• Korean Journal of Soil Science and Fertilizer
• /
• v.35 no.1
• /
• pp.12-26
• /
• 2002

The phylogenetic relationships for 33 strains belonging to the genera Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were conducted by the sequence analyses of the ITS regions. The sequence homologies of these strains showed the high variations(28.0 - 94.9%). According to the phylogenetic analysis of ITS regions. 37 ITS clones from 33 strains of 32 species were classified into four groups. Group I included all strains of the genus Sinorhizobium as core members and R. giardinii as a peripheral member. The genus Rhizobium strains were clustered into group II which was very heterogeneous and the tree toplogy of this group were very unstable. Among the members of group II. the taxonomic position of R. radiobacter and R. rubi was not clearly identified on the basis of ITS I regions. R. undicola and R. vitis were remotely related with other Rhizobium strains including R. leguminosarum, R. galegae, R. gallicum, R. mongolense, R. tropici, R. hainanense, R. rhizogense and R. huautlense of group II were supposed to be loosely related to R. leguminosarum. While the stains of the genera Bradyrhizobium constituted group III with Azorhizobium caulindans, the strains of the genus Mesorhizobium formed group IV on the relatively high sequence homology level.

• The Plant Pathology Journal
• /
• v.27 no.3
• /
• pp.242-248
• /
• 2011

Several soil bacteria were found to degrade N-Acylhomoserine lactones (NAHLs), thereby interfering with the bacterial quorum sensing system. In this research, fifteen strains of NAHL degrading rhizobacteria were isolated from potato rhizosphere. Based on phenotypic characteristics and 16S rDNA sequence analyses, the strains were identified as members of genera Bacillus, Streptomyces, Arthrobacter, Pseudomonas and Mesorhizobium. All tested isolates were capable to degrade both synthetic and natural NAHL produced by Pectobacterium carotovorum subsp. carotovorum (Pcc) strain EMPCC. In quorum quenching experiments selected isolates, especially Mesorhizobium sp., were markedly reduced the pathogenicity of Pcc strain EMPCC in potato tubers and totally suppressed tissue maceration on potato tubers. These led to consider the latter as a useful biocontrol agent against Pectobacterium spp.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.11
• /
• pp.1832-1836
• /
• 2006

Mesorhizobium sp. LUK, which utilizes 3-amino-3-phenylpropionic acid as the sole source of nitrogen with high enantioselectivity (E(S)>100), was isolated using enrichment culture. The enzyme involved in the utilization of (S)-3-amino-3-phenylpropionic acid was confirmed to be a transaminase and was purified by 235-folds with a specific activity of 0.72 U/mg. The molecular weight of the purified protein was ca. 47 kDa and the active enzyme was determined as a dimer on gel filtration chromatography. The N-terminal sequence was obtained from the purified protein. Spontaneous decarboxylation of produced ${\beta}-keto$ acids was observed during the chiral resolution of 3-amino-3-phenylpropionic acid.

• Journal of Microbiology and Biotechnology
• /
• v.21 no.6
• /
• pp.545-555
• /
• 2011

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included ${\alpha}$-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; ${\gamma}$-Proteobacteria genera Pseudomonas and Stenotrophomonas; and ${\beta}$-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

• Korean Journal of Microbiology
• /
• v.38 no.4
• /
• pp.247-253
• /
• 2002

The cellular responses of TNT-degrading bacterium, Stenotrophomonas sp. OK-5 to explosive 2,4,6-trini-trotoluene (TNT) as an environmental contaminant were examined. Survival of the strain OK-5 with time in the presence of different concentrations of TNT under sublethal conditions was monitored, and viable counts paralleled the production of the stress shock proteins in this bacterium. Total cellular fatty acids analysis showed that strain OK-5 produced or disappeared several different kinds of lipids when grown on TNT media than when grown on TSA. Under scanning electron microscope, the cells treated with 0.5 mM TNT for 12 hrs showed irregular rod shapes with wrinkled surfaces. Analyses of SDS-PAGE and Western blot using anti-DnaK and anti-GroEL revealed that several stress shock proteins including 70 kDa DnaK and 60 kDa GroEL in strain OK-5 were newly synthesized at different TNT concentrations in exponentially growing cultures. 2-D PAGE of soluble protein fractions from the culture of OK-5 exposed to TNT demonstrated that approximately 300 spots were observed on the silver stained gel ranging from pH 3 to pH 10. Among them, 10 spots significantly induced and expressed in response to TNT were selected and analyzed. As the result of internal amino acid sequencing with ESI-Q TOF, two proteins, spot #1 and spot #10 were assigned the DnaK protein XF2340 of Xylella fastidiosa and stress-induced protein of Mesorhizobium loti, respectively.

