Journal of Microbiology

Journal Articles

Influence of dragon bamboo with different planting patterns on microbial community and physicochemical property of soil on sunny and shady slopes: Weiyi Liu , Fang Wang , Yanmei Sun , Lei Yang , Huihai Chen , Weijie Liu , Bin Zhu , Chaomao Hui , Shiwei Wang; J. Microbiol. 2020;58(11):906-914. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0082-8

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Abstract: Dragon bamboo (Dendrocalamus giganteus) is a giant sympodial bamboo species widely distributed in Asia. However, it remains unclear how dragon bamboo and soil microbes interact to affect soil properties. In this study, we investigated the planting patterns (semi-natural and artificial) on different slopes (sunny and shady) to determine the effects on soil properties and microbial community. The results showed that the soil in which dragon bamboo was grown was acidic, with a pH value of ~5. Also, the soil organic matter content, nitrogen hydrolysate concentration, total nitrogen, available potassium, and total potassium of the dragon bamboo seminatural forest significantly improved, especially on the sunny slope. In contrast, the available phosphorus level was higher in the artificial bamboo forest, probably owing to the phosphate fertilizer application. The bacterial and fungal diversity and the bacterial abundance were all higher on the sunny slope of the semi-natural forest than those in the other samples. The microbial operational taxonomic units (OTUs) shared between the shady and sunny slopes accounted for 47.8–62.2%, but the core OTUs of all samples were only 24.4– 30.4% of each sample, suggesting that the slope type had a significant effect on the microbial community. Some acidophilic microbes, such as Acidobacteria groups, Streptomyces and Mortierella, became dominant in dragon bamboo forest soil. A PICRUSt analysis of the bacterial functional groups revealed that post-translational modification, cell division, and coenzyme transport and metabolism were abundant in the semi-natural forest. However, some microorganisms with strong stress resistance might be activated in the artificial forest. Taken together, these results illustrated the influence of dragon bamboo growth on soil physicochemical property and microbial community, which might help understand the growth status of dragon bamboo under different planting patterns.

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China: Pengyu Zhao , Jinxian Liu , Tong Jia , Zhengming Luo , Cui Li , Baofeng Chai; J. Microbiol. 2019;57(6):461-469. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8373-7

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Abstract: Microbial community assembly is affected by trade-offs between deterministic and stochastic processes. However, the mechanisms underlying the relative influences of the two processes remain elusive. This knowledge gap limits our ability to understand the effects of community assembly processes on microbial community structures and functions. To better understand community assembly mechanisms, the community dynamics of bacterial ecological groups were investigated based on niche breadths in 23 soil plots from subalpine coniferous forests on the Loess Plateau in Shanxi, China. Here, the overall community was divided into the ecological groups that corresponded to habitat generalists, ‘other taxa’ and specialists. Redundancy analysis based on Bray-Curtis distances (db-RDA) and multiple regression tree (MRT) analysis indicated that soil organic carbon (SOC) was a general descriptor that encompassed the environmental gradients by which the communities responded to, because it can explain more significant variations in community diversity patterns. The three ecological groups exhibited different niche optima and degrees of specialization (i.e., niche breadths) along the SOC gradient, suggesting the presence of a gradient in tolerance for environmental heterogeneity. The inferred community assembly processes varied along the SOC gradient, wherein a transition was observed from homogenizing dispersal to variable selection that reflects increasing deterministic processes. Moreover, the ecological groups were inferred to perform different community functions that varied with community composition, structure. In conclusion, these results contribute to our understanding of the trade-offs between community assembly mechanisms and the responses of community structure and function to environmental gradients.

