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Role of the LAMMER kinase LkhA in fungal development and aflatoxin production in Aspergillus flavus
Seong-Hwan Jeong, He-Jin Cho, Jae-Hyuk Yu, Hee-Moon Park, Hee-Soo Park
J. Microbiol. 2025;63(5):e2503007.   Published online May 27, 2025
DOI: https://doi.org/10.71150/jm.2503007
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AbstractAbstract PDF

A well-conserved LAMMER kinase in yeast and filamentous fungi, is a dual-specificity kinase with multiple roles in fungal biology. In this study, we assessed the roles of LkhA in Aspergillus flavus, a toxigenic fungus that produces aflatoxin B1. lkhA deletion mutants exhibited defects in fungal growth, conidiophore development, and sclerotia formation. These mutants exhibited impaired tolerance to oxidative and cell wall stresses. Moreover, the absence of lkhA resulted in a decrease in aflatoxin B1 production. The kernel assay revealed that the lkhA deletion mutants exhibited reduced production of conidia and aflatoxin B1, implying that LkhA can affect fungal toxigenesis and pathogenicity. Taken together, these results demonstrate that LkhA is important for differentiation, mycotoxin production, and pathogenicity in A. flavus.

Review
Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria
Yubin Yang, Hana Hyeon, Minju Joo, Kangseok Lee, Eunkyoung Shin
J. Microbiol. 2025;63(4):e2501027.   Published online April 2, 2025
DOI: https://doi.org/10.71150/jm.2501027
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AbstractAbstract PDF

The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.

Journal Article
Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil
Yong-Seok Kim , Eun-Mi Hwang , Chang-Myeong Jeong , Chang-Jun Cha
J. Microbiol. 2023;61(10):891-901.   Published online October 18, 2023
DOI: https://doi.org/10.1007/s12275-023-00081-1
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AbstractAbstract
Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rodshaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 ( C16:1 ω7c and/or C16: 1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).

Citations

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  • Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation
    Xu-Dong Lian, Yong Guan, Yue Jiang, Dong-Heui Kwak, Mi-Kyung Lee, Zhun Li
    Scientific Reports.2025;[Epub]     CrossRef
  • Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities
    Haojie Qiu, Weihua Zhao, Yingying Qin, Yanyan Wang, Meng Bai, Shaoqing Su, Chao Wang, Zhisheng Zhao
    Bioresource Technology.2025; 423: 132248.     CrossRef
  • mKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data
    Fangyu Mo, Qinghong Qian, Xiaolin Lu, Dihuai Zheng, Wenjie Cai, Jie Yao, Hongyu Chen, Yujie Huang, Xiang Zhang, Sanling Wu, Yifei Shen, Yinqi Bai, Yongcheng Wang, Weiqin Jiang, Longjiang Fan
    Briefings in Bioinformatics.2025;[Epub]     CrossRef
  • Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
    Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
    Journal of Microbiology.2024; 62(9): 739.     CrossRef
  • Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
    Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
    Current Microbiology.2024;[Epub]     CrossRef
  • Validation List no. 218. Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, Markus Göker
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
Editorial
Editorial] Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
J. Microbiol. 2023;61(3):273-276.   Published online April 3, 2023
DOI: https://doi.org/10.1007/s12275-023-00036-6
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AbstractAbstract
Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

