Network relationships of bacteria in a stable mixed culture

We investigated the network relationships of bacteria in a structurally stable mixed culture degrading cellulose. The mixed culture consists of four bacterial strains (a cellulose-degrading anaerobe [strain S], a saccharide-utilizing anaerobe [strain F], a peptide- and acetate-utilizing aerobe [strain 3] and a peptide-, glucose-, and ethanol-utilizing aerobe [strain 5]). Interspecies interactions were examined by analyzing the effects of culture filtrates on the growth of the other strains and by comprehensively analyzing population dynamics in the mixed-culture systems with all possible combinations of the four bacterial strains. The persistence of strain S depends on the effects of strain 5. However, strain 5 is a disadvantaged strain because strain 3 has bacteriocidal activity on strain 5. The extinction of strain 5 is indirectly prevented by strain F that suppresses the growth of strain 3. Although strain F directly has suppressive effects on the growth of strain S, strain F is essential for the persistence of strain S, considering the indirect effects (maintaining strain 5, which is essential for the survival of strain S, by inhibiting strain 3). These indirect relationships form a bacterial network in which all the relationships including suppressive effects were well balanced to maintain the structural stability. In addition to direct metabolite interactions, such kind of indirect relationships could have a great impact on microbial community structure in the natural environment.

Development of an enrichment culture growing at low temperature used for ensiling rice straw

To speed up the conversion of rice straw into feeds in a low-temperature region, a start culture used for ensiling rice straw at low temperature was selected by continuous enrichment cultivation. During the selection, the microbial source for enrichment was rice straw and soil from two places in Northeast China. Lab-scale rice straw fermentation at 10 degrees C verified, compared with the commercial inocculant, that the selected start culture lowered the pH of the fermented rice straw more rapidly and produced more lactic acid. The results from denatured gradient gel eletrophoresis showed that the selected start culture could colonize into the rice straw fermentation system. To analyze the composition of the culture, a 16S clone library was constructed. Sequencing results showed that the culture mainly consisted of two bacterial species. One (A) belonged to Lactobacillus and another (B) belonged to Leuconostoc. To make clear the roles of composition microbes in the fermented system, quantitative PCR was used. For species A, the DNA mass increased continuously until sixteen days of the fermentation, which occupied 65%. For species B, the DNA mass amounted to 5.5% at six days of the fermentation, which was the maximum relative value during the fermentation. To the authors' best knowledge, this is the first report on ensiling rice straw with a selected starter at low temperature and investigation of the fermented characteristics.

Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste

An anaerobic packed-bed reactor using carbon fiber textiles (CFT) as the supporting material was continuously operated using an artificial garbage slurry. 16S rRNA gene analysis showed that many bacteria in the biomass adhering to CFT were closely related to those observed from other anaerobic environments, although a wide variety of unidentified bacteria were also found. Dot blot hybridization results clarified that 16S rRNA levels of methanogens in the adhering biomass were higher than those in the effluent. Based on microscopic observation, the adhering biomass consisted of microorganisms, organic material, and void areas. Bacteria and Archaea detected by fluorescence in situ hybridization were distributed from the surface to the inner regions of the adhering biomass. Methanosarcina sp. tended to be more abundant in the inner part of the adhering biomass than at the surface. This is the first report to elucidate the structure of the microbial community on CFT in a packed-bed reactor.

Activation of mammalian target of rapamycin in postmenopausal ovarian endometriosis

The purpose of this study was to determine whether Akt and mammalian target of rapamycin (mTOR), downstream targets of phosphatidylinositol 3-kinase, are activated in endometriosis and ovarian cancer specimens. We measured total and phosphorylated levels of Akt and mTOR from 17 frozen ovarian cancers and 15 benign endometriosis specimens (nine from premenopausal women and six from postmenopausal women) by quantitation of signals from western blots using antibodies against these proteins. Elevated phospho-Akt was detected in ovarian cancer versus endometriosis specimens from premenopausal women and endometriosis specimens from postmenopausal women (2.3 +/- 0.45 versus 0.10 +/- 0.06 and 0.17 +/- 0.11; P < 0.05) when the western blot signal of activated kinase was normalized to total kinase levels. Elevated phospho-mTOR was detected in ovarian cancer and postmenopausal endometriosis versus premenopausal endometriosis (0.52 +/- 0.19 and 0.46 +/- 0.29 versus 0.13 +/- 0.08; P < 0.05). Expression of total kinases (normalized to beta-actin) was higher in carcinoma versus endometriosis specimens. Elevation of the active mTOR was specifically detected in postmenopausal endometriosis.