Antimicrobial effect and proposed action mechanism of cordycepin against Escherichia coli and Bacillus subtilis: Qi Jiang , Zaixiang Lou , Hongxin Wang , Chen Chen; J. Microbiol. 2019;57(4):288-297. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8113-z

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40 Citations

Abstract: The detailed antibacterial mechanism of cordycepin efficacy against food-borne germs remains ambiguous. In this study, the antibacterial activity and action mechanism of cordycepin were assessed. The results showed that cordycepin effectively inhibited the growth of seven bacterial pathogens including both Gram-positive and Gram-negative bacterial pathogens; the minimum inhibitory concentrations (MIC) were 2.5 and 1.25 mg/ml against Escherichia coli and Bacillus subtilis, respectively. Scanning electron microscope and transmission electron microscope examination confirmed that cordycepin caused obvious damages in the cytoplasmatic membranes of both E. coli and B. subtilis. Outer membrane permeability assessment indicated the loss of barrier function and the leakage of cytoplasmic contents. Propidium iodide and carboxyfluorescein diacetate double staining approach coupled with flow cytometry analysis indicated that the integrity of cell membrane was severely damaged during a short time, while the intracellular enzyme system still remained active. This clearly suggested that membrane damage was one of the reasons for cordycepin efficacy against bacteria. Additionally, results from circular dichroism and fluorescence analysis indicated cordycepin could insert to genome DNA base and double strand, which disordered the structure of genomic DNA. Basis on these results, the mode of bactericidal action of cordycepin against E. coli and B. subtilis was found to be a dual mechanism, disrupting bacterial cell membranes and binding to bacterial genomic DNA to interfere in cellular functions, ultimately leading to cell death.

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.

Research Support, Non-U.S. Gov't

Photosynthetic inhibition and oxidative stress to the toxic Phaeocystis globosa caused by a diketopiperazine isolated from products of algicidal bacterium metabolism: Shuo Tan , Xiaoli Hu , Pinghe Yin , Ling Zhao; J. Microbiol. 2016;54(5):364-375. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6012-0

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50 Citations

Abstract: Algicidal bacteria have been turned out to be available for inhibiting Phaeocystis globosa which frequently caused harmful algal blooms and threatened to economic development and ecological balance. A marine bacterium Bacillus sp. Ts-12 exhibited significant algicidal activity against P. globosa by indirect attack. In present study, an algicidal compound was isolated by silica gel column, Sephadex G-15 column and HPLC, further identified as hexahydropyrrolo[1,2-a]pyrazine- 1,4-dione, cyclo-(Pro-Gly), by GC-MS and 1H-NMR. Cyclo-(Pro-Gly) significantly increased the level of reactive oxygen species (ROS) within P. globosa cells, further activating the enzymatic and non-enzymatic antioxidant systems, including superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and ascorbic acid (AsA). The increase in methane dicarboxylic aldehyde (MDA) content showed that the surplus ROS induced lipid peroxidation on membrane system. Transmission electron microscope (TEM) and flow cytometry (FCM) analysis revealed that cyclo-(Pro-Gly) caused reduction of Chl-a content, destruction of cell membrane integrity, chloroplasts and nuclear structure. Real-time PCR assay showed that the transcriptions of photosynthesis related genes (psbA, psbD, rbcL) were significantly inhibited. This study indicated that cyclo-(Pro-Gly) from marine Bacillus sp. Ts-12 exerted photosynthetic inhibition and oxidative stress to P. globosa and eventually led to the algal cells lysis. This algicidal compound might be potential bio-agent for controlling P. globosa red tide.

Review

MINIREVIEW] Regulation of Escherichia coli RNase III activity: Boram Lim , Minji Sim , Howoon Lee , Seogang Hyun , Younghoon Lee , Yoonsoo Hahn , Eunkyoung Shin , Kangseok Lee; J. Microbiol. 2015;53(8):487-494. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5323-x

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12 Citations

Abstract: Bacterial cells respond to changes in the environment by adjusting their physiological reactions. In cascades of cellular responses to stresses of various origins, rapid modulation of RNA function is known to be an effective biochemical adaptation. Among many factors affecting RNA function, RNase III, a member of the phylogenetically highly conserved endoribonuclease III family, plays a key role in posttranscriptional regulatory pathways in Escherichia coli. In this review, we provide an overview of the factors affecting RNase III activity in E. coli.