Citations

Citations to this article as recorded by  
  • The PhoBR two-component system upregulates virulence in Aeromonas dhakensis C4–1
    Wei Feng, Xuesong Li, Nuo Yang, Lixia Fan, Guiying Guo, Jun Xie, Xiuqing Cai, Yuqi Meng, Jifeng Zeng, Yu Han, Jiping Zheng
    Aquaculture.2025; 595: 741665.     CrossRef
  • Molecular mechanisms of cold stress response in cotton: Transcriptional reprogramming and genetic strategies for tolerance
    Washu Dev, Fahmida Sultana, Hongge Li, Daowu Hu, Zhen Peng, Shoupu He, Haobo Zhang, Muhammad Waqas, Xiaoli Geng, Xiongming Du
    Plant Science.2025; 352: 112390.     CrossRef
  • PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
    Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
    mSystems.2024;[Epub]     CrossRef
  • Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems
    Mohit Yadav, Janhavi Sathe, Valentina Teronpi, Aditya Kumar
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
Journal Articles
Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11
Wonsik Lee
J. Microbiol. 2022;60(12):1123-1129.   Published online November 24, 2022
DOI: https://doi.org/10.1007/s12275-022-2476-2
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AbstractAbstract
Transposon mutant libraries are an important resource to study bacterial metabolism and pathogenesis. The fitness analysis of mutants in the libraries under various growth conditions provides important clues to study the physiology and biogenesis of structural components of a bacterial cell. A transposon library in conjunction with next-generation sequencing techniques, collectively named transposon sequencing (Tnseq), enables high-throughput genome profiling and synthetic lethality analysis. Tn-seq has also been used to identify essential genes and to study the mode of action of antibacterials. To construct a high-density transposon mutant library, an efficient delivery system for transposition in a model bacterium is essential. Here, I describe a detailed protocol for generating a high-density phage-based transposon mutant library in a Staphylococcus aureus strain, and this protocol is readily applicable to other S. aureus strains including USA300 and MW2.

Citations

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  • Optimizing phage-based mutant recovery and minimizing heat effect in the construction of transposon libraries in Staphylococcus aureus
    Sally W. Yousief, Nader Abdelmalek, Bianca Paglietti
    Scientific Reports.2024;[Epub]     CrossRef
Correlation between fat accumulation and fecal microbiota in crossbred pigs
Xin Li , Mengyu Li , Jinyi Han , Chuang Liu , Xuelei Han , Kejun Wang , Ruimin Qiao , Xiu-Ling Li , Xin-Jian Li
J. Microbiol. 2022;60(11):1077-1085.   Published online September 9, 2022
DOI: https://doi.org/10.1007/s12275-022-2218-5
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AbstractAbstract
Backfat thickness (BF) is an important indicator of fat deposition capacity and lean meat rate in pigs and is very important in porcine genetics and breeding. Intestinal microbiota plays a key role in nutrient digestion and utilization with a profound impact on fat deposition of livestock animals. To investigate the relationship between the pig gut microbiome and BF, 20 low-BF (L-BF) and 20 high-BF (H-BF) pigs were selected as two groups from Yunong Black pigs in the present study. Fecal samples from pigs were analyzed for microbial diversity, composition, and predicted functionality using 16S rRNA gene sequencing. The results showed that there were significant differences in microbial β diversity between the two groups. LEfSe analysis revealed a number of bacterial features being differentially enriched in either L-BF or H-BF pigs. Spearman correlation analysis identified the abundance of Oscillospira, Peptococcus, and Bulleidia were significantly positive correlations with BF (P < 0.05), while Sutterella and Bifidobacterium were significantly negatively correlated with BF (P < 0.05). Importantly, the bacteria significantly positively correlated with BF mainly belong to Clostridium, which can ferment host-indigestible plant polysaccharides into shortchain fatty acid (SCFA) and promote fat synthesis and deposition. Predictive functional analysis indicated that the pathway abundance of cell motility and glycan biosynthesis were significantly widespread in the microbiota of the H-BF group. The results of this study will be useful for the development of microbial biomarkers for predicting and improving porcine BF, as well as for the investigation of targets for dietary strategies.

