Journal of Microbiology

Volume 57(10); October 2019

Review

MINIREVIEW] Bacterial persistence: Fundamentals and clinical importance: Sung-Hee Jung , Choong-Min Ryu , Jun-Seob Kim; J. Microbiol. 2019;57(10):829-835. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9218-0

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51 Citations

Abstract: The threat of antibiotic-resistant bacteria is increasing worldwide. Bacteria utilize persistence and resistance to survive antibiotic stress. For a long time, persistence has been studied only under laboratory conditions. Hence, studies of bacterial persistence are limited. Recently, however, the high incidence of infection relapses caused by persister cells in immunocompromised patients has emphasized the importance of persister research. Furthermore, persister pathogens are one of the causes of chronic infectious diseases, leading to the overuse of antibiotics and the emergence of antibiotic-resistant bacteria. Therefore, understanding the precise mechanism of persister formation is important for continued use of available antibiotics. In this review, we aimed to provide an overview of the persister studies published to date and the current knowledge of persister formation mechanisms. Recent studies of the features and mechanisms of persister formation are analyzed from the perspective of the nature of the persister cell.

Journal Articles

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter: Soo-Jin Kim , Hayoung Cho , Jae-Hyung Ahn , Hang-Yeon Weon , Jae-Ho Joa , Jeong-Seon Kim , Soon-Wo Kwon; J. Microbiol. 2019;57(10):836-841. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9118-3

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Abstract: A Gram-stain-positive, rod-shaped, non-endospore-forming, motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4–35°C (optimum, 28–30°C), pH 5.0–9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae): Cely T. González , Kristin Saltonstall , Hermógenes Fernández-Marín; J. Microbiol. 2019;57(10):842-851. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-8639-0

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5 Citations

Abstract: Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.

Structure of bacterial and eukaryote communities reflect in situ controls on community assembly in a high-alpine lake: Eli Michael S. Gendron , John L. Darcy , Katherinia Hell , Steven K. Schmidt; J. Microbiol. 2019;57(10):852-864. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-8668-8

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9 Citations

Abstract: Recent work suggests that microbial community composition in high-elevation lakes is significantly influenced by microbes entering from upstream terrestrial and aquatic habitats. To test this idea, we conducted 18S and 16S rDNA surveys of microbial communities in a high-alpine lake in the Colorado Rocky Mountains. We compared the microbial community of the lake to water entering the lake and to uphill soils that drain into the lake. Utilizing hydrological and abiotic data, we identified potential factors controlling microbial diversity and community composition. Results show a diverse community entering the lake at the inlet with a strong resemblance to uphill terrestrial and aquatic communities. In contrast, the lake communities (water column and outlet) showed significantly lower diversity and were significantly different from the inlet communities. Assumptions of neutral community assembly poorly predicted community differences between the inlet and lake, whereas “variable selection” and “dispersal limitation” were predicted to dominate. Similarly, the lake communities were correlated with discharge rate, indicating that longer hydraulic residence times limit dispersal, allowing selective pressures within the lake to structure communities. Sulfate and inorganic nitrogen and phosphorus concentrations correlated with community composition, indicating “bottom up” controls on lake community assembly. Furthermore, bacterial community composition was correlated with both zooplankton density and eukaryotic community composition, indicating biotic controls such as “top-down” interactions also contribute to community assembly in the lake. Taken together, these community analyses suggest that deterministic biotic and abiotic selection within the lake coupled with dispersal limitation structures the microbial communities in Green Lake 4.

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes: Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul; J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9217-1

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19 Citations

Abstract: Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.

Whole genome analysis of Aspergillus sojae SMF 134 supports its merits as a starter for soybean fermentation: Kang Uk Kim , Kyung Min Kim , Yong-Ho Choi , Byung-Serk Hurh , Inhyung Lee; J. Microbiol. 2019;57(10):874-883. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9152-1

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14 Citations

Abstract: Aspergillus sojae is a koji (starter) mold that has been applied for food fermentation in Asia. The whole genome of A. sojae SMF 134, which was isolated from meju (Korean soybean fermented brick), was analyzed at the genomic level to evaluate its potential as a starter for soybean fermentation. The genome size was 40.1 Mbp, which was expected to be composed of eight chromosomes with 13,748 ORFs. Strain SMF 134 had a total of 151 protease genes, among which two more leucine aminopeptidase (lap) genes were found in addition to the previously known lap1, and three γ-glutamyltranspeptidase (ggt) genes were newly identified. Such genomic characteristics of SMF 134 with many protease and flavor-related (lap and ggt) genes support its merits as a starter for soybean fermentation. In addition, this first complete genome of A. sojae will allow for further genetic studies to better understand the production of various enzymes, including proteases, LAPs, and GGTs, as well as other characteristics as a starter mold for soybean fermentation.

