• 한국환경농학회지
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• 제30권4호
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• pp.367-376
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• 2011

논 토양의 미생물 생태 다양성을 조사하기 위한 효과적인 방법으로 qRT-PCR을 적용하고자 본 연구를 수행하였다. 논 토양 미생물의 gDNA를 분리하기 위하여 Mo Bio kit를 사용한 효과적이고 안정적인 gDNA 분리 방법을 확립하였다. 논 토양 미생물 다양성을 qRT-PCR로 검출하기 위하여 bacteria를 세분한 ${\alpha}$-Proteobacteria, ${\beta}$-Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes 다섯 가지 문과 전체 bacteria, 전체 fungi를 구분할 수 있는 특이 primer set을 선정하여 다양한 조건의 시험을 통하여 최종 조건을 확립하였으며 재현성 실험을 통하여 방법의 유의성을 검증하였다.

• 한국축산식품학회지
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• 제41권4호
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• pp.701-714
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• 2021

In this study, the microbial community succession and the protein hydrolysis of donkey meat during refrigerated (4℃) storage were investigated. 16S rDNA sequencing method was used to analyze the bacteria community structure and succession in the level of genome. Meanwhile, the volatile base nitrogen (TVB-N) was measured to evaluate the degradation level of protein. After sorting out the sequencing results, 1,274,604 clean data were obtained, which were clustered into 2,064 into operational taxonomic units (OTUs), annotated to 32 phyla and 527 genus. With the prolonging of storage time, the composition of microorganism changed greatly. At the same time, the diversity and richness of microorganism decreased and then increased. During the whole storage period, Proteobacteria was the dominant phyla, and the Photobacterium, Pseudompnas, and Acinetobacter were the dominant genus. According to correlation analysis, it was found that the abundance of these dominant bacteria was significantly positively correlated with the variation of TVB-N. And Pseudomonas might play an important role in the production of TVB-N during refrigerated storage of donkey meat. The predicted metabolic pathways, based on PICRUSt analysis, indicated that amino metabolism in refrigerated donkey meat was the main metabolic pathways. This study provides insight into the process involved in refrigerated donkey meat spoilage, which provides a foundation for the development of antibacterial preservative for donkey meat.

• 한국미생물·생명공학회지
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• 제33권3호
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• pp.226-230
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• 2005

The microbial community during composting of gargage was analyzed using 16S rDNA PCR - DGCE (denaturing gradient gel electrophoresis). Pseudomonas spp. was found throughout the process, and thermophilic Bacillus spp. was dominated at the thermophilic stage. Six thermophilic bacteria were isolated and identified as B. caldoxylolyticus, B. thermoalkalophilus, and B. thermodenitrificans.

• 미생물학회지
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• 제27권4호
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• pp.378-384
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• 1989

The numerical taxonomy of heterotrophic bacterial community in Lake Soyang was analysed. 95, 115, 88 and 75 strains which were isolated at each season from spring in 1987 to winter in 1988 were clustered by single matching coefficient. The diversity indices (H') were in the range of 0.511-1.684, and the community was most diverse in spring. THe seasonal variation of generic composition was significant. Of the domonant genera, Acinetobacter, Pseudomonas, and Flavobacterium were representative.

• Journal of Microbiology and Biotechnology
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• 제30권11호
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• pp.1688-1696
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• 2020

Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and nirK-, nirS- and nosZ-encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH₄⁺-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of nirK, nirS and nosZ in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that nirK, nirS and nosZ-type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by Gammaproteobacteria, Deltaproteobacteria, and Betaproteobacteria. Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.

• 한국환경농학회지
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• 제39권1호
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• pp.26-35
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• 2020

BACKGROUND: Microbes that govern a unique biochemical process of oxidizing ammonia into dinitrogen gas, such as anaerobic ammonium oxidation (anammox) have been reported to play a pivotal role in agricultural soils and in oceanic environments. However, limited information for anammox bacterial abundance and distribution in the terrestrial habitats has been known. METHODS AND RESULTS: Phylogenetic and next-generation sequencing analyses of bacterial 16S rRNA gene were performed to examine potential anammox bacteria in paddy soils. Through clone libraries constructed by using the anammox bacteria-specific primers, some clones showed sequence similarities with Planctomycetes (87% to 99%) and anammox bacteria (94% to 95%). Microbial community analysis for the paddy soils by using Illumina Miseq sequencing of 16S rRNA gene at phylum level was dominated by unclassified Bacteria at 33.2 ± 7.6%, followed by Chloroflexi at 20.4 ± 2.0% and Acidobacteria at 17.0 ± 6.5%. Planctomycetes that anammox bacteria are belonged to was 1.5% (± 0.3) on average from the two paddy soils. CONCLUSION: We suggest evidence of anammox bacteria in the paddy soil. In addition to the relatively well-known microbial processes for nitrogen-cycle, anammox can be a potential contributor on the cycle in terrestrial environments such as paddy soils.

