Journal of Microbiology

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Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea: Miryung Kim , Yong&# , Chang&#; J. Microbiol. 2023;61(1):37-47. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-022-00008-2

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Abstract: Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rodshaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 ( C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).

Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov.: Yun Jae Kim , Jhung-Ahn Yang , Jae Kyu Lim , Mi-Jeong Park , Sung-Hyun Yang , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon; J. Microbiol. 2020;58(4):252-259. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9376-0

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7 Citations

Abstract: An anaerobic, rod-shaped, mesophilic, chemolithoautotrophic, sulfate-reducing bacterial strain IOR2T was isolated from a newly found deep-sea hydrothermal vent (OVF, Onnuri Vent Field) area in the central Indian Ocean ridge (11°24􍿁88􍿂􀁇 S 66°25􍿁42􍿂􀁇E, 2021 m water depth). The 16S rRNA gene sequence analysis revealed that the strain IOR2T was most closely related to Desulfovibrio senegalensis BLaC1T (96.7%). However, it showed low similarity with the members of the family Desulfovibrionaceae, such as Desulfovibrio tunisiensis RB22T (94.0%), D. brasiliensis LVform1T (93.9%), D. halophilus DSM 5663T (93.7%), and Pseudodesulfovibrio aespoeensis Aspo-2T (93.2%). The strain IOR2T could grow at 23– 42°C (optimum 37°C), pH 5.0–8.0 (optimum pH 7.0) and with 0.5–6.5% (optimum 3.0%) NaCl. The strain could use lactate, pyruvate, H2, and glycerol as electron donors and sulfate, thiosulfate, and sulfite as electron acceptors. The major fatty acids of the strain IOR2T were iso-C15:0, iso-C17:0, anteiso- C15:0, and summed feature 9 (C16:0 methyl/iso-C17:1ω9c). Both the strains IOR2T and BLaC1T could grow with CO2 and H2 as the sole sources of carbon and energy, respectively. Genomic evidence for the Wood-Ljungdahl pathway in both the strains reflects chemolithoautotrophic growth. The DNA G + C content of the strain IOR2T and BLaC1T was 58.1–60.5 mol%. Based on the results of the phylogenetic and physiologic studies, Paradesulfovibrio onnuriensis gen. nov., sp. nov. with the type strain IOR2T (= KCTC 15845T = MCCC 1K04559T) was proposed to be a member of the family Desulfovibrionaceae. We have also proposed the reclassification of D. senegalensis as Paradesulfovibrio senegalensis comb. nov.

Identification of trehalose as a compatible solute in different species of acidophilic bacteria: Pedro A. Galleguillos , Barry M. Grail , Kevin B. Hallberg , Cecilia S. Demergasso , D. Barrie Johnson; J. Microbiol. 2018;56(10):727-733. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8176-2

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22 Citations

Abstract: The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response or adaptation to osmotic stress. In order to investigate the response to osmotic stress in these microorganisms, six species of acidophilic bacteria were grown at elevated osmotic strength in liquid media, and the compatible solutes synthesised were identified using ion chromatography and MALDI-TOF mass spectrometry. Trehalose was identified as one of, or the sole, compatible solute in all species and strains, apart from Acidithiobacillus thiooxidans where glucose and proline levels increased at elevated osmotic potentials. Several other potential compatible solutes were tentatively identified by MALDITOF analysis. The same compatible solutes were produced by these bacteria regardless of the salt used to produce the osmotic stress. The results correlate with data from sequenced genomes which confirm that many chemolithotrophic and heterotrophic acidophiles possess genes for trehalose synthesis. This is the first report to identify and quantify compatible solutes in acidophilic bacteria that have important roles in biomining technologies.

A murine colitis model developed using a combination of dextran sulfate sodium and Citrobacter rodentium: Jin-Il Park , Sun-Min Seo , Jong-Hyung Park , Hee-Yeon Jeon , Jun-Young Kim , Seung-Hyun Ryu , Yang-Kyu Choi; J. Microbiol. 2018;56(4):272-279. Published online April 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7504-x

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Abstract: Adult mice were treated with dextran sulfate sodium (DSS) and infected with Citrobacter rodentium for developing a novel murine colitis model. C57BL/6N mice (7-week-old) were divided into four groups. Each group composed of control, dextran sodium sulfate-treated (DSS), C. rodentiuminfected (CT), and DSS-treated and C. rodentium-infected (DSS-CT) mice. The DSS group was administered 1% DSS in drinking water for 7 days. The CT group was supplied with normal drinking water for 7 days and subsequently infected with C. rodentium via oral gavage. The DSS-CT group was supplied with 1% DSS in drinking water for 7 days and subsequently infected with C. rodentium via oral gavage. The mice were sacrificed 10 days after the induction of C. rodentium infection. The DSS-CT group displayed significantly shorter colon length, higher spleen to body weight ratio, and higher histopathological score compared to the other three groups. The mRNA expression levels of tumor necrosis factor (TNF)-α and interferon (INF)-γ were significantly upregulated; however, those of interleukin (IL)-6 and IL-10 were significantly downregulated in the DSS-CT group than in the control group. These results demonstrated that a combination of low DSS concentration (1%) and C. rodentium infection could effectively induce inflammatory bowel disease (IBD) in mice. This may potentially be used as a novel IBD model, in which colitis is induced in mice by the combination of a chemical and a pathogen.

