• Journal of Species Research
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• v.8 no.2
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• pp.161-175
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• 2019

During a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 46 bacterial strains assigned to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria were isolated from a diversity of habitats including freshwater, seawater, brackish water, ginseng soil, plant roots, natural caves, and tidal flats. Based on their high 16S rRNA gene sequence similarities (>98.7%) and formation of strongly-supported phylogenetic clades with the closest type species, each strain was assigned to an independent, predefined bacterial species. Since there were no published or official reports regarding the isolation of these 46 species in Korea, here we report them as new species to Korea: 34 species in 14 families in the five orders of Alphaproteobacteria, 10 species in five families in the three orders of Betaproteobacteria, one species of Deltaproteobacteria and one species of Epsilonproteobacteria. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.262-269
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• 2012

Seasonal differences of the cultivable bacterial communities associated with the marine sponge, Hymeniacidon sinapium, between spring and summer were analyzed through the Amplified Ribosomal DNA Restriction Analysis (ARDRA). For the cultivation of the bacterial isolates, modified Zobell and MA media were used. The 16S rDNA of individual strains were amplified and fragmented by using two restriction enzymes, HaeIII and MspI. As a result, 23 ARDRA types from the spring sponge and 28 types from the summer sponge were obtained. The partial sequencing result of 1 to 3 selected strains from each types showed over 94% similarities with the known species from the public database. The bacterial communities from the sponge, captured on spring, contained 4 phyla: Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. There were 5 phyla observed from the bacterial communities associated with the sponge, captured on summer: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes. Gammaproteobacteria was predominant group in both spring and summer, accounted for 33.8% of total in spring and 67.4% in summer, showed increase pattern on summer. Because Firmicutes and Actinobacteria participated in 30.2% and 8.3% of the spring sponge while they represented only 6.9% and 0% of the summer sponge, both bacterial groups showed decrease drift on summer. Betaproteobacteria (4.7%) and Bacteroidetes (4.7%) were only observed on the sponge captured on summer. On the sponge, Hymeniacidon sinapium, more diverse bacterial communities were shown on summer than on spring, and even from the same sponge, there were seasonal differences.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.278-285
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• 2010

We examined the distribution of exopolysaccharide (EPS) producing bacteria population in rhizosphere soils of domestic medicinal herbs; Angelica sinensis, Atractytodes japonica, Achyranthes japonica, Anemarrhena asphodeloides, and Astragalus membranaceus. Fifty-six percent of the total isolates from rhizosphere soil of Angelica sinensis were EPS producing bacteria, suggesting the dominance of EPS producing bacteria in rhizosphere soil of Angelica sinensis. EPS producing bacteria were enumerated in root system (rhizosphere soil, rhizoplane, inside of root) of Angelica sinensis. Bacterial density of rhizosphere soil, rhizoplane, and inside of root were distributed $9.0{\times}10^6CFU/g{\cdot}soil$, $7.0{\times}10^6CFU/g{\cdot}soil$, and $1.4{\times}10^3CFU/g{\cdot}soil$, respectively. EPS producing bacteria from rhizosphere soil were categorized into five major phylogenetic groups: Alphaproteobacteria (4 strains), Betaproteobacteria (6 strains), Firmicutes (2 strains), Actinobacteria (3 strains), and Bacteroidetes (1 strain) subdivisions. Also, the EPS producing isolates from rhizoplane were distributed as 7 strains in Alphaproteobacteria, 3 strains in Betaproteobacteria, 2 strains in Actinobacteria, 3 strains in Bacteroidetes, and 1 strain in Acidobacteria subdivisions. All of the EPS producing bacteria inside of root belong to genus Chitinophaga. Burkholderia caribiensis DR14, Terriglobus sp. DRP35, and Rhizobium hainanense SAP110 were selected in 112 EPS producing bacteria. These appeared to have produced high levels of exopolysaccharide 6,555 mpa.s, 3,275 mpa.s, and 1,873 mpa.s, respectively. The purified EPS was analyzed Bio-LC. As neutral sugars, glucose, galactose, mannose were detected and as amino sugars, galactosamine and glucosamine were detected. Especilally, analysis of Bio-LC showed that Rhizobium hainanense SAP110 produced glucose (60~89%) and glucosamine (8.5%) as major neutral sugar and amino sugar, respectively.

