cm) were more active in summer (approx. 25°C) than winter (approx. 5°C). Comparisons of TEA rates also indicated that sulfate reduction served as the dominant TEA process in summer, while methane production was the most active in winter. The contribution of metal reduction to total carbon oxidation was shown to be relatively minor. Anaerobic incubation of the sediment with various substrates indicated that trimethylamine was the best substrate for methane production whereas acetate, formate, ethanol, and H₂ served as good substrates for sulfate reduction, suggesting the presence of substrate partitioning. To identify methanogens likely responsible for methane production in the estuarine sediment, 16S rRNA gene clone libraries were constructed by using Euryarchaeota-specific PCR and analyzed. The libraries contained some Methanosarcinales-related clones as well as many clones which were neither affiliated with known orders nor related (<90%) to isolated organisms. These results suggest that methanogenesis is an important TEA process in estuarine sediment, particularly in winter, which may be catalyzed by yet uncultured groups of the order Methanosarcinales.

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We examined the distribution of antibiotic-resistant bacteria by analyzing 19 samples of feces of livestock, solid farmyard manure (FYM), soil from arable fields and orchards treated with FYM or not, and forest soils. Bacteria resistant to ampicillin, vancomycin, kanamycin, chloramphenicol, rifampicin, and tetracycline were enumerated by the dilution plate method at a rate of 50 mg l^-1. The total numbers of antibiotic-resistant bacteria in swine or poultry feces were the same as or up to eight orders of magnitude lower than the total numbers of culturable bacteria. The occurrence of antibiotic-resistant bacteria in the poultry feces increased with the use of antibiotics as feed additives. The occurrence of antibiotic-resistant bacteria was much lower in FYM samples than fecal samples with some exceptions. Of the soil samples, only that to which solid swine FYM at 40 t ha^-1 had been applied yearly for more than 10 years had significantly higher numbers of total and antibiotic-resistant bacteria than the upland soil that had not been treated with FYM. Resistant isolates from fecal samples showed a broad range of multi-drug resistance (MDR), but those from forest soil had a narrow-range MDR, suggesting that the use of antibiotics as feed additives influences the occurrence of broad-range MDR.

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To reveal predominant culturable Bacillus species in Japanese arable soils, aerobic spore-forming bacteria were isolated from different soils in Japan and their phylogenic positions were estimated from the 16S rDNA sequences. Bacillus species were also isolated from tomato roots grown in soils for 4 weeks to estimate the difference in phylogenic positions between soil and root isolates. The number of culturable Bacillus species ranged from 6.4 to 7.4 log cfu g^-1 soil and 4.7 to 6.7 log cfu g^-1 root in soils and tomato roots, respectively, and the proportion of Bacillus species among total culturable bacteria ranged from 3.8% to 17.9% and 0.1% to 6.7% in soils and roots, respectively. The differences in the number and percentage of culturable Bacillus species between the soils and roots were highly significant (P=0.0000 and 0.0023, respectively), indicating that Bacillus species were more predominant in soil than in root. A total of 108 isolates were characterized using the restriction fragment length polymorphism (RFLP) method and partial 16S rDNA sequences. They affiliated to 22 species including the genus Bacillus, Brevibacillus and Paenibacillus. No nitrogen fixers were isolated. The predominant species was Bacillus megaterium to which 42 isolates (39%) belonged. Some of the species, such as Bacillus luciferensis and Brevibacillus agri, were isolated only from the tomato roots and considered to be more adapted to the rhizosphere than soil. Among 108 isolates, only one strain, N2S6, belonging to Bacillus megaterium, showed consistent antagonistic activity against the bacterial wilt of tomato caused by Ralstonia solanacearum.

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The layer of mucus on the surface of bluegills (Lepomis macrochirus) captured in Lake Biwa was characterized as 1) large enough to host microbes (ca. 76 μm thick), 2) a physically different environment from the surrounding lake water in viscosity and buffering capacity, and 3) chemically rich in organic substances, which may be utilized as nutrients. Based on DAPI staining and on the number of colonies formed respectively, it was found that ca. 10³ times and 3 to 7 times the number of microbial cells were present in the mucus layer, as compared with the lake water. The bacterial flora of the mucus was greatly different from that of the lake water, according to a phylogenetic analysis. About 60% of the isolates from the mucus were Gram-positive. These Gram-positive isolates could be divided into two major groups. Each group consisted of strains sampled in one season, i.e., the strains sampled in July were closely related to the genus Staphylococcus, while the strains sampled in November were close to the genus Mycobacterium. In contrast, most isolates from the lake water were Gram-negative (72%); with all the strains closely related to β- and γ-Proteobacteria sampled in July. With the exception of one strain, the Gram-positive isolates from the lake water (6 strains) were all sampled in November. Almost all of the isolates from the mucus could metabolize glucose, whereas only half of the isolates from the lake water could do the same.

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