• ALGAE
• /
• v.39 no.2
• /
• pp.59-74
• /
• 2024

Terrestrial cyanobacteria are extremely diverse. In urban areas, they can be found as black stains on the surface of building walls, stone monuments, or man-made structures. Many of the terrestrial cyanobacteria are still understudied. To expand knowledge of terrestrial cyanobacterial diversity, a polyphasic characterization was performed to identify 12 strains isolated from campus of University of the Ryukyus, Okinawa, Japan. Multigene phylogenetic analyses based on 16S rRNA gene and 16S-23S rRNA internal transcribed spacer (ITS) region showed that the isolated strains formed two independent subclades within Nodosilinea, and were distantly related to all described Nodosilinea species. The 16S-23S rRNA ITS secondary structures showed variations for D1-D1' and Box B domain, while V3 domain was almost identical among entire species of Nodosilinea, including the studied strains. In addition, a unique morphological character, i.e. forming nodule or spiral shape, was also observed in certain studied strains. According to polyphasic characterization, Nodosilinea coculeatus sp. nov. and Nodosilinea terrestrialis sp. nov., were proposed as two new species of terrestrial cyanobacteria from Okinawa.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.8
• /
• pp.1379-1384
• /
• 2007

Four Gram-negative, chemoheterotrophic, non-motile, yellow-colored strains were isolated from the East Sea or from deep-sea sediments of Nankai Trough by standard dilution plating. Characterization by polyphasic approaches indicated that the four strains are members of the same species. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The dominant cellular fatty acids were i-C15:0, 3-OH i-C17:0, and 2-OH i-C15:0 and/or C16:1 ${\omega}7c$. Predominance of 2-OH i-C15:0 and/or C16:1 ${\omega}7c$ clearly differentiated the strains from closely related members. The DNA G+C contents ranged 35.1-36.2 mol%. It is proposed, from the polyphasic evidence, that the strains should be placed into a novel genus and species named Sufflavibacter maritimus gen. nov., sp. nov., with strain $IMCC1001^T(=KCCM\;42359^T=NBRC\;102039^T)$ as the type strain.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.1
• /
• pp.130-140
• /
• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.7
• /
• pp.1300-1305
• /
• 2017

A rod shaped, aerobic, Gram-stain-negative, and motile bacterium, strain $AR2^T$, was isolated from a water sample of Yeongsan river, Republic of Korea. Strain $AR2^T$ clustered closely with the members of the genus Chitinimonas and showed the highest 16S rRNA gene sequence similarity with Chitinimonas prasina $LY03^T$ (96.4%), Chitinimonas viridis $HMD2169^T$ (96.4%), Chitinimonas taiwanensis $cf^T$ (96.2%), and Chitinimonas koreensis $R2A43-10^T$ (94.2%). The predominant fatty acids of strain $AR2^T$ were identified to be summed feature 3 (comprising $C_{16:1}{\omega}7c$ and/or $C_{16:1}{\omega}6c$), $C_{16:0}$, and $C_{10:0}3-OH$. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were found to be the major polar lipids. The genomic DNA G+C content was 60.4 mol%. Based on the polyphasic characterization, the isolated strain $AR2^T$ is described as a representative of a novel species in the genus Chitinimonas, for which the name Chitinimonas naiadis sp. nov. (type strain =$AR2^T$ =KCTC $42755^T$ =JCM $31504^T$) is proposed.

• Journal of Microbiology and Biotechnology
• /
• v.32 no.5
• /
• pp.575-581
• /
• 2022

A Gram-stain-negative, white-coloured, and rod-shaped bacterium, strain DR4-4^T, was isolated from Daechung Reservoir, Republic of Korea, during Microcystis bloom. Strain DR4-4^T was most closely related to Caenimonas terrae SGM1-15^T and Caenimonas koreensis EMB320^T with 98.1% 16S rRNA gene sequence similarities. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DR4-4^T and closely related type strains were below 79.46% and 22.30%, respectively. The genomic DNA G+C content was 67.5%. The major cellular fatty acids (≥10% of the total) were identified as C_16:0, cyclo C_17:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Strain DR4-4^T possessed phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol as the main polar lipids and Q-8 as the respiratory quinone. The polyamine profile was composed of putrescine, cadaverine, and spermidine. The results of polyphasic characterization indicated that the isolated strain DR4-4^T represents a novel species within the genus Caenimonas, for which the name Caenimonas aquaedulcis sp. nov. is proposed. The type strain is DR4-4^T (=KCTC 82470^T =JCM 34453^T).

• Journal of Microbiology and Biotechnology
• /
• v.33 no.11
• /
• pp.1428-1436
• /
• 2023

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43^T, HBC28, and HBC61^T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43^T, HBC28, and HBC61^T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1^T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43^T and HBC61^T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43^T =KCTC 92793^T=LMG 32714^T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61^T =KCTC 92794^T=LMG 32713^T) are proposed.

