Journal of Microbiology

Full article

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

804 View
33 Download

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.

Journal Articles

Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.: Dong Hyeon Lee, Seung Bum Kim; J. Microbiol. 2024;62(6):449-461. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00131-2

336 View
8 Download
7 Web of Science
7 Crossref

Quorum quenching refers to any mechanism that inhibits quorum sensing processes. In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11(T), which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11(T) could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37(T), and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15(T) and Reyranella massiliensis 521(T), respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11(T) had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11(T). Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11(T). Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11(T) could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11( T) = KCTC 82780( T) = LMG 32365(T)).

Citations

Citations to this article as recorded by

Study of N-acyl homoserine lactone (AHL) degradation potential of bacteria isolated from environmental samples and their impact on quorum sensing regulated biofilm formation of Pseudomonas aeruginosa
Anju Tomy, Rakesh Yasarla
Journal of Environmental Chemical Engineering.2025; 13(2): 115974. CrossRef
Hepatotoxicity of imidacloprid in zebrafish and the alleviating role of 10-hydroxy-2-decenoi acid: Insights into oxidative stress, inflammation, and gut microbiota
Yujing Tang, Yandong Zhan, Shuangshuang Gao, Ting Li, Hongzhuan Xuan
Journal of Hazardous Materials.2025; 494: 138695. CrossRef
Description of Humidisolicoccus flavus gen. nov., sp. nov., a novel actinobacterium isolated from riverside soil
Da Chan Kim, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
The Causative Agent of Soft Rot in Plants, the Phytopathogenic Bacterium Pectobacterium carotovorum subsp. carotovorum: A Brief Description and an Overview of Methods to Control It
Alla I. Perfileva, Elena I. Strekalovskaya, Nadezhda V. Klushina, Igor V. Gorbenko, Konstantin V. Krutovsky
Agronomy.2025; 15(7): 1578. CrossRef
SynCom‐mediated herbicide degradation activates microbial carbon metabolism in soils
Yuxiao Zhang, Jack A. Gilbert, Xuan Liu, Li Nie, Xiyuan Xu, Guifeng Gao, Lihui Lyu, Yuying Ma, Kunkun Fan, Teng Yang, Yumeng Zhang, Jiabao Zhang, Haiyan Chu
iMeta.2025;[Epub] CrossRef
Research progress of bacterial quorum sensing systems in synthetic biology applications
Boyu Luo, Tuoyu Liu, Zhi Sun, Yue Teng
Chinese Science Bulletin.2024; 69(36): 5213. CrossRef
Validation List no. 220. 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

A comprehensive in silico analysis of sortase superfamily: Adeel Malik , Seung Bum Kim; J. Microbiol. 2019;57(6):431-443. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8545-5

305 View
0 Download
18 Web of Science
17 Crossref

Abstract PDF

Sortases are cysteine transpeptidases that assemble surface proteins and pili in their cell envelope. Encoded by all Grampositive bacteria, few Gram-negative bacteria and archaea, sortases are currently divided into six classes (A-F). Due to the steep increase in bacterial genome data in recent years, the number of sortase homologues have also escalated rapidly. In this study, we used protein sequence similarity networks to explore the taxonomic diversity of sortases and also to evaluate the current classification of these enzymes. The resultant data suggest that sortase classes A, B, and D predominate in Firmicutes and classes E and F are enriched in Actinobacteria, whereas class C is distributed in both Firmicutes and Actinobacteria except Streptomyces family. Sortases were also observed in various Gram-negatives and euryarchaeota, which should be recognized as novel classes of sortases. Motif analysis around the catalytic cysteine was also performed and suggested that the residue at 2nd position from cysteine may help distinguish various sortase classes. Moreover, the sequence analysis indicated that the catalytic arginine is highly conserved in almost all classes except sortase F in which arginine is replaced by asparagine in Actinobacteria. Additionally, class A sortases showed higher structural variation as compared to other sortases, whereas inter-class comparisons suggested structures of class C and D2 exhibited best similarities. A better understanding of the residues highlighted in this study should be helpful in elucidating their roles in substrate binding and the sortase function, and successively could help in the development of strong sortase inhibitors.

