• 보존과학회지
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• 제37권4호
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• pp.357-361
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• 2021

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple's soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple's soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

• Journal of Microbiology and Biotechnology
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• 제20권9호
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• pp.1339-1347
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• 2010

In this study, the identity and distribution of plants and the structure of their associated rhizobacterial communities were examined in an oil-contaminated site. The number of plant species that formed a community or were scattered was 24. The species living in soil highly contaminated with total petroleum hydrocarbon (TPH) (9,000-4,5000 mg/g-soil) were Cynodon dactylon, Persicaria lapathifolia, and Calystegia soldanella (a halophytic species). Among the 24 plant species, the following have been known to be effective for oil removal: C. dactylon, Digitaria sanguinalis, and Cyperus orthostachyus. Denaturing gradient gel electrophoresis (DGGE) profile analysis showed that the following pairs of plant species had highly similar (above 70%) rhizobacterial community structures: Artemisia princeps and Hemistepta lyrata; C. dactylon and P. lapathifolia; Carex kobomugi and Cardamine flexuosa; and Equisetum arvense and D. sanguinalis. The major groups of rhizobacteria were Beta-proteobacteria, Gamma-proteobacteria, Chloroflexi, Actinobacteria, and unknown. Based on DGGE analysis, P. lapathifolia, found for the first time in this study growing in the presence of high TPH, may be a good species for phytoremediation of oil-contaminated soils and in particular, C. soldanella may be useful for soils with high TPH and salt concentrations. Overall, this study suggests that the plant roots, regardless of plant species, may have a similar influence on the bacterial community structure in oil-contaminated soil.

• 농약과학회지
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• 제21권1호
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• pp.1-8
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• 2017

유기염소계 살충제 엔도설판은 2012년 국제적으로 사용이 금지되었으나 인도와 중국을 비롯한 국가들에서 여전히 사용되고 있으며 높은 잔류성과 이동성으로 인해 다양한 환경에서 검출되고 있다. 본 연구에서는 엔도설판이 토양세균의 군집구조에 미치는 영향을 16S rRNA 유전자 파이로시퀀싱 기법을 이용하여 분석하였다. 엔도설판을 100 mg/kg의 수준으로 밭토양에 처리했을 때 세균의 Operational taxonomic unit (OTU) 수와 다양성 지수가 감소했다가 서서히 증가하였으며 Proteobacteria와 Verrucomicrobia 문의 점유율은 증가하고 Chloroflexi와 Spirochaetes 문의 점유율은 감소한 것으로 나타나 엔도설판 처리가 토양세균 군집구조를 변화시키는 것을 확인하였다. 엔도설판 처리 시 Sphingomonas와 Burkholderia 속에 속하는 OTU의 점유율이 배양 초기에 높게 나타났으며 Pseudonocardia와 Opitutus 속에 속하는 OTU의 점유율은 배양 후기에 높게 나타났다. 이전 연구에서 Sphingomonas, Burkholderia, Pseudonocardia 속에 속하는 균주들이 엔도설판을 분해하였으므로 이 속에 속하는 OTU들이 토양에서 엔도설판의 분해에 단계적으로 관여했을 것으로 추정된다.

• The Plant Pathology Journal
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• 제35권4호
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• pp.362-371
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• 2019

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 $1^{st}$ transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 $1^{st}$ transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.

• Journal of Ecology and Environment
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• 제41권9호
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• pp.271-280
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• 2017

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, ${\beta}$-1,4-glucosidase, cellobiohydrolase, ${\beta}$-1,4-xylosidase, ${\beta}$-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was $125.9({\pm}5.7({\pm}1SE))$, $30.9({\pm}0.9)$, $15.7({\pm}0.6)$, $6.7({\pm}0.9)$, and $3.3({\pm}0.3)nmol\;g^{-1}\;h^{-1}$ at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

• Journal of Ecology and Environment
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• 제31권4호
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• pp.309-316
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• 2008

To develop a monitoring method for soil microbial communities in rice paddy fields, we used terminal restriction fragment length polymorphism (T-RFLP) to compare soil bacterial community structure in rice paddy fields experiencing different management practices: organic practices, conventional practices without a winter barley rotation, and conventional practices with a winter barley rotation. Restriction fragment length profiles from soils farmed using organic practices showed very different patterns from those from conventional practices with and without barley rotation. In principal component analyses, restriction fragment profiles in organic practice samples were clearly separated from those in conventional practice samples, while principal component analysis did not show a clear separation for soils farmed using conventional practices with and without barley rotation. The cluster analysis showed that the bacterial species compositions of soils under organic practices were significantly different from those under conventional practices at the 95% level, but soils under conventional practice with and without barley rotation did not significantly differ. Although the loadings from principal component analyses and the Ribosomal DNA Project II databases suggested candidate species important for soils under organic farming practices, it was very difficult to get detailed bacterial species information from terminal restriction fragment length polymorphism. Rank-abundance diagrams and diversity indices showed that restriction fragment peaks under organic farming showed high Pielou's Evenness Index and the reciprocal of Simpson Index suggesting high bacterial diversity in organically farmed soils.

