Journal of Microbiology

Volume 55(7); July 2017

Review

Minireview] Microbial radiation-resistance mechanisms: Kwang-Woo Jung , Sangyong Lim , Yong-Sun Bahn; J. Microbiol. 2017;55(7):499-507. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7242-5

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45 Citations

Abstract: Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.

Journal Articles

Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(7):508-513. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6645-7

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24 Citations

Abstract: Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39T, were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2T (97.41– 97.68%), Limnobacter litoralis KP1-19T (95.55–95.76%), and various genera belonging to the class Betaproteobacteria (90.34–93.34%). DNA-DNA hybridization showed 79.3–83.9% similarity between the genomic DNA of UCM-39T, UCM-30, and UCM-33, while the sequence similarity between UCM- 39T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C16:1ω7c and/or C16:1ω6c) and 8 (C18:1ω7c and/or C18:1ω6c), and C16:0. The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39T (=KACC 18574T =NBRC 111650T).

Viridibacterium curvum gen. nov., sp. nov., isolated from freshwater: Ji Young Kang , Jeesun Chun , Young Cheol Jung , Kwang Yeop Jahng; J. Microbiol. 2017;55(7):514-519. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7003-5

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Abstract: A Gram stain-negative, yellowish green-pigmented, facultatively anaerobic, motile, curved rod-shaped bacterium designated as strain JJ016T was isolated from an artificial lake in South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ016T indicated that the isolate belonged to the family Rhodocyclaceae and exhibited 95.0% identity to Uliginosibacterium gangwonense 5YN10-9T. The major cellular fatty acids of the novel strain were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0, C14:0, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The DNA G+C content of strain JJ016T was 61.9 mol%. The major respiratory quinone and major polar lipid of strain JJ016T were ubiquinone-8 and phosphatidylethanolamine, respectively. Based on the morphological and physiological properties and the biochemical evidence presented, we concluded that strain JJ016T represents a novel species of a new genus in the family Rhodocyclaceae, for which the name Viridibacterium curvum gen. nov., sp. nov. is proposed. The type strain is JJ016T (=KACC 16899T =JCM 18715T).

Ensifer collicola sp. nov., a bacterium isolated from soil in South Korea: Jun Hyeong Jang , Dongwook Lee , Seho Cha , Taegun Seo; J. Microbiol. 2017;55(7):520-524. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6608-z

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5 Citations

Abstract: Strain Mol12T, which presented in the form of Gram-negative, motile, non-spore forming rod-shaped, was isolated from soil in South Korea and characterized to determine its taxonomic position. The strain grew at 20–30°C (optimum 30°C) and pH 7.0–10.0 (optimum pH 8.0) with 1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain Mol12T was most closely related to Ensifer terangae LMG 7834T (96.78%), Rhizobium daejeonense KCTC 12121T (96.43%), Ensifer adhaerens Casida AT (96.28%). Chemotaxonomic data showed that the predominant fatty acids were Summed Feature 8 (C18:1 ω7c and/or C18:1 ω6c; 53.02%) and C18:1 ω7c 11-methyl (24.01%). Its complex polar lipid contained major amounts of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and Q-10 as the predominant ubiquinone. The DNA G+C content of strain Mol12T was determined to be 60.9 mol%. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain Mol12T (=KCTC 42816T =JCM 31049T) ought to be classified as a type strain of a novel species, for which the name Ensifer collicola sp. nov. is proposed.

Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain: Qingmei Liu , Muhammad Zubair Siddiqi , Mi-Sun Kim , Sang Yong Kim , Wan-Taek Im; J. Microbiol. 2017;55(7):525-530. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7180-2

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6 Citations

Abstract: A Gram-negative, non-motile, aerobic, and rod-shaped bacterial strain designated as BR5-28T was isolated from the soil of a ginseng field at Baekdu Mountain Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BR5-28T grew at 10–42°C (optimum temperature, 30°C) and pH 5.5–8.5 (optimum pH, 7.0) on R2A agar medium without additional NaCl supplementation. Strain BR5- 28T exhibited β-glucosidase activity, which was responsible for its ability to transform the ginsenosides Rb1 and Rd (the two dominant active components of ginseng) to compound-K. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Mucilaginibacter of the family Sphingobacteriaceae, and formed clusters with Mucilaginibacter frigoritolerans FT22T (95.8%) and Mucilaginibacter gotjawali SA3-7T (95.7%). The G+C content of the genomic DNA was 45.1%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c), iso-C15:0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain BR5- 28T was differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter hankyongensis sp. nov. is proposed, with the type strain BR5-28T (=KCTC 22274T =DSM 21151T).

Exploring the oral microflora of preschool children: Wen Ren , Qun Zhang , Xuenan Liu , Shuguo Zheng , Lili Ma , Feng Chen , Tao Xu , Baohua Xu; J. Microbiol. 2017;55(7):531-537. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-6474-8

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22 Citations

Abstract: The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences. We found the highest α diversity, microbial richness, and evenness in plaque, compared with saliva and tongue coating. Plaque was also distinguished from saliva and tongue coating by phylogenetic distances (weighted UniFrac). Taxa with different relative abundances were further identified, confirming the existence of microbial differences across the three niches. Core microbiomes were defined of each niche; however, only a small proportion of operational taxonomic units (8.07%) were shared by the three niches. Coaggregation between Actinomyces spp. and Streptococcus spp. and other correlations among periodontal pathogens, such as Prevotella, Fusobacteria, Capnocytophaga, and Tannerella, were shown by a co-occurrence network. In summary, our study provides a framework of oral microbial communities in the population of preschool children as a baseline for further studies of oral diseases related to microbes.

Evaluation and application of constitutive promoters for cutinase production by Saccharomyces cerevisiae: Juan Zhang , Yanqiu Cai , Guocheng Du , Jian Chen , Miao Wang , Zhen Kang; J. Microbiol. 2017;55(7):538-544. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6514-4

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Abstract: died and applied in processes targeted for industrial scale. In this work, the cutinase gene tfu from Thermobifida fusca was artificially synthesized according to codon usage bias of Saccharomyces cerevisiae and investigated in Saccharomyces cerevisiae. Using the α-factor signal peptide, the T. fusca cutinase was successfully overexpressed and secreted with the GAL1 expression system. To increase the cutinase level and overcome some of the drawbacks of induction, four different strong promoters (ADH1, HXT1, TEF1, and TDH3) were comparatively evaluated for cutinase production. By comparison, promoter TEF1 exhibited an outstanding property and significantly increased the expression level. By fed-batch fermentation with a constant feeding approach, the activity of cutinase was increased to 29.7 U/ml. The result will contribute to apply constitutive promoter TEF1 as a tool for targeted cutinase production in S. cerevisiae cell factory.

Identification of cyst wall proteins of the hypotrich ciliate Euplotes encysticus using a proteomics approach: Bangzheng Wang , Tao Niu , Muhammad Zeeshan Bhatti , Fenfen Chen , Lin Wu , Jiwu Chen; J. Microbiol. 2017;55(7):545-553. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6422-7

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13 Citations

Abstract: Euplotes encysticus is a species of Hypotrich ciliates, which form cyst wall by secreting the special substances on encounter of adverse environment. It has critical significance to study the component and mechanism underlying resting cyst, during resisting unfavorable conditions in dormancy induction. The present study was aimed to investigate the effects of cyst wall proteins of Euplotes encysticus by using biochemical
methods
. Therefore, protein extracts were separated by SDSPAGE, identified and analyzed by MALDI-TOF MS and Bioinformatics tools. We detected 42 cyst wall proteins, 26 were functional proteins and 16 proteins consist of unknown function; which is consistent with cyst wall specificity. These results partially revealed the components of resting cyst wall formed after the cells differentiation of Euplotes encysticus. In addition, our data suggested that the function of cyst wall proteins are more likely involved in the mechanical protection, signal transduction, material transport, protein degradation and energy metabolism to survival, with potentially importance implications in the molecular mechanism of eukaryocyte dormancy under stress condition.