Citations

Citations to this article as recorded by

Advances and challenges in drug design against dental caries: Application of in silico approaches
Zhongxin Chen, Xinyao Zhao, Hanyu Zheng, Yufei Wang, Linglin Zhang
Journal of Pharmaceutical Analysis.2025; 15(6): 101161. CrossRef
Rolling down the pilus formation of gram-positive bacteria: underlining the importance of Sortase C as a drug target
Himanshi Kain, Ena Gupta, Prashant Sharma, Akanksha Haldiya, Vijay Kumar Srivastava, Ravi Ranjan Kumar Neeraj, Pradeep Sharma, S. L. Kothari, Sandip Patil, Shaowei Dong, Anupam Jyoti, Sanket Kaushik
Biofouling.2025; 41(1): 1. CrossRef
Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase
José Jesús Gallego-Parrilla, Emmanuele Severi, Govind Chandra, Tracy Palmer
Microbiology .2024;[Epub] CrossRef
Sortases: structure, mechanism, and implications for protein engineering
Jeanine F. Amacher, John M. Antos
Trends in Biochemical Sciences.2024; 49(7): 596. CrossRef
A unique binding mode of P1′ Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage
Brandon A. Vogel, Jadon M. Blount, Hanna M. Kodama, Noah J. Goodwin-Rice, Devin J. Andaluz, Sophie N. Jackson, John M. Antos, Jeanine F. Amacher
RSC Chemical Biology.2024; 5(1): 30. CrossRef
GPApred: The first computational predictor for identifying proteins with LPXTG-like motif using sequence-based optimal features
Adeel Malik, Watshara Shoombuatong, Chang-Bae Kim, Balachandran Manavalan
International Journal of Biological Macromolecules.2023; 229: 529. CrossRef
Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes
Melody Gao, D. Alex Johnson, Isabel M. Piper, Hanna M. Kodama, Justin E. Svendsen, Elise Tahti, Frederick Longshore‐Neate, Brandon Vogel, John M. Antos, Jeanine F. Amacher
Protein Science.2022; 31(3): 701. CrossRef
Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities
Jordan D. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, Isabel M. Piper, Justin E. Svendsen, D. Alex Johnson, Brandon A. Vogel, John M. Antos, Michael J. Harms, Jeanine F. Amacher
Bacteria.2022; 1(2): 121. CrossRef
SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information
Adeel Malik, Sathiyamoorthy Subramaniyam, Chang-Bae Kim, Balachandran Manavalan
Computational and Structural Biotechnology Journal.2022; 20: 165. CrossRef
Prevalent association with the bacterial cell envelope of prokaryotic expansins revealed by bioinformatics analysis
Andrés de Sandozequi, Juan José Salazar‐Cortés, Irán Tapia‐Vázquez, Claudia Martínez‐Anaya
Protein Science.2022;[Epub] CrossRef
Intramolecular Covalent Bonds in Gram‐Positive Bacterial Surface Proteins
Quan Ma, Hai Lei, Yi Cao
ChemBioChem.2022;[Epub] CrossRef
The ever-expanding tcp conjugation locus of pCW3 from Clostridium perfringens
Sarah A. Revitt-Mills, Thomas D. Watts, Dena Lyras, Vicki Adams, Julian I. Rood
Plasmid.2021; 113: 102516. CrossRef
A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains
Kira S. Makarova, Yuri I. Wolf, Svetlana Karamycheva, Eugene V. Koonin
Frontiers in Microbiology.2021;[Epub] CrossRef
Sorting out the Superbugs: Potential of Sortase A Inhibitors among Other Antimicrobial Strategies to Tackle the Problem of Antibiotic Resistance
Nikita Zrelovs, Viktorija Kurbatska, Zhanna Rudevica, Ainars Leonchiks, Davids Fridmanis
Antibiotics.2021; 10(2): 164. CrossRef
Chemoenzymatic Semisynthesis of Proteins
Robert E. Thompson, Tom W. Muir
Chemical Reviews.2020; 120(6): 3051. CrossRef
Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium
Adeel Malik, Yu Ri Kim, In Hee Jang, Sunghoon Hwang, Dong-Chan Oh, Seung Bum Kim
BMC Genomics.2020;[Epub] CrossRef
Proteases as Secreted Exoproteins in Mycoplasmas from Ruminant Lungs and Their Impact on Surface-Exposed Proteins
Sarah Ganter, Guylaine Miotello, Lucía Manso-Silván, Jean Armengaud, Florence Tardy, Patrice Gaurivaud, François Thiaucourt, Rebecca E. Parales
Applied and Environmental Microbiology.2019;[Epub] CrossRef

Mucibacter soli gen. nov., sp. nov., a new member of the family Chitinophagaceae producing mucin: Min-Kyeong Kim , Sewook Park , Tae-Su Kim , Yochan Joung , Ji-Hye Han , Seung Bum Kim; J. Microbiol. 2019;57(5):356-361. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8512-1

280 View
0 Download
8 Web of Science
8 Crossref

Abstract PDF

A Gram-stain-negative, mucus-forming, motile by gliding, non-spore-forming and short rod-shaped bacterial strain designated R1-15T was isolated from soil and its taxonomic position was evaluated using a polyphasic approach. Strain R1-15T grew at 15–37°C (optimum, 30°C), at pH 6–7 (optimum, pH 6) and in the presence of 0–1% (w/v) NaCl (optimum, 0%) on 0.1X TSA. On the basis of 16S rRNA gene sequence similarity, the novel strain was assigned to the family Chitinophagaceae of the phylum Bacteroidetes, and its closest related taxa were species of the genera Taibaiella (88.76– 90.02% sequence similarity), Lacibacter (89.24–90.00%), Chitinophaga (88.61–89.76%), and Terrimonas (89.04%). Flexirubin- type pigments were produced. The only isoprenoid quinone was MK-7, and the major polar lipid was phosphatidylethanolamine. Based on whole genome comparisons between the strain R1-15T and the type strains of relatives, the orthologous average nucleotide identity values were 66.9– 67.0%. The DNA G+C content of strain R1-15T was 43.8 mol%. The combination of phylogenetic, chemotaxonomic and phenotypic data clearly supported separation of strain R1-15T from related taxa, and thus the name Mucibacter soli gen. nov., sp. nov. is proposed. The type strain is R1-15T (= KCTC 62274T = JCM 31190T).