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).

A lactic acid bacterium isolated from kimchi ameliorates intestinal inflammation in DSS-induced colitis: Jin-Soo Park , Inseong Joe , Paul Dong Rhee , Choon-Soo Jeong , Gajin Jeong; J. Microbiol. 2017;55(4):304-310. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6447-y

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48 Citations

Abstract: Some species of lactic acid bacteria have been shown to be beneficial in inflammatory bowel disease (IBD). In the pre-sent study, a strain of lactic acid bacterium (Lactobacillus paracasei LS2) was isolated from the Korean food, kimchi, and was shown to inhibit the development of experimental colitis induced by dextran sulfate sodium (DSS). To inves-tigate the role of LS2 in IBD, mice were fed DSS in drinking water for seven days along with LS2 bacteria which were administered intragastrically to some of the mice, while phos-phate-buffered saline (PBS) was administered to others (the controls). The administration of LS2 reduced body weight loss and increased survival, and disease activity indexes (DAI) and histological scores indicated that the severity of colitis was significantly reduced. The production of inflammatory cy-tokines and myeloperoxidase (MPO) activity also decreased. Flow cytometry analysis showed that the number of Th1 (IFN-γ) population cells was significantly reduced in the LS2- administered mice compared with the controls. The admini-stration of LS2 induced the increase of CD4+FOXP3+ Treg cells, which are responsible for IL-10. Numbers of macro-phages (CD11b+ F4/80+), and neutrophils (CD11b+ Gr-1+) among lamina propria lymphocytes (LPL) were also reduced. These results indicate that LS2 has an anti-inflammatory effect and ameliorates DSS-induced colitis.

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

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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.

Research Support, Non-U.S. Gov'ts

Low-Scale Expression and Purification of an Active Putative Iduronate 2-Sulfate Sulfatase-Like Enzyme from Escherichia coli K12: Edwin David Morales-Álvarez , Claudia Marcela Rivera-Hoyos , Angélica María Baena-Moncada , Patricia Landázuri , Raúl A. Poutou-Piñales , Homero Sáenz-Suárez , Luis A. Barrera , Olga Y. Echeverri-Peña; J. Microbiol. 2013;51(2):213-221. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2416-2

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15 Citations

Abstract: The sulfatase family involves a group of enzymes with a large degree of similarity. Until now, sixteen human sulfatases have been identified, most of them found in lysosomes. Human deficiency of sulfatases generates various genetic disorders characterized by abnormal accumulation of sulfated intermediate compounds. Mucopolysaccharidosis type II is characterized by the deficiency of iduronate 2-sulfate sulfatase (IDS), causing the lysosomal accumulation of heparan and dermatan sulfates. Currently, there are several cases of genetic diseases treated with enzyme replacement therapy, which have generated a great interest in the development of systems for recombinant protein expression. In this work we expressed the human recombinant IDS-Like enzyme (hrIDS-Like) in Escherichia coli DH5α. The enzyme concentration revealed by ELISA varied from 78.13 to 94.35 ng/ml and the specific activity varied from 34.20 to 25.97 nmol/h/mg. Western blotting done after affinity chromatography purification showed a single band of approximately 40 kDa, which was recognized by an IgY polyclonal antibody that was developed against the specific peptide of the native protein. Our 100 ml-shake-flask assays allowed us to improve the enzyme activity seven fold, compared to the E. coli JM109/pUC13-hrIDS-Like system. Additionally, the results obtained in the present study were equal to those obtained with the Pichia pastoris GS1115/ pPIC-9-hrIDS-Like system (3 L bioreactor scale). The system used in this work (E. coli DH5α/pGEX-3X-hrIDS-Like) emerges as a strategy for improving protein expression and purification, aimed at recombinant protein chemical characterization, future laboratory assays for enzyme replacement therapy, and as new evidence of active putative sulfatase production in E. coli.

