• Mycobiology
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• v.51 no.2
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• pp.72-78
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• 2023

In this study, a fungal strain KNUF-22-025 belonging to the genus Botryotrichum was isolated from the soil in Korea. The cultural and morphological characteristics of this strain differed from those of closely related species. On malt extract agar, strain KNUF-22-025 showed slower growth than most of the related species, except B. domesticum. The conidia size (9.6-21.1×9.9-18.4 ㎛) of strain KNUF-22-025 was larger than those of B. piluliferum, B. domesticum, and B. peruvianum but smaller than those of B. atrogriseum and B. iranicum. Conidiophores in strain KNUF-22-025 (137 ㎛) were longer than those in other closely related species but shorter than those in B. atrogriseum. Multi-locus analysis of molecular markers, such as ITS, 28S ribosomal DNA, RBP2, and TUB2 revealed that strain KNUF-22-025 was distinct from other Botryotrichum species. Thus, this strain is proposed as a novel species based on morphological characteristics along with molecular phylogeny and named Botryotrichum luteum sp. nov.

• The Korean Journal of Mycology
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• v.51 no.2
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• pp.101-109
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• 2023

A fungal strain designated KNUF-21-66Q1 was isolated from soil in Chungcheongbuk Province, Korea. Moderate growth of colonies was observed on potato dextrose agar, oatmeal agar (OA), malt extract agar, and cornmeal agar media at 25℃, and the detailed morphology was examined on OA medium. The colonies on OA medium were flat, had entire margin, hyaline, and yellow concentric rings in 3-4 weeks. Conidiomata were pycnidial, solitary or clustered, globose to subglobose, black-brown, and 300-500 ㎛ in diameter. Conidiogenous cells were smooth, hyaline, globose to ampulliform, and 6.0-9.0×3.0-6.0 ㎛ in size (n=15). Conidia were hyaline to pale brown, slightly golden, obovoid to slightly ellipsoidal, smooth, guttulate, and 3.0-4.7×2.1-3.3 ㎛ in size (n=100). The strain was confirmed based on phylogenetic analysis using internal transcribed spacer regions, the partial 28S rDNA of large subunit, and β-tubulin gene sequences. The morphological observations and phylogenetic analysis revealed that the strain KNUF-21-66Q1 was similar to the previously described Paraconiothyrium kelleni. To our knowledge, this is the first report of P. kelleni in Korea.

• Microbiology and Biotechnology Letters
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• v.52 no.1
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• pp.94-96
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• 2024

Pseudarthrobacter sp. IC2-21 is isolated from the greenhouse soil in Icheon, Gyeonggi, Korea. This strain IC2-21 is a first fluquinconazole degrading soil bacterium. We analyze the whole genome sequence of Pseudarthrobacter sp. IC2-21. The sequence analysis revealed that Pseudarthrobacter sp. IC2-21 possesses a single 4,265,009 bps circular chromosome with a DNA G+C-content of 65.4%. This chromosome contains 3,942 protein-coding sequences and 12 rRNA and 51 tRNA genes. In the result of sequence analysis, it is revealed that strain IC2-21 possessed genes coding the triazole pesticides degradation related enzymes, such as oxygenase, and fluquinconazole degradation related genes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.245-245
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• 2017

Heavy metal pollution of agricultural soils affects land productivity and has impact on the quality of surrounding ecosystem. Soil microbial community parameters are used as reliable indices for assessing quality of agricultural lands under metal stress. This study investigated bacterial community structure of polluted and undisturbed paddy soils to elucidate soil factors that are related to alteration of bacterial communities under conditions of metal pollution. No obvious differences in the richness or diversity of bacterial communities were observed between samples from polluted and control areas. The bacterial communities of three locations were distinct from one another, and each location possessed distinctive set of bacterial phylotypes. The abundances of several phyla and genera differed significantly between study locations. Variation of bacterial community was mostly related to soil general properties at phylum level while at finer taxonomic levels concentrations of arsenic and lead were significant factors. According to results of bacterial community functional prediction, the soil bacterial communities of metal polluted locations were characterized by more abundant DNA replication and repair, translation, transcription and nucleotide metabolism pathway enzymes while amino acid and lipid metabolism as well as xenobiotic biodegradation potential was reduced.Our results suggest that the soil microbial communities had adapted to the elevated metal concentrations in the polluted soils as evidenced by changes in relative abundances of particular groups of microorganisms at different taxonomic resolution levels, and by altered functional potential of the microbial communities.