Citations

Citations to this article as recorded by

Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery
Xing Chen, Yuan-Dong Li, Xiu-Ming Liu, Li Gao, Xing-Kui Zhou, Li-Min Dong, Gang Du, Neeli Habib, Wen-Jun Li, Yan-Qing Duan
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Saline soil improvement promotes the transformation of microbial salt tolerance mechanisms and microbial-plant-animal ecological interactions
Keyu Yao, Guanghao Wang, Wen Zhang, Qiang Liu, Jian Hu, Mao Ye, Xin Jiang
Journal of Environmental Management.2024; 372: 123360. CrossRef
Cast from the Past? Microbial Diversity of a Neolithic Stone Circle
Mercedes Martín-Cereceda, Amaya de Cos-Gandoy, Richard A. J. Williams, David Elliott, Andrea Serrano-Bellón, Blanca Pérez-Uz, Abel Sanchez-Jimenez
Microorganisms.2024; 12(11): 2338. CrossRef
Dyella sedimenti sp. nov., Isolated from the Sediment of a Winery
Li Gao, Yuan-Dong Li, Xing-Kui Zhou, Xiu-Ming Liu, Hui-Tian Li, Wen-Jun Li, Yan-Qing Duan
Current Microbiology.2022;[Epub] CrossRef
Utilization of three-layered polyvinyl alcohol gel cubes for treating low-strength ammonium wastewater in a single-stage autotrophic nitrogen removal process
Dawoon Jeong, Hyunman Lim, Myoung-Soo Ko, Weonjae Kim
Journal of Environmental Chemical Engineering.2022; 10(1): 106934. CrossRef
Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil
Su Gwon Roh, Chan Lee, Min-Kyeong Kim, Hye-Jeong Kang, Yeong Seok Kim, Min Ji Kim, Adeel Malik, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2682. CrossRef
Gordonia insulae sp. nov., isolated from an island soil
Yeong Seok Kim, Su Gwon Roh, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 2079. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(1): 1. CrossRef

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

Diversity and Physiological Properties of Root Endophytic Actinobacteria in Native Herbaceous Plants of Korea: Tae-Ui Kim , Sung-Heun Cho , Ji-Hye Han , Young Min Shin , Hyang Burm Lee , Seung Bum Kim; J. Microbiol. 2012;50(1):50-57. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1417-x

211 View
0 Download
32 Crossref

Abstract

Endophytic actinobacterial diversity in the native herbaceous plant species of Korea was analyzed using a culturebased approach. Sixty one actinobacterial strains were isolated, and assigned to 15 genera based on 16S rRNA gene analysis. The members of the genus Streptomyces comprised 45.9% of the total isolates, followed by Micromonospora (18.8%), Rhodococcus (6.6%), Microbispora (4.9%), and Micrococcus (4.9%). Other minor constituents included members of Microbacterium, Streptacidiphilus, Arthrobacter, Dietzia, Kitasatospora, Herbiconiux, Mycobacterium, Nocardia, Rathayibacter, and Tsukamurella. Among the isolates, 65.6% exhibited at least one hydrolytic enzyme activity out of four, and 45.9% exhibited antagonistic activity against at least one fungal pathogen out of five, thus demonstrating that endophytic actinobacteria can be an important source of bioactive compounds. Notably, most strains of Streptomyces proved active for both enzymatic and antagonistic activities.

