• Journal of Microbiology
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• v.45 no.6
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• pp.479-484
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• 2007

Bacterial communities at 10 cm, 100 cm, and 200 cm depths in a 100-year-old lead-zinc tailing heap were evaluated by constructing 16S rRNA gene libraries. In total, 98 operational taxonomic units (OTUs) were identified from 193 clones at a 3% sequence difference level. The OTU number and species richness decreased with the depth. Species composition was significantly different between the three libraries. Fifty-seven percent of the examined clones were Acidobacteria and 27% belonged to Proteobacteria. Other sequences included Chloroflexi, Firmicutes, Chlamydiae, Actinobacteria, Gemmatimonadetes, Nitrospira, and three unclassified OTUs. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were mainly distributed in the rhizosphere of naturally colonizing plants; however, Deltaproteobacteria, Acidobacteria, and Chloroflexi tended to inhabit the deeper tailings (below the 100 cm-depth).

• Journal of Species Research
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• v.10 no.2
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• pp.134-141
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• 2021

During a survey of indigenous prokaryotic species diversity of the upstream Nakdong River, South Korea, 12 bacterial strains were isolated for further analysis. These bacterial strains were identified showing at least 98.7% 16S rRNA gene sequence similarity with known bacterial species that were previously unreported in South Korea. The 12 bacterial strains were phylogenetically diverse and assigned to four classes, eight orders, nine families, and ten different genera. The isolates were identified as Leucobacter holotrichiae (99.1%), Leucobacter tardus (99.9%), Rhodococcus rhodochrous (99.9%), Tessaracoccus oleiagri (100%), and Paeniglutamicibacter cryotolerans (99.3%), of the class Actinobacteria; Bacillus coagulans (99.7%) and Bacillus wudalianchiensis (99.1%) of the class Bacilli; Ochrobactrum pseudogrignonense (99.2%) and Paracoccus thiocyanatus (100%) of the class Alphaproteobacteria; and Ideonella azotifigens (99.0%), Polaromonas glacialis(99.3%), and Herbaspirillum seropedicae (99.5%) of the class Betaproteobacteria. The cellular and colonial morphology, biochemical properties, and phylogenetic position of these isolates were examined, and species descriptions are provided.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.329-337
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• 2015

All known genomes (N=10) in the order Nitrosomonadales were analyzed to contain 9,808 and 908 gene clusters in their pan-genome and core genome, respectively. Analyses with reference genomes belonging to other orders in Betaproteobacteria revealed that sizes of pan-genome and core genome were dependent on the number of genomes compared and the differences of genomes within a group. The sizes of pan-genomes of the genera Nitrosomonas and Nitrosospira were 7,180 and 4,586 and core genomes, 1,092 and 1,600, respectively, which implied that similarity of genomes in Nitrosospira were higher than Nitrosomonas. The genomes of Nitrosomonas contributed mostly to the size of the pan-genome and core genomes of Nitrosomonadales. COG analysis of gene clusters showed that the J (translation, ribosomal structure and biogenesis) category occupied the biggest proportions (9.7-21.0%) among COG categories in core genomes and its proportion increased in the group which genetic distances among members were high. The unclassified category (-) occupied very high proportions (34-51%) in pan-genomes. Ninety seven gene clusters existed only in Nitrosomonadales and not in reference genomes. The gene clusters contained ammonia monooxygenase (amoA and amoB) and -related genes (amoE and amoD) which were typical genes characterizing the order Nitrosomonadales while they contained significant amount (16-45%) of unclassified genes. Thus, these exclusively-conserved gene clusters might play an important role to reveal genetic specificity of the order Nitrosomonadales.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Korean Journal of Microbiology
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• v.52 no.2
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• pp.175-182
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• 2016

In this study, we isolated aromatic compounds (lignin polymers) utilizing bacteria in humus layer of oak forest and investigated phylogenetic characteristics and correlation with major bacterial populations in the humus layer by pyrosequencing. Forty-two isolates using aromatic compounds such as p-anisic acid, benzoic acid, ferulic acid and p-coumaric acid were isolated and phylogentic analyses based on 16S rRNA gene sequences showed that the isolates belonged to the genus Rhizobium, Sphingomonas, Burkhorlderia, and Pseudomonas. Among these, Burkhorlderia species which belong to Betaproteobacteria class occupied 83% among the isolates. The bacterial populations in humus layer of oak forest were characterized by next generation pyrosequencing based on 16S rRNA gene sequences. The humus sample produced 7,862 reads, 1,821 OTUs and 6.76 variability index with 97% of significance level, respectively. Bacterial populations consist of 22 phyla and Betaproteobacteria were the major phylum consisting of 15 genera including Burkholderia, Polaromonas, Ralstoria, Zoogloea, and Variovorax. Approximately fifty percentage of them was Burkholderia. Burkholderia as the majority of population in the humus was considered to play a role in degrading lignin in humus layer of oak forest.