Archaeal population on supporting material in methanogenic packed-bed reactor

The population of methanogenic archaea in a packed-bed reactor was determined. A difference between populations on the supporting material and in effluent was observed at operation under a high organic loading rate and a short hydraulic retention time. This difference was characterized by the predominance of Methanosarcina sp. on the supporting material.

Changes in bacterial community during fermentative hydrogen and acid production from organic waste by thermophilic anaerobic microflora

AIMS

Changes in fermentation pattern during the treatment of organic wastes containing solid materials by thermophilic anaerobic microflora were investigated with respect to product formation and bacterial community structure during hydrogen production.

METHODS AND RESULTS

Anaerobic microflora enriched from sludge compost was cultivated using artificial garbage slurry in a continuous flow-stirred tank reactor. Product formation varied depending on pH and hydraulic retention time (HRT) applied. Community analysis by terminal restriction fragment length polymorphism and clone library analysis of polymerase chain reaction-amplified bacterial 16S rDNA indicated that difference in the fermentative product distribution could be caused by different populations of micro-organisms in the microflora.

CONCLUSION

Hydrogen fermentation with acetate/butyrate formation was optimized at <1.0 d HRT at pH 5.0 and 6.0. Thermoanaerobacterium thermosaccharolyticum was the dominant hydrogen-producing micro-organism. Conversely, unidentified organisms became dominant after 4.0 d HRT at pH 7.0 and 8.0, where relatively high-solubilization efficiency of solid materials was observed with no production of hydrogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report describing product formation in the fermentation of solid organic wastes by a mixed population of micro-organisms. Various fermentation patterns including hydrogen fermentation were characterized and evaluated from engineering and microbial aspects.

Microbial community in methanogenic packed-bed reactor successfully operating at short hydraulic retention time

The microbial community in a thermophilic anaerobic packed-bed reactor, which had been successfully operated to convert acetic and butyric acids to methane at a short hydraulic retention time (from 24 h to 1.9 h), was investigated. Archaea closely related to known methanogens were detected by 16S rRNA gene analyses of the effluents, together with diverse types of unidentified bacteria.

Direct comparison of single-strand conformation polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) to characterize a microbial community on the basis of 16S rRNA gene fragments

Characterization of microbial communities using single-strand conformation polymorphism (SSCP) was compared with that using denaturing gradient gel electrophoresis (DGGE). This comparison was based on the V3-4 region (Escherichia coli positions: 341-806) of 16S rRNA gene of bacterial or archaeal communities obtained from a methanogenic bioreactor. Significant differences in the bacterial banding profiles were observed while attempting to detect the diversity of the community and its succession during the reactor operation. The SSCP produced a number of sharp bands and differentiated the bacterial community structures to which the DGGE gave an identical pattern. On the other hand, the SSCP and DGGE provided similar succession patterns for archaeal community.

Diversity of a stable enrichment culture which is useful for silage inoculant and its succession in alfalfa silage

Alfalfa is a kind of forage that is difficult to ensile for good quality. Therefore, inoculants are always used to enhance the preservation of alfalfa silage. Through continuous restricted subcultivation, a lactic acid bacteria community (Al2) was selected from well-fermented alfalfa silage, which sharply decreased the pH level and produced a large amount of lactic acid. The adding of Al2 to alfalfa at ensiling resulted in a more rapid drop in pH and higher levels of lactic acid, and it also reduced the ammonia-nitrogen content significantly (P < 0.01). Plate isolation, denaturing gradient gel electrophoresis (DGGE) and the construction of a 16S rRNA gene clone library were used to identify the composition diversity of the Al2 community; seven strains were detected in the community, the predominant strain belonging to Lactobacillus plantarum. Samples of alfalfa silages of duration 0, 2, 5, 10, 20 and 30 days were studied with DGGE analysis. The DGGE band patterns of Al2-treated and non inoculated were rather different, and the components of Al2 were the dominant bacteria in Al2-treated silages, especially L. plantarum, while Pediococcus pentosaceaus was predominant in naturally fermented alfalfa silage.

Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.

Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester

In this study, the microbial community succession in a thermophilic methanogenic bioreactor under deteriorative and stable conditions that were induced by acidification and neutralization, respectively, was investigated using PCR-mediated single-strand conformation polymorphism (SSCP) based on the 16S rRNA gene, quantitative PCR, and fluorescence in situ hybridization (FISH). The SSCP analysis indicated that the archaeal community structure was closely correlated with the volatile fatty acid (VFA) concentration, while the bacterial population was impacted by pH. The archaeal community consisted mainly of two species of hydrogenotrophic methanogen (i.e., a Methanoculleus sp. and a Methanothermobacter sp.) and one species of aceticlastic methanogen (i.e., a Methanosarcina sp.). The quantitative PCR of the 16S rRNA gene from each methanogen revealed that the Methanoculleus sp. predominated among the methanogens during operation under stable conditions in the absence of VFAs. Accumulation of VFAs induced a dynamic transition of hydrogenotrophic methanogens, and in particular, a drastic change (i.e., an approximately 10,000-fold increase) in the amount of the 16S rRNA gene from the Methanothermobacter sp. The predominance of the one species of hydrogenotrophic methanogen was replaced by that of the other in response to the VFA concentration, suggesting that the dissolved hydrogen concentration played a decisive role in the predominance. The hydrogenotrophic methanogens existed close to bacteria in aggregates, and a transition of the associated bacteria was also observed by FISH analyses. The degradation of acetate accumulated during operation under deteriorative conditions was concomitant with the selective proliferation of the Methanosarcina sp., indicating effective acetate degradation by the aceticlastic methanogen. The simple methanogenic population in the thermophilic anaerobic digester significantly responded to the environmental conditions, especially to the concentration of VFAs.

Characteristics of sediments in a newly constructed reservoir in Japan

The sediment formation mechanisms of a newly constructed reservoir in Ehime, Japan were evaluated by characterizing the soil particles (SP) and particulate phosphorus (PP) in the runoff and reservoir sediments. The SP and PP loads from the runoffs of the main river in the watershed considerably increased, when the specific discharge rates were over 300 l/s/km2 (high flow conditions). When the specific discharge rates exceeded over 300 l/s/km2, 19% of the watershed generated over 80% of the SP and PP loads. When the specific discharge rates were under 300 l/s/km2 (low flow conditions), the contributions of the previously mentioned 19% area to the SP and PP loads were smaller. Significant amounts of smectite were found in the sediments in the reservoir and in the soil samples obtained at the forest exposed area in this 19% area while it was negligible in citrus orchards and paddy fields that constituted the remaining land surfaces. The forest area exposed by recent landslides was significant for the SP and PP in the reservoir. Judging from the outcomes, land use information alone may not be sufficient to detect critical sources of SP and PP in the runoffs and reservoirs. To identify and confirm crucial areas for the SP and PP in the runoffs, the investigations should be conducted under high flow conditions and the composition of clay minerals in the sediments should be checked against the clay mineral distributions of soils in the watershed.

Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria

A stable cellulose-degrading microflora enriched from composting materials has been analyzed in our laboratory. Cellulose-degrading efficiency of an anaerobic cellulolytic isolate, Clostridium straminisolvens CSK1, was remarkably lower than that of the original microflora. We successfully constructed bacterial communities with effective cellulose degradation by mixing C. straminisolvens CSK1 with aerobic non-cellulolytic bacteria isolated from the original microflora. Comparison of the cellulose degradation processes of the pure culture of C. straminisolvens CSK1 and the mixed-culture indicated that non-cellulolytic bacteria essentially contribute to cellulose degradation by supplying anaerobic environment, consuming metabolites, which otherwise deteriorate the cellulolytic activity, and by neutralizing pH.

