Journal of Microbiology

Volume 54(12); December 2016

Review

MINIREVIEW] Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria: Kyung Sook Bae , Mi Sun Kim , Ji Hee Lee , Joo Won Kang , Dae In Kim , Ji Hee Lee , Chi Nam Seong; J. Microbiol. 2016;54(12):789-795. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6446-4

7 View
0 Download
5 Citations

Abstract: To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

Journal Articles

Deinococcus rubellus sp. nov., bacteria isolated from the muscle of antarctic fish: Seok-Gwan Choi , Seon Hwa Jeon , Jae-Bong Lee , Eun Sun Joo , Sangyong Lim , Hee-Young Jung , Myung Kyum Kim; J. Microbiol. 2016;54(12):796-801. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6390-3

6 View
0 Download
1 Citations

Abstract: Two new bacterial strains designated as Ant6T and Ant18 were isolated from the muscle of a fish which had been caught in the Antarctic Ocean. Both strains are Gram-stain-positive, catalase positive, oxidase negative, aerobic, and coccoid bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences of strains Ant6T and Ant18 revealed that the strains Ant6T and Ant18 belong to the genus Deinococcus in the family Deinococcaceae in the class Deinococci. The highest degrees of sequence similarities of strains Ant6T and Ant18 were found with Deinococcus alpinitundrae LMG 24283T by 96.4% and 96.8%, respectively. Strain Ant6T exhibited a high level of DNA- DNA hybridization values with strain Ant18 (82 ± 0.6%). Chemotaxonomic data revealed that the predominant fatty acids were C17􍾙:􍾙0 cyclo, 16:0, and feature 3 (C16:1 ω6c/ω7c) for both strains. A complex polar lipid profile consisted of major amounts of unknown phosphoglycolipids (PGL) and unknown aminophospholipid (APL). Based on the phylogenetic, phenotypic, and chemotaxonomic data, strains Ant6T (=KEMB 9004-169T =JCM 31434T) and Ant18 (=KEMB 9004- 170) should be classified as a new species, for which the name Deinococcus rubellus sp. nov. is proposed.

Deinococcus sedimenti sp. nov. isolated from river sediment: Jae-Jin Lee , Yeon-Hee Lee , Su-Jin Park , Sangyong Lim , Sun-Wook Jeong , Seung-Yeol Lee , Sangkyu Park , Hyo-Won Choi , Myung Kyum Kim , Hee-Young Jung; J. Microbiol. 2016;54(12):802-808. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6361-8

3 View
0 Download
5 Citations

Abstract: A novel Gram-positive, oval-shaped, non-motile bacterium designated strain 16F1LT was isolated from sediment collected from the Han River in Seoul, Republic of Korea. Based on the 16S rRNA gene sequence (1,448 bp), this strain was identified as a member of the genus Deinococcus that belongs to the class Deinococci. Similarities in the 16S rRNA gene sequence were shown with Deinococcus daejeonensis MJ27T (99.0%), D. grandis DSM 3963T (98.1%), D. radiotolerans C1T (97.5%), and D. caeni Ho-08T (97.2%). Strain 16F1LT was classified as a different genomic species from closely related Deinococcus members, based on less than 70% DNA-DNA relatedness. Genomic DNA G+C content of strain 16F1LT was 67.2 mol%. Strain 16F1LT was found to grow at temperatures of 10–37°C (optimum 25°C) and pH 7–8 (optimum pH 7) on R2A medium, and was catalase-positive and oxidase-negative. Strain 16F1LT showed resistance to gamma radiation (D10 > 2 kGy). In addition, this strain had the following chemotaxonomic characteristics: the major fatty acids were C15:1 ω6c and C16:1 ω7c; the polar lipid profile contained phosphoglycolipids, unknown aminophospholipids, an unknown aminoglycolipid, unknown aminolipids, an unknown glycolipid, an unknown phospholipid, and an unknown polar lipid; the major quinone was MK-8. Phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicated that strain 16F1LT represents a novel species within the genus Deinococcus, for which the name Deinococcus sedimenti sp. nov. is proposed. The type strain is 16F1LT (=KCTC 33796T =JCM 31405T).

Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni: Jae-Bong Lee , Seon Hwa Jeon , Seok-Gwan Choi , Hee-Young Jung , Myung Kyum Kim , Sathiyaraj Srinivasan; J. Microbiol. 2016;54(12):809-813. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6473-1

2 View
0 Download
4 Citations

Abstract: In this paper, a new bacterial strain designated as 16MFT21T is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21T is a Gram-staining-positive, catalase- oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21T revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21T is with Bacillus licheniformis ATCC 14580T (96.6%) and Bacillus sonorensis NBRC 101234T (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH􍾘from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone- 7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21T (=KCTC 18866T =JCM 31664T) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea: Jin-Woo Lee , Kae Kyoung Kwon , Jang-Jun Bahk , Dong-Hun Lee , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee; J. Microbiol. 2016;54(12):814-822. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6379-y

6 View
0 Download
6 Citations

Abstract: We have previously identified a sulfate methane transition zone (SMTZ) within the methane hydrate-bearing sediment in the Ulleung Basin, East Sea of Korea, and the presence of ANME-1b group in the sediment has been shown by phylogenetic analysis of a 16S rRNA gene. Herein, we describe taxonomic and functional profiling in the SMTZ sample by metagenomic analysis, comparing with that of surface sediment. Metagenomic sequences of 115 Mbp and 252 Mbp were obtained from SMTZ and surface sediments, respectively. The taxonomic profiling using BLASTX against the SEED within MG-RAST showed the prevalence of methanogens (19.1%), such as Methanosarcinales (12.0%) and Methanomicrobiales (4.1%) predominated within the SMTZ metagenome. A number of 185,200 SMTZ reads (38.9%) and 438,484 surface reads (62.5%) were assigned to functional categories, and methanogenesis-related reads were statistically significantly overrepresented in the SMTZ metagenome. However, the mapping analysis of metagenome reads to the reference genomes, most of the sequences of the SMTZ metagenome were mapped to ANME-1 draft genomes, rather than those of methanogens. Furthermore, the two copies of the methyl-coenzyme M reductase gene (mcrA) segments of the SMTZ metagenome were clustered with ANME-1b in the phylogenetic cluster. These results indicate that ANME- 1b reads were miss-annotated to methanogens due to limitation of database. Many of key genes necessary for reverse methanogenesis were present in the SMTZ metagenome, except for N5,N10-methenyl-H4MPT reductase (mer) and CoBCoM heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary player the anaerobic methane oxidation in the SMTZ, of the methane hydrate-bearing sediment at the Ulleung Basin, East Sea of Korea.

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches: Shin Ae Lee , Jiyoung Park , Bora Chu , Jeong Myeong Kim , Jae-Ho Joa , Mee Kyung Sang , Jaekyeong Song , Hang-Yeon Weon; J. Microbiol. 2016;54(12):823-831. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6410-3

4 View
0 Download
43 Citations

Abstract: The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culturedependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These
results
showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.

Mycobiota of ground red pepper and their aflatoxigenic potential: Hyeonheui Ham , Sosoo Kim , Min-Hee Kim , Soohyung Lee , Sung Kee Hong , Jae-Gee Ryu , Theresa Lee; J. Microbiol. 2016;54(12):832-837. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6480-2

3 View
0 Download
21 Citations

Abstract: To investigate contamination of ground red pepper with fungi and mycotoxin, we obtained 30 ground red pepper samples from 15 manufacturers in the main chili-pepper-producing areas in Korea. Fungal contamination was evaluated by spreading diluted samples on potato dextrose agar plates. The total fungi counts ranged from 0 to 7.3 × 103 CFU/g. In the samples, the genus Aspergillus had the highest incidence, while Paecilomyces was isolated most frequently. The next most frequent genera were Rhizopus, Penicillium, Cladosporium, and Alternaria. Within Aspergillus, A. ruber was predominant, followed by A. niger, A. amstelodami, A. ochraceus, A. terreus, A. versicolor, A. flavus, and A. fumigatus. The samples were analyzed for aflatoxins, ochratoxin A, and citrinin by ultraperfomance liquid chromatography (UPLC) with a fluorescence detector. Ochratoxin A was detected from three samples at 1.03‒2.08 μg/kg, whereas no aflatoxins or citrinin were detected. To test the potential of fungal isolates to produce aflatoxin, we performed a PCR assay that screened for the norB-cypA gene for 64 Aspergillus isolates. As a result, a single 800-bp band was amplified from 10 A. flavus isolates, and one Aspergillus sp. isolate. UPLC analyses confirmed aflatoxin production by nine A. flavus isolates and one Aspergillus sp. isolate, which produced total aflatoxins at 146.88‒909.53 μg/kg. This indicates that continuous monitoring of ground red pepper for toxigenic fungi is necessary to minimize mycotoxin contamination.

