Denaturing Gradient Gel Electrophoresis Analyses of Microbial Community from Field-Scale Composter.

Pedro, Mannix S.; Haruta, Shin; Hazaka, Masaru; Shimada, Rumiko; Yoshida, Chie; HIURA, KOICHIRO; Ishii, Masaharu; Igarashi, Yasuo

doi:10.1263/jbb.91.159

Cited by 61 publications

(46 citation statements)

References 16 publications

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“…A consortium adapts well to environmental variation via a change in the predominant species 18,19,26) . If a particular species decreases during stressful conditions, its numbers are restored under optimum conditions.…”

Section: Discussionmentioning

confidence: 99%

Change in the Predominant Bacteria in a Microbial Consortium Cultured on Media Containing Aromatic and Saturated Hydrocarbons as the Sole Carbon Source

2007

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A No.22 consortium was isolated from contaminated soils at oilfields by repeated transfer on a mineral salts medium with the aromatic hydrocarbon fraction from crude petroleum. The consortium was able to degrade aromatic hydrocarbons at high rates. Fourteen major DNA bands were detected in the consortium by PCR-DGGE. Three strains were capable of forming colonies on agarose plates containing mineral salts and aromatic hydrocarbons, and identified as Pandoraea sp. Y1, Hyphomicrobium facile Y3, and Burkholderia multivorans Y4 by 16S rRNA gene sequencing. The consortia of three cultures; an aromatic subculture, a saturated culture transferred from the subculture, and an aromatic obtained culture from the transferred culture, were compared using PCR-DGGE, a clone library, and quantitative real-time PCR. Burkholderia species containing strain Y4 became the dominant species in the saturated culture whereas its abundance decreased in the aromatic culture. Pandoraea sp. Y1, which was of low abundance in the saturated culture, and an unisolated bacterium, Brachymonas sp. F, in contrast, increased in the aromatic culture. The aromatic hydrocarbons were degraded by Pandoraea sp. Y1 and B. multivorans Y4, whereas the saturates were only degraded by B. multivorans Y4. The results indicate that the No.22 consortium adapts well to different carbon sources through a change in its predominant species. This study provides some basic information regarding bioremediation using the consortium.

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Section: Discussionmentioning

confidence: 99%

Change in the Predominant Bacteria in a Microbial Consortium Cultured on Media Containing Aromatic and Saturated Hydrocarbons as the Sole Carbon Source

2007

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“…Amplification was done in a standard reaction mixture containing 25 mM Tris (hydroxymethyl) methyl aminopropane sulfonic acid (pH 9.3), 50 mM KCl, 2.0 mM MgCl 2 , 0.2 mM dNTP, 2.5 U of Taq polymerase, 1.0 mM each primer, and the DNA template. The PCR was run with an initial denaturation at 95°C for 10 min, and 30 cycles of denaturation at 93°C for 30 s, annealing at 65°C (first 10 cycles), 60°C (second 10 cycles), or 55°C (last 10 cycles) for 30 s, and extension at 72°C for 1 min, with a final extension at 72°C for 5 min (Pedro et al, 2001). The reaction was conducted in a PCR thermal cycler (Dice, Takara Bio Inc., Shiga, Japan).…”

Section: Dggementioning

confidence: 99%

Ensiling of Soybean Curd Residue and Wet Brewers Grains With or Without Other Feeds as a Total Mixed Ration

Wang

Nishino

2008

Journal of Dairy Science

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Wet brewers grains and soybean curd residue were stored in laboratory-scale silos without (BG and SC silages, respectively) or with other ingredients as total mixed rations (BGT and SCT silages, respectively). Silages were opened after 14 and 56 d, and microbial counts, fermentation products, and aerobic stability were determined. Denaturing gradient gel electrophoresis was carried out to examine bacterial communities, and several bacteria that appeared to be involved in fermentation were identified. Lactic acid content was greater in SCT than in BGT silage, but lower in SC than in BG silage. Ethanol content was greater in BG than in SC regardless of silage type. Aerobic deterioration occurred promptly in ensiling materials (nonensiled by-products and total mixed ration mixtures) and in silages stored alone; however, SCT and BGT silages resisted deterioration and no heating was found for more than 5.5 d regardless of storage period. Silages were stable even with high yeast populations at silo opening, whereas prolonged ensiling decreased yeast counts in the 2 total mixed ration silages. The denaturing gradient gel electrophoresis profiles appeared similar between SCT and BGT silages but not between SC and BG silages. Weissella spp. and Lactobacillus brevis were common in aerobically stable SCT and BGT silages, and Lactobacillus buchneri was detected only in BGT silage. Both L. brevis and L. buchneri were found in silage but not in ensiling materials. Several other lactic acid bacteria were also identified in SCT and BGT silages, but did not appear to be related to fermentation and aerobic stability.

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“…The community structure was investigated with both PCR-based and cultivation-isolation-based techniques (8,31,32). The succession of the microbial community was observed with PCR-based techniques (12,17,30,31,32). Using other biomarkers, including phospholipid fatty acids and lipoquinones, succession of the microbial community was examined (13,15).…”

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confidence: 99%

Enzyme Production-Based Approach for Determining the Functions of Microorganisms within a Community

Nakamura

Haruta

Nguyen

et al. 2004

Appl Environ Microbiol

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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.

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Denaturing Gradient Gel Electrophoresis Analyses of Microbial Community from Field-Scale Composter.

Cited by 61 publications

References 16 publications

Change in the Predominant Bacteria in a Microbial Consortium Cultured on Media Containing Aromatic and Saturated Hydrocarbons as the Sole Carbon Source

Change in the Predominant Bacteria in a Microbial Consortium Cultured on Media Containing Aromatic and Saturated Hydrocarbons as the Sole Carbon Source

Ensiling of Soybean Curd Residue and Wet Brewers Grains With or Without Other Feeds as a Total Mixed Ration

Enzyme Production-Based Approach for Determining the Functions of Microorganisms within a Community

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