Journal of Microbiology

Journal Article

Flaviflexus equikiangi sp. nov. isolated from faeces of Equus kiang (Tibetan wild ass) and carrying a class 1 integron gene cassette in its genome: Caixin Yang , Xingxing Lian , Yanpeng Cheng , Yifan Jiao , Jing Yang , Kui Dong , Shan Lu , Xin-He Lai , Dong Jin , Han Zheng , Ji Pu , Suping Wang , Liyun Liu , Jianguo Xu; J. Microbiol. 2022;60(6):585-593. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1673-3

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Abstract: Two Gram-stain-positive, catalase-negative, non-spore-forming, cocci-shaped strains (dk850T and JY899) were isolated from the feces of Equus kiang in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based phylogenetic analyses showed that strains dk850T and JY899 belong to the genus Flaviflexus, closest to F. salsibiostraticola KCTC 33148T, F. ciconiae KCTC 49253T and F. huanghaiensis H5T. The DNA G + C content of strain dk850T was 62.9%. The digital DNADNA hybridization values of strain dk850T with the closely related species were below the 70% threshold for species demarcation. The two strains grew best at 28°C on brain heart infusion (BHI) agar with 5% sheep blood. All strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-9(H4) was the major menaquinone in strain dk850T. The major polar lipids included diphosphatidylglycerol and an unidentified phospholipid. Strains dk850T and JY899 were identified as carrying a class 1 integron containing the aminoglycoside resistance gene aadA11, both strains were resistant to spectinomycin and streptomycin. Based on several lines of evidence from phenotypic and phylogenetic analyses, strains dk850T and JY899 represent a novel species of the genus Flaviflexus, for which the name Flaviflexus equikiangi sp. nov. is proposed. The type strain is dk850T (= CGMCC 1.16593T = JCM 33598T).

Review

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

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Journal Articles

Mesorhizobium denitrificans sp. nov., a novel denitrifying bacterium isolated from sludge: Muhammad Zubair Siddiqi , Ngo Thi Phuong Thao , Gyumin Choi , Dae-Cheol Kim , Young-Woo Lee , Sang Young Kim , Ji-Hyang Wee , Wan-Taek Im; J. Microbiol. 2019;57(4):238-242. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8590-0

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Abstract

A Gram-stain-negative, non-spore-forming, facultative, rodshaped bacterium (designated LA-28T) was isolated from a sludge sample from a wastewater treatment plant in Hanam city, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-28T clustered with species of the genus Mesorhizobium and appeared closely related to M. jarvisii LMG 28313T (96.8%), M. waimense ICMP 19557T (96.7%), and M. huakuii LMG 14107T (96.7%). Growth occurs at 18– 40°C on R2A medium in the presence of 1–4% NaCl (w/v) and at pH 6–8. The DNA G+C content was 61.2 mol%, and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (> 5%) were C16:0, C19:0 ω8c cyclo, C18:1 ω7c 11-methyl, and C18:1 ω7c and/or C18:1 ω6c (summed feature 8). Major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidyl-N-methylethanolamine (PME), and phosphatidylcholine (PC). Physiological and biochemical characteristics indicated that strain LA-28T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium denitrificans sp. nov. is proposed. The type strain is LA-28T (= KACC 19675T = LMG 30806T).

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Lara Costa, Mathieu Martinez, Marcel Suleiman, Rolf Keiser, Moritz Lehmann, Markus Lenz
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S. Sáez-Orviz, R. Lebrero, L. Terrén, S. Doñate, M.D. Esclapez, L. Saúco, R. Muñoz
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Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
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Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer
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Minkyung Kim, Wonjae Kim, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
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Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation: May Nyan Taw , Hae-In Lee , Sang-Ho Lee , Woo-Suk Chang; J. Microbiol. 2015;53(8):518-525. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5313-z

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Abstract

Bradyrhizobium japonicum is a Gram-negative soil bacterium that can fix nitrogen into ammonia by developing a symbiotic relationship with the soybean plant. MocR proteins make up a subfamily of GntR superfamily, one of the most widely distributed and prolific groups of the helix-turn-helix transcription factors. In this study, we constructed a mutant strain for mocR (blr6977) to investigate its role in cellular processes and symbiosis in B. japonicum. Although growth rate and morphology of the mutant were indistinguishable from those of the wild type, the mutant showed significant differences in motility and attachment (i.e., biofilm formation) from the wild type. The mutant displayed a decrease in biofilm formation, but was more motile than the wild type. The inactivation of mocR did not affect the number of nodules on soybean roots, but caused delayed nodulation. Delayed nodulation intrigued us to study competitiveness of the mutant infecting soybeans. The mutant was less competitive than the wild type, indicating that delayed nodulation might be due to competitiveness. Gene expressions of other MocR subfamily members were also compared between the wild type and mutant strains. None of the mocR-like genes examined in this study were differentially expressed between both strains.