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea: Jeong Myeong Kim , An-Sung Roh , Seung-Chul Choi , Eun-Jeong Kim , Moon-Tae Choi , Byung-Koo Ahn , Sun-Kuk Kim , Young-Han Lee , Jae-Ho Joa , Seong-Soo Kang , Shin Ae Lee , Jae-Hyung Ahn , Jaekyeong Song , Hang-Yeon Weon; J. Microbiol. 2016;54(12):838-845. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6526-5

2 View
0 Download
142 Citations

Abstract: Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis. A total of 11,865 operational taxonomic units at a 97% similarity cutoff level were detected from 847,560 sequences. Among nine soil factors evaluated; pH, electrical conductivity (EC), exchangeable cations (Ca2+, Mg2+, Na+, and K+), available P2O5, organic matter, and NO3-N, soil pH was most strongly correlated with bacterial richness (polynomial regression, pH: R2 = 0.1683, P < 0.001) and diversity (pH: R2 = 0.1765, P < 0.001). Community dissimilarities (Bray-Curtis distance) were positively correlated with Euclidean distance for pH and EC (Mantel test, pH: r = 0.2672, P < 0.001; EC: r = 0.1473, P < 0.001). Among dominant phyla (> 1%), the relative abundances of Proteobacteria, Gemmatimonadetes, Acidobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were also more strongly correlated with pH and EC values, compared with other soil cation contents, such as Ca2+, Mg2+, Na+, and K+. Our results suggest that, despite the heterogeneity of various environmental variables, the bacterial communities of the intensively cultivated greenhouse soils were particularly influenced by soil pH and EC. These findings therefore shed light on the soil microbial ecology of greenhouse cultivation, which should be helpful for devising effective management strategies to enhance soil microbial diversity and improving crop productivity.

Helicobacter pylori outer membrane protein, HomC, shows geographic dependent polymorphism that is influenced by the Bab family: Aeryun Kim , Stephanie L. Servetas , Jieun Kang , Jinmoon Kim , Sungil Jang , Yun Hui Choi , Hanfu Su , Yeong-Eui Jeon , Youngmin A. Hong , Yun-Jung Yoo , D. Scott Merrell , Jeong-Heon Cha; J. Microbiol. 2016;54(12):846-852. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6434-8

4 View
0 Download
10 Citations

Abstract: The array of outer membrane proteins (OMPs) found in Helicobacter pylori provides a crucial component for persistent colonization within the gastric niche. Not only does H. pylori harbor a wide number of OMPs, but these OMPs often vary across strains; this likely contributes to immune evasion, adaptation during long term colonization, and potentially differential disease progression. Previous work from our group described OMP differences among the Bab family (babA, babB, and babC) and Hom family (homA and homB) from 80 American H. pylori clinical isolates (AH) and 80 South Korean H. pylori clinical isolates (KH). In the current study, we expanded our investigation to include the less well characterized Hom family member, HomC. Overall, we identified and genotyped three homC variants: homCS, homCL, and homCM, in both populations. Similar to other polymorphic genes, the KH group showed less overall diversity, with 97.5% of strains harboring homCL. In contrast, a more heterogeneous profile was observed in strains derived from an American population; we found nearly equal distribution of homCS and homCL. Further analysis of the AH group identified associations between homC polymorphism and bab genotype; in AH strains, there was a significant association between homCL and carriage of babA at locus A. Since babA is an important virulence factor for the development of severe gastric disease, these data may suggest that homC polymorphism plays a role in H. pylori pathogenesis.

Inhibitory effects of bee venom and its components against viruses in vitro and in vivo: Md Bashir Uddin , Byeong-Hoon Lee , Chamilani Nikapitiya , Jae-Hoon Kim , Tae-Hwan Kim , Hyun-Cheol Lee , Choul Goo Kim , Jong-Soo Lee , Chul-Joong Kim; J. Microbiol. 2016;54(12):853-866. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6376-1

2 View
0 Download
92 Citations

Abstract: Bee venom (BV) from honey bee (Apis Melifera L.) contains at least 18 pharmacologically active components including melittin (MLT), phospholipase A2 (PLA2), and apamin etc. BV is safe for human treatments dose dependently and proven to possess different healing properties including antibacterial and antiparasitidal properties. Nevertheless, antiviral properties of BV have not well investigated. Hence, we identified the potential antiviral properties of BV and its component against a broad panel of viruses. Co-incubation of non-cytotoxic amounts of BV and MLT, the main component of BV, significantly inhibited the replication of enveloped viruses such as Influenza A virus (PR8), Vesicular Stomatitis Virus (VSV), Respiratory Syncytial Virus (RSV), and Herpes Simplex Virus (HSV). Additionally, BV and MLT also inhibited the replication of non-enveloped viruses such as Enterovirus-71 (EV-71) and Coxsackie Virus (H3). Such antiviral properties were mainly explained by virucidal mechanism. Moreover, MLT protected mice which were challenged with lethal doses of pathogenic influenza A H1N1 viruses. Therefore, these results provides the evidence that BV and MLT could be a potential source as a promising antiviral agent, especially to develop as a broad spectrum antiviral agent.

First
Prev
Page of 1
Next
Last

Previous issues