Citations

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  • Carboxymethyl chitosan-dialdehyde glucan/polydopamine carrier targeted delivery Bacillus subtilis on enhancing oral utilization and intestinal colonization in mice
    Lulu Chu, Luyu Xie, Bingzhi Chen, Yuji Jiang, Wenjie Wang
    International Journal of Biological Macromolecules.2024; 280: 135574.     CrossRef
  • Impact of Early Weaning on Development of the Swine Gut Microbiome
    Benoit St-Pierre, Jorge Yair Perez Palencia, Ryan S. Samuel
    Microorganisms.2023; 11(7): 1753.     CrossRef
  • Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
    Kang Xiao, Zhengyu Chen, Qin Long
    Journal of Microbiology.2023; 61(5): 571.     CrossRef
The novel antifungal agent AB-22 displays in vitro activity against hyphal growth and biofilm formation in Candida albicans and potency for treating systemic candidiasis
Kyung-Tae Lee , Dong-Gi Lee , Ji Won Choi , Jong-Hyun Park , Ki Duk Park , Jong-Seung Lee , Yong-Sun Bahn
J. Microbiol. 2022;60(4):438-443.   Published online March 14, 2022
DOI: https://doi.org/10.1007/s12275-022-2016-0
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AbstractAbstract
Systemic candidiasis, which is mainly caused by Candida albicans, is a serious acute fungal infection in the clinical setting. In a previous study, we reported that compound 22h (designated as AB-22 in this study), a vinyl sulfate compound, is a fast-acting fungicidal agent against a broad spectrum of fungal pathogens. In this study, we aimed to further analyze the in vitro and in vivo efficacy of AB-22 against filamentation, biofilm formation, and virulence of C. albicans. Under in vitro hyphal growth-inducing condition, AB-22 effectively inhibited germ tube formation and hyphal growth, which are required for the initiation of biofilm formation. Indeed, AB-22 significantly suppressed C. albicans biofilm formation in a dose-dependent manner. Moreover, AB-22 treatment inhibited the normal induction of ALS3, HWP1, and ECE1, which are all required for hyphal transition in C. albicans. Furthermore, AB-22 treatment increased the survival of mice systemically infected with C. albicans. In conclusion, in addition to its fungicidal activity, AB-22 inhibits filamentation and biofilm formation in C. albicans, which could collectively contribute to its potent in vivo efficacy against systemic candidiasis.

Citations

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  • Preparation and analysis of quinoa active protein (QAP) and its mechanism of inhibiting Candida albicans from a transcriptome perspective
    Xufei Zhang, Chunmei Zheng, Wenxuan Ge, Xueying Li, Xiuzhang Wang, Yanxia Sun, Xiaoyong Wu
    PeerJ.2025; 13: e18961.     CrossRef
Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China
Ju-Wei Wang , Pei-Jie Han , Da-Yong Han , Sen Zhou , Kuan Li , Peng-Yu He , Pan Zhen , Hui-Xin Yu , Zhen-Rong Liang , Xue-Wei Wang , Feng-Yan Bai
J. Microbiol. 2021;59(8):753-762.   Published online July 5, 2021
DOI: https://doi.org/10.1007/s12275-021-1115-7
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AbstractAbstract
The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55–18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85–23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.

