• Journal of Microbiology and Biotechnology
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• v.23 no.11
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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).

• Ocean and Polar Research
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• v.27 no.2
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.

• Korean Journal of Microbiology
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• v.48 no.1
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• pp.8-15
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• 2012

Bioaerosols generated from composting facilities and landfills may create health risks for workers and nearby residents. To determine the levels of culturable airborne bacteria and fungi in bioaerosols, samples were seasonally collected at a composting facility and a landfill in Ulsan, Korea with an impaction-type sampler. Concentrations of heterotrophic bacteria averaged (in $MPN/m^3$) $6.5{\times}10^3$ (range $1.5{\times}10^2-1.5{\times}10^4$) in the composting facility and $3.9{\times}10^3$ (range $6.0{\times}10^1-9.3{\times}10^3$) at the entrance of the facility. These concentrations were 460 and 280 times higher than those of reference sites. Coliform bacteria were detected both inside and entrance of the facility. On the landfill, heterotrophic bacterial concentrations averaged (in $MPN/m^3$) $4.9{\times}10^2$ (range $1.7{\times}10^2-1.0{\times}10^3$), while they averaged $3.7{\times}10^2$ (range $4.8{\times}10^1-1.3{\times}10^3$) at the parking lot of the landfill. These concentrations were 35 and 26 times higher than those of reference sites. When we isolated and tentatively identified heterotrophic bacteria, Pseudomonas luteola was the most dominant species in bioaerosols from the composting facility, whereas the most abundant one in reference samples was Micrococcus sp. Average concentrations of airborne fungi were measured between $4.8{\times}10^2$ and $7.9{\times}10^2\;MPN/m^3$ depending on sites, which were 2.1-3.4 times higher compared to those of reference sites. While Cladosporium, Alternaria, and Penicillium were commonly identified fungal genera, genus Aspergillus was identified only in bioaerosols from the composting facility.

• The Plant Pathology Journal
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• v.34 no.3
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• pp.241-249
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• 2018

Commercial biocontrol of microbial plant diseases and plant pests, such as nematodes, requires field-effective formulations. The isolate Pseudomonas chlororaphis O6 is a Gram-negative bacterium that controls microbial plant pathogens both directly and indirectly. This bacterium also has nematocidal activity. In this study, we report on the efficacy of a wettable powder-type formulation of P. chlororaphis O6. Culturable bacteria in the formulated product were retained at above $1{\times}10^8$ colony forming units/g after storage of the powder at $25^{\circ}C$ for six months. Foliar application of the diluted formulated product controlled leaf blight and gray mold in tomato. The product also displayed preventative and curative controls for root-knot nematode (Meloidogyne spp.) in tomato. Under laboratory conditions and for commercially grown melon, the control was at levels comparable to that of a standard commercial chemical nematicide. The results indicated that the wettable powder formulation product of P. chlororaphis O6 can be used for control of plant microbial pathogens and root-knot nematodes.

• Journal of Microbiology
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• v.37 no.4
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• pp.193-199
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• 1999

Fifty-eight strains showing different colony morphological characteristics on various media were isolated from marine coral (Plexauridae sp.) and ambient seawater near Mun-Sum, Cheju-Island in 1998. Bacterial diversity was studies by phylogenetic analysis of the partial 16S rRNA gene sequences. All isolates representing the bacterial domain included affiliates of the high G+C (59%) and los G+C (3%) subdivision of Gram positive bacteria, and the alpha (33%) and gamma (5%) subdivision of the Proteobacteria. The 16S rDNA sequence similarity of the isolates was in the 88.3 to 100% range (average, 95.6%) to reported sequence data. In the comparison of the isolates from marine coarl and ambient seawater, more diverse groups belonging to ${\alpha}$-Proteobacteria were preferentially obtained from seawater.

• Tuberculosis and Respiratory Diseases
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• v.84 no.1
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• pp.1-12
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• 2021

Mycobacterium tuberculosis has infected more than two billion individuals worldwide, of whom 5%-10% have clinically active disease and 90%-95% remain in the latent stage with a reservoir of viable bacteria in the macrophages for extended periods of time. The tubercle bacilli at this stage are usually called dormant, non-viable, and/or non-culturable microorganisms. The patients with latent bacilli will not have clinical pictures and are not infectious. The infections in about 2%-23% of the patients with latent status become reactivated for various reasons such as cancer, human immunodeficiency virus infection, diabetes, and/or aging. Many studies have examined the mechanisms involved in the latent state of Mycobacterium and showed that latency modified the expression of many genes. Therefore, several mechanisms will change in this bacterium. Hence, this study aimed to briefly examine the genes involved in the latent state as well as the changes that are caused by Mycobacterium tuberculosis. The study also evaluated the relationship between the functions of these genes.