Poly-γ-glutamic acid productivity of Bacillus subtilis BsE1 has positive function in motility and biocontrol against Fusarium graminearum: Luyao Wang , Ning Wang , Dandan Mi , Yuming Luo , Jianhua Guo; J. Microbiol. 2017;55(7):554-560. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6589-y

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14 Citations

Abstract: In this study, we investigate the relationship between γ-PGA productivity and biocontrol capacity of Bacillus subtilis BsE1; one bacterial isolate displayed 62.14% biocontrol efficacy against Fusarium root rot. The γ-PGA yield assay, motility assay, wheat root colonization assay, and biological control assay were analysed in different γ-PGA yield mutants of BsE1. The pgsB (PGA-synthase-CapB gene) deleted mutant of BsE1 reduced γ-PGA yield and exhibited apparent decline of in vitro motile ability. Deletion of pgsB impaired colonizing capacity of BsE1 on wheat root in 30 days, also lowered biocontrol efficacies from 62.08% (wild type BsE1) to 14.22% in greenhouse experiment against Fusarium root rot. The knockout of pgdS and ggt (genes relate to two γ-PGA degrading enzymes) on BsE1, leads to a considerable improvement in polymer yield and biocontrol efficacy, which attains higher level compared with wild type BsE1. Compared with ΔpgsB mutant, defense genes related to reactive oxygen species (ROS) and phytoalexin expressed changes by notable levels on wheat roots treated with BsE1, demonstrating the functional role γ-PGA plays in biocontrol against Fusarium root rot. γ-PGA is not only important to the motile and plant root colonization ability of BsE1, but also essential to the biological control performed by BsE1 against Fusarium root rot. Our goal in this study is to reveals a new perspective of BCAs screening on bacterial isolates, without good performance during pre-assays of antagonism ability.

Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5: Kiyoung Yoon , Ju Yeon Song , Min-Jung Kwak , Soon-Kyeong Kwon , Jihyun F. Kim; J. Microbiol. 2017;55(7):561-567. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-6427-2

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Abstract: Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes. Comparison of average nucleotide identities among six available Polaribacteria genomes including DSW-5 suggested that the DSW-5 genome is most similar to that of Polaribacter sp. MED152, which is a proteorhodopsin-containing marine bacterium. A phylogenomic analysis of the six Polaribacter strains and 245 Flavobacteriaceae bacteria confirmed a close relationship of the genus Polaribacter with Tenacibaculum and Kordia. DSW-5’s genome has a gene encoding proteorhodopsin and genes encoding 85 enzymes belonging to carbohydrate-active enzyme families and involved in polysaccharide degradation, which may play important roles in energy metabolism of the bacterium in the marine ecosystem. With genes for 238 CAZymes and 203 peptidases, DSW-5 has a relatively high number of degrading enzymes for its genome size suggesting its characteristics as a free-living marine heterotroph.

Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species: Thao Thi Nguyen , Tae-Soo Chon , Jaehan Kim , Young-Su Seo , Muyoung Heo; J. Microbiol. 2017;55(7):568-582. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7085-0

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Abstract: Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM) – based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus: Jhung-Ahn Yang , Sung-Hyun Yang , Junghee Kim , Kae Kyoung Kwon , Hyun-Myung Oh; J. Microbiol. 2017;55(7):583-591. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7172-2

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Abstract: Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden–Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

Letter

Letter to the Editor] Comment on Primary lymphocyte infection models for KSHV and its putative tumorigenesis mechanisms in B cell lymphomas (Journal of Microbiology 2017, 55(5): 319-329): Giovanna Rappocciolo , Frank Jenkins , Charles R. Rinaldo; J. Microbiol. 2017;55(7):592-593.; DOI: https://doi.org/10.1007/s12275-017-0670-4

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