Citations

Citations to this article as recorded by  
  • Isolation of Saccharomycopsis species from plant material
    Carmen Dost, Florian Michling, Davies Kaimenyi, Mareike Rij, Jürgen Wendland
    Microbiological Research.2024; 283: 127691.     CrossRef
  • Microbial enzymes: the bridge between Daqu flavor and microbial communities
    Zelong Zhong, Tianyi Liu, Kaiping He, Min Zhong, Xiaoxue Chen, Yansong Xue, Beizhong Han, Diqiang Wang, Jun Liu
    Food Innovation and Advances.2024; 3(4): 426.     CrossRef
  • Exploring the heterogeneity of community and function and correspondence of “species-enzymes” among three types of Daqu with different fermentation peak-temperature via high-throughput sequencing and metagenomics
    Ying Huang, Dong Li, Yu Mu, Zhiyu Zhu, Yuzhang Wu, Qi Qi, Yingchun Mu, Wei Su
    Food Research International.2024; 176: 113805.     CrossRef
  • Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review
    Jiamu Kang, Xiaoning Huang, Rengshu Li, Yuandi Zhang, Xiao-Xue Chen, Bei-Zhong Han
    Food Research International.2024; 188: 114497.     CrossRef
  • Correlational analysis of physicochemical indexes, microbial communities, and volatile components in light-flavor Daqu from north and south regions of China
    Qi Yu, Feiyan Mou, Junwen Xiao, Cheng Zhan, Liang Li, Xu Chang, Xiaoyuan Dong, Maobin Chen, Xinrui Wang, Mei Chen, Shangling Fang
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • Dynamic changes in volatile profiles and bacterial communities during natural fermentation of Mei yu, traditional Chinese fermented fish pieces
    Hongmei Yin, Qiang Hong, Xiang Yu, Hui Wang, Xiaodan Shi, Wei Liu, Tao Yuan, Zongcai Tu
    Food Research International.2024; 194: 114882.     CrossRef
  • Exploring the relationship between GuaYi levels and microbial-metabolic dynamics in Daqu
    Boyang Xu, Shanshan Xu, Hao Zhou, Ruijuan Wang, Chao Jiang, Dongdong Mu, Xuefeng Wu, Xiaolei Wu, Shaotong Jiang, Xingjiang Li
    Food Bioscience.2024; 60: 104347.     CrossRef
  • Exploring the Role of Active Functional Microbiota in Flavor Generation by Integrated Metatranscriptomics and Metabolomics during Niulanshan Baijiu Fermentation
    Yuanyuan Pan, Ying Wang, Wenjun Hao, Sen Zhou, Chengbao Duan, Qiushi Li, Jinwang Wei, Gang Liu
    Foods.2023; 12(22): 4140.     CrossRef
  • Dynamic changes and correlations of microbial communities, physicochemical properties, and volatile metabolites during Daqu fermentation of Taorong-type Baijiu
    Yanbo Liu, Haideng Li, Shumei Dong, Zhou Zhou, Zhenke Zhang, Runna Huang, Suna Han, Jianguang Hou, Chunmei Pan
    LWT.2023; 173: 114290.     CrossRef
  • The differences in carbohydrate utilization ability between six rounds of Sauce-flavor Daqu
    Qi Zhu, Liangqiang Chen, Zheng Peng, Qiaoling Zhang, Wanqiu Huang, Fan Yang, Guocheng Du, Juan Zhang, Li Wang
    Food Research International.2023; 163: 112184.     CrossRef
  • Microbial Community Affects Daqu Quality and the Production of Ethanol and Flavor Compounds in Baijiu Fermentation
    Pei-Jie Han, Lu-Jun Luo, Ying Han, Liang Song, Pan Zhen, Da-Yong Han, Yu-Hua Wei, Xin Zhou, Zhang Wen, Jun-Zhi Qiu, Feng-Yan Bai
    Foods.2023; 12(15): 2936.     CrossRef
  • Comparison of physicochemical characteristics and microbiome profiles of low-temperature Daqu with and without adding tartary buckwheat
    Jiamu Kang, Liangliang Jia, Zhongxiao Zhang, Min Zhang, Xiaoning Huang, Xiaoxue Chen, Bei-Zhong Han
    Food Bioscience.2022; 49: 101931.     CrossRef
  • What Are the Main Factors That Affect the Flavor of Sauce-Aroma Baijiu
    Jiao Niu, Shiqi Yang, Yi Shen, Wei Cheng, Hehe Li, Jinyuan Sun, Mingquan Huang, Baoguo Sun
    Foods.2022; 11(21): 3534.     CrossRef
  • Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu
    Jiamu Kang, Xiaoxue Chen, Bei-Zhong Han, Yansong Xue
    Food Research International.2022; 158: 111488.     CrossRef
Isolation of a novel strain, Sphingorhabdus sp. YGSMI21 and characterization of its enantioselective epoxide hydrolase activity
Jung-Hee Woo , Hae-Seon Kim , Nyun-Ho Park , Ho Young Suk
J. Microbiol. 2021;59(7):675-680.   Published online June 1, 2021
DOI: https://doi.org/10.1007/s12275-021-1023-x
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AbstractAbstract
Sphingorhabdus sp. YGSMI21, a novel microbial strain with an enantioselective epoxide hydrolase activity, was isolated from tidal samples contaminated by accidental oil spills subjected to enriched culture with polycyclic aromatic hydrocarbon. This strain was able to optically decompose (R)-styrene oxide (SO) and showed 100% optical purity. In addition, it showed a good enantioselectivity for the derivatives of (S)- SO, (S)-2-chlorostyrene oxide (CSO), (S)-3-CSO and (S)-4- CSO. For (S)-2-CSO, (S)-3-CSO and (S)-4-CSO, 99.9%ee was obtained with the yield of 26.2%, 24.8%, and 11.0%, respectively, when using 10 mg cells of Sphingorhabdus sp. YGSMI21 at pH 8.0 with 4 mM racemic substrates at pH 8.0 and 25°C. The values obtained in this study for (S)-2-CSO, particularly the yield of 26.2%, is noteworthy, considering that obtaining an enantiomerically pure form is difficult. Taken together, Sphingorhabdus sp. YGSMI21 can be regarded as a wholecell biocatalyst in the production of various (S)-CSO with the chlorine group at a different position.

