• Journal of Microbiology
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• 제42권1호
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• pp.1-8
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• 2004

Changes in the bacterial populations of a 5-stage biological nutrient removal (BNR) process, with a step feed system for wastewater treatment, were monitored by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments. DGGE analysis indicated seasonal community changes were observed, however, community profiles of the total bacteria of each reactor showed only minor differences in the samples obtained from the same season. The number of major bands was higher in the summer samples, and decreased during the winter period, indicating that the microbial community structure became simpler at low temperatures. Since the nitrogen and phosphate removal efficiencies were highly maintained throughout the winter operation period, the bacteria which still remaining in the winter sample can be considered important, playing a key role in the present 5-stage BNR sludge. The prominent DGGE bands were excised, and sequenced to gain insight into the identities of the predominant bacterial populations present, and most were found to not be closely related to previously characterized bacteria. These data suggest the importance of culture-independent methods for the quality control of wastewater treatment.

• 한국환경농학회지
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• 제40권1호
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• pp.49-59
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• 2021

BACKGROUND: Soil salinity causes reduction of crop productivity. Rhizosphere microbes have metabolic capabilities and ability to adaptation of plants to biotic and abiotic stresses. Plant growth-promoting bacteria (PGPB) could play a role as elicitors for inducing tolerance to stresses in plants by affecting resident microorganism in soil. This study was conducted to demonstrate the effect of selected strains on rhizosphere microbial community under salinity stress. METHODS AND RESULTS: The experiments were conducted in tomato plants in pots containing field soil. Bacterial suspension was inoculated into three-week-old tomato plants, one week after inoculation, and -1,000 kPa-balanced salinity stress was imposed. The physiological and biochemical attributes of plant under salt stress were monitored by evaluating pigment, malondialdehyde (MDA), proline, soil pH, electrical conductivity (EC) and ion concentrations. To demonstrate the effect of selected Bacillus strains on rhizosphere microbial community, soil microbial diversity and abundance were evaluated with Illumina MiSeq sequencing, and primer sets of 341F/805R and ITS3/ITS4 were used for bacterial and fungal communities, respectively. As a result, when the bacterial strains were inoculated and then salinity stress was imposed, the inoculation decreases the stress susceptibility including reduction in lipid peroxidation, enhanced pigmentation and proline accumulation which subsequently resulted in better plant growth. However, bacterial inoculations did not affect diversity (observed OTUs, ACE, Chao1 and Shannon) and structure (principle coordinate analysis) of microbial communities under salinity stress. Furthermore, relative abundance in microbial communities had no significant difference between bacterial treated- and untreated-soils under salinity stress. CONCLUSION: Inoculation of Bacillus strains could affect plant responses and soil pH of tomato plants under salinity stress, whereas microbial diversity and abundance had no significant difference by the bacterial treatments. These findings demonstrated that Bacillus strains could alleviate plant's salinity damages by regulating pigments, proline, and MDA contents without significant changes of microbial community in tomato plants, and can be used as effective biostimulators against salinity stress for sustainable agriculture.

• 한국해양바이오학회지
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• 제7권2호
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• pp.42-51
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• 2015

The community structure of cultivable bacteria associated with the marine sponge, Petrosia corticata, collected from Jeju Island in summer (September) of 2012 and winter (January) of 2013, were compared by the PCR-ARDRA method. Bacterial strains were cultured for 4 days at $26^{\circ}C$ on Zobell medium and marine agar medium. After PCR amplification of 16S rRNA gene of individual strains, the restriction enzymes MspI and HaeIII were used to make restriction patterns. As a result, 24 ARDRA patterns from the summer sponge and 20 ARDRA patterns from the winter sponge were obtained. The sequencing result of 1-3 selected strains from each pattern showed over 98% similarities with the known sequences from the public database. At the phylum level, the bacterial community structures of both sponges (summer and winter) were identical qualitatively and composed of 4 phyla : Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Alphaproteobacteria accounted for 42.5% of total in summer sponge and 25.2% in winter, decreasing in the winter sample. Gammaproteobacteria accounted for 27.5% of total in summer sponge and 35.2% in winter, increasing in the winter sample. At the genus and species level, summer sponge had more diverse bacterial communities than winter sponge. Actinobacteria, Bacteroidetes, and Firmicutes increased in the winter sample.

• Journal of Microbiology and Biotechnology
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• 제21권3호
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• pp.293-298
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• 2011

Nitrifying bacterial community structures of suspended and attached biomasses in a full-scale integrated fixed-film activated sludge process were investigated by analyzing 16S rRNA gene sequences obtained from pyrosequencing. The suspended biomass had a higher number of ammonia-oxidizing bacterial sequences (0.8% of total sequences) than the attached biomass (0.07%), although most of the sequences were within the Nitrosomonas oligotropha lineage in both biomasses. Nitrospira-like nitrite-oxidizing bacterial sequences were retrieved in the suspended biomass (0.06%), not in the attached biomass, whereas the existence of Nitrobacter-like sequences was not evident. The suspended biomass had higher nitrification activity (1.13 mg N/TSS/h) than the attached biomass (0.07 mg N/TSS/h). Overall, the results made it possible to conclude the importance of the suspended biomass, rather than the attached biomass, in nitrification in the wastewater treatment process studied.

