• Ocean and Polar Research
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• 제25권1호
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• pp.21-30
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• 2003

Seasonal fluctuations of physico-chemical and biological aspects of the environment were studied in Vladivostok harbour (Golden Horn Bay, the East Sea/Sea of Japan). The benthic community structure was described with a focus on size-spectra (bacteria, meio- and macrofauna) related with the chemical environment and chemical fluxes in sediment and to reveal their possible ecological role in the process of bioremediation of the environment. Samples from two sites with different concentrations of heavy metals (Fe, Zn, Cu, Pb, Mn, Cr, Ni Cd, Co) and petroleum hydrocarbon were assessed by a number of methods. These included plate counts of culturable bacteria, observation through a scanning electron (SEM) and transmission electron microscope (TEM). These approaches were complemented with microscopic assessments of the diversity of the benthic community. The specific communities had a limited number of species, tolerant to abnormally high levels of toxic compounds. The dominant species were presented by several sho.1-lived small polychaetes (Capitella capitata) and nematodes (Oncholaimium ramosum). The highest population density was recorded in microbenthos, in various diatoms, various physiological groups of bacteria which participate in biomineralization: marine heterotrophic bacteria, which oxidized oil, black oil in addition to groups resistant to heavy metals. They have the entire set of mechanisms for neutralizing the negative effect of those compounds, forming the detrital food web and biogeochemical circulation of material in sediments, which results in the biological self-recycling of sea basins. Macro- and meiobenthic organisms were more sensitive to a greater extent of $H_2S$ and petroleum hydrocarbons than to metal content, but the within-site rankings were the same as those achieved for microbiological analyses.

• 한국응용과학기술학회지
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• 제37권6호
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• pp.1698-1705
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• 2020

나이가 20-25세인 남녀 성인들 20명(남성 5명, 여성 15명)의 엄지손가락 표면에 상재하는 세균을 채취하고 Luria-Bertani agar에서 배양하였다. 배양된 세균들의 16S rDNA를 polymerase chain reaction을 통하여 증폭하고, 그 염기서열을 분석하였다. 이렇게 얻어진 염기서열을 genbank의 자료들과 비교하여 세균들을 동정한 결과, 총 14종의 세균들이 확인되었다. 개인별로는 평균 2.5종의 배양 가능한 세균들을 손의 피부에 보유하는 것으로 확인되었다. 확인된 세균 중에서는 Staphylococcus 종들이 가장 널리 존재하고 있었으며, 다음으로는 Micrococcus luteus이었다. Staphylococcus 종들의 경우에는 그 분포에 있어서 성별에 따른 차이가 적었으나, Micrococcus luteus의 경우에는 남자보다 여자에게서 훨씬 더 많이 분리되는 경향을 보였다. 이러한 결과는 피부 질환에 대한 연구, 피부질환에 대한 치료제 개발, 피부에 사용하는 화장품개발 등의 분야에 도움이 될 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제12권1호
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• pp.77-83
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• 1999

Molecular biological techniques that recently developed, have made it possible to realize some of new attempts in the research field of rumen microbiology. Those are 1) cloning of genes from rumen microorganisms mainly in E. coli, 2) transformation of rumen bacteria and 3) ecological analysis with nonculturing methods. Most of the cloned genes are for polysaccharidase enzymes such as endoglucanase, xylanase, amylase, chitinase and others, and the cloning rendered gene structural analyses by sequencing and also characterization of the translated products through easier purification. Electrotransformation of Butyrivibrio fibrisolvens and Prevotella ruminicola have been made toward the direction for obtaining more fibrolytic, acid-tolerant, depoisoning or essential amino acids-producing rumen bacterium. These primarily required stable and efficient gene transfer systems. Some vectors, constructed from native plasmids of rumen bacteria, are now available for successful gene introduction and expression in those rumen bacterial species. Probing and PCR-based methodologies have also been developed for detecting specific bacterial species and even strains. These are much due to accumulation of rRNA gene sequences of rumen microbes in databases. Although optimized analytical conditions are essential to reliable and reproducible estimation of the targeted microbes, the methods permit long term storage of frozen samples, providing us ease in analytical work as compared with a traditional method based on culturing. Moreover, the methods seem to be promissing for obtaining taxonomic and evolutionary information on all the rumen microbes, whether they are culturable or not.