Citations

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  • Epoxide Hydrolases: Multipotential Biocatalysts
    Marek Bučko, Katarína Kaniaková, Helena Hronská, Peter Gemeiner, Michal Rosenberg
    International Journal of Molecular Sciences.2023; 24(8): 7334.     CrossRef
  • Effects of submerged macrophytes (Elodea nuttallii) on water quality and microbial communities of largemouth bass (Micropterus salmoides) ponds
    Zhijuan Nie, Zhaowei Zheng, Haojun Zhu, Yi Sun, Jun Gao, Jiancao Gao, Pao Xu, Gangchuan Xu
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
    Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(6): 576.     CrossRef
Effect of biostimulation and bioaugmentation on hydrocarbon degradation and detoxification of diesel-contaminated soil: a microcosm study
Patricia Giovanella , Lídia de Azevedo Duarte , Daniela Mayumi Kita , Valéria Maia de Oliveira , Lara Durães Sette
J. Microbiol. 2021;59(7):634-643.   Published online May 15, 2021
DOI: https://doi.org/10.1007/s12275-021-0395-2
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AbstractAbstract
Soil contamination with diesel oil is quite common during processes of transport and storage. Bioremediation is considered a safe, economical, and environmentally friendly approach for contaminated soil treatment. In this context, studies using hydrocarbon bioremediation have focused on total petroleum hydrocarbon (TPH) analysis to assess process effectiveness, while ecotoxicity has been neglected. Thus, this study aimed to select a microbial consortium capable of detoxifying diesel oil and apply this consortium to the bioremediation of soil contaminated with this environmental pollutant through different bioremediation approaches. Gas chromatography (GC-FID) was used to analyze diesel oil degradation, while ecotoxicological bioassays with the bioindicators Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis sativus were used to assess detoxification. After 90 days of bioremediation, we found that the biostimulation and biostimulation/ bioaugmentation approaches showed higher rates of diesel oil degradation in relation to natural attenuation (41.9 and 26.7%, respectively). Phytotoxicity increased in the biostimulation and biostimulation/bioaugmentation treatments during the degradation process, whereas in the Microtox test, the toxicity was the same in these treatments as that in the natural attenuation treatment. In both the phytotoxicity and Microtox tests, bioaugmentation treatment showed lower toxicity. However, compared with natural attenuation, this approach did not show satisfactory hydrocarbon degradation. Based on the microcosm experiments results, we conclude that a broader analysis of the success of bioremediation requires the performance of toxicity bioassays.