• Korean Journal of Ecology and Environment
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• v.51 no.4
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• pp.299-310
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• 2018

Odor compounds (geosmin, 2-MIB) have been causing problems in the Bukhan River system, but the causative organisms have not been clearly identified. To evaluate the relationship between dynamics of microbial community and odor compounds, two times monthly monitoring of water quality and microbial community from the three serial lakes (Lake Uiam, Lake Cheongpyeong and Lake Paldang) in the Bukhan River system were conducted from April to October 2017. The odor compounds were analyzed by HS-SPME analysis method using GC/MS. Bacteria communities were identified at the class level by NGS analysis. Actinobacteria and Betaproteobacteria were dominant taxon in bacteria community of three serial lakes. In the case of phytoplankton communities showed that seasonal changes by Bacillariophyceae and Cryptophyceae in spring, Cyanobacteria in summer, and Bacillariophyceae and Cryptophyceae in autumn. Dominant species was Dolichospermum (=Anabaena), Microcystis and Pseudanabaena in Bukhan River system in all study period. At the same time the odors geosmin and 2-MIB were also detected at high concentration. There is a significant positive correlation between proportion of Actinobaceria and 2-MIB concentration (r=0.491, p<0.01). In addition, proportion of cyanobacteria showed a significant correlation of geosmin (r=0.381, p<0.05) and 2-MIB (r=0.386, p<0.05) concentration. In this study, odor compounds in the Bukhan River system are considered to be a direct relationship between with Actinobacteria and cyanobacteria.

• Journal of Microbiology and Biotechnology
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• v.17 no.1
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• pp.168-175
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• 2007

We report here on the cultivation of numerous novel bacterial species from a eutrophic freshwater pond. A total of 60 strains, 15 strains per each culture medium, were obtained from the surface of a eutrophic freshwater pond by employing a conventional dilution-plating method with four different kinds of culture media, including R2A, 1/10R2A, PCA, and 1/10PCA. Among the 60 strains isolated, 27 strains showed less than 97% 16S rRNA gene sequence similarities to validly published species, and thus they are considered to comprise 19 novel species. Of the 27 strains assigned to the novel species, the majority of the strains (20 strains) were affiliated with the Alphaproteobacteria and Betaproteobacteria. The remaining 7 strains were affiliated with the Gammaproteobacteria, Firmicutes, Actinobacteria, and Deinococci. Because we have isolated 19 novel species from a usual freshwater pond using a conventional culturing technique, our results suggest that an unexplored ecosystem, even if it looks like a common ecosystem found elsewhere, harbors diverse unidentified microbes, which will be definitely further characterized.

• Journal of Microbiology and Biotechnology
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• v.19 no.7
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• pp.651-657
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• 2009

Shifts in the activity and diversity of microbes involved in aliphatic and aromatic hydrocarbon degradation in contaminated soil were investigated. Subsurface soil was collected from a gas station that had been abandoned since 1995 owing to ground subsidence. The total petroleum hydrocarbon content of the sample was approximately 2,100 mg/kg, and that of the soil below a gas pump was over 23,000 mg/kg. Enrichment cultures were grown in mineral medium that contained hexadecane (H) or naphthalene (N) at a concentration of 200 mg/l. In the Henrichment culture, a real-time PCR assay revealed that the 16S rRNA gene copy number increased from $1.2{\times}10^5$to $8.6{\times}10^6$with no lag phase, representing an approximately 70-fold increase. In the N-enrichment culture, the 16S rRNA copy number increased about 13-fold after 48 h, from $6.3{\times}10^4$to $8.3{\times}10^5$. Microbial communities in the enrichment cultures were studied by denaturing gradient gel electrophoresis and by analysis of 16S rRNA gene libraries. Before the addition of hydrocarbons, the gas station soil contained primarily Alpha- and Gammaproteobacteria. During growth in the H-enrichment culture, the contribution of Bacteriodetes to the microbial community increased significantly. On the other hand, during N-enrichment, the Betaproteobacteria population increased conspicuously. These results suggest that specific phylotypes of bacteria were associated with the degradation of each hydrocarbon.

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

• Korean Journal of Environmental Biology
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• v.38 no.2
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• pp.289-298
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• 2020

As part of the research program "2018 Rapid screening and identification of freshwater microorganisms using MALDI-TOF/MS library" freshwater samples were collected from a branch of the Nakdong River. Almost 300 antibiotic-resistant bacterial strains were isolated from freshwater samples and subsequently identified by 16S rRNA gene sequencing. Seventeen strains among the isolates shared high 16S rRNA gene sequence similarity (>99.0%) with known species that were not previously recorded in Korea, and each of the isolates also formed a robust phylogenetic clade with the closest species. These species were phylogenetically diverse, belonging to four phyla, seven classes, 10 orders, and 13 genera. At the genus and class level, the previously unrecorded species belonged to Rhodovarius, Xanthobacter, and Shinella of the class Alphaproteobacteria; Ottowia, Simplicispira, and Zoogloea of Betaproteobacteria; Pseudomonas, Acinetobacter, and Shewanella of Gammaproteobacteria; Arcobacter of Epsilonproteobacteria; Sphingobacterium of Sphingobacteriia; Trichococcus of Bacilli; and Leucobacter of Actinobacteria. The previously unrecorded species were further characterized by examining their gram-staining, colony and cell morphology, biochemical properties, and phylogenetic position.