Citations

Citations to this article as recorded by

Diversity and Bioactivity of Endophytic Actinobacteria Associated with the Roots of Artemisia herba-alba Asso from Algeria
Nadjette Djemouai, Atika Meklat, Khadidja Oulad Hadj Youcef, Asma Nacer, Sid Ahmed Saadi, Carol Verheecke-Vaessen
Current Microbiology.2024;[Epub] CrossRef
Endophytic fungus Neopestalotiopsis clavispora AUMC15969: biosynthesis and characterization of exopolysaccharides and biodiesel production
Mostafa M. Koutb, Elhagag A. Hassan, Nemmat A. Hussein, Fahd M. Abdelkarem, Hussein H. Abulreesh, Khaled Elbanna, Yulu Yang, El-Sayed Salama, Maysa M. Ali
Biomass Conversion and Biorefinery.2024; 14(19): 24539. CrossRef
Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization
Louis Garneau, Pascale B. Beauregard, Sébastien Roy
Canadian Journal of Microbiology.2023; 69(2): 72. CrossRef
Assessing the growth-promoting traits of actinobacteria spp. isolated from Cleome africana: Implications on growth and root enhancement of Medicago sativa
Anas Raklami, Francisco Quintas-Nunes, Francisco X. Nascimento, Martin Jemo, Khalid Oufdou, Asad Syed, Ali H. Bahkali, Meenakshi Verma, Ahmed Nafis
Journal of King Saud University - Science.2023; 35(6): 102722. CrossRef
Microbial Endophytes: Emerging Trends and Biotechnological Applications
Shruti Agrawal, Arun Bhatt
Current Microbiology.2023;[Epub] CrossRef
The characteristics of actinomyces strptomyces griseorubiginosus 83 – the effective biosorbent of silver
Nigora Bekmukhamedova, Khurshida Khamidova, A. Muratov, S. Khasanov
E3S Web of Conferences.2023; 371: 01038. CrossRef
Endophytic bacteria of wheat and the potential to improve microelement composition of grain
O. O. Makar, N. D. Romanyuk
Studia Biologica.2022; 16(3): 101. CrossRef
Isolation and identification of endophytic actinobacteria from Citrullus colocynthis (L.) Schrad and their antibacterial properties
Aram R. Ali, Yadollah Bahrami, Elham Kakaei, Sara Mohammadzadeh, Sasan Bouk, Nastaran Jalilian
Microbial Cell Factories.2022;[Epub] CrossRef
Comparative Secretome Analyses of Toxigenic and AtoxigenicRathayibacterSpecies
Matthew A. Tancos, Michael B. McMahon, Wesley M. Garrett, Douglas G. Luster, Elizabeth E. Rogers
Phytopathology®.2021; 111(9): 1530. CrossRef
Evaluation of Rpf protein of Micrococcus luteus for cultivation of soil actinobacteria
Yuhui Wang, Jiangli Shi, Lingjie Tang, Yufan Zhang, Yujia Zhang, Xinyu Wang, Xiumin Zhang
Systematic and Applied Microbiology.2021; 44(5): 126234. CrossRef
Diversity and function of culturable actinobacteria in the root-associated of Salvia miltiorrhiza Bunge
Yu-Rui Wu, Cui-Bai Li, Yan-Hong Wu, Lan Li, Bo Li, Wen-Bo Li, Bu-Jin Ma, Zhu-Yun Yan
PeerJ.2021; 9: e11749. CrossRef
Diversity and Antimicrobial Potential of Cultivable Endophytic Actinobacteria Associated With the Medicinal Plant Thymus roseus
Zulpiya Musa, Jinbiao Ma, Dilfuza Egamberdieva, Osama Abdalla Abdelshafy Mohamad, Gulsumay Abaydulla, Yonghong Liu, Wen-Jun Li, Li Li
Frontiers in Microbiology.2020;[Epub] CrossRef
Seasonal Variation Influence Endophytic Actinobacterial Communities of Medicinal Plants from Tropical Deciduous Forest of Meghalaya and Characterization of Their Plant Growth-Promoting Potentials
Dina Barman, Mamtaj S. Dkhar
Current Microbiology.2020; 77(8): 1689. CrossRef
Molecular and biotechnological aspects of secondary metabolites in actinobacteria
Richa Salwan, Vivek Sharma
Microbiological Research.2020; 231: 126374. CrossRef
Isolation and screening of actinomycetes producing cellulase and xylanase from Mamasa soil, West Sulawesi
A L Putri, R Setiawan
IOP Conference Series: Earth and Environmental Science.2019; 308(1): 012035. CrossRef
Plant Growth-Promoting Potential of Endophytic Bacteria Isolated from Costus speciosus in Tropical Deciduous Forest of Eastern Himalaya
Dina Barman, Mamtaj S. Dkhar
Proceedings of the National Academy of Sciences, India Section B: Biological Sciences.2019; 89(3): 841. CrossRef
Endophyte: Understanding the Microbes and its Applications
Raymond Oriebe Anyasi, Harrison Ifeanyichuk Atagana
Pakistan Journal of Biological Sciences.2019; 22(4): 154. CrossRef
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity
Anne van der Meij, Joost Willemse, Martinus A. Schneijderberg, René Geurts, Jos M. Raaijmakers, Gilles P. van Wezel
Antonie van Leeuwenhoek.2018; 111(5): 679. CrossRef
Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds
Zothanpuia, Ajit Kumar Passari, Vincent Vineeth Leo, Preeti Chandra, Brijesh Kumar, Chandra Nayak, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdulaziz A. Alqarawi, Bhim Pratap Singh
Microbial Cell Factories.2018;[Epub] CrossRef
Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters
Raghavan Dinesh, Veeraraghavan Srinivasan, Sheeja T. E., Muthuswamy Anandaraj, Hamza Srambikkal
Critical Reviews in Microbiology.2017; 43(5): 546. CrossRef
RETRACTED: Production of Potent Antimicrobial Compounds from Streptomyces cyaneofuscatus Associated with Fresh Water Sediment
Zothanpuia, Ajit K. Passari, Preeti Chandra, Vincent V. Leo, Vineet K. Mishra, Brijesh Kumar, Bhim P. Singh
Frontiers in Microbiology.2017;[Epub] CrossRef
Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India
Ramya Krishnan, Rahul Ravikumar Menon, Naoto Tanaka, Hans-Jürgen Busse, Srinivasan Krishnamurthi, Natarajan Rameshkumar, Pankaj Kumar Arora
PLOS ONE.2016; 11(3): e0150322. CrossRef
Diversity of Culturable Plant Growth-Promoting Bacterial Endophytes Associated with Sugarcane Roots and Their Effect of Growth by Co-Inoculation of Diazotrophs and Actinomycetes
Worarat Kruasuwan, Arinthip Thamchaipenet
Journal of Plant Growth Regulation.2016; 35(4): 1074. CrossRef
Distribution and Identification of Endophytic Streptomyces Species from Schima wallichii as Potential Biocontrol Agents against Fungal Plant Pathogens
AJIT KUMAR PASSARI, VINEET KUMAR MISHRA, VIJAI KUMAR GUPTA, RATUL SAIKIA, BHIM PRATAP SINGH
Polish Journal of Microbiology.2016; 65(3): 319. CrossRef
Isolation and antimicrobial activities of actinobacteria closely associated with liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza inflate BAT. in Xinjiang, China
Ke Zhao, Chong Zhao, Ping Liao, Qin Zhang, Yanbing Li, Maoke Liu, Xiaoling Ao, Yunfu Gu, Decong Liao, Kaiwei Xu, Xiumei Yu, Quanju Xiang, Chengyi Huang, Qiang Chen, Lili Zhang, Xiaoping Zhang, Petri Penttinen
Microbiology.2016; 162(7): 1135. CrossRef
Continuing hunt for endophytic actinomycetes as a source of novel biologically active metabolites
Meeta Masand, Polpass Arul Jose, Ekta Menghani, Solomon Robinson David Jebakumar
World Journal of Microbiology and Biotechnology.2015; 31(12): 1863. CrossRef
Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants
Martha E. Trujillo, Raúl Riesco, Patricia Benito, Lorena Carro
Frontiers in Microbiology.2015;[Epub] CrossRef
Biodiversity and plant growth promoting traits of culturable endophytic actinobacteria associated with Jatropha curcas L. growing in Panxi dry-hot valley soil
Sheng Qin, Qian Miao, Wei-Wei Feng, Yu Wang, Xiao Zhu, Ke Xing, Ji-Hong Jiang
Applied Soil Ecology.2015; 93: 47. CrossRef
Isolation, abundance and phylogenetic affiliation of endophytic actinomycetes associated with medicinal plants and screening for their in vitro antimicrobial biosynthetic potential
Ajit K. Passari, Vineet K. Mishra, Ratul Saikia, Vijai K. Gupta, Bhim P. Singh
Frontiers in Microbiology.2015;[Epub] CrossRef
Microbispora sp. LGMB259 Endophytic Actinomycete Isolated from Vochysia divergens (Pantanal, Brazil) Producing β-Carbolines and Indoles with Biological Activity
Daiani C. Savi, Khaled A. Shaaban, Nathalia Vargas, Larissa V. Ponomareva, Yvelise M. Possiede, Jon S. Thorson, Chirlei Glienke, Jürgen Rohr
Current Microbiology.2015; 70(3): 345. CrossRef
Endophytic microorganisms—promising applications in bioremediation of greenhouse gases
Z. Stępniewska, A. Kuźniar
Applied Microbiology and Biotechnology.2013; 97(22): 9589. CrossRef
Micromonospora is a normal occupant of actinorhizal nodules
Lorena Carro, Petar Pujic, Martha E Trujillo, Philippe Normand
Journal of Biosciences.2013; 38(4): 685. CrossRef