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

The Intracellular Mechanism of Action on Escherichia coli of BF2-A/C, Two Analogues of the Antimicrobial Peptide Buforin 2: Gang Hao , Yong-Hui Shi , Ya-Li Tang , Guo-Wei Le; J. Microbiol. 2013;51(2):200-206. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2441-1

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32 Citations

Abstract: In the present study, the antimicrobial peptides BF2-A and BF2-C, two analogues of Buforin 2, were chemically synthesized and the activities were assayed. To elucidate the bactericidal mechanism of BF2-A/C and their different antimicrobial activities, the influence of peptides to E. coli cell membrane and targets of intracellular action were researched. Obviously, BF2-A and BF2-C did not induce the influx of PI into the E. coli cells, indicating nonmemebrane permeabilizing killing action. The FITC-labeled BF2-A/C could penetrate the E. coli cell membrane and BF2-C penetrated the cells more efficiently. Furthermore, BF2-A/C could bind to DNA and RNA respectively, and the affinity of BF2-C to DNA was powerful at least over 4 times than that of BF2-A. The present results implied that BF2-A and BF2-C inhibited the cellular functions by binding to DNA and RNA of cells after penetrating the cell membranes, resulting in the rapid cell death. The structure-activity relationship analysis of BF2-A/C revealed that the cell-penetrating efficiency and the affinity ability to DNA were critical factors for determining the antimicrobial potency of both peptides. The more efficient cellpenetrating and stronger affinity to DNA caused that BF2-C displayed more excellent antimicrobial activity and rapid killing kinetics than BF2-A.

The Use of Pseudomonas fluorescens P13 to Control Sclerotinia Stem Rot (Sclerotinia sclerotiorum) of Oilseed Rape: Hui Li , Huaibo Li , Yan Bai , Jing Wang , Ming Nie , Bo Li , Ming Xiao; J. Microbiol. 2011;49(6):884-889. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1261-4

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28 Citations

Abstract: Sclerotinia stem rot (SSR) caused by the fungus Sclerotinia sclerotiorum has been an increasing threat to oilseed rape (Brassica napus L.) cultivation. Efficient and environment‐friendly treatments are much needed. Here we focus on microbial control. The Pseudomonas fluorescens P13 that was isolated from oilseed rape cultivation soil, proved to be a useful biocontrol strain for application. Morphology, physiological and biochemical tests and 16S rDNA analysis demonstrated that it was P. fluorescens P13 and that it had a broad antagonistic spectrum, significantly lessening the mycelial growth of S. sclerotiorum by 84.4% and suppressing sclerotial formation by 95‐100%. Scanning electron microscopy studies attested that P13 deformed S. sclerotiorum mycelia when they were cultured together. P13 did not produce chitinase but did produce hydrogen cyanide (HCN) which was likely one of the antagonistic mechanisms. The density of P13 remained at a high level (≥106 CFU/ml) during 5 weeks in the rhizosphere soil and roots. P13 reduced SSR severity at least by 59% in field studies and also promoted seedling growth (p<0.05) at the seedling stage. From these data, our work provided evidence that P13 could be a good alternative biological resource for biocontrol of S. sclerotiorum.

Antifungal Activity and Mechanism of Fengycin in the Presence and Absence of Commercial Surfactin Against Rhizopus stolonifer: Yang Tao , Xiao-mei Bie , Feng-xia Lv , Hai-zhen Zhao , Zhao-xin Lu; J. Microbiol. 2011;49(1):146-150. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0171-9

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81 Citations

Abstract: The antifungal activity and mechanism of fengycin in the presence and absence of commercial surfactin against Rhizopus stolonifer were investigated. The MIC (minimal inhibitory concentration) of fengycin without commercial surfactin added was 0.4 mg/ml while the MIC of fengycin with commercial surfactin added was 2.0 mg/ml. Fengycin acted on cell membrane and cellular organs and inhibited DNA synthesis. The antifungal effect of fengycin was reduced after commercial surfactin was added. All these results suggest that the fungal cell membrane may be the primary target of fengycin action and commercial surfactin may reduce the antifungal activity of fengycin.