• Journal of Microbiology and Biotechnology
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• 제21권9호
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• pp.885-892
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• 2011

The bacterial communities in the intestinal tracts of earthworm were investigated by culture-dependent and -independent approaches. In total, 72 and 55 pure cultures were isolated from the intestinal tracts of earthworms under aerobic and anaerobic conditions, respectively. Aerobic bacteria were classified as Aeromonas (40%), Bacillus (37%), Photobacterium (10%), Pseudomonas (7%), and Shewanella (6%). Anaerobic bacteria were classified as Aeromonas (52%), Bacillus (27%), Shewanella (12%), Paenibacillus (5%), Clostridium (2%), and Cellulosimicrobium (2%). The dominant microorganisms were Aeromonas and Bacillus species under both aerobic and anaerobic conditions. In all, 39 DNA fragments were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. Aeromonas sp. was the dominant microorganism in feeds, intestinal tracts, and casts of earthworms. The DGGE band intensity of Aeromonas from feeds, intestinal tracts, and casts of earthworms was 12.8%, 14.7%, and 15.1%, respectively. The other strains identified were Bacillus, Clostridium, Enterobacter, Photobacterium, Pseudomonas, Shewanella, Streptomyces, uncultured Chloroflexi bacterium, and uncultured bacterium. These results suggest that PCR-DGGE analysis was more efficient than the culturedependent approach for the investigation of bacterial diversity and the identification of unculturable microorganisms.

• 한국환경농학회지
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• 제38권3호
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• pp.185-196
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• 2019

BACKGROUND: This study investigated the effects of rice genetically modified to be resistant against rice blast and rice bacterial blight on the soil microbial community. A comparative analysis of the effects of rice genetically modified rice choline kinase (OsCK1) gene for disease resistance (GM rice) and the Nakdong parental cultivar (non-GM rice) on the soil microbial community at each stage was conducted using rhizosphere soil of the OsCK1 and Nakdong rice. METHODS AND RESULTS: The soil chemistry at each growth stage and the bacterial and fungal population densities were analyzed. Soil DNA was extracted from the samples, and the microbial community structures of the two soils were analyzed by pyrosequencing. No significant differences were observed in the soil chemistry and microbial population density between the two soils. The taxonomic analysis showed that Chloroflexi, Proteobacteria, Firmicutes, Actinobacteria, and Acidobacteria were present in all soils as the major phyla. Although the source tracking analysis per phylogenetic rank revealed that there were differences in the bacteria between the GM and non-GM soil as well as among the cultivation stages, the GM and non-GM soil were grouped according to the growth stages in the UPGMA dendrogram analysis. CONCLUSION: The difference in bacterial distributions between Nakdong and OsCK1 rice soils at each phylogenetic level detected in microbial community analysis by pyrosequencing may be due to the genetic modification done on GM rice or due to heterogeneity of the soil environment. In order to clarify this, it is necessary to analyze changes in root exudates along with the expression of transgene. A more detailed study involving additional multilateral soil analyses is required.

• 미생물학회지
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• 제42권2호
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• pp.103-110
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• 2006

들잔디(zoysia japonica)에 제초제를 살포 한 다음, 아미노산을 포함한 액비(LFcAA)를 처리한 들잔디 토양의 미생물 군집구조 및 다양성을 비교하기 위하여 16S rDNA서열에 기초한 T-RFLP (terminal restriction fragment length polymorphism)분식과 클론의 염기서열 분석을 실시하였다. 제한효소 HaeIII을 이용한 T-RFLP 분석결과 아미노산 액비를 처리한 실험구 KD3과 KD4에서, 32, 38개의 유효한 피크를 가진 T-RFs가 나타났다. 23개를 나타낸 아미노산 무처리구인 KD2가 KD3,4에 비해 미생물군집구조가 단순한 것으로 조사되었다. 네 개의 실험구 KDl (대조구), KD2 (무처리구), KD3 (LFcAA 1X)., KD4 (LFcAA 2X)에서 각각 110개의 클론의 16S rDNA부분 염기서열 분석결과 대부분이 $91{\sim}99%$ 유사도 수준에서 GeneBank에 등록된 염기서열 중 대부분 uncultured bacterium으로 BLAST결과 조사되었다. 이외의 대부분의 클론들은 Proteobacteria, Acidobacteria, Actinobacteria, Sphingobacteria, Planctomycetes 그룹들의 클론들이 조사되었고, 특히 LEcAA 2X 처리구인 KD4에서는 KD2에서와는 다르게 Alphaproteobacteria의 Rhizobiales, Shigomonadales,그리고 Caulobacterales목에 속하는 미생물들의 클론이 조사되었으며, Gammaproteobactetia의 Pseudomonas 속의 세균들이 주로 나타났으며, Betaproteobaderia 의 Nitrosomonadales 목의 Nitrosospira 속들이 주로 조사되었다. 이 외에도 Acidobacteria 그룹, Actinobacteria 그룰, Planctomycetacia, Sphingobacteria 그룹들이 다양하게 조사되었다. 이러한 결과는 제초제를 살포한 미생물 군집구조가 LFcAA 첨가로 들잔디의 미생물 군집 구조에 큰 영향을 주고 있음을 시사하였다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.161-161
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• 2017