The NADP+-dependent glutamate dehydrogenase Gdh1 is subjected to glucose starvation-induced reversible aggregation that affects stress resistance in yeast: Woo Hyun Lee , Ju Yeong Oh , Pil Jae Maeng; J. Microbiol. 2019;57(10):884-892. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9065-z

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Abstract: The yeast Saccharomyces cerevisiae has two isoforms of NADP+-dependent glutamate dehydrogenase (Gdh1 and Gdh3) that catalyze the synthesis of glutamate from α-ketoglutarate and NH4 +. In the present study, we confirmed that Gdh3, but not Gdh1, mainly contributes to the oxidative stress resistance of stationary-phase cells and found evidence suggesting that the insignificance of Gdh1 to stress resistance is possibly resulted from conditional and reversible aggregation of Gdh1 into punctuate foci initiated in parallel with postdiauxic growth. Altered localization to the mitochondria or peroxisomes prevented Gdh1, which was originally localized in the cytoplasm, from stationary phase-specific aggregation, suggesting that some cytosolic factors are involved in the process of Gdh1 aggregation. Glucose starvation triggered the transition of the soluble form of Gdh1 into the insoluble aggregate form, which could be redissolved by replenishing glucose, without any requirement for protein synthesis. Mutational analysis showed that the N-terminal proximal region of Gdh1 (NTP1, aa 21-26, TLFEQH) is essential for glucose starvation-induced aggregation. We also found that the substitution of NTP1 with the corresponding region of Gdh3 (NTP3) significantly increased the contribution of the mutant Gdh1 to the stress resistance of stationary-phase cells. Thus, this suggests that NTP1 is responsible for the negligible role of Gdh1 in maintaining the oxidative stress resistance of stationary- phase cells and the stationary phase-specific stresssensitive phenotype of the mutants lacking Gdh3.

The velvet repressed vidA gene plays a key role in governing development in Aspergillus nidulans: Min-Ju Kim , Won-Hee Jung , Ye-Eun Son , Jae-Hyuk Yu , Mi-Kyung Lee , Hee-Soo Park; J. Microbiol. 2019;57(10):893-899. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9214-4

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14 Citations

Abstract: Fungal development is regulated by a variety of transcription factors in Aspergillus nidulans. Previous studies demonstrated that the NF-κB type velvet transcription factors regulate certain target genes that govern fungal differentiation and cellular metabolism. In this study, we characterize one of the VosA/VelB-inhibited developmental genes called vidA, which is predicted to encode a 581-amino acid protein with a C2H2 zinc finger domain at the C-terminus. Levels of vidA mRNA are high during the early and middle phases of asexual development and decrease during the late phase of asexual development and asexual spore (conidium) formation. Deletion of either vosA or velB results in increased vidA mRNA accumulation in conidia, suggesting that vidA transcript accumulation in conidia is repressed by VosA and VelB. Phenotypic analysis demonstrated that deletion of vidA causes decreased colony growth, reduced production of asexual spores, and abnormal formation of sexual fruiting bodies. In addition, the vidA deletion mutant conidia contain more trehalose and β-glucan than wild type. Overall, these results suggest that VidA is a putative transcription factor that plays a key role in governing proper fungal growth, asexual and sexual development, and conidia formation in A. nidulans.

Kinetic characterization of laccase from Bacillus atrophaeus, and its potential in juice clarification in free and immobilized forms: Lokesh Kumar Narnoliya , Neera Agarwal , Satya N. Patel , Sudhir P. Singh; J. Microbiol. 2019;57(10):900-909. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9170-z

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21 Citations

Abstract: In the present study, a laccase gene (BaLc) from a lignin degrading bacterium, Bacillus atrophaeus, has been cloned and expressed in Escherichia coli. The optimal catalytic activity of the protein was achieved at 5.5 pH and 35°C temperature, measured by oxidation of ABTS. The Km and Vmax values were determined as 1.42 mM and 4.16 μmole/min, respectively. To achieve the enzyme recovery, the biocatalyst (BaLc) was covalently attached onto the functionalized iron magnetic-nanoparticles. The nanoparticles were characterized by zeta-potential and FTIR analyses. The immobilized BaLc enzyme was physico-kinetically characterized, exhibiting retention of 60% of the residual activity after ten reaction cycles of ABTS oxidation. The immobilized biocatalyst system was tested for its biotechnological exploitability in plant juice processing, achieving 41–58% of phenol reduction, 41–58% decolorization, 50–59% turbidity reduction in the extracts of banana pseudo-stem and sweet sorghum stalk, and apple fruit juice. This is the first study to demonstrate the use of nanoparticle- laccase conjugate in juice clarification. The findings suggest that B. atrophaus laccase is a potential catalytic tool for plant juice bioprocessing activities.