DRA0336, Another OxyR Homolog, Involved in the Antioxidation Mechanisms in Deinococcus radiodurans: Longfei Yin , Liangyan Wang , Huiming Lu , Guangzhi Xu , Huan Chen , Hongdan Zhan , Bing Tian , Yuejin Hua; J. Microbiol. 2010;48(4):473-479. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0043-8

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29 Citations

Abstract: A novel OxyR (DR0615) with one conserved cysteine that senses hydrogen peroxide in Deinococcus radiodurans had been identified in our previous work. Comparative genomics revealed that D. radiodurans possesses another OxyR homolog, OxyR2 (DRA0336). In this study, we constructed the deletion mutant of oxyR2 and the double mutant of both the OxyR homologs to investigate the role of OxyR in response to oxidative stress in D. radiodurans. Deletion of oxyR2 resulted in an obviously increased sensitivity to hydrogen peroxide, and the double mutant for oxyR and oxyR2 was significantly more sensitive than any of the two single mutants. The total catalase activity of the double mutant was lower than that of any of the single mutants, and reactive oxygen species (ROS) accumulated to a greater extent. DNA microarray analysis further suggested that oxyR2 was involved in antioxidation mechanisms. Site-direct mutagenesis and complementation analysis revealed that C228 in OxyR2 was essential. This is the first report of the presence of two OxyR in one organism. These results suggest that D. radiodurans OxyR and OxyR2 function together to protect the cell against oxidative stress.

Physiological characterization of kinetics and action mechanism of vibrio hemolysin: Choe, Young Chool , Jeong, Ga Jin; J. Microbiol. 1995;33(4):289-294.

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Abstract: The action mechanism of hemolysin rendering virulency of Vibrio anguilarum has not clarified as yet, even though there were several possible factors explained. We have studied hemolytic kinetics performed by hemolysin from V. anguillarum strain V7 as well as binding of hemolysin to RBC membrane. Maximal rate of hemolysis and duration of lag phase were directly and inversly correlated to the concentration of hemolysin used. Hemolysin molecules are known to bind consumptively with proper diameter, while other protectants with smaller diameter could not. In conclusion, hemolysin should bind irreversibly to RBC membrane exert hemolysis distorting osmotic pressure. The binding could be hindered by spatial structure of the RBC surfacem which might be caused by sialic acid.

Catalytic mechanism and inhibition studies of purine nucleoside phosphorylase (PNP) in micrococcus luteus: Choi , Hye Seon; J. Microbiol. 1997;35(1):15-20.

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Abstract: Kinetic studies were done to elucidate the reaction mechanism of purine nucleoside phosphorylase (PNP) in Micrococcus Luteus. PNP catalyzes the reversible phosphorolysis of ribonucleosides to their respective base. The effect of alternative competing substrates suggested that a single enzyme was involved in binding to the active site for all purine nucleosides, inosine, deoxyiosine, guanosine, deoxyguanosine, adenosine and deoxyadenosine. Affinity studies showed that pentose moiety reduced the binding capacity and methylation of ring N-1 of inosine and guanosine had little effect on binding to bacterial enzyme, whereas these compounds did not bind to the mammalian enzymes. The initial velocity and product inhibition studies demonstrated that the predominant mechanism of reaction was an ordered bi, bi reaction. The nucleoside bound to the enzyme first, followed by phosphate. Ribose 1-phosphate was the first product to leave, followed by base.

Laboratory Developed fluoroquinolone Resistant Escherichia coli Has a new Missense Mutation in QRDR of PartC: Lee, Soon Deuk , Lee, Yeon Hee; J. Microbiol. 1998;36(2):106-110.

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Abstract: The fluoroquinolone resistance mechanism of four laboratory developed fluorquinolone resistant strains of Escherichia coli was studied. Fluoroquinolone concentrations inside the resistant cells were similar to the concentrations in the susceptible cells. DNA sequencing of the quinolone resistance determining regions (QRDR) in gyrA and parC revealed the presence of Ser 83Leu and Asp87Gly mutations in GyrA, and Gly78Cys and Ser80Arh mutations in ParC of the ofloxacin, norfloxacin, and HK3140 resistant strains, while the ciprofloxacin resistant strain had Ser83Leu and Aasp87Tyr mutations in GyrA, and Gly78Cys and Ser80Ile mutations in ParC. A Gly78Cys substitution in ParC was newly detected in this work and seemed to be responsible for the extremely high MICs to fluroquinolones.

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