• The Korean Journal of Pesticide Science
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• v.21 no.1
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• pp.1-8
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• 2017

Although a global ban on the use of endosulfan, an organochloline insecticide, has taken effect in mid-2012, it has been still used in several countries, including India and China, and detected in diverse environments in the world due to its relative persistence and semi-volatility. In this study, the effect of endosulfan on soil bacterial community was investigated using 16S rRNA gene pyrosequencing method. When endosulfan was applied to an upland soil at a rate of 100 mg/kg soil (ES soil), the number of operational taxonomic units (OTU) and diversity indices for bacteria initially decreased and gradually recovered to the level of the non-treated soil (NT soil) during an eight-week incubation period. At bacterial phylum level, relative abundances of Proteobacteria and Verrucomicrobia were higher while those of Chloroflexi and Spirochaetes were lower in the ES soil than in the NT soil, suggesting that an endosulfan application affects the bacterial community structure in soil. In the ES soil, the relative abundances of the OTUs affiliated to the genera Sphingomonas and Burkholderia increased in the initial period of incubation while those affiliated to the genera Pseudonocardia and Opitutus increased in the late period of incubation. Because the first three genera contain bacterial strains reported to degrade endosulfan, they are expected to be involved in the degradation of endosulfan, probably one after another.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.9
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• pp.1464-1473
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• 2018

Objective: To describe in-depth sequencing, the bacterial community diversity and its succession during ensiling of whole-plant maize and subsequent exposure to air. Methods: The microbial community dynamics of fermented whole-plant maize for 60 days (sampled on day 5, 10, 20, 40, 60) and subsequent aerobic exposure (sampled on day 63 after exposure to air for 3 days) were explored using Illumina Miseq sequence platform. Results: A total of 227,220 effective reads were obtained. At the genus level, there were 12 genera with relative abundance >1%, Lactobacillus, Klebsiella, Sporolactobacillus, Norank-c-cyanobacteria, Pantoea, Pediococcus, Rahnella, Sphingomonas, Serratia, Chryseobacterium, Sphingobacterium, and Lactococcus. Lactobacillus consistently dominated the bacterial communities with relative abundance from 49.56% to 64.17% during the ensiling process. Klebsiella was also an important succession bacterium with a decrease tendency from 15.20% to 6.41% during the ensiling process. The genus Sporolactobacillus appeared in late-ensiling stages with 7.70% abundance on day 40 and 5.32% on day 60. After aerobic exposure, the Lactobacillus decreased its abundance from 63.2% on day 60 to 45.03% on d 63, and Klebsiella from 5.51% to 5.64%, while Sporolactobacillus greatly increased its abundance to 28.15%. These bacterial genera belong to 5 phyla: Firmicutes (relative abundance: 56.38% to 78.43%) was dominant, others were Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria. The bacterial communities clearly clustered into early-ensiling (d 5), medium-ensiling (d 10, d 20), late-ensiling (d 40, d 60), and aerobic exposure (d 63) clusters, with early- and late-ensiling communities more like each other than to the aerobic exposure communities. Conclusion: High-throughput sequencing based on 16S rRNA genes proved to be a useful method to explore bacterial communities of silage. The results indicated that the bacterial communities varied during fermentation and more dramatically during aerobic exposure. The study is valuable for understanding the mechanism of population change and the relationship between bacteria and ensilage characteristics.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.287-295
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• 2005

In order to compare bacteria] community structure and diversity in activated sludges, terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16s rDNAs was analyzed for 31 domestic and industrial wastewater treatment plants (WTPs). Regardless of the characteristics of the wastewaters, the bacteria] community structures of activated sludges appeared diverse and complex. In particular, activated sludges in domestic WTPs contained higher bacterial diversity than those in industrial WTPs. It was also found that terminal restriction fragment (T-RF) profiles derived from domestic WTPs were very similar with each other, although activated sludges were collected from different plants at different locations. Interestingly, activated sludges of a WTP where restaurant and toilet sewages of a company were managed showed a bacterial community structure similar to that of domestic WTPs. Activated sludges in leather industria] WTPs also showed a high similarity. However, other wastewaters possessed different bacterial communities, so that overall similarity was as low as about $30\%$. Since activated sludges from WTPs for domestic wastewaters and a company sewage appeared to hold similar bacterial communities, it was necessary to confirm if similar wastewaters induce a similar bacterial community. To answer this question, analysis of T-RFs for activated sludges, taken from another 12 domestic WTPs, was conducted by using a 6­FAM$^{TM}$-Iabeled primer and an automated DNA sequencer for higher sensitivity. Among 12 samples, it was again found that T-RF profiles of activated sludges from Yongin, Sungnam, Suwon, and Tancheon domestic WTPs in Kyonggi-do were very similar with each other. On the other hand, T-RF profiles of activated sludges from Shihwa and Ansan WTPs were quite different from each other. It was thought that this deviation was caused by wastewaters, since Ansan and Shihwa WTPs receive both domestic and industrial wastewaters. From these results, it was tentatively concluded that similar bacterial communities might be developed in activated sludges, if WTPs treat similar wastewaters.