Citations

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  • Heavy fuel oil-contaminated soil remediation by individual and bioaugmentation-assisted phytoremediation with Medicago sativa and with cold plasma-treated M. sativa
    Jūratė Žaltauskaitė, Rimas Meištininkas, Austra Dikšaitytė, Laima Degutytė-Fomins, Vida Mildažienė, Zita Naučienė, Rasa Žūkienė, Kazunori Koga
    Environmental Science and Pollution Research.2024; 31(20): 30026.     CrossRef
  • Soil Corrosivity Under Natural Attenuation
    Larissa O. da Silva, Sara H. de Oliveira, Rafael G. C. da Silva, Magda R. S. Vieira, Ivanilda R. de Melo, Severino L. Urtiga Filho
    Materials Research.2024;[Epub]     CrossRef
  • Updating risk remediation-endpoints for petroleum-contaminated soils? A case study in the Ecuadorian Amazon region
    Daniel Hidalgo-Lasso, Karina García-Villacís, Jeaneth Urvina Ulloa, Darwin Marín Tapia, Patricio Gómez Ortega, Frederic Coulon
    Heliyon.2024; 10(9): e30395.     CrossRef
  • Recent advances in the development and applications of luminescent bacteria–based biosensors
    Yingying Li, Yuankun Zhao, Yiyang Du, Xuechun Ren, He Ding, Zhimin Wang
    Luminescence.2024;[Epub]     CrossRef
  • Oil biodegradation studies with an immobilized bacterial consortium in plant biomass for the construction of bench-scale bioreactor
    Rachel M. Ferreira, Bernardo D. Ribeiro, Danielle.M.A. Stapelfeldt, Rodrigo P. do Nascimento, Maria de.F.R. Moreira
    Cleaner Chemical Engineering.2023; 6: 100107.     CrossRef
  • Application of Luminescent Bacteria Bioassay in the Detection of Pollutants in Soil
    Kai Zhang, Meng Liu, Xinlong Song, Dongyu Wang
    Sustainability.2023; 15(9): 7351.     CrossRef
  • Salicylate or Phthalate: The Main Intermediates in the Bacterial Degradation of Naphthalene
    Vasili M. Travkin, Inna P. Solyanikova
    Processes.2021; 9(11): 1862.     CrossRef
Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing
Shuai Yang , Wei Xu , Yuanhao Gao , Xiaoyao Chen , Zhu-Hua Luo
J. Microbiol. 2020;58(10):841-852.   Published online September 2, 2020
DOI: https://doi.org/10.1007/s12275-020-0198-x
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AbstractAbstract
There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.

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    Eun-Bi Kim, Se-Jong Ju, Yeon Jee Suh
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Short-term effects of returning granulated straw on soil microbial community and organic carbon fractions in dryland farming
Wei Fan , Jinggui Wu
J. Microbiol. 2020;58(8):657-667.   Published online June 25, 2020
DOI: https://doi.org/10.1007/s12275-020-9266-5
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AbstractAbstract
We conducted a 2-year field experiment which was comprised of five treatments, namely no straw returning (CK), straw mulching (SM), straw plowed into the soil (SP), and straw returned in granulated form (SG). The aim of this study was to investigate the effects of different straw returning modes on soil bacterial and fungal community structure and their relationships to soil organic carbon (SOC) fractions at three different soil depths (0–20, 20–40, and 40–60 cm) in a dryland under maize cultivation in Northeast (NE) China. SM, SP, and SG treatments significantly increased SOC content. Compared with SM and SP treatments, SG treatment significantly increased the content of SOC and easily oxidizable carbon (EOC) in the topsoil (0–20 cm depth), and increased dissolved organic carbon (DOC) and SOC content of the light fraction (LFOC) in the 20–40 cm layer. Meanwhile, SG treatment exhibited the highest microbial biomass C (MBC) content in all of the three soil depths. SG treatment also enhanced bacterial richness as well as fungal richness and diversity in the upper 40 cm of soil. In addition, SG treatment increased the relative abundance of Proteobacteria in all depths, and had the highest relative abundance of Basidiomycota in the first 20 cm of soil. SP treatment showed the lowest soil organic carbon content in all fractions and soil microbial community composition. SM treatment exhibited similar results to SG treatment in SOC, DOC, and LFOC contents, and bacterial diversity in the topsoil and subsoil. As a whole, treatment SG improved soil quality and maize yield, hence we recommend returning granulated straw as the most effective practice for enhancing labile SOC fractions as well as maintaining soil diversity and microbial richness of arid farmlands in NE China.