Application of Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Monitor Effect of Biocontrol Agents on Rhizosphere Microbial Community of Hot Pepper (Capsicum annuum L.): Young Tae Kim , Myoungho Cho , Je Yong Jeong , Hyang Burm Lee , Seung Bum Kim; J. Microbiol. 2010;48(5):566-572. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0126-6

178 View
0 Download
11 Scopus

Abstract PDF: Microbial communities in hot pepper (Capsicum annuum L.) cultivation fields under different cultivation methods were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis. Rhizosphere soil and leaf samples were collected from control, conventional and nature-friendly cultivation fields between May and July, 2009. Two Bacillus subtilis strains were applied to nature-friendly cultivation fields as biocontrol agents during the sampling period. Relative abundances of bacteria and plant pathogenic fungi related T-RFs were also measured to monitor the effect of biocontrol agents on potential plant pathogenic fungi. In the principal component analysis (PCA) based on T-RFLP profiles, the microbial communities from rhizosphere soil samples in July, including bacteria and fungi, showed distinct difference between nature-friendly cultivation fields and other cultivation fields. However, there was no correlation between cultivation methods and leaf microbial communities at any sampling period. Changes in the abundance of bacteria related T-RF in the rhizosphere of nature-friendly cultivation fields were observed clearly two months after application of biocontrol agent, while the abundance of plant pathogenic fungi related T-RFs significantly decreased.

Evaluation of Insecticidal Activity of a Bacterial Strain, Serratia sp. EML-SE1 against Diamondback Moth: Hyung Uk Jeong , Hye Yeon Mun , Hyung Keun Oh , Seung Bum Kim , Kwang Yeol Yang , Iksoo Kim , Hyang Burm Lee; J. Microbiol. 2010;48(4):541-545. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0221-9

144 View
0 Download
24 Scopus

Abstract PDF: To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th instar larvae of the diamondback moth was investigated on a Chinese cabbage leaf housed in a round plastic cage (Ø 10×6 cm). 72 h after spraying the cabbage leaf with LBB and NB cultures containing the bacterial strain, the mortalities of the larvae were determined to be 91.7% and 88.3%, respectively. In addition, the insecticidal activity on potted cabbage containing 14 leaves in a growth cage (165×83×124 cm) was found to be similar to that of the plastic cage experiment. The results of this study provided valuable information on the insecticidal activity of the liquid culture of a Serratia species against the diamondback moth.