Stable coexistence of five bacterial strains as a cellulose-degrading community

A cellulose-degrading defined mixed culture (designated SF356) consisting of five bacterial strains (Clostridium straminisolvens CSK1, Clostridium sp. strain FG4, Pseudoxanthomonas sp. strain M1-3, Brevibacillus sp. strain M1-5, and Bordetella sp. strain M1-6) exhibited both functional and structural stability; namely, no change in cellulose-degrading efficiency was observed, and all members stably coexisted through 20 subcultures. In order to investigate the mechanisms responsible for the observed stability, "knockout communities" in which one of the members was eliminated from SF356 were constructed. The dynamics of the community structure and the cellulose degradation profiles of these mixed cultures were determined in order to evaluate the roles played by each eliminated member in situ and its impact on the other members of the community. Integration of each result gave the following estimates of the bacterial relationships. Synergistic relationships between an anaerobic cellulolytic bacterium (C. straminisolvens CSK1) and two strains of aerobic bacteria (Pseudoxanthomonas sp. strain M1-3 and Brevibacillus sp. strain M1-5) were observed; the aerobes introduced anaerobic conditions, and C. straminisolvens CSK1 supplied metabolites (acetate and glucose). In addition, there were negative relationships, such as the inhibition of cellulose degradation by producing excess amounts of acetic acid by Clostridium sp. strain FG4, and growth suppression of Bordetella sp. strain M1-6 by Brevibacillus sp. strain M1-5. The balance of the various types of relationships (both positive and negative) is thus considered to be essential for the stable coexistence of the members of this mixed culture.

Isolation and characterization of predominant microorganisms during decomposition of waste materials in a field-scale composter

A self-heating field-scale composter treating agro-industrial wastes within a period of 30 d was analyzed by denaturing gradient gel electrophoresis (DGGE) (Pedro et al., J. Biosci. Bioeng., 91, 159-165, 2001). Three major bands were derived from Propionibacterium acnes, Methylobacterium mesophilicum or M. radiotolerans, and Bacillus thermocloacae. Strains MSP09A and MSP06G with close affiliation to P. acnes and B. thermocloacae, respectively, were successfully isolated. Based on quantitative-PCR results, the relative population of MSP09A increased towards the end of the composting process (mesophilic stage) while MSP06G seemed to predominate during the middle period (thermophilic stage). These results correlated highly with their growth temperatures. MSP09A and MSP06G had different metabolic profiles which were largely affected by culture conditions. MSP09A was able to utilize large complex molecules of lipids and proteins. An interspecies relationship in terms of metabolites such as propionic acid was expected between the two microorganisms.

Characterization of a microorganism isolated from the effluent of hydrogen fermentation by microflora

The hydrogen production yield from glucose by an isolate was investigated and compared to that by microflora. The isolate, Thermoanaerobacterium thermosaccharolyticum KU001, from the microflora demonstrated approximately 2.4 mol/mol-glucose of hydrogen production with acetate/butyrate formation in an artificial medium. The fermentation pattern was similar to that observed for the hydrogen fermentation of wastewater by the microflora. A PCR-DGGE analysis of the bacterial 16S rDNA detected T. thermosaccharolyticum in the microflora with strong intensity of the characteristic 16S rDNA band, although the microflora was enriched from an artificial medium. These results imply that T. thermosaccharolyticum could be a predominant species of the microflora that is involved in hydrogen-producing acetate/butyrate fermentation. The nitrogen source in the medium affected the carbohydrate metabolism of KU001, and caused a change in hydrogen yield.