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Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli
Jungwook Park , Hyun-Hee Lee , Hyejung Jung , Young-Su Seo
J. Microbiol. 2019;57(9):781-794.   Published online August 27, 2019
DOI: https://doi.org/10.1007/s12275-019-9330-1
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AbstractAbstract
The phytopathogenic Burkholderia species B. glumae and B. plantarii are the causal agents of bacterial wilt, grain rot, and seedling blight, which threaten the rice industry globally. Toxoflavin and tropolone are produced by these phytopathogens and are considered the most hostile biohazards with a broad spectrum of target organisms. However, despite their nonspecific toxicity, the effects of toxoflavin and tropolone on bacteria remain unknown. RNA-seq based transcriptome analysis was employed to determine the genome-wide expression patterns under phytotoxin treatment. Expression of 2327 and 830 genes was differentially changed by toxoflavin and tropolone, respectively. Enriched biological pathways reflected the down-regulation of oxidative phosphorylation and ribosome function, beginning with the inhibition of membrane biosynthesis and nitrogen metabolism under oxidative stress or iron starvation. Conversely, several systems such as bacterial chemotaxis, flagellar assembly, biofilm formation, and sulfur/taurine transporters were highly expressed as countermeasures against the phytotoxins. In addition, our findings revealed that three hub genes commonly induced by both phytotoxins function as the siderophore enterobactin, an ironchelator. Our study provides new insights into the effects of phytotoxins on bacteria for better understanding of the interactions between phytopathogens and other microorganisms. These data will also be applied as a valuable source in subsequent applications against phytotoxins, the major virulence factor.

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Review
MINIREVIEW] The therapeutic applications of antimicrobial peptides (AMPs): a patent review
Hee-Kyoung Kang , Cheolmin Kim , Chang Ho Seo , Yoonkyung Park
J. Microbiol. 2017;55(1):1-12.   Published online December 30, 2016
DOI: https://doi.org/10.1007/s12275-017-6452-1
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AbstractAbstract
Antimicrobial peptides (AMPs) are small molecules with a broad spectrum of antibiotic activities against bacteria, yeasts, fungi, and viruses and cytotoxic activity on cancer cells, in addition to anti-inflammatory and immunomodulatory activities. Therefore, AMPs have garnered interest as novel therapeutic agents. Because of the rapid increase in drug-resistant pathogenic microorganisms, AMPs from synthetic and natural sources have been developed using alternative antimicrobial strategies. This article presents a broad analysis of patents referring to the therapeutic applications of AMPs since 2009. The review focuses on the universal trends in the effective design, mechanism, and biological evolution of AMPs.

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Journal Article
Potential for colonization of O111:H25 atypical enteropathogenic E. coli
Marta O. Domingos , Keyde C.M. Melo , Irys Viana Neves , Cristiane M. Mota , Rita C. Ruiz , Bruna S. Melo , Raphael C. Lima , Denise S.P.Q. Horton , Monamaris M. Borges , Marcia R. Franzolin
J. Microbiol. 2016;54(11):745-752.   Published online October 29, 2016
DOI: https://doi.org/10.1007/s12275-016-6015-x
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AbstractAbstract
Using clonal phylogenetic methods, it has been demonstrated that O111:H25 atypical enteropathogenic E. coli (aEPEC) strains belong to distinct clones, suggesting the possibility that their ability to interact with different hosts and abiotic surfaces can vary from one clone to another. Accordingly, the ability of O111:H25 aEPEC strains derived from human, cat and dogs to adhere to epithelial cells has been investigated, along with their ability to interact with macrophages and to form biofilms on polystyrene, a polymer used to make biomedical devices. The results demonstrated that all the strains analyzed were able to adhere to, and to form pedestals on, epithelial cells, mechanisms used by E. coli to become strongly attached to the host. The strains also show a Localized-Adherence- Like (LAL) pattern of adhesion on HEp-2 cells, a behavior associated with acute infantile diarrhea. In addition, the O111:H25 aEPEC strains derived either from human or domestic animals were able to form long filaments, a phenomenon used by some bacteria to avoid phagocytosis. O111:H25 aEPEC strains were also encountered inside vacuoles, a characteristic described for several bacterial strains as a way of protecting themselves against the environment. They were also able to induce TNF-α release via two routes, one dependent on TLR-4 and the other dependent on binding of Type I fimbriae. These O111:H25 strains were also able to form biofilms on polystyrene. In summary the results suggest that, regardless of their source (i.e. linked to human origin or otherwise), O111:H25 aEPEC strains carry the potential to cause human disease.

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