• Microbiology and Biotechnology Letters
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• v.38 no.4
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• pp.448-454
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• 2010

This study investigated the effect of PCE and TCE as electron acceptors on the bacterial composition of dechlorinating communities. The enrichment cultures reductively dechlorinating PCE and TCE were developed from three environment samples using acetate as electron donor. The cultures were prepared by sequential enrichment, which was seeded with sediment and dredged soil. Denatured gradient gel electrophresis (DGGE) of 16S rRNA gene fragment was used to compare the microbial communities of these three enrichment cultures. After incubation for 4 weeks, the removal efficiencies of PCE and TCE were highest from Yeocheon site (87.37% and 84.46%, respectively). PCE and TCE as electron acceptors affected the bacterial diversity and community profiles in the enrichment cultures. DGGE analysis showed that the dominant bacteria in PCE and TCE enrichment were belonged to Clostridium sp., Desulfotomaculum sp., and uncultured bacteria.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1561-1569
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• 2006

Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE profiles were compared using different pairs of primers targeting different hypervariable regions of thirteen representative soil bacteria and clones. The primer set (1070f-1392r) for the E. coli numbering 1,071-1,391 region could not resolve all the 16S rDNA fragments of the representative bacteria and clones, and moreover, yielded spurious bands in DGGE profiles. For the E. coli numbering 353-514 region, various forward primers were designed to investigate the efficiency of PCR amplification. A degenerate forward primer (F357IW) often yielded multiple bands for a certain single 16S rDNA fragment in DGGE analysis, whereas nondegenerate primers (338f, F338T2, F338I2) differentially amplified each of the fragments in the mixture according to the position and the number of primer-template mismatches. A forward primer (F352T) designed to have one internal mismatch commonly with all the thirteen 16S rDNA fragments efficiently produced and separated all the target DNA bands with similar intensities in the DGGE profiles. This primer set F352T-519r consistently yielded the best DGGE banding profiles when tested with various soil samples. Touchdown PCR intensified the uneven amplification, and lowering the annealing temperature had no significant effect on the DGGE profiles. These results showed that PCR amplification bias could be much improved by properly designing primers for use in fingerprinting soil bacterial communities with the DGGE technique.

• Microbiology and Biotechnology Letters
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• v.42 no.1
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• pp.41-50
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• 2014

In this study, the performances of PVA-encapsulation and non-encapsulation in a fed-batch bioreactor system were compared for biohydrogen production. Hydrogen production in the PVA-encapsulation bioreactor was not significantly different in comparison to the non-encapsulation bioreactor. However, the hydrogen gas in the encapsulation bioreactor could be stably produced when it was exposed to environmental difficulties such as pH impact by the accumulation of organic acids as fermentative metabolic products. Bacterial communities by DGGE analysis were differently shifted between the PVA-encapsulation and non-encapsulation bioreactors from the initial sludge. The community of hydrogen producing bacteria was stable during the experimental period in the PVA-encapsulation bioreactor compared to the non-encapsulation method. The absolute quantitation of the DNA copy number by a high-throughput droplet digital PCR system for six genera contributed to hydrogen production showing that the numbers of dominant bacteria existed at similar levels in the two bioreactors regardless of encapsulation. In both of two bioreactors, not only Clostridium and Enterobacter, which are known as anaerobic hydrogen producing bacteria, but also Firmicutes, Ruminococcus and Escherichia existed with $1{\times}10^5-1{\times}10^6$ copy numbers of ml-samples exhibiting rapid growth during the initial operation period.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.6
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• pp.1164-1168
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• 2011

This study evaluated the soil microbial communities by fatty acid methyl ester (FAME) method in soils (6 sites for immatured paddy, 9 sites for normal paddy, and 5 sites for sandy paddy) in Gyeongnam Province. The soil microbial biomass carbon content in normal and sandy paddy were 1,235 and $441mg\;kg^{-1}$, respectively, showing the soil microbial biomass carbon content in normal paddy was higher than that in sandy paddy. The soil organic matter contents $33g\;kg^{-1}$ of immatured and normal paddy were higher than sandy paddy $18g\;kg^{-1}$ (p<0.05). The communities of total bacteria and Gram-negative bacteria in normal paddy were significantly higher than those in sandy paddy (p<0.05). Total bacteria communities should be considered as a potential responsible factor for the obvious microbial community differentiation.