• Journal of Microbiology and Biotechnology
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• v.20 no.5
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• pp.862-870
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• 2010

Cyperus rotundus L. is a perennial herb that was found to be dominating an area in northeast Brazil previously contaminated with petroleum. In order to increase our knowledge of microorganism-plant interactions in phytoremediation, the bacterial community present in the rhizosphere and roots of C. rotundus was evaluated by culture-dependent and molecular approaches. PCR-DGGE analysis based on the 16S rRNA gene showed that the bacterial community in bulk soil, rhizosphere, and root samples had a high degree of similarity. A complex population of alkane-utilizing bacteria and a variable nitrogen-fixing population were observed via PCR-DGGE analysis of alkB and nifH genes, respectively. In addition, two clone libraries were generated from alkB fragments obtained by PCR of bulk and rhizosphere soil DNA samples. Statistical analyses of these libraries showed that the compositions of their respective populations were different in terms of alkB gene sequences. Using culturedependent techniques, 209 bacterial strains were isolated from the rhizosphere and rhizoplane/roots of C. rotundus. Dot-blot analysis showed that 17 strains contained both alkB and nifH gene sequences. Partial 16S rRNA gene sequencing revealed that these strains are affiliated with the genera Bosea, Cupriavidus, Enterobacter, Gordonia, Mycoplana, Pandoraea, Pseudomonas, Rhizobium, and Rhodococcus. These isolates can be considered to have great potential for the phytoremediation of soil with C. rotundus in this tropical soil area.

• Ocean and Polar Research
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• v.26 no.1
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• pp.51-58
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• 2004

We isolated and identified culturable Arctic bacteria that had inhabited soils around the Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The collected soils were diluted in distilled water; the diluted soil-water was spread on 3M petri-films at Dasan Station. The petri-films were transported to the laboratory at KORDI, and cultured at $4^{\circ}C$. Colonies grown on the petri-films were subsequently cultured on nutrient agar plates at $4^{\circ}C$ every 7 days. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 165 rDNA sequences. A total of 227 strains of bacteria were isolated. Among them, 16S rDNA sequences of 185 strains were identical with those of known strains isolated in this study, and 42 strains were finally identified. Phylogenetic analysis using 16S rDNA indicated that the 30 strains belonged to Pseudomonas, 7 strains to Arthrobacter, two strains to Flavobacterium, and the remaining to Achromobacter, Pedobacter, and Psychrobacter. Among the 42 strains, 14 bacteria produced protease: they were 6 strains of Pseudomonax, 4 strains of Arthrobater, an Achromobacter strain, 2 strains of Flavobacterium, and a Pedohacter strain. We expect these Arctic bacteria can be used for screening to develop new industrial enzymes that are active at low temperatures.

• Parasites, Hosts and Diseases
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• v.40 no.1
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• pp.17-24
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• 2002

We have cloned a cDNA encoding a cysteine proteinase of the Acanthamoeba healui OC-3A strain isolated from the brain of a granulomatous amoebic encephalitis patient. A DNA probe for an A. healui cDNA library screening was amplified by PCR using degenerate oligonucleotide primers designed on the basis of conserved amino acids franking the active sites of cysteine and asparagine residues that are conserved in the eukaryotic cysteine proteinases. Cysteine proteinase gene of A. healui (AhCPI) was composed of 330 amino acids with signal sequence, a proposed pro-domain and a predicted active site made up of the catalytic residues, $Cys^{25},{\;}His^{159},{\;}and{\;}Asn^{175}$. Deduced amino acid sequence analysis indicates that AhCPI belong to ERFNIN subfamily of C 1 peptidases. By Northern blot analysis. no direct correlation was observed between AhCPI mRNA expression and virulence of Acanthamoeba, but the gene was expressed at higher level in amoebae isolated from soil than amoeba from clinical samples. These findings raise the possibility that AhCPI protein may play a role in protein metabolism and digestion of phagocytosed bacteria or host tissue debris rather than in invasion of amoebae into host tissue.