• Journal of Microbiology and Biotechnology
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• 제19권12호
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• pp.1656-1664
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• 2009

Bioaugmentation of bioreactors focuses on the removal of numerous organics, with little attention typically paid to the maintenance of high and stable nitrite accumulation in partial nitrification. In this study, a bioaugmented membrane bioreactor (MBR) inoculated with enriched ammonia-oxidizing bacteria (AOB) was developed, and the effects of dissolved oxygen (DO) and temperature on the stability of partial nitrification and microbial community structure, in particular on the nitrifying community, were evaluated. The results showed that DO and temperature played the most important roles in the stability of partial nitrification in the bioaugmented MBR. The optimal operation conditions were found at 2-3 mgDO/l and $30^{\circ}C$, achieving 95% ammonia oxidization efficiency and nitrite ratio ($NO_2^-/{NO_x}^-$) of 0.95. High DO (5-6 mg/l) and low temperature ($20^{\circ}C$) had negative impacts on nitrite accumulation, leading to nitrite ratio drop to 0.6. However, the nitrite ratio achieved in the bioaugmented MBR was higher than that in most previous literatures. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) were used to provide an insight into the microbial community. It showed that Nitrosomonas-like species as the only detected AOB remained predominant in the bioaugmented MBR all the time, and coexisted with numerous heterotrophic bacteria. The heterotrophic bacteria responsible for mineralizing soluble microbial products (SMP) produced by nitrifiers belonged to the Cytophaga-Flavobacterium-Bacteroides (CFB) group, and $\alpha$-, $\beta$-, and $\gamma$- Proteobacteria. The fraction of AOB ranging from 77% to 54% was much higher than that of nitrite-oxidizing bacteria (0.4-0.9%), which might be the primary cause for the high and stable nitrite accumulation in the bioaugmented MBR.

• 미생물학회지
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• 제45권2호
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• pp.155-162
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• 2009

계통적으로 근연하며 지리적 분포가 유사한 두 종의 Spirastrella 속의 해양 해면, S. panis와 S. abata의 배양 가능한 공생세균 군집구조를 16S rDNA-RFLP 방법에 의해 분석하였다. 공생세균의 배양은 해면추출물 3%를 포함하는 MA 배지를 사용하였다. 증폭된 16S rDNA의 RFLP (restriction fragment length polymorphism) 분석을 위한 제한효소로 HaeIII와 MspI을 이용하였으며, 그 결과 24개의 RFLP type을 구별할 수 있었다. 각 패턴별로 1~5개의 분리균주를 선별하여 부분 염기서열 분석 결과, 알려진 세균 종과 98.4% 이상의 유사도를 나타내었으며 2종의 Spirastrella 해면으로부터 분리된 세균들은 모두 Alphaproteobacteria, Gammaproteobacteria, Firmicutes, Actinobacteria 4개의 강(class)에 포함되었다. Alphaproteobacteria는 S. abata에서 39.3%, S. panis에서 47.6%가 관찰되어 두 해면에서 우점하는 세균 군집이었다. Gammaproteobacteria의 경우 S. abata에서 38.5%로 관찰된 반면 S. panis에서 1.6%의 아주 적은 비율로 관찰되었다. 또한 Bacillus (phylum Firmicutes) 종은 S. abata에서 9.7%를 나타낸 반면, S. panis에서는 44.3%의 분포를 나타내었다. Planococcus maritimus (8.1%, phylum Firmicutes)와 Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria)는 S. abata에서만 관찰되어 이들은 S. abata에 특이적인 세균 종임을 알 수 있었다. 같은 장소에 서식하는 계통적으로 근연한 두 종의 해면에서 공생세균의 군집 구조는 차이가 큰 것으로 나타났다.

• 한국지하수토양환경학회지:지하수토양환경
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• 제17권1호
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• pp.47-54
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• 2012

When quicklime is added into soil for various purposes, abrupt changes in soil chemistry may affect essential ecological functions played by indigenous bacterial communities in soil. The magnitude of influence was estimated by observing changes in abundance and diversity of soil bacteria after quicklime treatment. When several soil samples were treated up to 20% (w/w) quicklime, plate count of viable cells ranged $10^2{\sim}10^3$ CFU $g^{-1}$, showing a reduction of more than $10^4$ times from viable counts of the untreated sample. Diversity of the bacterial isolates that survived after quicklime treatment was analyzed by conducting $GTG_5$ rep-PCR fingerprinting. There were only two types of fingerprints common to both 5% and 20% quicklime samples, implying that bacteria surviving at different strength of quicklime treatment differed depending on their tolerance to quicklime-treated condition. Isolates surviving the quicklime treatments were further characterized by Gram staining and endospore staining. All isolates were found to be Gram positive bacteria, and 85.4% of them displayed endospores state. In conclusion, most bacteria surviving quicklime treatment appear to be endospores. This finding suggests that most of ecological functions of bacteria in soil are lost with quicklime treatment.

• 한국해양바이오학회지
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• 제13권1호
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• pp.10-19
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• 2021

This study investigated how ozone treatment can successfully inactivate pathogenic bacteria in both artificial seawater and effluents discharged from the fishery quarantine station in Pyeongtaek Port, Korea. Vibrio sp. and Streptococcus sp. were initially inoculated into the artificial seawater. All microbes were almost completely inactivated within 10 min and 30 min by injecting 6.4 mg/min and 2.0 mg/min of ozone, respectively. It was discovered that the water storing Pleuronichthys, Pelteobagrus, and Cyprinus imported from China contained the indicator bacteria, Vibrio sp., Enterococcus sp., total coliforms, and heterotrophic microorganisms. Compared to the control, three indicator bacteria were detected at two to six times higher concentrations. The water samples displayed a diverse microbial community, comprising the following four phyla: Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria. Almost all indicator bacteria were inactivated in 5 min at 2.0 mg/min of ozonation; comparatively, 92.9%-98.2% of the less heterotrophic microorganisms were deactivated within the same time period. By increasing the dosage to 6.4 mg/min, 100% deactivation was achieved after 10 min. Despite the almost complete inactivation of most indicator bacteria at high doses after 10 min, several bacterial strains belonging to the Proteobacteria have still been found to be resistant under the given operational conditions.