Journal of Microbiology

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Exploring the biosynthetic potential of Korean Actinobacteria for antibacterial metabolite discovery: Sehong Park, Hyun-Woo Je, Yujin Cha, Boncheol Gu, Yeojeong Cho, Jin-Il Kim, Ji Won Seo, Seung Bum Kim, Jino Son, Moonsuk Hur, Changmin Sung, Min-Kyu Oh, Hahk-Soo Kang; J. Microbiol. 2025;63(9):e2504002. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2504002

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Abstract PDF Supplementary Material: Actinobacteria, a phylum of Gram-positive bacteria, are renowned for their remarkable ability to produce antibacterial natural products. The National Institute of Biological Resources (NIBR) of Korea maintains a collection of Korean native actinobacteria. In this study, we explored the phylogenetic and biosynthetic diversity of the NIBR actinobacteria collection to assess its potential as a source of new antibacterial natural products. A 16S rDNA-based phylogenetic analysis revealed a high level of genetic diversity within the collection, with a predominance of Streptomyces, along with rare actinobacterial genera such as Kitasatospora and Micromonospora. Additionally, genetic network analysis of biosynthetic gene clusters (BGCs) from 15 sequenced NIBR actinobacterial strains demonstrated extensive BGC diversity, with many clusters identified as cryptic. Screening of culture extracts for antibacterial activity, followed by dereplication of active extracts, suggested the presence of potentially novel antibacterial natural products. Activity-guided isolation and whole-genome sequencing of the active strain KU57 led to the isolation of one new and three known svetamycin congeners along with their BGC. Overall, our findings highlight the NIBR actinobacteria collection as a valuable source for the discovery of new antibacterial natural products.

Review

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives: Ok Kyung Lee, Jong Seok Lee, Yoonyong Yang, Moonsuk Hur, Kyung Jin Lee, Eun Yeol Lee; J. Microbiol. 2025;63(3):e2412024. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2412024

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Methane gas is recognized as a promising carbon substrate for the biosynthesis of value-added products due to its abundance and low price. Methanotrophs utilized methane as their sole source of carbon and energy, thus they can serve as efficient biocatalysts for methane bioconversion. Methanotrophs-catalyzed microbial bioconversion offer numerous advantages, compared to chemical processes. Current indirect chemical conversions of methane suffer from their energy-intensive processes and high capital expenditure. Methanotrophs can be cell factories capable of synthesizing various value-added products from methane such as methanol, organic acids, ectoine, polyhydroxyalkanoates, etc. However, the large-scale commercial implementation using methanotrophs remains a formidable challenge, primarily due to limitations in gas-liquid mass transfer and low metabolic capacity. This review explores recent advancements in methanotroph research, providing insights into their potential for enabling methane bioconversion.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Journal Articles

Medium Chain Length Polyhydroxyalkanoate Production by Engineered Pseudomonas gessardii Using Acetate-formate as Carbon Sources: Woo Young Kim, Seung-Jin Kim, Hye-Rin Seo, Yoonyong Yang, Jong Seok Lee, Moonsuk Hur, Byoung-Hee Lee, Jong-Geol Kim, Min-Kyu Oh; J. Microbiol. 2024;62(7):569-579. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00136-x

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Abstract PDF

Production of medium chain length polyhydroxyalkanoate (mcl-PHA) was attempted using Pseudomonas gessardii NIBRBAC000509957, which was isolated from Sunchang, Jeollabuk-do, Republic of Korea (35°24'27.7"N, 127°09'13.0"E) and effectively utilized acetate and formate as carbon sources. We first evaluated the utilization of acetate as a carbon source, revealing optimal growth at 5 g/L acetate. Then, formate was supplied to the acetate minimal medium as a carbon source to enhance cell growth. After overexpressing the acetate and formate assimilation pathway enzymes, this strain grew at a significantly higher rate in the medium. As this strain naturally produces PHA, it was further engineered metabolically to enhance mcl-PHA production. The engineered strain produced 0.40 g/L of mcl-PHA with a biomass content of 30.43% in fed-batch fermentation. Overall, this strain can be further developed to convert acetate and formate into valuable products.