• Journal of Microbiology and Biotechnology
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• 제33권6호
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• pp.760-770
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• 2023

Continuous cropping obstacles have become a serious factor restricting sustainable development in modern agriculture, while companion planting is one of the most common and effective methods for solving this problem. Here, we monitored the effects of companion planting on soil fertility and the microbial community distribution pattern in pepper monoculture and companion plantings. Soil microbial communities were analyzed using high-throughput sequencing technology. Companion plants included garlic (T1), oat (T2), cabbage (T3), celery (T4), and white clover (T5). The results showed that compared with the monoculture system, companion planting significantly increased the activities of soil urease (except for T5) and sucrase, but decreased catalase activity. In addition, T2 significantly improved microbial diversity (Shannon index) while T1 resulted in a decrease of bacterial OTUs and an increase of fungal OTUs. Companion planting also significantly changed soil microbial community structures and compositions. Correlation analysis showed that soil enzyme activities were closely correlated with bacterial and fungal community structures. Moreover, the companion system weakened the complexity of microbial networks. These findings indicated that companion plants can provide nutrition to microbes and weaken the competition among them, which offers a theoretical basis and data for further research into methods for reducing continuous cropping obstacles in agriculture.

• 한국환경농학회지
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• 제38권4호
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• pp.219-224
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• 2019

BACKGROUND: Soil bacteria play important roles in organic matter decomposition and nutrient cycling during the non-growing season. The purpose of this study was to investigate the effects of soil management and chemical properties on the utilization of carbon sources by soil bacteria in paddy fields. METHODS AND RESULTS: The Biolog EcoPlate was used for analyzing community-level carbon substrate utilization profiles of soil bacteria. Soils were collected from the following three types of areas: plain, interface and mountain areas, which were tested to investigate the topology effect. The results of canonical correspondence analysis and Kendall rank correlation analysis showed that soil C/N ratio and NH₄⁺ influenced utilization of carbon sources by bacteria. The utilization of carbohydrates and complex carbon sources were positively correlated with NH₄⁺ concentration. Cultivated paddy fields were compared with adjacent abandoned fields to investigate the impact of cultivation cessation. The level of utilization of putrescine was lower in abandoned fields than in cultivated fields. Monoculture fields were compared with double cropping fields cultivated with barley to investigate the impact of winter crop cultivation. Cropping system altered bacterial use of carbon sources, as reflected by the enhanced utilization of 2-hydroxy benzoic acid under monoculture conditions. CONCLUSION: These results show that soil use intensity and topological characteristics have a minimal impact on soil bacterial functioning in relation to carbon substrate utilization. Moreover, soil chemical properties were found to be important factors determining the physiological profile of the soil bacterial community in paddy fields.

• Journal of Ecology and Environment
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• 제40권1호
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• pp.75-83
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• 2016

Background: In order to evaluate the effect of pH, known as a critical factor for shaping the biogeographical microbial patterns in the studies by others, on the bacterial diversity, we selected two sites in a similar geographical location (site 1; north latitude 35.3, longitude 127.8, site 2; north latitude 35.2, longitude 129.2) and compared their soil bacterial diversity between them. The mountain soil at site 1 (Jiri National Park) represented naturally acidic but almost pollution free (pH 5.2) and that at site 2 was neutral but exposed to the pollutants due to the suburban location of a big city (pH 7.7). Methods: Metagenomic DNAs from soil bacteria were extracted and amplified by PCR with 27F/518R primers and pyrosequenced using Roche 454 GS FLX Titanium. Results: Bacterial phyla retrieved from the soil at site 1 were more diverse than those at site 2, and their bacterial compositions were quite different: Almost half of the phyla at site 1 were Proteobacteria (49 %), and the remaining phyla were attributed to 10 other phyla. By contrast, in the soil at site 2, four main phyla (Actinobacteria, Bacteroidetes, Proteobacteria, and Cyanobacteria) composed 94 %; the remainder was attributed to two other phyla. Furthermore, when bacterial composition was examined on the order level, only two Burkholderiales and Rhizobiales were found at both sites. So depending on pH, the bacterial community in soil at site 1 differed from that at site 2, and although the acidic soil of site 1 represented a non-optimal pH for bacterial growth, the bacterial diversity, evenness, and richness at this site were higher than those found in the neutral pH soil at site 2. Conclusions: These results and the indices regarding diversity, richness, and evenness examined in this study indicate that pH alone might not play a main role for bacterial diversity in soil.

• Journal of Microbiology and Biotechnology
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• 제13권2호
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• pp.251-255
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• 2003

The bacterial compositions of seven hot-pepper sown soil were compared in this study. From the 624 isolates, 95 species and 49 genera were identified by fatty acid methyl ester analysis (FAME). The FAME results of seven soil showed two distinct clusters for aerobic and Gram-negative bacteria in the high productivity and monoculture soil samples. While Arthrobacter ($17\%$), Kocuria ($11\%$), Pseudomonas ($8\%$), and Bacillus ($8\%$) were predominant among bacteria which were cultured on heterotrophic (YG) agar medium, Pseudomonas ($56\%$), Stenotrophomonas ($16\%$), and Burkholderia ($8\%$) were predominant on crystal violet agar medium. Shannon Weaver indices (H) indicated that colonies obtained from heterotrophic agar medium (3.1) were found to be more diverse than those obtained from the crystal violet media (1.9). The results suggest that FAME analysis may be a potential indicator for of soil quality.