• Korean Chemical Engineering Research
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• v.48 no.2
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• pp.147-156
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• 2010

There are four key factors for gas-phase biofilters; biocatalysts(microorganisms), packing materials, design/operating techniques, and diagnosis/management techniques. Biofilter performance is significantly affected by microbial community structures as well as loading conditions. The microbial studies on biofilters are mostly performed on basis of culture-dependent methods. Recently, advanced methods have been proposed to characterize the microbial community structure in environmental samples. In this study, the physiological, biochemical and molecular methods for profiling microbial communities are reviewed, and their applicability to biofilters is discussed. Community-level physiological profile is based on the utilization capability of carbon substrate by heterotrophic community in environmental samples. Phospholipid fatty acid analysis method is based on the variability of fatty acids present in cell membranes of different microorganisms. Molecular methods using DNA directly extracted from environmental samples can be divided into "partial community DNA analysis" and "whole community DNA analysis" approaches. The former approaches consist in the analysis of PCR-amplified sequence, the genes of ribosomal operon are the most commonly used sequences. These methods include PCR fragment cloning and genetic fingerprinting such as denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism, ribosomal intergenic spacer analysis, and random amplified polymorphic DNA. The whole community DNA analysis methods are total genomic cross-DNA hybridization, thermal denaturation and reassociation of whole extracted DNA and extracted whole DNA fractionation using density gradient.

• Korean Journal of Agricultural and Forest Meteorology
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• v.9 no.3
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• pp.161-169
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• 2007

Global climate changes including elevated $CO_2$, drought, and global warming may influence greenhouse gas emissions in wetlands. A variety of microbial communities including denitrifiers and methanogens play a key role in determining such processes. In this paper we summarize current knowledge on the effects of climate changes on $CO_2,\;CH_4$, and $N_2O$ production and microbial communities mediating those processes in wetlands. Elevated atmospheric $CO_2$ and warming generally increase gas emissions, but effects of droughts differ with gas type and drying level. The responses of microbial community to climate changes in terms of composition, diversity and abundance are still in question due to lack of studies in wetlands. Based on the present review, it is suggested that future studies on microbial processes should consider microbial community and relationships between microbial function and structure with diverse environmental factors including climate changes. Such knowledge would be crucial to better understand and predict accurately any shifts in ecological functions of wetlands.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.2
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• pp.139-143
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• 2009

We examined the vertical distribution of specific microbial groups and the patterns of microbial community structure within the soil profile using phospholipid fatty acid (PLFA). Samples were collected from the soil surface down to 15 cm in depth from paddy and upland fields located in Daegu, Korea. The two fields have been fertilized with only chemical fertilizers N, P, K for 33 years. Principal component analysis of the PLFA signatures indicated that the composition of the soil microbial communities changed significantly with the cultivation practices and soil depth, suggesting that cultivation practices of paddy and upland fields had more significant influence on soil microbial community than the soil depth did. The soil microbial communities changed more drastically with soil depth in upland field than in paddy field, with making thicker soil surface in paddy field in terms of soil microbial community. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the deeper soil horizons are more carbon-limited and anaerobic than surface soil. The community analysis using PLFAs as biomarkers revealed that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundance of Gram-negative bacteria and fungi were highest at the soil surface and substantially lower in the subsurface.

• Proceedings of the Korea Water Resources Association Conference
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• 2023.05a
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• pp.487-487
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• 2023

농업 분야에서 미생물은 영양분 가용화, 유기물 분해 등 토양 영양분 공급에 중요한 역할을 하며, 토양 건강성 증진, 식량 안보 및 식품 건강 면에서 많은 활용 가능성을 지니고 있다. 최근 유역 환경 건강성, 생물 다양성 보존, 효율적인 고품질 농산물 생산에 대한 관심이 커져, 지속 가능한 농업 중 하나인 유기농업과 관행농업 토양의 이화학적 및 생물학적 특성에 관한 비교 연구가 진행되고 있다. 미생물은 지속 가능한 농업 발전의 중요한 요소 중 하나로써, 미생물 다양성이 풍부할수록 토양 비옥도, 작물 성장 면에서 긍정적인 영향을 미친다고 알려져 있다. 본 연구는 이에 대한 기초 데이터를 제공하기 위해 논 경작지를 대상으로 유기 및 관행농업 토양의 미생물 군집조성과 Alpha diversity analysis(Chao1, Shannon, Simpson index)을 통해 비교하였다. 경기도 양평군에서 유기 및 관행 논 지역을 각각 1지점씩 선정하였으며, 8월부터 11월까지 총 4회 현장 조사를 진행하였다. 미생물 분석은 차세대염기서열분석을 실시하였으며, bacteria는 16S rRNA V3-4 영역, fungi는 ITS 3-4 영역을 sequencing 하였다. 미생물 군집조성은 문수준에서는 큰 차이가 없었으나, 속수준에서는 fungi 군집조성에 차이를 보였다. 예로 Ustilaginoidea 속은 관행 논 토양에서만 발견되었으며, 벼 이삭누룩병을 일으키는 병원균으로 과도한 질소 비료 시비가 원인으로 추정된다. 종 다양성은 bacteria diversity의 경우 관행 논 토양에서 높게 측정되는 반면, fungi diversity의 경우 유기 논 토양에서 높게 측정되었다. 결론적으로 체계적인 시비 관리 통해 미생물 군집은 조절될 수 있으며, 관행농업은 적절한 시비를 통해 토양 건강성 및 식품 건강성 면에서 유기농업과 비슷한 효과를 보여줄 가능성이 있다고 판단된다.