• Journal of Microbiology and Biotechnology
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• 제5권4호
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• pp.181-187
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• 1995

The cells of Vibrio vulnificus can be induced to the viable but nonculturable (VBNC) state by natural environmental parameters. The V. vulnificus cells in the VBNC state can not be recovered by ordinary laboratory techniques. This nonculturability could often hamper development of effective processing strategies to minimize the number of V. vulnificus in seafoods. Even with V. vulnificus cells in a culturable state, the length of time required to identify the bacteria in contaminated food by phenotyphic characterization may prevent appropriate in-time responses by public health agencies to infections of the bacteria. In the present study, we used polymerase chain reaction (PCR) to develop a rapid and direct detection method for V. vulnificus in small octopus (Octopus variabilis) which is consumed as a raw food in Korea. The region targeted was a 704-base pair (bp) portion of the hemolysin gene, vvhA, of V. vulnificus. The primers designed for PCR amplification were specific for all V. vulnificus sp. tested. Several methods were examined to extract total DNA directly from V. vulnificus seeded into the octopus homogenate and the guanidine isothiocyanate (CITC) method appeared to be most effective. From the octopus homogenate seeded by V. vulnificus at an initial level of $10^2$ CFU/ml of the homogenate and then incubated for 12 h, the targeted sequence was successfully amplified by PCR and the 704-bp DNA fragment was observed by gel electrophoresis. The total completion of this assay requires less than one day.

• Journal of Microbiology
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• 제43권spc1호
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• pp.93-100
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• 2005

It had long been assumed that a bacterial cell was dead when it was no longer able to grow on routine culture media. We now know that this assumption is simplistic, and that there are many situations where a cell loses culturability but remains viable and potentially able to regrow. This mini-review defines what the 'viable but nonculturable' (VBNC) state is, and illustrates the methods that can be used to show that a bacterial cell is in this physiological state. The diverse environmental factors which induce this state, and the variety of bacteria which have been shown to enter into the VBNC state, are listed. In recent years, a great amount of research has revealed what occurs in cells as they enter and exist in this state, and these studies are also detailed. The ability of cells to resuscitate from the VBNC state and return to an actively metabolizing and culturable form is described, as well as the ability of these cells to retain virulence. Finally, the question of why cells become nonculturable is addressed. It is hoped that this mini-review will encourage researchers to consider this survival state in their studies as an alternative to the conclusion that a lack of culturability indicates the cells they are examining are dead.

• Journal of Microbiology and Biotechnology
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• 제22권3호
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• pp.283-291
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• 2012

Bioremediation efforts often rely on the application of surfactants to enhance hydrocarbon bioavailability. However, synthetic surfactants can sometimes be toxic to degrading microorganisms, thus reducing the clearance rate of the pollutant. Therefore, surfactant-resistant bacteria can be an important tool for bioremediation efforts of hydrophobic pollutants, circumventing the toxicity of synthetic surfactants that often delay microbial bioremediation of these contaminants. In this study, we screened a natural surfactant-rich compartment, the estuarine surface microlayer (SML), for cultivable surfactant-resistant bacteria using selective cultures of sodium dodecyl sulfate (SDS) and cetyl trimethylammonium bromide (CTAB). Resistance to surfactants was evaluated by colony counts in solid media amended with critical micelle concentrations (CMC) of either surfactants, in comparison with non-amended controls. Selective cultures for surfactant-resistant bacteria were prepared in mineral medium also containing CMC concentrations of either CTAB or SDS. The surfactantresistant isolates obtained were tested by PCR for the Pseudomonas genus marker gacA gene and for the naphthalene-dioxygenase-encoding gene ndo. Isolates were also screened for biosurfactant production by the atomized oil assay. A high proportion of culturable bacterioneuston was tolerant to CMC concentrations of SDS or CTAB. The gacA-targeted PCR revealed that 64% of the isolates were Pseudomonads. Biosurfactant production in solid medium was detected in 9.4% of tested isolates, all affiliated with genus Pseudomonas. This study shows that the SML is a potential source of surfactant-resistant and biosurfactant-producing bacteria in which Pseudomonads emerge as a relevant group.

• 한국환경과학회지
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• 제10권3호
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• pp.239-245
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• 2001

This research was performed to investigate the dynamics of microbial community by RBC (Rotating Biological Contactor) using Rhodococcus sp. EL-GT and activated sludge. Cell counts revealed by DAPI were compared with culturable bacterial counts from nutrient agar. Colony counts on nutrient agar gave values 20~25% and 1~15% of cell counts (DAPI). The cell counts for the dynamics of bacterial community were determined by combination of in situ hybridization with fluorescently-labelled oligonyucleotide probes and epifluorescence microscopy. Around 90~80% of total cells visualized DAPI were also detected by the bacteria probe EUB 338. For both reactors proteobacteria belonging to the gamma subclass were dominant in the first stage (1 and 2 stage) and proteobacteria belonging to the gamma subclass were dominant in the last stage (3 and 4 stage).