• Journal of Species Research
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• v.9 no.2
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• pp.105-116
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• 2020

A total of 37 anaerobic bacteria strains within the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidia, Flavobacteriia, Bacilli, Clostridia, and Fusobacteriia were isolated from freshwater and sediment of the Geum River in Korea. The unreported species were related with Rhizobium and Oleomonas of the class Alphaproteobacteria; Acidovorax, Pseudogulbenkiania, and Aromatoleum of the class Betaproteobacteria; Tolumonas, Aeromonas, Cronobacter, Lonsdalea, and Phytobacter of the class Gammaproteobacteria; Bacteroides, Dysgonomonas, Macellibacteroides, and Parabacteroides of the class Bacteroidia; Flavobacterium of the class Flavobacteriia; Bacillus and Paenibacillus of the class Bacilli; Clostridium, Clostridioides, Paraclostridium, Romboutsia, Sporacetigenium, and Terrisporobacter of the class Clostridia; and Cetobacterium and Ilyobacter of the class Fusobacteriia. A total of 37 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species, but not reported in Korea, were determined to be unrecorded anaerobic bacterial species in Korea.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.326-328
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• 2017

Herbaspirillum sp. meg3 belonging to Betaproteobacteria was isolated from soil in Jeju island. Here, we report the complete genome sequence of strain meg3 with a size of approximately 5.47 Mb and a mean G + C content of 57.1%. The genome included 4,816 coding sequences, and 9 ribosomal RNA and 51 transfer RNA genes. In the genome, two incomplete prophage regions have been identified. Also, we propose that strain meg3 has a potential capability for aromatic-compounds degradation based on the result of genome analysis.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.791-807
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• 2017

The type II secretion system (T2SS), which transports selected periplasmic proteins across the outer membrane, has rarely been studied in nonpathogens or in organisms classified as Betaproteobacteria. Therefore, we studied Cupriavidus metallidurans (Cme), a facultative chemilithoautotroph. Gel analysis of extracellular proteins revealed no remarkable differences between the wild type and the T2SS mutants. However, enzyme assays revealed that native extracellular alkaline phosphatase is a T2SS substrate, because activity was 10-fold greater for the wild type than a T2SS mutant. In Cme engineered to produce three Ralstonia solanacearum (Rso) exoenzymes, at least 95% of their total activities were extracellular, but unexpectedly high percentages of these exoenzymes remained extracellular in T2SS mutants cultured in rich broth. These conditions appear to permit an alternative secretion process, because neither cell lysis nor periplasmic leakage was observed when Cme produced a Pectobacterium carotovorum exoenzyme, and wild-type Cme cultured in minimal medium secreted 98% of Rso polygalacturonase, but 92% of this exoenzyme remained intracellular in T2SS mutants. We concluded that Cme has a functional T2SS despite lacking any abundant native T2SS substrates. The efficient secretion of three foreign exoenzymes by Cme is remarkable, but so too is the indication of an alternative secretion process in rich culture conditions. When not transiting the T2SS, we suggest that Rso exoenzymes are probably selectively packaged into outer membrane vesicles. Phylogenetic analysis of T2SS proteins supports the existence of at least three T2SS subfamilies, and we propose that Cme, as a representative of the Betaproteobacteria, could become a new useful model system for studying T2SS substrate specificity.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1717-1723
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• 2010

The integrated fixed-film activated sludge (IFAS) system is a variation of the activated sludge wastewater treatment process, in which hybrid suspended and attached biomass is used to treat wastewater. Although the function and performance of the IFAS system are well studied, little is known about its microbial community structure. In this study, the composition and diversity of the bacterial community of suspended and attached biomass samples were investigated in a full-scale IFAS system using a high-throughput pyrosequencing technology. Distinct bacterial community compositions were examined for each sample and appeared to be important for its features different from conventional activated sludge processes. The abundant bacterial groups were Betaproteobacteria (59.3%), Gammaproteobacteria (8.1%), Bacteroidetes (5.2%), Alphaproteobacteria (3.9%), and Actinobacteria (3.2%) in the suspended sample, whereas Actinobacteria (14.6%), Firmicutes (13.6%), Bacteroidetes (11.6%), Betaproteobacteria (9.9%), Gammaproteobacteria (9.25%), and Alphaproteobacteria (7.4%) were major bacterial groups in the attached sample. Regarding the diversity, totals of 3,034 and 1,451 operational taxonomic units were identified at the 3% cutoff for the suspended and attached samples, respectively. Rank abundance and community analyses demonstrated that most of the diversity was originated from rare species in the samples. Taken together, the information obtained in this study will be a base for further studies relating to the microbial community structure and function of the IFAS system.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.309-315
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• 2017

Most of acidophiles are found in the various low pH environments and affect to metal cycle through oxidation and reduction reactions. The present study was carried out above 50 strains as acidophiles isolated from acidic soils of exhausted mine and Jeju Gotjawal. Finally, total 19 strains obtained and were tentatively identified based on comparative similarity analysis for 16S rRNA gene sequence and physiological characterizations. These isolates belonged to Gammaproteobacteria (6 strains), Actinobacteria (5 strains), Betaproteobacteria (4 strains), Alphaproteobacteria (2 strains), and Bacilli (2 strains). We observed that these isolates can grow under low pH culture condition. This case study for analysis physiological characterizations of indigenous microorganisms in acidic soil might provide basic information on useful application.