Impact of cry1AC-Carrying Brassica rapa subsp. pekinensis on Leaf Bacterial Community: Young Tae Kim , Kang Seon Lee , Moon Jung Kim , Seung Bum Kim; J. Microbiol. 2009;47(1):33-39. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0254-4

146 View
0 Download
1 Scopus

Abstract PDF: The effects of Chinese cabbage (Brassica rapa subsp. pekinensis) carrying cry1AC derived from Bacillus thuringiensis (Bt) on leaf bacterial community were examined by analyzing the horizontal transfer of transgene fragments from plants to bacteria. The effect of plant pathogenic bacteria on the gene transfer was also examined using Pseudomonas syringae pathovar. maculicola. The frequency of hygromycin-resistant bacteria did not alter in Bt leaves, though slight increase was observed in Pseudomonas-infected Bt leaves with no statistical significance. The analysis of bacterial community profiles using the denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated that there were slight differences between Bt and control Chinese cabbage, and also that infected tissues were dominated by P. syringae pv. maculicola. However, the cultured bacterial pools were not found to contain any transgene fragments. Thus, no direct evidence of immediate gene transfer from plant to bacteria or acquisition of hygromycin resistance could be observed. Still, long-term monitoring on the possibility of gene transfer is necessary to correctly assess the environmental effects of the Bt crop on bacteria.

Description of Streptomyces neopeptinius sp. nov., an Actinobacterium with Broad Spectrum Antifungal Activities: Ji Hye Han , In Cheon Hwang , Sung Heun Cho , Cheol Jang , Nam Gyu Kim , Seung Hun Yu , Yong Man Yu , Seung Bum Kim; J. Microbiol. 2008;46(3):295-299. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-008-0011-8

258 View
0 Download
7 Crossref

Abstract PDF

A streptomycete strain producing broad-spectrum antifungal substances was taxonomically characterized. The strain, designated KNF 2047T (= SH-09T= KCTC 10586BPT), was found to form extensively branching aerial and substrate mycelia, and produce spiny-ornamented spores with loose spiral chains. The whole cell hydrolyzates contained major amount of LL-diaminopimelic acid. The major fatty acids of the phospholipids were saturated and branched fatty acids containing 14~17 carbons, and the major isoprenoid quinones were hexa- and octa-hydrogenated menaquinones with 9 isoprene units. The phylogenetic analysis using the 16S rRNA gene indicated that the strain belongs to the genus Streptomyces but forms an independent phyletic line. These results clearly demonstrate that strain KNF2047T forms a new center of taxonomic variation within Streptomyces, for which the name Streptomyces neopeptinius sp. nov. is proposed.

Citations

Citations to this article as recorded by

Isolation, Antibacterial Activity and Molecular Identification of Avocado Rhizosphere Actinobacteria as Potential Biocontrol Agents of Xanthomonas sp.
Jesús Rafael Trinidad-Cruz, Gabriel Rincón-Enríquez, Zahaed Evangelista-Martínez, Luis López-Pérez, Evangelina Esmeralda Quiñones-Aguilar
Microorganisms.2024; 12(11): 2199. CrossRef
Structural diversity, biosynthesis, and biological functions of lipopeptides fromStreptomyces
Songya Zhang, Yunliang Chen, Jing Zhu, Qiujie Lu, Max J. Cryle, Youming Zhang, Fu Yan
Natural Product Reports.2023; 40(3): 557. CrossRef
Streptomyces sp. strain SK68, isolated from peanut rhizosphere, promotes growth and alleviates salt stress in tomato (Solanum lycopersicum cv. Micro-Tom)
Karthiyaini Damodharan, Sasikumar Arunachalam Palaniyandi, Bao Le, Joo-Won Suh, Seung Hwan Yang
Journal of Microbiology.2018; 56(10): 753. CrossRef
Isolation and characterisation of rhizosphere bacteria active against Meloidogyne incognita, Phytophthora nicotianae and the root knot–black shank complex in tobacco
Ying Huang, Li Ma, Dun Huang Fang, Jia Qin Xi, Ming Liang Zhu, Ming He Mo, Ke Qin Zhang, Yan Ping Ji
Pest Management Science.2015; 71(3): 415. CrossRef
Antimicrobial Cyclic Peptides for Plant Disease Control
Dong Wan Lee, Beom Seok Kim
The Plant Pathology Journal.2015; 31(1): 1. CrossRef
Reassessment of the status of Streptomyces setonii and reclassification of Streptomyces fimicarius as a later synonym of
Kyoung-Ok Kim, Kwang-Soo Shin, Mi Na Kim, Kee-Sun Shin, David P. Labeda, Ji-Hye Han, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_12): 2978. CrossRef
Screening of Local Actinomycete Isolates in Manipur for Anticandidal Activity
Suchitra Sanasam, Debananda S. Ningtho
Asian Journal of Biotechnology.2010; 2(2): 139. CrossRef

Dominance of Endospore-forming Bacteria on a Rotating Activated Bacillus Contactor Biofilm for Advanced Wastewater Treatment: Seong Joo Park , Jerng Chang Yoon , Kwang-Soo Shin , Eung Ho Kim , Soobin Yim , Yeon-Je Cho , Gi Moon Sung , Dong-Geun Lee , Seung Bum Kim , Dong-Uk Lee , Sung-Hoon Woo , Ben Koopman; J. Microbiol. 2007;45(2):113-121.; DOI: https://doi.org/2525 [pii]