• Korean Journal of Microbiology
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• v.45 no.1
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• pp.1-9
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• 2009

Microbes within complex communities show quite different physiology from pure cultured microbes. However, historically the study of microbes has focused on single species in pure culture and most of microbes are unculturable in our labs, so understanding of complex communities lags behind understanding of pure cultured cells. Methodologies including stable isotope probing (SIP), a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR), isotope micrarray, and metagenomics have given insights into the uncultivated majority to link phylogenetic and functional information. Here, we review some of the most recent literatures, with an emphasis on methodological improvements to the sensitivity and utilities of these methods to link phylogeny and function in complex microbial communities.

• Korean Journal of Microbiology
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• v.33 no.1
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• pp.55-65
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• 1997

16S rRNA를 분석한 연구들은 자연 생태계에서 추출한 핵산을 이용하여 16rRNA 유전자의 염기서열을 분석하거나 특정 DNA probe를 이용한 hybridization 실험이 주류를 이루어 왔다. 특히 PCR 기법이 개발됨에 따라 적은 양의 시료를 대량으로 손쉽게 증폭시킬 수 있어 다양한 분야에 응용되고 있다. 세균 군집의 구조를 이해하는데 있어서 PCR 방법의 적용 대상은 주로 16S rRNA 유전자의 염기서열 해독분야이며 해양 생태계를 대상으로 많은 연구 결과가 보고되었다(11,13,21,26). 한편 자연 생태계의 개별적 미생물 분류룬들을 검출하기 위한 특정 oligonucleotide probe의 개발방법들은 미생물 군집의 유전적 다양성에 대한 정보 파악 이외에 배양이 어려운 혐기성 세균과 같은 특정 세균들의 동정에도 이용되고 있다(3,24,55). 본고에서는 세균 군집의 구조와 다양성을 연구하는데 적용 가능한 rRNA 분석방법들을 수계 생태계를 중심으로 살펴보고자 한다.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.220-225
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• 2019

Studies based on microbial community analyses have increased in the recent decade since the development of next generation sequencing technology. Associations of gut microbiota with host's health are one of the major outcomes of microbial ecology filed. The major approach for microbial community analysis includes the sequencing of variable regions of 16S rRNA genes, which does not provide the information of bacterial activities. Here, we conducted RNA-based microbial community analysis and compared results obtained from DNA- and its cDNA-based microbial community analyses. Our results indicated that these two approaches differed in the ratio of Firmicutes and Bacteroidetes, known as an obesity indicator, as well as abundance of some key bacteria in gut metabolisms such as butyrate producers and probiotics strains. Therefore, cDNA-based microbial community may provide different insights regarding roles of gut microbiota compared to the previous studies where DNA-based microbial community analyses were performed.

• Korean Journal of Microbiology
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• v.22 no.4
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• pp.243-247
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• 1984

The effect of the heavy metals copper and cadmium on the natural populations of surface microlayer and subsurface water was investigated. Two microbiological parameters, number of colony-forming bacteria and $^{14}C-glucose$ uptake rate, were evalated. The two natural bacterial populations showed different tolerances of the heavy metals. The ingibition of bacterial growth and activity occurred more strongly in the 1m-depth samples than in neuston populations. The results support the existence of autochthonous bacterioneuston populations in marine environment.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.170-179
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• 2017

Tea is the most popular beverage in the world. In fact, there are mainly three different kinds of tea (Green tea, black tea, and post-fermented tea). Post-fermented tea is produced by the microbial fermentation process using sun-dried green tea leaves (Camellia sinensis) as the raw material. Chungtaejeon was a traditional tea introduced in the age of the ancient three states and is the only "Ddeok-cha or Don-cha" culture in the world that survived on the southwestern shore of Republic of Korea. In this study, the structures of the bacterial community involved in the production of oriental traditional post-fermented tea (Chungtaejeon) were investigated using 16S rRNA gene analysis. The 16S rRNA gene analysis of dominant microbial bacteria in post-fermented tea confirmed the presence of Pantoea sp., and Klebsiella oxytoca. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the post-fermented tea was ${\gamma}$-proteobacteria. As a result of the microbial community size analysis, it was confirmed that the size of the microbial communities of Chungtaejeon was the largest compared to other teas

• Journal of Korean Society of Environmental Engineers
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• v.32 no.1
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• pp.87-96
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• 2010

The electrode material is one of the factors affecting the power production of microbial fuel cell. In this study, effects of carbon electrode material, thickness and configuration on the power density, biofilm formation and microbial community diversity of microbial fuel cell were investigated. To optimize the anode-cathode electrode assembly, seven lab-scale reactors which had various carbon electrode constructions were operated in continuous mode. Under the steady state condition, the electrode combination of graphite felt (6 mm) with hole showed the highest cell voltage of 238 mV and the coulombic efficiency of 37%. As a result of SEM analysis, the bacteria growing on surface of knitted type of carbon cloth and graphite felt electrode ncreased significantly. The change of dominant species between seeding sludge and biofilm on the surface of anode electrode, microbial analysis with PCR-DGGE showed that the dominant species of seeding sludge are quite different from those of biofilm on the surface of each anode electrode. Especially Geobacter sp., a well known electrochemical bacteria, was found as the dominant species of the electrode combination with graphite felt.