• The Plant Pathology Journal
• /
• v.27 no.4
• /
• pp.360-366
• /
• 2011

Bacterial leaf spot of Euphorbia pulcherrima has been reported in many countries. Characterization by polyphasic approaches indicated that the isolates from India, USA and New Zealand could be distinguished based on rep-PCR profiles and gyrB phylogenies, while the Chinese isolates should be ascribed to Xanthomonas axonopodis pv. poinsettiicola.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.9
• /
• pp.1536-1541
• /
• 2018

A yellowish, flexirubin-pigment-producing strain $I3-3^T$ was isolated from river water in Iksan, the Republic of Korea. The strain was gram-negative, aerobic, non-motile, showed catalase and oxidase activities, and could grow at a temperature range of $10-35^{\circ}C$, pH 5.0-10 and 0-2.0% (w/v) of NaCl. The major fatty acids were iso-$C_{15:0}$, iso-$C_{17:0}$ 3-OH and summed feature 3 (comprising $C_{16:1}{\omega}7c$ and/or $C_{16:1}{\omega}6c$). The isolate contained phosphatidylethanolamine, one aminolipid, and two unidentified lipids as the major polar lipids. Menaquinone-6 (MK6) was the major respiratory quinone. The G+C content of the genomic DNA of strain $I3-3^T$ was 35.6%. Comparison of the 16S rRNA gene sequence with the sequences of the closely related type strains showed highest sequence similarity of 96.95% and 96.93% to Flavobacterium nitrogenifigens $NXU-44^T$ and Flavobacterium compostarboris $15C3^T$, respectively. Based on phenotypic and phylogenetic distinctiveness, strain $I3-3^T$ is considered as a member of novel species within the genus Flavobacterium, for which Flavobacterium amnigenum sp. nov. is proposed. The type strain is $I3-3^T$ (=KCTC $52884^T$ =NBRC $112871^T$).

• Journal of Animal Science and Technology
• /
• v.51 no.6
• /
• pp.527-536
• /
• 2009

A potent protein degrading bacterium was isolated from soil samples of different environments. Polyphasic taxonomic studies and phylogenetic 16S rRNA sequence analyses led to identify the isolate IB No. 11 as a strain of Bacillus subtilis. The isolated strain was recognized to produce protease constitutively, and the maximum production (1.64 units/ml) was attained in a shake flask culture when the isolate was grown at $40^{\circ}C$, for 32 h in basal medium supplemented with starch (0.25%) and gelatin (1.25%) as sole carbon and nitrogen source, respectively. The optimum pH and temperature for the protease activity were determined to be pH 7.0 and $50^{\circ}C$, respectively. $Ca^{2+}$ and $Mn^{2+}$ enhanced remarkably the protease activity but neither showed positive effect on the protease's thermal stability. In addition, it was observed that the protease was fairly stable in the pH range of 6.5-8.0 and at temperatures below $50^{\circ}C$, and it could be a good candidate for an animal feed additive. The inhibition profile of the protease by various inhibitors indicated that the enzyme is a member of serine-proteases. A combination of UV irradiation and NTG mutagenesis allowed to develop a protease hyper-producing mutant strain coded as IB No. 11-4. This mutant strain produced approximately 3.23-fold higher protease activity (6.74 units/mg) than the parent strain IB No. 11 when grown at $40^{\circ}C$ for 32h in the production medium. The protease production profile of the selected mutants was also confirmed by the zymography analysis.

• Journal of Environmental Science International
• /
• v.22 no.11
• /
• pp.1403-1413
• /
• 2013

The effects of cadmium ions ($Cd^{2+}$) on the Chl a fluorescence of Ricciocarpos natans were investigated in order to determine whether Chl fluorescence can be used as a biomarker to estimate the physiological responses of plants to cadmium stress. In all plants treated with $Cd^{2+}$, the image of Fv/Fm, which represents the maximum photochemical efficiency of PSII, changed as the $Cd^{2+}$ concentration increased, when treated for 48 h or more. Changes of ${\Phi}_{PSII}$ and $Q_P$ images were recognized even at 10 ${\mu}M$ $Cd^{2+}$. The Chl a O-J-I-P fluorescence transient was also affected even at 10 ${\mu}M$ $Cd^{2+}$. The fluorescence yield decreased considerably in steps J, I and P in plants treated with $Cd^{2+}$, although a typical polyphasic rise was observed in non-treated plants. The Chl fluorescence parameters, Fm, Fv/Fo, Sm, SFIabs, PIabs and ETo/CS, decreased as the $Cd^{2+}$ concentration increased, while the Mo and Kn parameters increased. Peroxidase activity decreased significantly and catalase activity increased as the $Cd^{2+}$ concentration increased. Because of its sensitivity to $Cd^{2+}$ Ricciocarpos natans is useful in experiments investigating the responses of plants to cadmium exposure. Several parameters (Fm, Fv/Fo, Sm, SFIabs, PIabs, ETo/CS, Mo and Kn) can be applied to determine quantitatively the physiological states of plants under cadmium stress.