• Animal Bioscience
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• v.34 no.9
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• pp.1466-1478
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• 2021

Objective: Ruminants are completely dependent on their microbiota for rumen fermentation, feed digestion, and consequently, their metabolism for productivity. This study aimed to evaluate the rumen bacteria of lactating yaks with different milk protein yields, using high-throughput sequencing technology, in order to understand the influence of these bacteria on milk production. Methods: Yaks with similar high milk protein yield (high milk yield and high milk protein content, HH; n = 12) and low milk protein yield (low milk yield and low milk protein content, LL; n = 12) were randomly selected from 57 mid-lactation yaks. Ruminal contents were collected using an oral stomach tube from the 24 yaks selected. High-throughput sequencing of bacterial 16S rRNA gene was used. Results: Ruminal ammonia N, total volatile fatty acids, acetate, propionate, and isobutyrate concentrations were found to be higher in HH than LL yaks. Community richness (Chao 1 index) and diversity indices (Shannon index) of rumen microbiota were higher in LL than HH yaks. Relative abundances of the Bacteroidetes and Tenericutes phyla in the rumen fluid were significantly increased in HH than LL yaks, but significantly decreased for Firmicutes. Relative abundances of the Succiniclasticum, Butyrivibrio 2, Prevotella 1, and Prevotellaceae UCG-001 genera in the rumen fluid of HH yaks was significantly increased, but significantly decreased for Christensenellaceae R-7 group and Coprococcus 1. Principal coordinates analysis on unweighted UniFrac distances revealed that the bacterial community structure of rumen differed between yaks with high and low milk protein yields. Furthermore, rumen microbiota were functionally enriched in relation to transporters, ABC transporters, ribosome, and urine metabolism, and also significantly altered in HH and LL yaks. Conclusion: We observed significant differences in the composition, diversity, fermentation product concentrations, and function of ruminal microorganisms between yaks with high and low milk protein yields, suggesting the potential influence of rumen microbiota on milk protein yield in yaks. A deeper understanding of this process may allow future modulation of the rumen microbiome for improved agricultural yield through bacterial community design.

• Journal of Life Science
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• v.33 no.6
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• pp.481-489
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• 2023

The taste and quality of soy sauce, a fermented liquid condiment, is greatly influenced by microbial metabolism during fermentation. To investigate the microbiological characteristics of ganjang during the initial fermentation process, we prepared meju (fermented soybean) blocks fermented with starter cultures and solar salts and analyzed the microbial community quantitively using 16S rRNA gene profiling from ganjang that had been fermented over a five-week period. The ganjang samples were collected and analyzed after soaking for week one (1W), three (3W), and five (5W) weeks. We found that Halomonadaceae was significantly higher in the 1W group (89.83%) than the 3W and 5W groups (14.46%, and 13.78%, respectively). At a species level, Chromohalobacter beijerinckii and Chromohalobacter canadensis were the dominant species in the 1W group but several taxa such as Bacillus subtilis, Pediococcus acidilactici, and Enterococcus faecalis were more abundant in the 3W and 5W groups. Pearson correlation analysis of the relative abundance of the bacteria showed a negative correlation between Chromohalobacter and two bacterial genera Bacillus and Enterococcus. Beta-diversity showed a statistical distinction between the 1W and the 3W and 5W groups, while no significance was evident between the 3W and 5W groups. Linear discriminant effect size analysis was used to identify biomarkers and significant differences in the relative abundance of several halophilic bacteria, Bacillus sp. and lactic acid bacteria at 1W, 3W, and 5W, recpectively, which indicates the important role of the bacterial community at these time points.