• Journal of Korean Society of Environmental Engineers
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• v.28 no.7
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• pp.757-763
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• 2006

In our previous studies, we have isolated bacteria from BTEX-contaminated sediment, which utilized BTEX as a sole carbon source and $NO_3$-N as an electron acceptor. For the possibility of field application, we have applied co-culture of those isolates in the BTEX-contaminated soil and evaluated their biodegradation efficiencies. To investigate the relationship between the isolates and indigenous microorganism in soil, changes of microbial community structure in soil samples with respect to time were monitored. To examine this, soil samples were artificially contaminated with benzene, toluene, ethylbenzene and o-xylene. BTEX-degrading bacteria such as Pseudomonas stutzeri strain 15(DQ 202712), Klebsiells sp. strain 20(DQ 202715) and Citrobacter sp. strain A(DQ 202713) were injected into the soil samples in the ratio of 2:1:1. Our results showed that the highest BTEX biodegradation efficiency was achieved when both BTEX and $NO_3-N$ existed simultaneously. The change in soil microbial community structure was characterized by PCR-DGGE analysis comparing the relative DGGE band intensities. The band intensities of indigenous microorganisms in the soil were reduced by injecting co-culture of the three isolates. On the contrary, the relative band intensities of the isolates were increased. Among the three isolates, Pseudomonas stutzeri strain 15 rendered the highest band intensity. This indicates that the Pseudomonas stutzeri was the dominant microbial species found in the soil samples.

• Korean Journal of Ecology and Environment
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• v.51 no.4
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• pp.299-310
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• 2018

Odor compounds (geosmin, 2-MIB) have been causing problems in the Bukhan River system, but the causative organisms have not been clearly identified. To evaluate the relationship between dynamics of microbial community and odor compounds, two times monthly monitoring of water quality and microbial community from the three serial lakes (Lake Uiam, Lake Cheongpyeong and Lake Paldang) in the Bukhan River system were conducted from April to October 2017. The odor compounds were analyzed by HS-SPME analysis method using GC/MS. Bacteria communities were identified at the class level by NGS analysis. Actinobacteria and Betaproteobacteria were dominant taxon in bacteria community of three serial lakes. In the case of phytoplankton communities showed that seasonal changes by Bacillariophyceae and Cryptophyceae in spring, Cyanobacteria in summer, and Bacillariophyceae and Cryptophyceae in autumn. Dominant species was Dolichospermum (=Anabaena), Microcystis and Pseudanabaena in Bukhan River system in all study period. At the same time the odors geosmin and 2-MIB were also detected at high concentration. There is a significant positive correlation between proportion of Actinobaceria and 2-MIB concentration (r=0.491, p<0.01). In addition, proportion of cyanobacteria showed a significant correlation of geosmin (r=0.381, p<0.05) and 2-MIB (r=0.386, p<0.05) concentration. In this study, odor compounds in the Bukhan River system are considered to be a direct relationship between with Actinobacteria and cyanobacteria.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.283-294
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• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.678-684
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• 2017

The aim of this study was to elucidate the changes in the microbial community and biochemical properties of a traditional sweet paste during fermentation. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that Aspergillus oryzae was the predominant species in the koji (the fungal mixture), and the majority of the fungi isolated belonged to two Zygosaccharomyces species in the mash. The bacterial DGGE profiles revealed the presence of Bacillus subtilis during fermentation, and Lactobacillus acidipiscis, Lactobacillus pubuzihii, Lactobacillus sp., Staphylococcus kloosi, and several uncultured bacteria were also detected in the mash after 14 days of main fermentation. Additionally, during main fermentation, amino-type nitrogen and total acid increased gradually to a maximum of $6.77{\pm}0.25g/kg$ and $19.10{\pm}0.58g/kg$ (30 days) respectively, and the concentration of reducing sugar increased to $337.41{\pm}3.99g/kg$ (7 days). The 180-day fermented sweet paste contained $261.46{\pm}19.49g/kg$ reducing sugar and its pH value remained at around 4.65. This study has used the PCR-DGGE technique to demonstrate the microbial community (including bacteria and fungi) in sweet paste and provides useful information (biochemical properties) about the assessment of the quality of sweet paste throughout fermentation.

• Journal of Microbiology and Biotechnology
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• v.26 no.3
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• pp.540-548
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• 2016

Microbially induced calcium carbonate precipitation (CCP) is a long-standing but re-emerging environmental engineering process for production of self-healing concrete, bioremediation, and long-term storage of CO₂. CCP-capable bacteria, two Bacillus strains (JH3 and JH7) and one Sporosarcina strain (HYO08), were isolated from two samples of concrete and characterized phylogenetically. Calcium carbonate crystals precipitated by the three strains were morphologically distinct according to field emission scanning electron microscopy. Energy dispersive X-ray spectrometry mapping confirmed biomineralization via extracellular calcium carbonate production. The three strains differed in their physiological characteristics: growth at alkali pH and high NaCl concentrations, and urease activity. Sporosarcina sp. HYO08 and Bacillus sp. JH7 were more alkali- and halotolerant, respectively. Analysis of the community from the same concrete samples using barcoded pyrosequencing revealed that the relative abundance of Bacillus and Sporosarcina species was low, which indicated low culturability of other dominant bacteria. This study suggests that calcium carbonate crystals with different properties can be produced by various CCP-capable strains, and other novel isolates await discovery.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.287-292
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• 2002

The composition of bacterial communities was detected in surface water of Cheonho Reservoir dominated by cyanobacteria, using fluorescent in situ hybridization (FISH) method. Total bacterial numbers were very high ranging from 0.6～$1.3{\times}10^7 \cells{\cdot}ml^-1$, whereas the ratio of Eubacteria to total bacteria was 29.8~45.8%, which was lower than that in other freshwater ecosystems. On average only 2.1% of DAPI-stained bacteria were detected by FISH with probes for $\alpha$, $\beta$, and $\gamma$-groups, respectively. Unknown eubacteria which was not bound to any probes except EUB 338, was relatively high. On the other hand, the Cytophaga-Flavobacterium group increased following the change of dominant species from Anabaena sp. to Microcystis sp. This result showed that bacterial communities could be affected by phytoplanktons, especially cyanobacteria.