• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1013-1022
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• 2023

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

• 문화기술의 융합
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• 제10권3호
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• pp.873-878
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• 2024

우리는 Loperamide로 유도한 변비 Sprague-Dawley 랫드 모델에서 프락토올리고당 및 과채류복합 추출물을 2 주간 경구 투여 한 후 랫 분변의 그룹 기간별로 수집 한 후 장내 마크로바이옴 변화 경향을 분석하였다. 프락토올리고당 및 과채복합추출물(FVCE)에 대한 미생물 군집 분석을 16S rDNA 클로닝 및 pyrosequencing을 통해 수행하여 표준화 및 체계화를 위한 기초 데이터를 얻었다. 과채복합추출물(FVCE) 제조 공정은 원핵생물 군집에 대한 미생물 분석을 통해 문 수준에서 미생물 verrucomicrobiota의 약간의 차이가 우세한 것으로 나타났다. 속 수준에서는 prevotella와 muribaculaceae가 종 수준에서 더 많은 차이를 보였다. 이러한 결과는 사용된 미생물 군집이 생산되는 과일 및 채소 복합 추출물(FVCE)의 품질에 영향을 미친다는 것을 시사한다고 할 수 있다. 따라서, 일관된 품질의 과일 및 채소 복합 추출물(FVCE)을 생산하기 위해서는 안정적인 미생물 군집이 유지되어야 한다.

• 한국토양비료학회지
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• 제44권6호
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• pp.1169-1175
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• 2011

시설재배지의 토양미생물 분포 특성을 밝히고 토양의 건전성을 평가하고자, 전국 주요 시설재배 8개 주산단지에서 각각 5포장을 선정하여 토양화학성, 미생물분포 및 생화학적 특성을 조사하였다. 토양화학성은 가용성인산, 칼륨, 칼슘의 함량이 적정범위보다 크게 상회하여 상당량의 염류 집적을 확인하였다. 토양미생물의 배양적 방법을 통해 조사한 시설재배지의 주요 우점 박테리아는 Bacillus 속, Microbacterium 속, Arthrobacter 속, Lysobacter 속 등이었으며, 형광성 Pseudomonas 속의 밀도는 상추와 오이 재배지에서 각각 $0.018-7.3{\times}10^4\;cfu\;g^{-1}$, $0.0013-9.6{\times}10^4\;cfu\;g^{-1}$으로 시료에 따라 큰 변이를 보였다. 비배양학적 방법을 통한 토양미생물 분포 조사를 위해 수행한 인지질지방산 (PLFA)의 주성분 분석 결과, 작물 및 지역별 군집구조의 큰 차이는 없었다. 따라서 토양화학성 및 미생물군집구조 측면에서 시설재배지 조사지역의 토양은 대체로 건전한 것으로 판단된다.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2004년도 임시총회 및 추계학술발표회
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• pp.164-167
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• 2004

To investigate the chemical and microbiological characteristics of groundwater and surface waters in contaminated sites, hydrochemical and microbial community analysis were executed. Different indigenous bacteria were observed at 4 contaminated sites and this is considered to decompose the contaminants of groundwater. The research results showed the close relationship between hydrochemistry and microbial characteristics and those are used for the information of natural attenuation and enhanced bioremediation.

• Bulletin of the Korean Chemical Society
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• 제32권1호
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• pp.356-358
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• 2011

• Journal of Microbiology and Biotechnology
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• 제27권1호
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• pp.130-140
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• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.

• Environmental Engineering Research
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• 제12권4호
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• pp.129-135
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• 2007

This study evaluated microbial risk that could develop within soil microbial communities after amended with organic fertilizers from stabilized swine manure waste. For this purpose, we assessed the occurrences and competitiveness of antibiotic resistance and pathogenicity in soil microbial communities that were amended with swine manure wastes stabilized by a traditional lagoon fermentation process and an autothermal thermophilic aerobic digestion process, respectively. According to laboratory cultivation detection analysis, soil applications of the stabilized organic fertilizers resulted in increases in absolute abundances of antibiotic resistant bacteria and of two tested pathogenic bacteria indicators. The increase in occurrences might be due to the overall growth of microbial communities by the supplement of nutrients from the fertilizers. Meanwhile, the soil applications were found to reduce competitiveness for various types of antibiotic resistant bacteria in the soil microbial communities, as indicated by the decrease in relative abundances (of total viable heterotrophic bacteria). However, competitiveness of pathogens in response to the fertilization was pathogens-specific, since the relative abundance of Staphylococcus was decreased by the soil applications, while the relative abundance of Salmonella was increased. Further testes revealed that no MAR (multiple antibiotic resistance) occurrence was detected among cultivated pathogen colonies. These findings suggest that microbial risk in the soil amended with the fertilizers may not be critical to public health. However, because of the increased occurrences of antibiotic resistance and pathogenicity resulted from the overall microbial growth by the nutrient supply from the fertilizers, potential microbial risk could not be completely ruled out in the organic-fertilized soil samples.

• 생명과학회지
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• 제31권10호
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• pp.922-928
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• 2021

본 연구는 우리나라 전통 장류인 된장과 청국장의 미생물 분포와 시료간의 미생물학적 차이에 대해 차세대 염기서열 분석법(NGS)을 이용하여 분석하였다. α-diversity 분석 결과 된장에서 종 추정치와 풍부도가 통계학적으로 유의한 수준으로 높은 것으로 나타났다. 세균 분포를 분석한 결과 문 수준에서 Firmicutes가 된장에서 97.02%, 청국장에서 99.67%를 차지하여 공통적으로 가장 우점하는 것으로 나타났으며, 속 수준에서는 된장과 청국장에서 Bacillus가 각각 71.70%, 59.87%를 차지하여 가장 우점하는 것으로 확인되었다. 된장과 청국장의 미생물 분포에 차이가 있는지 분석하기 위해 PERMANOVA 분석을 수행한 결과 된장과 청국장의 미생물 분포에 통계학적으로 유의한 수준으로 차이가 나는 것으로 나타났다. 각 된장과 청국장 미생물 군집을 대표하는 biomarker를 분석하기 위해 LEfSe분석을 수행한 결과 된장에서 Bacillus subtilis, Tetragenococcus halophilus, Clostridium arbusti가 상대적으로 많이 분포하였으며, 청국장에서는 Bacillus thermoamylovorans, Enterococcus faecium, Lactobacillus sakei가 상대적으로 많이 분포하는 것으로 나타났다. 본 연구를 통해 콩을 주원료로 하는 우리나라 대표 전통장류인 된장과 청국장의 시료별 유사성과 차이점에 대한 미생물 분포를 정의하고 전통장류의 생화학적, 생리학적 특성과 미생물 분포의 상관관계를 규명하기 위한 기초 연구자료로 활용할 수 있을 것으로 기대된다.

• 한국토양비료학회지
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• 제45권6호
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• pp.1073-1085
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• 2012

Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.