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1386-1392
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• 2010

A bacterial strain designated GR5$^T$, previously isolated from a freshwater culture pond in Taiwan while screening for bacteria for antimicrobial compounds, was characterized using a polyphasic taxonomic approach. Strain GR5$^T$ was found to be Gram-negative, aerobic, greenish-yellow colored, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at $10-40^{\circ}C$ (optimum, $35^{\circ}C$), pH 7.0-8.0 (optimum pH 8.0), and with 0-2.0% NaCl (optimum, 0.5-1.0%). The major fatty acids were $C_{16:1}{\omega}7c$(36.3%), $C_{16:0}$(16.6%), $C_{12:0}$ 3-OH (12.5%), and $C_{18:1}{\omega}7c$(9.1%). The major respiratory quinone was Q-8, and the DNA G+C content of the genomic DNA was 51.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GR5$^T$ belongs to the genus Rheinheimera, where its most closely related neighbors are Rheinheimera texasensis A62-14B$^T$ and Rheinheimera tangshanensis JA3-B52$^T$ with sequence similarities of 98.1% and 97.5%, respectively, and the sequence similarities to any other recognized species within Gammaproteobacteria are less than 96.5%. The mean level of DNA-DNA relatedness between strain GR5$^T$ and R. texasensis A62-14B$^T$, the strain most closely related to the isolate, was $26.5{\pm}7.6%$. Therefore, based on the phylogenetic and phenotypic data, strain GR5$^T$ should be classified as a novel species, for which the name Rheinheimera aquatica sp. nov. is proposed. The type strain is GR5$^T$ (=BCRC 80081$^T$=LMG 25379$^T$).

• Environmental Analysis Health and Toxicology
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• v.21 no.4 s.55
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• pp.375-380
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• 2006

Endocrine disrupting chemicals (EDC) have been emphasized due to their threats in human health. Waste incinerator emission has been emphasized as a source of EDC including polychlorinateddibenzofurans(PCDD/F) and other carcinogenic polycyclic aromatic hydrocarbons (PAHs). Urinary 1-hydroxypyrene (1-OHP) has been used as an exposure biomarker for the PAHs. On the other hand, etheno-DNA adducts, e.g. 1, $N^6-ethenodeoxyadenosine({\varepsilon}dA)$, has been developed as an useful effective or response biomarker for carcinogenesis. Thus, I investigated association between urinary 1-OHP and ${\varepsilon}dA$ levels due to distance from an incinerator which was built more 10 years ago in the middle of a farm in P city. I designated the EDC-high and low exposed group due to distance from the incinerator, i.e. within 2.5km and $5.0{\sim}7.5km$ from the incinerator, respectively. The study subjects were age and sex-matched males and females (mean age, $61.3{\pm}9.6$ yrs; total 40 persons, male, 10; female, 10 for the each group). Urinary 1-OHP and ${\varepsilon}dA$ were analyzed with HPLC-FD and IP-HPLC-FD, respectively. As results, the distance from the incinerator was not associated with urinary 1-OHP nor ${\varepsilon}dA$ levels (p=0.43 and 0.82, respectively). On the other hand, urinary ${\varepsilon}dA$ levels were significantly higher in the hyperlipidemia group (N=10) than normal group (N=30). In conclusion, urinary 1-OHP nor ${\varepsilon}dA$ levels can not be suggested as an incinerator-related exposure nor effective biomarker. However, not only distance from the incinerator bot also systemic approaches including wind and soil contamination are required to assume exposure levels of incinerator-related EDC.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.86-95
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• 2015

To study the halobacterial diversity at the rhizospheric soil of coastal plant native to Dokdo islands, several host plant were selected and its rhizospheric soil was sampled. Soil sample was diluted serially and pure isolation was done by sub-culture using marine agar media. 26 halophilic strains cultivable at the marine medium containig concentration of 9.0% sodium chloride were selected among total 161 isolates. Their partial 16S rRNA gene sequences extracted from genomic DNA were analyzed and partially identified. Furthermore, to identify their genetic relationship, phylogenetic tree was deduced. Total 26 strains were belongs to Firmicutes (30.8%), Gamma proteobacteria (53.8%), Bacteroidetes (7.7%), Alpha proteobacteria (7.7%), and Actinobacteria (7.7%). These results showed the specific difference from previous researches which has been reported the microbial flora of soil or sea water around the Dokdo islands. Furthermore, 4 among 26 halophilic strains grew at above 12.0% NaCl concentrated marine broth, and 2 strains Idiomarina abyssalis LM4H23 and Halomonas huangheensis AS4H13 grew at 15.0% concentration. These halophilic strains thought to overcoming the severe stress like high salt concentration or variation derived from Dokdo-specific climate and might have unknown, specific relationship with their host coastal plant native to Dokdo islands.