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Formate-driven photoautotrophic growth and biopolymer storage in anaerobic purple bacteria
Mohammad Adib Ghazali Abdul Rahman, Bronwyn Laycock, Steven Pratt, Damien J. Batstone
Bioresource Technology.2025; 434: 132753. CrossRef
Sulphide and oleic acid synergism in accelerating mcl-PHA biopolymer production in Pseudomonas aeruginosa MCC 5300 by modulating electron transport system
Raghavendra Paduvari, Divyashree Somashekara
Biochemistry and Biophysics Reports.2025; 44: 102286. CrossRef
Unlocking efficient polyhydroxyalkanoate production by Gram-positive Priestia megaterium using waste-derived feedstocks
Xinyi Bai, Libo Xu, Kang Li, Guangbao Zhang, Mengjun Zhang, Yi Huang
Microbial Cell Factories.2025;[Epub] CrossRef

Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Abstract PDF

Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Ammonium bicarbonate alleviates apple replant disease: Inhibiting Fusarium and improving soil environment
Mei Wang, Li Xiang, Weixiao Tang, Xuesen Chen, Chuanrong Li, Chengmiao Yin, Zhiquan Mao
Scientia Horticulturae.2024; 325: 112652. CrossRef
Regulation of root-associated microbiomes and root exudates by different tobacco species
Mengli Gu, Jingjing Jin, Peng Lu, Shizhou Yu, Huan Su, Haihong Shang, Zhixiao Yang, Jianfeng Zhang, Peijian Cao, Jiemeng Tao
Chemical and Biological Technologies in Agriculture.2024;[Epub] CrossRef
MAPK Cascades in Plant Microbiota Structure and Functioning
Thijs Van Gerrewey, Hoo Sun Chung
Journal of Microbiology.2024; 62(3): 231. CrossRef
Land-use change alters the bacterial community structure, but not forest management
Viviana Rodríguez Rivera, Yendi E. Navarro-Noya, Luc Dendooven, Marco Luna Guido
Folia Microbiologica.2023; 68(2): 277. CrossRef
Soil Microbial Communities Associated with Three Arctic Plants in Different Local Environments in Ny–Ålesund, Svalbard
Deokjoo Son, Eun Ju Lee
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The root microbiome: Community assembly and its contributions to plant fitness
Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang, Yang Bai
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Phytobiomes Journal.2020; 4(2): 103. CrossRef
Tomato-Associated Archaea Show a Cultivar-Specific Rhizosphere Effect but an Unspecific Transmission by Seeds
Julian Taffner, Alessandro Bergna, Tomislav Cernava, Gabriele Berg
Phytobiomes Journal.2020; 4(2): 133. CrossRef
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
Journal of Microbiology.2020; 58(11): 906. CrossRef

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

Fungal Community Associated with Genetically Modified Poplar During Metal Phytoremediation: Moonsuk Hur , Young Woon Lim , Jae Jeong Yu , Se Uk Cheon , Young Im Choi , Seok-Hwan Yoon , Sang-Cheol Park , Dong-Il Kim , Hana Yi; J. Microbiol. 2012;50(6):910-915. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2491-9

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Abstract PDF

Due to the increasing demand for phytoremediation, many transgenic poplars have been developed to enhance the bioremediation of heavy metals. However, structural changes to indigenous fungal communities by genetically modified organisms (GMO) presents a major ecological issue, due to the important role of fungi for plant growth in natural environments. To evaluate the effect of GM plant use on environmental fungal soil communities, extensive sequencing-based community analysis was conducted, while controlling the influence of plant clonality, plant age, soil condition, and harvesting season. The rhizosphere soils of GM and wild type (WT) poplars at a range of growth stages were sampled together with unplanted, contaminated soil, and the fungal community structures were investigated by pyrosequencing the D1/D2 region of the 28S rRNA gene. The results show that the overall structure of the rhizosphere fungal community was not significantly influenced by GM poplars. However, the presence of GM specific taxa, and faster rate of community change during poplar growth, appeared to be characteristic of the GM plant-induced effects on soil-born fungal communities. The results of this study provide additional information about the potential effects of GM poplar trees aged 1.5–3 years, on the soil fungal community.

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Jihwi Jang
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Di Liu, Kuanyu Zheng, Yue Wang, Yan Zhang, Ruimin Lao, Zhiyang Qin, Tao Li, Zhiwei Zhao
Journal of Hazardous Materials.2022; 424: 127430. CrossRef
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Environmental Science and Pollution Research.2022; 29(23): 35350. CrossRef
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Jianxiu Guo, Saman Bowatte, Fujiang Hou
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C. S. Schmidt, P. Lovecká, L. Mrnka, A. Vychodilová, M. Strejček, M. Fenclová, K. Demnerová
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Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study
Katrina L. Callender, Sébastien Roy, Damase P. Khasa, Lyle G. Whyte, Charles W. Greer, Zhili He
PLOS ONE.2016; 11(2): e0150181. CrossRef
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