• 미생물학회지
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• 제47권1호
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• pp.38-49
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• 2011

하수처리시설에서 발생하는 공기중 미생물은 작업자 및 주민에게 건강상 위해의 요인이 될 수 있다. 이들 시설에서 공기중 세균과 진균의 농도 수준을 파악하기 위해 울산시에 위치한 위생처리장 1곳(YC-STP)과 하수처리장 3곳(YY-, OS-, HY-STP)의 포기조와 포기조 근처 지점에서 계절별로 공기중 미생물을 포집하였다. YC-STP의 공기중 세균 농도는 포기조에서 $1.3({\pm}0.2){\times}10^3-2.6({\pm}1.1){\times}10^4$ MPN/$m^3$, 포기조 근처에서 $1.7 ({\pm}1.0){\times}10^2-7.2({\pm}2.2){\times}10^3$ MPN/$m^3$로 매우 높았으며, 대장균군도 검출되었다. YY-, OS-, HY-STP의 공기중 세균 농도는 포기조에서 $1.9({\pm}1.2){\times}10^1-1.8({\pm}1.2){\times}10^4$ MPN/$m^3$, 포기조 근처에서 $5.0({\pm}2.8){\times}10^0-6.6({\pm}2.0){\times}10^3$ MPN/$m^3$의 범위였다. YC-, OS-, YY-STP에서의 공기중 세균 농도는 대조군 지점에 비해 평균값 기준으로 포기조에서는 16-1,200배, 포기조 근처에서는 9-280배 정도 더 높은 수치였으며, 포기조 근처(10 m)보다 포기조(0 m)에서 1.7-4.4배 정도 더 높았다. 공기중 세균을 분리하여 동정한 결과 하수처리시설에서는 Pseudomonas luteola, 대조군 지점에서는 Micrococcus sp.가 우점하였다. 공기중 진균의 농도는 포기조 보다 포기조 근처에서 더 높았으며 포기조 외에 다른 주요 발생원이 존재함을 시사한다. Cladosporium, Alternaria, Penicillium의 3속이 주로 검출되었다.

• 생명과학회지
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• 제13권5호
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• pp.723-731
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• 2003

Lipase 유전자들의 보존적 영역을 탐색하기 위해 LED(Lipase Engineering Database)와 COG (Clusters of Orthologous Groups of proteins)를 통하여 각각 132개와 24개의 서열을 얻어 분석하였다. Lipase 유전자의 염기서열은 아주 다양하였고 LED의 각 상동성그룹 (homologous family) 별로 독특한 아미노산 서열이 보존적인 것을 확인 할 수 있었다. COG0657에 속하는 lipase들은 LED의 Moraxella lipase 1 homologous group과 유사한 아미노산 보존적 영역이 있음을 확인하였다. 다양한 반응 조건에 적응하는 혹은 높은 활성을 갖는 새로운 lipase 유전자를 원핵생물에서 탐색하기 위하여 다양한 시도들이 수행되어 왔지만 그들은 모두 배양가능한 미생물에 국한되어 있었다. 배양할 수 없는 세균의 유전자원을 포함하는 메타게놈에 대한 유용성 역시 최근에 널리 인식되고 있다. Lipase 유전자의 다양성으로 보았을 때 메타게놈을 이용한 새로운 lipase 유전자를 찾는 작업도 가능할 것으로 사료되어 lipase유전자 일부를 (222∼713 bp) 증폭시키는 총 10개의 PCR primer를 설계하였으며 그 가능성을 NCBI의 BLAST를 통하여 검증하였다. Lipase 유전자의 염기서열은 아미노산 서열보다 아주 다양하여 비교적 많은 수의 primer set이 필요하였다. 각 primer set의 증폭효율은 각 LED group의 16.7%와 60.0% 사이였고 개별적인 primer set을 이용할 때 보다 3.6배 효율이 높은 것으로 드러났다. Lipase 유전자의 다양성은 설계된 primer set들을 이용하여 새로운 lipase 유전자를 검출할 가능성을 높이는 것으로 사료되었다.

• Journal of Microbiology and Biotechnology
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• 제23권11호
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• pp.1617-1626
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• 2013

The Bacterial community structure and its complexity of the enrichment culture during the isolation and screening of imidacloprid-degrading strain were studied using denaturating gradient gel electrophoresis analysis. The dominant bacteria in the original tea rhizosphere soil were uncultured bacteria, Rhizobium sp., Sinorhizobium, Ochrobactrum sp., Alcaligenes, Bacillus sp., Bacterium, Klebsiella sp., and Ensifer adhaerens. The bacterial community structure was altered extensively and its complexity reduced during the enrichment process, and four culturable bacteria, Ochrobactrum sp., Rhizobium sp., Geobacillus stearothermophilus, and Alcaligenes faecalis, remained in the final enrichment. Only one indigenous strain, BCL-1, with imidacloprid-degrading potential, was isolated from the sixth enrichment culture. This isolate was a gram-negative rod-shaped bacterium and identified as the genus Ochrobactrum based on its morphological, physiological, and biochemical properties and its 16S rRNA gene sequence. The degradation test showed that approximately 67.67% of the imidacloprid (50 mg/l) was degraded within 48 h by strain BCL-1. The optimum conditions for degradation were a pH of 8 and $30^{\circ}C$. The simulation of imidacloprid bioremediation by strain BCL-1 in soil demonstrated that the best performance in situ (tea soil) resulted in the degradation of 92.44% of the imidacloprid (100 mg/g) within 20 days, which was better than those observed in the ex situ simulations that were 64.66% (cabbage soil), 41.15% (potato soil), and 54.15% (tomato soil).