155 View
0 Download

Abstract PDF: The bacterial diversity inherent to the biofilm community structure of a modified rotating biological contactor wastewater treatment process, referred to as the Rotating Activated Bacillus Contactor (RABC) process, was characterized in this study, via both culture-dependent and culture-independent methods. On the basis of culture-dependent methods, Bacillus sp. were found to exist in large numbers on the biofilm (6.5% of the heterotrophic bacteria) and the microbial composition of the biofilms was quite simple. Only three phyla were identified-namely, the Proteobacteria, the Actinobacteria (High G+C Gram-positive bacteria), and the Firmicutes (Low G+C Gram-positive bacteria). The culture-independent partial 16S rDNA sequence analysis revealed a considerably more diverse microbial composition within the biofilms. A total of eight phyla were recovered in this case, three of which were major groups: the Firmicutes (43.9%), the Proteobacteria (28.6%), and the Bacteroidetes (17.6%). The remaining five phyla were minor groups: the Planctomycetes (4.4%), the Chlorobi (2.2%), the Actinobacteria (1.1%), the Nitrospirae (1.1%), and the Verrucomicrobia (1.1%). The two most abundant genera detected were the endospore-forming bacteria (31.8%), Clostridium and Bacillus, both of which are members of the Firmicutes phylum. This finding indicates that these endospore-forming bacteria successfully colonized and dominated the RABC process biofilms. Many of the colonies or clones recovered from the biofilms evidenced significantly high homology in the 16S rDNA sequences of bacteria stored in databases associated with advanced wastewater treatment capabilities, including nitrification and denitrification, phosphorus accumulation, the removal of volatile odors, and the removal of chlorohydrocarbons or heavy metals. The microbial community structures observed in the biofilms were found to correlate nicely with the enhanced performance of advanced wastewater treatment protocols.

Phylogenetic Diversity of Acidophilic Sporoactinobacteria Isolated from Various Soils: Sung-Heun Cho , Ji-Hye Han , Chi Nam Seong , Seung Bum Kim; J. Microbiol. 2006;44(6):600-606.; DOI: https://doi.org/2468 [pii]

148 View
0 Download

Abstract PDF: Spore forming actinobacteria (sporoactinobacteria) isolated from soils with an acidic pH in Pinus thunbergii forests and coal mine waste were subjected to taxonomic characterization. For the isolation of acidophilic actinobacteria, acidified starch casein agar (pH adjusted to 4-5) was used. The numbers of actinobacteria growing in acidic media were between 3.2 × 104 and 8.0 × 106 CFU/g soil. Forty three acidophilic actinobacterial strains were isolated and their 16S rDNA sequences were determined. The isolates were divided into eight distinctive phylogenetic clusters within the variation encompassed by the family Streptomycetaceae. Four clusters among them were assigned to the genus Streptacidiphilus, whereas the remaining four were assigned to Streptomyces. The clusters belonging to either Streptomyces or Streptacidiphilus did not form monophyletic clade. The growth pH profiles indicated that the representative isolates grew best between pH 5 and 6. It is evident from this study that acidity has played a critical role in the differentiation of the family Streptomycetaceae, and also that different mechanisms might have resulted in the evolution of two groups, Streptacidiphilus (strict acidophiles) and neutrotolerant acidophilic Streptomyces. The effect of geographic separation was clearly seen among the Streptacidiphilus isolates, which may be a key factor in speciation of the genus.

Diversity of Denitrifying Bacteria Isolated from Daejeon Sewage Treatment Plant: Young-Woon Lim , Soon-Ae Lee , Seung Bum Kim , Hae-Young Yong , Seon-Hee Yeon , Yong-Keun Park , Dong-Woo Jeong , Jin-Sook Park; J. Microbiol. 2005;43(5):383-390.; DOI: https://doi.org/2286 [pii]

160 View
0 Download

Abstract PDF: The diversity of the denitrifying bacterial populations in Daejeon Sewage Treatment Plant was examined using a culture-dependent approach. Of the three hundred and seventy six bacterial colonies selected randomly from agar plates, thirty-nine strains that showed denitrifying activity were selected and subjected to further analysis. According to the morphological and biochemical properties, the thirty nine isolates were divided into seven groups. This grouping was supported by an unweighted pair group method, using an arithmetic mean (UPGMA) analysis with fatty acid profiles. Restriction pattern analysis of 16S rDNA with four endonucleases (AluI, BstUI, MspI and RsaI) again revealed seven distinct groups, consistent with those defined from the morphological and biochemical properties and fatty acid profiles. Through the phylogenetic analysis using the 16S rDNA partial sequences, the main denitrifying microbial populations were found to be members of the phylum, Proteobacteria; in particular, classes Gammaproteobacteria (Aeromonas, Klebsiella and Enterobacter) and Betaproteobacteria (Acidovorax, Burkholderia and Comamonas), with Firmicutes, represented by Bacillus, also comprised a major group.

Isolation and Characterization of Bacteria Associated with Two Sand Dune Plant Species, Calystegia soldanella and Elymus mollis: Myung Soo Park , Se Ra Jung , Myoung Sook Lee , Kyoung Ok Kim , Jin Ok Do , Kang Hyun Lee , Seung Bum Kim , Kyung Sook Bae; J. Microbiol. 2005;43(3):219-227.; DOI: https://doi.org/2223 [pii]