Analyses of microbial community within a composter operated using household garbage with special reference to the addition of soybean oil

A commercially available composter was operated using fixed composition of garbage with or without the addition of soybean oil. The composter was operated without adding seed microorganisms or bulking materials. Microflora within the composter were analyzed by denaturing gradient gel electrophoresis (DGGE) in the case of oil addition, or by 16/18 S rRNA gene sequencing of the isolated microorganisms in the case of no oil addition. The results showed that, irrespective of the addition of oil, the bacteria identified were all gram positive, and that lactobacilli seemed to be the key microorganisms. Based on the results, suitable microflora for use in a household composter are discussed.

Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter

The diversity of microbial community during the decomposition of waste in a field-scale composter (Hazaka system) was investigated by denaturing gradient gel electrophoresis (DGGE). The composter operates at a high temperature through a self-heating system, creating a thermophilic (60-76 degrees C) stage during the initial phase and a mesophilic (45 degrees C) stage towards the later phase of the composting period. The pH of the system (pH 7.75-8.10) did not vary significantly during the process while moisture content was reduced from 48.8% to 25.1%. DGGE and 16S rDNA analyses showed that the following genera were found throughout the process: Propionibacterium sp., Methylobacterium sp., Pseudomonas sp., and Bradyrhizobium sp. Different Bacillus spp. thrive at the thermophilic or the mesophilic stage while Clostridium sp. was only found at the initial phase of the process. Staphylococcus sp. and Caulobacter sp. or Brevundimonas sp. existed during the later phase of the composting period.

Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community

A novel anaerobic, thermophilic and cellulolytic bacterium (strain CSK1(T)) was isolated from a cellulose-degrading bacterial community. On the basis of 16S rRNA gene sequence similarity, strain CSK1(T) was mapped to cluster III of the genus Clostridium. Strain CSK1(T) is closely related to Clostridium thermocellum (96.2 %) and Clostridium aldrichii (95.1 %). Strain CSK1(T) is a non-motile, spore-forming, straight or slightly curved rod. The optimum temperature and initial pH for its growth and cellulose degradation are 50-55 degrees C and pH 7.5. Strain CSK1(T) grew under a gas phase containing up to 4 % O(2). Phylogenetic and phenotypic analyses support the differentiation of strain CSK1(T) from its closest relatives. Strain CSK1(T) therefore represents a novel species, for which the name Clostridium straminisolvens sp. nov. is proposed, with CSK1(T) (=DSM 16021(T)=IAM 15070(T)) as the type strain.

Microbial diversity in biodegradation and reutilization processes of garbage

With particular focus on the microbial diversity in garbage treatment, the current status of garbage treatment in Japan and microbial ecological studies on various bioprocesses for garbage treatment are described in detail. The future direction of research in this field is also discussed.

Enzyme production-based approach for determining the functions of microorganisms within a community

The functions of specific microorganisms in a microbial community were investigated during the composting process. Cerasibacillus quisquiliarum strain BLx(T) and Bacillus thermoamylovorans strain BTa were isolated and characterized in our previous studies based on their dominance in the composting system. Strain BLx(T) degrades gelatin, while strain BTa degrades starch. We hypothesized that these strains play roles in gelatinase and amylase production, respectively. The relationship between changes in the abundance ratios of each strain and those of each enzyme activity during the composting process was examined to address this hypothesis. The increase in gelatinase activity in the compost followed a dramatic increase in the abundance ratio of strain BLx(T). Zymograph analysis demonstrated that the pattern of active gelatinase bands from strain BLx(T) was similar to that from the compost. Gelatinases from both BLx(T) and compost were partially purified and compared. Homologous N-terminal amino acid sequences were found in one of the gelatinases from strain BLx(T) and that of compost. These results indicate strain BLx(T) produces gelatinases during the composting process. Meanwhile, the increase in the abundance ratio of strain BTa was not concurrent with that of amylase activity in the compost. Moreover, the amylase activity pattern of strain BTa on the zymogram was different from that of the compost sample. These results imply that strain BTa may not produce amylases during the composting process. To our knowledge, this is the first report demonstrating that the function of a specific microorganism is directly linked to a function in the community, as determined by culture-independent and enzyme-level approaches.