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Peng Zhang, Xiaofang Wu, Lei Ji, Wei Yan, Liping Chen, Zhonghao Lu, Deshun Xu, Yunfeng Zha, Dafang Xu, Fenfen Dong
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The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135
Si‐Qiong Xu, Xiao Wang, Lu Xu, Ke‐Xin Wang, Yin‐Hu Jiang, Fu‐Yin Zhang, Qing Hong, Jian He, Shuang‐Jiang Liu, Ji‐Guo Qiu
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The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus
Yangyang Li, Weidong Sun, Quan Wang, Ying Yu, Ying Wan, Kai Zhou, Rong Guo, Xiangan Han, Zhaoguo Chen, Weihuan Fang, Wei Jiang
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PrbP modulates biofilm formation in Liberibacter crescens
Lei Pan, Christopher L. Gardner, Reagan Beliakoff, Danilo da Silva, Ran Zuo, Fernando A. Pagliai, Kaylie A. Padgett‐Pagliai, Marcelo L. Merli, Erol Bahadiroglu, Claudio F. Gonzalez, Graciela L. Lorca
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The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism
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Research Support, Non-U.S. Gov'ts

Two Rhizobacterial Strains, Individually and in Interactions with Rhizobium sp., Enhance Fusarial Wilt Control, Growth, and Yield in Pigeon Pea: Swarnalee Dutta , Pranjal Morang , Nishanth Kumar S , B.S. Dileep Kumar; J. Microbiol. 2014;52(9):778-784. Published online September 2, 2014; DOI: https://doi.org/10.1007/s12275-014-3496-3

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Abstract

A Pseudomonas aeruginosa strain, RRLJ 04, and a Bacillus cereus strain, BS 03, were tested both individually and in combination with a Rhizobium strain, RH 2, for their ability to enhance plant growth and nodulation in pigeon pea (Cajanus cajan L.) under gnotobiotic, greenhouse and field conditions. Both of the rhizobacterial strains exhibited a positive effect on growth in terms of shoot height, root length, fresh and dry weight, nodulation and yield over the non-treated control. Co-inoculation of seeds with these strains and Rhizobium RH 2 also reduced the number of wilted plants, when grown in soil infested with Fusarium udum. Gnotobiotic studies confirmed that the suppression of wilt disease was due to the presence of the respective PGPR strains. Seed bacterization with drug-marked mutants of RRLJ 04 and BS 03 confirmed their ability to colonize and multiply along the roots. The results suggest that co-inoculation of these strains with Rhizobium strain RH 2 can be further exploited for enhanced growth, nodulation and yield in addition to control of fusarial wilt in pigeon pea.

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P. Morang, S.P. Devi, D.K. Jha, B.K. Dutta, B.S. Dileep Kumar
Rhizosphere.2018; 6: 89. CrossRef
Lettuce and rhizosphere microbiome responses to growth promotingPseudomonasspecies under field conditions
Matheus A. P. Cipriano, Manoeli Lupatini, Lucilene Lopes-Santos, Márcio J. da Silva, Luiz F. W. Roesch, Suzete A. L. Destéfano, Sueli S. Freitas, Eiko E. Kuramae, Angela Sessitsch
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Bradyrhizobium yuanmingense related strains form nitrogen-fixing symbiosis with Cajanus cajan L. in Dominican Republic and are efficient biofertilizers to replace N fertilization
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Scientia Horticulturae.2015; 192: 421. CrossRef

Arsenite Oxidation by a Facultative Chemolithotrophic Bacterium SDB1 Isolated from Mine Tailing: Rovimar T. Lugtu , Sung-Chan Choi , Young-Sook Oh; J. Microbiol. 2009;47(6):686-692. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0279-3

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Abstract: An arsenite (As[III])-oxidizing bacterium, SDB1, was isolated from mine tailing collected from the Sangdong mine area in Korea and showed chemolithotrophic growth on As[III] and CO2 as the respective electron and carbon sources. SDB1 is Gram-negative, rod-shaped, and belongs to the Sinorhizobium-Ensifer branch of α-Proteobacteria. Growth and As[III] oxidation was enhanced significantly by the presence of yeast extract (0.005%) in minimal salt medium containing 5 mM As[III]; decreasing the doubling time from 9.8 to 2.1 h and increasing the As[III] oxidation rate from 0.014 to 0.349 pmol As[III] oxidized cell-1 h-1. As[III] oxidation nearly stopped at pH around 4 and should be performed at pH 7~8 to be most effective. SDB1 was immobilized in calcium-alginate beads and the oxidation capacity was investigated. Specific As[III] oxidation rates obtained with SDB1 (10.1~33.7 mM As[III] oxidized g-1 dry cell h-1) were 10~16-times higher than those reported previously with a heterotrophic bacterial strain (Simeonova et al., 2005). The stability and reusability of immobilized SDB1 strongly suggested that the immobilized SDB1 cell system can make the As[III] oxidation process technically and economically feasible in practical applications.

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