RNase G controls tpiA mRNA abundance in response to oxygen availability in Escherichia coli: Jaejin Lee , Dong-Ho Lee , Che Ok Jeon , Kangseok Lee; J. Microbiol. 2019;57(10):910-917. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9354-6

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9 Citations

Abstract: Studies have shown that many enzymes involved in glycolysis are upregulated in Escherichia coli endoribonuclease G (rng) null mutants. However, the molecular mechanisms underlying the RNase G-associated regulation of glycolysis have not been characterized. Here, we show that RNase G cleaves the 5􍿁􀁇untranslated region of triosephosphate isomerase A (tpiA) mRNA, leading to destabilization of the mRNA in E. coli. Nucleotide substitutions within the RNase G cleavage site in the genome resulted in altered tpiA mRNA stability, indicating that RNase G activity influences tpiA mRNA abundance. In addition, we observed that tpiA expression was enhanced, whereas that of RNase G was decreased, in E. coli cells grown anaerobically. Our findings suggest that RNase G negatively regulates tpiA mRNA abundance in response to oxygen availability in E. coli.

Autophagic elimination of Trypanosoma cruzi in the presence of metals: Laís Pessanha de Carvalho , Edésio José Tenório de Melo; J. Microbiol. 2019;57(10):918-926. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9018-6

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Abstract: Trypanosoma cruzi is an obligate intracellular parasite transmitted to vertebrate hosts by blood-sucking insects. Molecules present in parasites and mammalian cells allow the recognition and parasite internalization. Metallic ions play an essential role in the establishment and maintenance of hostparasite interaction. However, little is known about how parasites handle with essential and nonessential metal quotas. This study aimed to investigate the influence of metal ions on the biological processes of T. cruzi infected cells. Infected cells were incubated with ZnCl2, CdCl2, and HgCl2 for 12 h and labeled with different specific dyes to investigate the cellular events related to intracellular parasite death and elimination. Infected host cells and parasite’s mitochondria underwent functional and structural disorders, in addition to parasite’s DNA condensation and pH decrease on host cells, which led to parasite death. Further investigations suggested that lysosomes were involved in pH decrease and the double membrane of the endoplasmic reticulum formed vacuoles surrounding damaged parasites, which indicate the occurrence of autophagy for parasite elimination. In conclusion, low concentrations of nonessential and essential metals cause a series of damage to Trypanosoma cruzi organelles, leading to its loss of viability, death, and elimination, with no removal of the host cells.

Molecular genomic characterization of severe fever with thrombocytopenia syndrome virus isolates from South Korea: Yu Jung Won , Lae Hyung Kang , Sung Geun Lee , Seung Won Park , Jae Ik Han , Soon Young Paik; J. Microbiol. 2019;57(10):927-937. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9174-8

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6 Citations

Abstract: Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne emerging infectious disease caused by the SFTS virus (SFTSV) and is a threat to public health due to its high fatality rate. However, details on tick-to-human transmission of SFTSV are limited. In this study, we determined the wholegenome sequence of a South Korean SFTSV strain (CUKJJ01), compared it to those of other recent human SFTSV isolates, and identified the genetic variations and relationships among the SFTSV strains. The genome of CUK-JJ01 was consistent with the genome of other members of the genus Phlebovirus, including the large (L), medium (M), and small (S) segments of 6368, 3378, and 1744 nucleotides, respectively. Based on amino acid sequences of the M and S segments, which are used to distinguish the six SFTSV genotypes, CUK-JJ01 was classified as genotype B. Segment analysis revealed that the L, M, and S segments were 97.49%, 97.18%, and 97.94% similar to those of KAJNH2/2013/ Korea, ZJZHSH-FDE/2012/China, and KADGH/2013/Korea, respectively. Currently, only few studies on SFTSV have been conducted in Korean population and most were limited to serological analysis. Although the present study has limitations in terms of number of sample analyzed, the findings may serve as basis to understand the transmission and spread of SFTSV, as well as for the development of diagnostic and detection methods for viral recombinants by comparing the whole genome sequence of SFTSV isolates from South Korea and that of foreign isolates.

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