• Journal of Microbiology and Biotechnology
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• v.22 no.8
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• pp.1044-1053
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• 2012

The gene encoding an esterase enzyme was cloned from a metagenomic library of cow rumen bacteria. The esterase gene (est5S) was 1,026 bp in length, encoding a protein of 366 amino acid residues with a calculated molecular mass of 40,168 Da. The molecular mass of the enzyme was estimated to be 40,000 Da. The Est5S protein contains the Gly-X-Ser-X-Gly motif found in most bacterial and eukaryotic serine hydrolases. However, the Asp or Glu necessary for the catalytic triad [Ser-Asp-(Glu)-His] was not present, indicating Est5S represents a novel member of the GHSQG family of esterolytic enzymes. BlastP in the NCBI database analysis of Est5S revealed homology to hypothetical proteins and it had no homology to previous known lipases and esterases. Est5S was optimally active at pH 7.0 and $40^{\circ}C$. Among the p-nitrophenyl acylesters tested, high enzymatic activities were observed on the short-chain p-nitrophenyl acylesters, such as p-nitrophenyl acetate, etc. The conserved serine residue ($Ser_{190}$) was shown to be important for Est5S activity. The primers that amplified the est5S gene did not show any relative band with 49 species of culturable rumen bacteria. This implies that a new group esterase gene, est5S, may have come from a noncultured cow rumen bacterium.

• Journal of Microbiology and Biotechnology
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• v.31 no.9
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• pp.1218-1230
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• 2021

Cold-adapted plant growth-promoting bacteria (PGPB) with multiple functions are an important resource for microbial fertilizers with low-temperature application. In this study, culturable cold-adapted PGPB strains with nitrogen fixation and phosphorus solubilization abilities were isolated. They were screened from root and rhizosphere of four dominant grass species in nondegraded alpine grasslands of the Qilian Mountains, China. Their other growth-promoting characteristics, including secretion of indole-3-acetic acid (IAA), production of siderophores and ACC deaminase, and antifungal activity, were further studied by qualitative and quantitative methods. In addition, whether the PGPB strains could still exert plant growth-promoting activity at 4℃ was verified. The results showed that 67 isolates could maintain one or more growth-promoting traits at 4℃, and these isolates were defined as cold-adapted PGPB. They were divided into 8 genera by 16S rRNA gene sequencing and phylogenetic analysis, of which Pseudomonas (64.2%) and Serratia (13.4%) were the common dominant genera, and a few specific genera varied among the plant species. A test-tube culture showed that inoculation of Elymus nutans seedlings with cold-adapted PGPB possessing different functional characteristics had a significant growth-promoting effect under controlled low-temperature conditions, including the development of the roots and aboveground parts. Pearson correlation analysis revealed that different growth-promoting characteristics made different contributions to the development of the roots and aboveground parts. These cold-adapted PGPB can be used as excellent strain resources suitable for the near-natural restoration of degraded alpine grasslands or agriculture stock production in cold areas.

• Journal of Microbiology and Biotechnology
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• v.32 no.1
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• pp.91-98
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• 2022

Tetanus is a potentially fatal public health illness resulted from the neurotoxins generated by Clostridium tetani. C. tetani is not easily culturable and culturing the relevant bacteria from infected wounds has rarely been useful in diagnosis; PCR-based assays can only be conducted at highly sophisticated laboratories. Therefore, a real-time recombinase polymerase amplification assay (Exo-RPA) was constructed to identify the fragments of the neurotoxin gene of C. tetani. Primers and the exo probe targeting the conserved region were designed, and the resulting amplicons could be detected in less than 20 min, with a detection limit of 20 copies/reaction. The RPA assay displayed good selectivity, and there were no cross-reactions with other infectious bacteria common in penetrating wounds. Tests of target-spiked serum and pus extract revealed that RPA is robust to interfering factors and has great potential for further development for biological sample analysis. This method has been confirmed to be reliable for discriminating between toxic and nontoxic C. tetani strains. The RPA assay dramatically improves the diagnostic efficacy with simplified device architecture and is a promising alternative to real-time PCR for tetanus detection.

• Journal of Life Science
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• v.17 no.9 s.89
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• pp.1284-1289
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• 2007

The Biological Activated Carbon (BAC) process in the water treatments represents a kind of biofiltration process which capabilities of bacteria to remove organic matters are maximized. It enables to eliminate organic matters and effectively reduce microbial regrowth potentials. As attached bacteria employ natural organic matter as a substrate, they are significantly dependent on indigenous microorganisms. In this study, characteristics of bacterial community by culturable and unculturable Methods have been conducted in a pilot plant using SAC in water treatment process at the downstream of the Nakdong River. Based on the results, HPC and bacterial- production for coal-based activated carbon material were $1.20{\sim}56.2{\times}l0^7$ cfu/g and $1.2{\sim}3.7\;mgC/m^{3}h$, respectively, in the SAC process. The highest level of attached bacteria biomass and organic carbon removal efficiency was found in the coal-based activated carbon. The genera Pseudomonas, Flavobacterium, Alcaligenes, Acilzetobacter, and Spingomonas were identified for each activated carbon material. Pseudomonas vesicularis was the dominant species in the coconut- and coal-based materials, where as Pseudomonas cepacia was the dominant species in the wood-based material. The Scanning Electron Microscope (SEM) observation of the activated carbon surface also found the widespread distribution of rod form and coccus. The community of attached bacteria was investigated by performing Fluorescent in situ hybridization (FISH) analysis. a group was dominant in coal, wood and coccunt-based materials, ${\alpha},\;{\beta}\;and\;{\gamma}$ group ranged from 27.0 ${\sim}$ 43.0%, 7.1 ${\sim}$ 22.0%, 11.3 ${\sim}$ 28.6%, respectively. These results suggest that a group bacterial community appears to be regulated removal efficiency of organic material in water treatment process.