The Role and Regulation of Trx1, a Cytosolic Thioredoxin in Schizosaccharomyces pombe: Ji-Yoon Song , Jung-Hye Roe; J. Microbiol. 2008;46(4):408-414. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0076-4

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35 Citations

Abstract: The genome of fission yeast Schizosaccharomyces pombe harbors two genes for thioredoxins, trx1+ and trx2+, which encode cytosolic and mitochondrial thioredoxins, respectively. The Δtrx1 mutant was found sensitive to diverse external stressors such as various oxidants, heat, and salt, whereas Δtrx2 mutant was not sensitive except to paraquat, a superoxide generator. Both Δtrx1 and Δtrx2 mutants were more resistant to diamide, a thiol-specific oxidant, than the wild type. The trx1+ gene expression was induced by H2O2 and menadione, being mediated through a stress-responsive transcription factor Pap1. In Δtrx1 cells, the basal expression of Pap1-regulated genes were elevated, suggesting a role for Trx1 as a reducer for oxidized (activated) Pap1. The Δtrx1 mutant exhibited cysteine auxotrophy, which can be overcome by adding sulfite. This suggests that Trx1 serves as a primary electron donor for 3’-phosphoadenosine-5’-phosphosulfate (PAPS) reductase and thus is an essential protein for sulfur assimilation in S. pombe. These results suggest that, in contrast to Trx2 whose role is more confined to mitochondrial functions, Trx1 plays a major role in protecting S. pombe against various stressful conditions and enables proper sulfur metabolism.

Effects of Sulfate Concentration on the Anaerobic Dechlorination of Polychlorinated Biphenyls in Estuarine Sediments: Young-Cheol Cho , Kyoung-Hee Oh; J. Microbiol. 2005;43(2):166-171.; DOI: https://doi.org/2167 [pii]

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Abstract: In order to determine the effects of sulfate concentration on the anaerobic dechlorination of polychlorinated biphenyls, sediments spiked with Aroclor 1242 were made into slurries using media which had various sulfate concentrations ranging from 3 to 23 mM. The time course of dechlorination clearly demonstrated that dechlorination was inhibited at high concentration of sulfate due to less dechlorination of meta-substituted congeners. When the dechlorination patterns were analyzed by the calculation of Euclidean distance, the dechlorination pathway in the 3 mM sulfate samples was found to be different from that observed in the 13 mM samples, although the extent of dechlorination in these two samples was similar. It is possible that the dechlorination in the high sulfate concentration samples is inhibited by the suppression of growth of methanogen, which have been shown to be meta-dechlorinating microorganisms.

Distribution and activity of sulfate-reducing bacteria in lake soyang sediments: Jin, Ho Yong , Lee, Dong Hun , Zo, Young Gun , Kang Chan Su , Kim Sang Jong; J. Microbiol. 1996;34(2):131-136.

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Abstract: In order to known the extend of contribution to the degradation of organic materials and nutrient recycling by sulfate-reducing bacteria (SRB) and methane-producing bacteria (MPB) in sediment, the distribution and activity of these two groups of microorganisms were studied montly in 1994 at two sites, one littoral (Sanggulri) and the other profundal (DAM), in Lake Soyang. In the seasonal distribution of two microorganisms, SRB were 1.07 × 10^3 - 2.42 × 10^5 cells/g-dry weight at Sanggulri, 2.40 × 10^5 - 1.29 × 10^6 at Dam and MPB were 0.52 × 10^3 cells/g-dry weight at Sangguri and 1.44 × 10^3 - 6.89 × 10^3 at Dam. In these results, the density of SRB in Lake Soyang is much higher than other lakes. These high values might be due to higher sulfate concentration, 0.69-4.05 mM, than normal freshwater, 0.01-1.2 mM. And a good correlation of SRB and chlorophyll a concentration implied that the important environmental factor on distribution of SRB might be the concentration of available organic matter. In a comparison of sulfate-reducing rate and methane producing rate in 1995, the activity of SRB for the degradation of organic matter was higher than MPB by factor of 359. Conclusively SRB superior to MPB in the distribution and activity are more important anaerobic bacteria in Lake Soyang sediments.

Fate of genetically engineered 2,4-D-Degrading microorganisms in natural soils and waters: Hong, Seok Myeong , Lee, Yin Won , Kim, Chi Kyung , Ka, Jong Ok; J. Microbiol. 1996;34(4):320-326.

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Abstract: To analyze the effects of host versus plasmid on survival of 2,4-degrading bacteria in environmental samples, strains Pseudomonas cepacia/pJP4, Alcaligenes JMP228/pJP4, P. cepacia/p712, and Alcaligenes JMP228/p712 were separately inoculated into samples of field soil, paddy soil, lake water, and river water, and then the changes of their populations were measured. The strains used contained a 2,4-D degradative plasmid, either pJP4 conferring fast-growing property to the host or p712 conferring slow-growing property, and were resistant to antibiotics such that the inoculated strains could be enumerated against the indigenous microbial populations. In sterile environmental samples, these strains were stably maintained at the levels used for inoculation, except in sterile paddy soil where Alcaligenes JMP228 strains died drapidly. In natural soil samples for four strains declined steadily with time, but in natural water samples their populations fell rapidly at the early phase and then remained almost constant. When the environmental samples were treated with 2, 4-D, P. cepacia/pJP4 and P. cepacia/p712 maintained significant numbers, while Alcaligenes JMP228/pJP4 and Alcaligenes JMP228/p712 declined significantly in most of the samples. The results indicated that the survivability of genetically modified microorganisms could vary depending on the environments and that their abundance in the environments under 2,4-D selection was markedly influenced by the nature of the 2,4-D degradative plasmid as well as type of the host strain.

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