• Journal of Life Science
• /
• v.26 no.6
• /
• pp.711-720
• /
• 2016

To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/ absence and gene content trees were analyzed. The number of COGs was in the range of 103–2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30–99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.

• Journal of Species Research
• /
• v.6 no.2
• /
• pp.163-170
• /
• 2017

As a part of the research program 'Survey of freshwater organisms and specimen collection', freshwater samples were collected from Lakes Soyang and Chungju in 2016. Hundreds of bacterial strains were isolated from the samples and were identified based on 16S rRNA gene sequences. Among the bacterial isolates, strains showing higher than 98.7% sequence similarity with validly published bacterial species not reported in Korea were selected as unrecorded bacterial species. Based on 16S rRNA gene sequence similarity, 17 strains were identified as unrecorded bacterial species in Korea. The 17 bacterial strains were phylogenetically diverse and belonged to four phyla, seven classes, 13 orders, 14 families, and 16 genera. At generic level, the unreported species were affiliated with Caulobacter, Paracoccus, and Mesorhizobium of the class Alphaproteobacteria, Deefgea, Undibacterium, Chitinimonas, Inhella, and Sphaerotilus of the class Betaproteobacteria, Vibrio and Cellvibrio of the class Gammaproteobacteria, Sanguibacter and Clavibacter of the phylum Actinobacteria, Lactococcus of the phylum Firmicutes, Deinococcus of the class Deinococci, and Chryseobacterium and Flavobacterium of the phylum Bacteroidetes. The unreported species were further characterized by examining Gram reaction, colony and cell morphology, biochemical properties, and phylogenetic position. The detailed description of the 17 unreported species are also provided.

• Journal of Korean Society on Water Environment
• /
• v.22 no.6
• /
• pp.1014-1021
• /
• 2006

SMMIAR (Submerged Moving Media Intermittent Aeration Reactor) Process is a very efficient system which remove ammonia to nitrogen gas in one reactor. In this study, we determined the diversity of ammonia oxidizing bacteria and denitrifying bacteria using specific PCR amplification and the clone library construction. An ammonia monooxygenase gene(amoA) was analyzed to investigate the diversity of nitrifiers. Most of amoA gene fragments (27/29, 93%) were same types and they are very similar (>99%) to the sequences of Nitrosomonas europaea and other clones isolated from anoxic ammonia oxidizing reactors. ANAMMOX related bacteria have not determined by specific PCR amplification. A nitrite reductase gene(nirK) was analyzed to investigate the diversity of denitrifying bacteria. About half (9/20, 45%) of denitrifiers were clustered with Rhodobacter and most of others were clustered with Mesorhizobium (6/20, 30%) and Rhizobium (3/20, 15%). All of these nirK gene clones were clustered in alpha-Proteobacteria and this result is coincide with other system which also operate nitrification and denitrification in one reactor. The molecular monitoring of the population of nitrifiers and denitrifiers would be helpful for the system stabilization and scale-up.

• Genomics & Informatics
• /
• v.10 no.4
• /
• pp.249-255
• /
• 2012

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.190-190
• /
• 2017

Chemical fertilizers have been used to increase crop production and contributed to escaping food shortages. However, excessive use of chemical fertilizers over a long period caused many problems such as environmental pollution and the hampered production potential of the land. Thus, it is necessary to develop eco-friendly bio-fertilizers that can replace the use of chemical fertilizers. Here, we tested the effect of some nitrogen-fixing microorganims on the plant growth promotion. Seventy free-living nitrogen fixing microorganisms were isolated from rhizosphere of crop cultivation fields, streamside soils and sludge in Ansung, Korea. Of them, three strains (NF2-4-1, Yeast; EMM409, Mesorhizobium; Gsoil662, Burkholderia) were selected to be most efficient in the capacity of N-fixing nitrogen based on colony forming cell assay in N-free media. To investigate the ability to promote plant growth, these strains were inoculated into the soil and cabbage were grown for 4 weeks in the grown chamber. Fresh weight, dry weight, and leaf area were measured from 4-week-old plants. Phenotypic analysis revealed that the growth of the plants inoculated with NF2-4-1 and EMM409 strains were significantly promoted compared to the mock-treated control plants, while Gsoil662-inoculated plants did not show statically significant promotion. These results indicate that these nitrogen-fixing microorganims can be used to develop plant growth promoting bio-fertilizers. Further analysis on nitrogen fixing level in soil by these strains will be tested.