145 View
0 Download

Abstract PDF: Little is known about the bacterial communities associated with the plants inhabiting sand dune ecosystems. In this study, the bacterial populations associated with two major sand dune plant species, Calystegia soldanella (beach morning glory) and Elymus mollis (wild rye), growing along the costal areas in Tae-An, Chungnam Province, were analyzed using a culture-dependent approach. A total of 212 bacteria were isolated from the root and rhizosphere samples of the two plants, and subjected to further analysis. Based on the analysis of the 16S rDNA sequences, all the bacterial isolates were classified into six major phyla of the domain Bacteria. Significant differences were observed between the two plant species, and also between the rhizospheric and root endophytic communities. The isolates from the rhizosphere of the two plant species were assigned to 27 different established genera, and the root endophytic bacteria were assigned to 21. Members of the phylum Gammaproteobacteria, notably the Pseudomonas species, comprised the majority of both the rhizospheric and endophytic bacteria, followed by members of Bacteroidetes and Firmicutes in the rhizosphere and Alphaproteobacteria and Bacteroidetes in the root. A number of isolates were recognized as potentially novel bacterial taxa. Fifteen out of 27 bacterial genera were commonly found in the rhizosphere of both plants, which was comparable to 3 out of 21 common genera in the root, implying the host specificity for endophytic populations. This study of the diversity of culturable rhizospheric and endophytic bacteria has provided the basis for further investigation aimed at the selection of microbes for the facilitation of plant growth.

Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Community Profiles in the Rhizosphere of cry1AC-carrying Brassica rapa subsp. pekinensis: Sera Jung , Semi Park , Daeha Kim , Seung Bum Kim; J. Microbiol. 2008;46(1):12-15.; DOI: https://doi.org/10.1007/s12275-007-0190-8

242 View
0 Download
10 Crossref

Abstract PDF

The effect of genetically modified (GM) Brassica rapa subsp. pekinensis (Chinese cabbage) expressing Bt toxin gene (cry1AC) to the rhizosphere bacterial community was examined using the denaturing gradient gel electrophoresis (DGGE) fingerprinting method. From the visual comparison of the DGGE profiles, there were no significant differences between the profiles of Bt and control rhizosphere in both Suwon and Yesan samples. From the sequence analysis of the individual bands, Sphingomonas sp. of Alphaproteobacteria and several actinobacterial members were identified as the main bacterial taxa in both Suwon and Yesan samples. In the multiple correspondence analysis, no clear separation between Bt and control rhizosphere was seen in both Suwon and Yesan datasets. The profiles of bulk soils were separated from those of rhizosphere. The DGGE fingerprinting analyses indicated that Bt crops did not significantly alter the genetic composition of rhizosphere bacterial communities.

Citations

Citations to this article as recorded by

Current trends in Bt crops and their fate on associated microbial community dynamics: a review
Amit Kishore Singh, Suresh Kumar Dubey
Protoplasma.2016; 253(3): 663. CrossRef
Do genetically modified plants affect adversely on soil microbial communities?
Zheng-jun Guan, Shun-bao Lu, Yan-lin Huo, Zheng-Ping Guan, Biao Liu, Wei Wei
Agriculture, Ecosystems & Environment.2016; 235: 289. CrossRef
Plant growth promoting traits of phosphate-solubilizing rhizobacteria isolated from apple trees in trans Himalayan region of Himachal Pradesh
Preeti Mehta, Abhishek Walia, Anjali Chauhan, C. K. Shirkot
Archives of Microbiology.2013; 195(5): 357. CrossRef
Effects of Bacillus thuringiensis agent on bacterial population and diversity in cotton rhizosphere soil
Mei-Zhe HAN, Xiao-Xian WANG, Chang-Hong LIU, Ya-Rong XUE, Yuan-Qing BU, Ming ZHANG
Chinese Journal of Eco-Agriculture.2013; 21(10): 1277. CrossRef
Microbial community in seawater reverse osmosis and rapid diagnosis of membrane biofouling
Jinwook Lee, In S. Kim
Desalination.2011; 273(1): 118. CrossRef
Microbial communities associated with the root system of wild olives (Olea europaea L. subsp. europaea var. sylvestris) are good reservoirs of bacteria with antagonistic potential against Verticillium dahliae
Sergio Aranda, Miguel Montes-Borrego, Rafael M. Jiménez-Díaz, Blanca B. Landa
Plant and Soil.2011; 343(1-2): 329. CrossRef
Culturable bacterial community analysis in the root domains of two varieties of tree peony (Paeonia ostii)
Jigang Han, Yao Song, Zhigang Liu, Yonghong Hu
FEMS Microbiology Letters.2011; 322(1): 15. CrossRef
Impact of cry1AC-carrying Brassica rapa subsp. pekinensis on leaf bacterial community
Young Tae Kim, Kang Seon Lee, Moon Jung Kim, Seung Bum Kim
The Journal of Microbiology.2009; 47(1): 33. CrossRef
Rhizosphere Communities of Genetically Modified Zeaxanthin-Accumulating Potato Plants and Their Parent Cultivar Differ Less than Those of Different Potato Cultivars
Nicole Weinert, Remo Meincke, Christine Gottwald, Holger Heuer, Newton C. M. Gomes, Michael Schloter, Gabriele Berg, Kornelia Smalla
Applied and Environmental Microbiology.2009; 75(12): 3859. CrossRef
Diversity of Culturable Bacteria Isolated from Root Domains of Moso Bamboo (Phyllostachys edulis)
Jigang Han, Dongliang Xia, Lubin Li, Lei Sun, Kai Yang, Liping Zhang
Microbial Ecology.2009; 58(2): 363. CrossRef

First
Prev
Page of 1
Next
Last

Search