• Economic and Environmental Geology
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• v.57 no.3
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• pp.305-317
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• 2024

To investigate the effect of changes in microbial communities on arsenic release in soil, experiments were conducted on arsenic-contaminated soils (F1, G7, and G10). The experiments involved three groups of the experimental sets; ① BAC: sterilized soil + Bacillus fungorum, ② IND: indigenous bacteria, and ③ MIX: indigenous bacteria + B. fungorum, and incubated them for seven weeks using lactate as a carbon source under anaerobic conditions. The experimental results showed that higher concentrations of arsenic were released from the IND and MIX soils, where indigenous bacterial communities existed, compared to BAC. Significantly higher levels of arsenic were released from the G10 soil, which showed higher pH, compared to the F1 and G7 soils. In the G10 soil, unlike other soils, the proportion of As(III) among the released arsenic was also low. These results may be attributed to differences in microbial community composition that vary depending on the soil. By the seventh week, the diversity of microbial species in the IND and MIX soils had significantly decreased, with dominant orders such as Eubacteriales and Bacillales thriving. Bacteroidales in the seventh week of the MIX in the F1 soil, Rummeliibacillus in the seventh week of the IND and MIX of the G7 soil, and Enterobacterales in the IND and MIX of the G10 soil were dominant. At present, it is not known which mechanisms of microbial community changes affect the geochemical behavior of arsenic; however, these results indicate that microbiome in the soil may function as one of the factors regulating arsenic release.

• Journal of Life Science
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• v.17 no.9 s.89
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• pp.1284-1289
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• 2007

The Biological Activated Carbon (BAC) process in the water treatments represents a kind of biofiltration process which capabilities of bacteria to remove organic matters are maximized. It enables to eliminate organic matters and effectively reduce microbial regrowth potentials. As attached bacteria employ natural organic matter as a substrate, they are significantly dependent on indigenous microorganisms. In this study, characteristics of bacterial community by culturable and unculturable Methods have been conducted in a pilot plant using SAC in water treatment process at the downstream of the Nakdong River. Based on the results, HPC and bacterial- production for coal-based activated carbon material were $1.20{\sim}56.2{\times}l0^7$ cfu/g and $1.2{\sim}3.7\;mgC/m^{3}h$, respectively, in the SAC process. The highest level of attached bacteria biomass and organic carbon removal efficiency was found in the coal-based activated carbon. The genera Pseudomonas, Flavobacterium, Alcaligenes, Acilzetobacter, and Spingomonas were identified for each activated carbon material. Pseudomonas vesicularis was the dominant species in the coconut- and coal-based materials, where as Pseudomonas cepacia was the dominant species in the wood-based material. The Scanning Electron Microscope (SEM) observation of the activated carbon surface also found the widespread distribution of rod form and coccus. The community of attached bacteria was investigated by performing Fluorescent in situ hybridization (FISH) analysis. a group was dominant in coal, wood and coccunt-based materials, ${\alpha},\;{\beta}\;and\;{\gamma}$ group ranged from 27.0 ${\sim}$ 43.0%, 7.1 ${\sim}$ 22.0%, 11.3 ${\sim}$ 28.6%, respectively. These results suggest that a group bacterial community appears to be regulated removal efficiency of organic material in water treatment process.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Journal of Wetlands Research
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• v.9 no.1
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• pp.123-131
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• 2007

Effect of nitrogen-load condition on hydrogen ($H_2$) production and bacterial community in a continuous anaerobic hydrogen fermentation were investigated. The slight $H_2$ production on extremely low nitrogen-load condition (C/N ratio: 180) at the start-up period. The highest $H_2$ production was obtained when the C/N ratio was 36, the $H_2$ production yield ($mol-H_2/mol-glucose$) reached to 1.7, and it was indicated that Clostridium pasteurianum mainly contributed to the $H_2$ production. The $H_2$ production was decreased on both the lower (C/N: 72) and higher (C/N: 18) nitrogen-load conditions. The excess nitrogen-load was not always suitable for the hydrogen production. The fluctuation of $H_2$ production seemed to be caused by a change in the bacterial community according to the nitrogen-load condition, while a recovery of $H_2$ productivity was possible by a control of nitrogen-load condition through the bacterial community change. When the nitrogen-load condition was not suitable for hydrogen production, the lactic acid concentration was increased and also lactic acid bacteria were definitely detected, which suggested that the competition between hydrogen fermentator and lactic acid producer was occurred. These results demonstrated that the nitrogen-load condition affect on the $H_2$ productivity through the change of bacterial community in anaerobic hydrogen fermentation.