Seed endophytes are very remarkable groups of bacteria for their unique abilities of being vertically transmitted and conserved. As plants attain hybrid vigor and heterosis in the process of crossbreeding, this might also lead to the changes in the community structure and diversity of plant endophytes in the hybrid plants ultimately affecting the endophytes of the seeds. It would be interesting to characterize how seed endophyte composition change over time. The objective of this study is to gain insights into the influence of natural crossbreeding and parental lineage in the seed bacterial endophytic communities of two pure inbred lines exploring contributions of the two most important sources of plant endophytes - colonization from external sources and vertical transmission via seeds. Total genomic DNA was isolated from rice seeds and bacterial DNA was selectively amplified by PCR. The diversity of endophytic bacteria was studied through Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Diversity between the original parents and the pure inbred line may show significant differences in terms of richness, evenness and diversity indices. Heat maps reveal astonishing contributions of both or either parents (IR29 ${\times}$ Pokkali and AT401 ${\times}$ IR31868) in the shaping of the bacterial seed endophytes of the hybrid, FL478 and IC32, respectively. Most of the T-RFs of the subsequent pure inbred line could be traced to any or both of the parents. Comparison of common and genotype-specific T-RFs of parents and their offspring reveals that majority of the T-RFs are shared suggesting higher transmission of bacterial communities common to both parents. The parents influence the bacterial community of their offspring. Unique T-RFs of the offspring also suggest external sources of colonization particularly as the seeds are cultivated in different ecogeographical locations. This study showed that host parental lines contributed greatly in the shaping of bacterial seed endophytes of their offspring. It also revealed transmission and potential conservation of core seed bacterial endophytes that generally become the dominant microbiota in the succeeding generations of plant hosts.

• 한국환경보건학회지
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• 제37권2호
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• pp.124-132
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• 2011

Biofilm and aeration tank of pilot and full RABC (rotating activated Bacillus contactor) plant were analyzed to characterize and determine bacterial community structure in food wastewater treatment system at winter. Concentration of heterotrophic bacteria and Bacillus group was $10^7$ and $10^5$ CFU/ml, respectively, at biofilm of pilot-plant while others represented $10^6$ and $10^4$ CFU/ml, respectively. Five and eight phyla were detected at biofilm of pilot- and full-plant, respectively, by 16S rDNA sequencing. Biofilm of pilot-plant was dominated by ${\beta}$-Proteobacteria (38.8%), ${\gamma}$-Proteobacteria (22.4%), and Bacteroidetes (12.2%), and the most dominant genus was Zoogloeae genus (22.4%). Candidate division TM7 (12.5%) was only detected at biofilm of full-plant and it was dominated by Bacteroidetes (33.3%), ${\gamma}$-Proteobacteria (29.2%), and ${\beta}$-Proteobacteria (20.8%). Clostridium genus specific primer set enabled to detect the sequences of Clostridium genus. These suggested that anaerobic and aerobic bacteria were coexisted even from the initial period of biofilm formation and ${\beta}$-Proteobacteria, ${\gamma}$-Proteobacteria and Bacteroidetes were major phyla in biofilm of food wastewater treatment system at winter.

• Animal Bioscience
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• 제35권12호
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• pp.1860-1870
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• 2022

Objective: The observation that temperate C₃ and tropical C₄ forage silages easily produce large amounts of ethanol or acetic acid has puzzled researchers for many years. Hence, this study aimed to assess the effects of epiphytic microbiota from C₃ forages (Italian ryegrass and oat) on fermentative products and bacterial community structure in C₄ forage (sorghum) silage. Methods: Through microbiota transplantation and γ-ray irradiation sterilization, the irradiated sorghum was treated: i) sterile distilled water (STSG); ii) epiphytic microbiota from sorghum (SGSG); iii) epiphytic microbiota from Italian ryegrass (SGIR); iv) epiphytic microbiota from oat (SGOT). Results: After 60 days, all the treated groups had high lactic acid (>63.0 g/kg dry matter [DM]) contents and low pH values (<3.70), acetic acid (<14.0 g/kg DM) and ammonia nitrogen (<80.0 g/kg total nitrogen) contents. Notably, SGIR (59.8 g/kg DM) and SGOT (77.6 g/kg DM) had significantly (p<0.05) higher ethanol concentrations than SGSG (14.2 g/kg DM) on day 60. After 60 days, Lactobacillus were predominant genus in three treated groups. Higher proportions of Chishuiella (12.9%) and Chryseobacterium (7.33%) were first found in silages. The ethanol contents had a positive correlation (p<0.05) with the abundances of Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium. Conclusion: The epiphytic bacteria on raw materials played important roles in influencing the silage fermentation products between temperate C₃ and tropical C₄ forages. The quantity and activity of hetero-fermentative Lactobacillus, Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium may be the key factors for the higher ethanol contents and DM loss in silages.