• 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.50 no.2
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• pp.119-127
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• 2014

The affiliations and physiological characteristics of culturable bacteria isolated from the sediments of Ross Sea, Antarctica were investigated. Sixty-three isolates obtained by cultivation were grouped into 21 phylotypes affiliated with the phyla Actinobacteria and Bacteroidetes and with the classes Alphaproteobacteria and Gammaproteobacteria by phylogenetic analysis of 16S rRNA gene sequences. Based on phylogenetic analysis (<98.65% sequence similarity), approximately 49% of total isolates represented potentially novel species or genus. Among them, extracellular protease, lipase, and exopolysaccharide activities at $10^{\circ}C$ or $20^{\circ}C$ were detected in approximately 46%, 25%, and 32% of the strains, respectively. Forty-three isolates produced at least one type of extracellular material and 21 of them produced at least two extracellular protease, lipase, and/or exopolysaccharides. Our findings indicate that culturable bacterial diversity present within the marine sediments of Ross Sea, Antarctica may contribute to the hydrolysis of the major organic constituents which is closely related with carbon and nitrogen cycling in this environment.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.19 no.2
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• pp.147-154
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• 2014

Bacteria play an important role in biogeochemical cycles in marine environments and their functional attributes in ecosystems depend primarily on species composition. In this study, seasonal variation of bacterial diversity was investigated by pyrosequencing of 16S rDNA in surface sediment and overlying seawater collected in the south East Sea, planned for the site of $CO_2$ sequestration by the carbon capture and storage (CCS) project. Gammaproteobacteria was dominant in the sediment in most seasons, whereas Alphaproteobacteria was a most dominant group in the overlying water. Thus, the bacterial diversity greatly differ between sediment and seawater samples. On the genus level, bacterial diversity between two habitats was also different. However, the number of genera found over 5% were less than 10 in both habitats and the bacterial community was composed of a number of diverse minor or rare genera. Elevation of $CO_2$ concentration during a $CO_2$ storage process, could result in change of bacterial diversity. Thus, this study will be very useful to access the effect of $CO_2$ on bacterial diversity and to predict functional change of the ecosystem during the process of CCS project.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1100-1107
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• 2012

Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.

• Korean Journal of Environmental Biology
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• v.37 no.3
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• pp.380-388
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• 2019

The studies regarding soil bacterial community and correlation analysis of wild-simulated ginseng cultivation area are insufficient. The purpose of this study was to investigate the correlation between soil bacterial community and growth characteristics of wild-simulated ginseng for selection of suitable cultivation area. The bacterial community was investigated by high throughput sequencing technique (Illumina platform). The correlation coefficient between soil bacterial community and growth characteristics were analyzed using Spearman's rank correlation. The soil bacterial community from soil samples of 8 different wild-simulated ginseng cultivated area exhibited two distinct clusters, cluster 1 and cluster 2. The relative abundance of Proteobacteria (35.4%) and Alphaproteobacteria(24.4%) was observed to be highest in all soil samples. The lower soil pH and higher abundance of Acidobacteria resulted in increased growth of wild-simulated ginseng. Additionally, abundance of Acidobacteriia (class) and Koribacteraceae (family) demonstrated significant positive correlation with fresh weight of wild-simulated ginseng. The results of this study clearly state the correlation between growth characteristic and soil bacterial community of wild-simulated ginseng cultivation area, thereby offering effective insight into selection of suitable cultivation area of wild-simulated ginseng.

• 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.26 no.5
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• pp.883-890
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• 2016

Marine sediments are a microbial biosphere with an unknown physiology, and the sediments harbor numerous distinct phylogenetic lineages of Bacteria and Archaea that are at present uncultured. In this study, the structure of the archaeal and bacterial communities was investigated in the surface and subsurface sediments of Jeju Island using a next-generation sequencing method. The microbial communities in the surface sediments were distinct from those in the subsurface sediments; the relative abundance of sequences for Thaumarchaeota, Actinobacteria, Bacteroides, Alphaproteobacteria, and Gammaproteobacteria were higher in the surface than subsurface sediments, whereas the sequences for Euryarchaeota, Acidobacteria, Firmicutes, and Deltaproteobacteria were relatively more abundant in the subsurface than surface sediments. This study presents detailed characterization of the spatial distribution of benthic microbial communities of Jeju Island and provides fundamental information on the potential interactions mediated by microorganisms with the different biogeochemical cycles in coastal sediments.

• Journal of Microbiology and Biotechnology
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• v.23 no.5
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• pp.602-613
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• 2013

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

• 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.