Journal of Microbiology

Reviews

The Role of Extracellular Vesicles in Pandemic Viral Infections: Woosung Shim, Anjae Lee, Jung-Hyun Lee; J. Microbiol. 2024;62(6):419-427. Published online June 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00144-x

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Extracellular vesicles (EVs), of diverse origin and content, are membranous structures secreted by a broad range of cell types. Recent advances in molecular biology have highlighted the pivotal role of EVs in mediating intercellular communication, facilitated by their ability to transport a diverse range of biomolecules, including proteins, lipids, DNA, RNA and metabolites. A striking feature of EVs is their ability to exert dual effects during viral infections, involving both proviral and antiviral effects. This review explores the dual roles of EVs, particularly in the context of pandemic viruses such as HIV-1 and SARS-CoV-2. On the one hand, EVs can enhance viral replication and exacerbate pathogenesis by transferring viral components to susceptible cells. On the other hand, they have intrinsic antiviral properties, including activation of immune responses and direct inhibition of viral infection. By exploring these contrasting functions, our review emphasizes the complexity of EV-mediated interactions in viral pathogenesis and highlights their potential as targets for therapeutic intervention. The insights obtained from investigating EVs in the context of HIV-1 and SARS-CoV-2 provide a deeper understanding of viral mechanisms and pathologies, and offer a new perspective on managing and mitigating the impact of these global health challenges.

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Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2024; 34(12): 2506. CrossRef

MAPK Cascades in Plant Microbiota Structure and Functioning: Thijs Van Gerrewey, Hoo Sun Chung; J. Microbiol. 2024;62(3):231-248. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00114-3

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Abstract

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, infuencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent fndings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

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Lipid transfer protein VAS inhibits the hypersensitive response via reactive oxygen species signaling in Nicotiana benthamiana
Rina Koyama, Akira Suzuki, Kouhei Ohnishi, Yasufumi Hikichi, Akinori Kiba, Stefanie Ranf
Journal of Experimental Botany.2025; 76(4): 1285. CrossRef
Short-Term Fertilization with the Nitrogen-Fixing Bacterium (NFB) Kosakonia radicincitans GXGL-4A Agent Can Modify the Transcriptome Expression Profiling of Cucumber (Cucumis sativus L.) Root
Baoyun Feng, Erxing Wang, Yating Zhang, Lurong Xu, Yanwen Xue, Yunpeng Chen
Microorganisms.2025; 13(3): 506. CrossRef
Pharmacological effects and the related mechanism of scutellarin on inflammation-related diseases: a review
Yang Zhou, Chenlin Gu, Yan Zhu, Yuting Zhu, Yutong Chen, Li Shi, Yang Yang, Xin Lu, Hanqing Pang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications
Yuqing Yan, Hui Wang, Yan Bi, Fengming Song
Plant Communications.2024; 5(12): 101128. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
The microbiome orchestrates contaminant low-dose phytostimulation
Evgenios Agathokleous, Edward J. Calabrese, Stavros D. Veresoglou
Trends in Plant Science.2024;[Epub] CrossRef

Journal Articles

Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus: Sung&# , Mi&# , Hyun&# , Kae Kyoung Kwon; J. Microbiol. 2023;61(2):175-187. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00022-y

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Abstract

Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. ( MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. ( MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.

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An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023
Sara D. Lawhon, Claire R. Burbick, Trinity Krueger, Elena Ruiz-Reyes, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[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
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Non-mitochondrial aconitase regulates the expression of iron-uptake genes by controlling the RNA turnover process in fission yeast: Soo-Yeon Cho , Soo-Jin Jung , Kyoung-Dong Kim , Jung-Hye Roe; J. Microbiol. 2021;59(12):1075-1082. Published online October 26, 2021; DOI: https://doi.org/10.1007/s12275-021-1438-4

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Abstract

Aconitase, a highly conserved protein across all domains of life, functions in converting citrate to isocitrate in the tricarboxylic acid cycle. Cytosolic aconitase is also known to act as an iron regulatory protein in mammals, binding to the RNA hairpin structures known as iron-responsive elements within the untranslated regions of specific RNAs. Aconitase-2 (Aco2) in fission yeast is a fusion protein consisting of an aconitase and a mitochondrial ribosomal protein, bL21, residing not only in mitochondria but also in cytosol and the nucleus. To investigate the role of Aco2 in the nucleus and cytoplasm of fission yeast, we analyzed the transcriptome of aco2ΔN mutant that is deleted of nuclear localization signal (NLS). RNA sequencing revealed that the aco2ΔN mutation caused increase in mRNAs encoding iron uptake transporters, such as Str1, Str3, and Shu1. The half-lives of mRNAs for these genes were found to be significantly longer in the aco2ΔN mutant than the wild-type strain, suggesting the role of Aco2 in mRNA turnover. The three conserved cysteines required for the catalytic activity of aconitase were not necessary for this role. The UV cross-linking RNA immunoprecipitation analysis revealed that Aco2 directly bound to the mRNAs of iron uptake transporters. Aco2-mediated degradation of iron-uptake mRNAs appears to utilize exoribonuclease pathway that involves Rrp6 as evidenced by genetic interactions. These results reveal a novel role of non-mitochondrial aconitase protein in the mRNA turnover in fission yeast to fine-tune iron homeostasis, independent of regulation by transcriptional repressor Fep1.

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Iron-mediated post-transcriptional regulation in Toxoplasma gondii
Megan A. Sloan, Adam Scott, Dana Aghabi, Lucia Mrvova, Clare R. Harding, Dominique Soldati-Favre
PLOS Pathogens.2025; 21(2): e1012857. CrossRef
The Key Enzymes of Carbon Metabolism and the Glutathione Antioxidant System Protect Yarrowia lipolytica Yeast Against pH-Induced Stress
Tatyana I. Rakhmanova, Natalia N. Gessler, Elena P. Isakova, Olga I. Klein, Yulia I. Deryabina, Tatyana N. Popova
Journal of Fungi.2024; 10(11): 747. CrossRef
The intricate link between iron, mitochondria and azoles in Candida species
Wouter Van Genechten, Rudy Vergauwen, Patrick Van Dijck
The FEBS Journal.2024; 291(16): 3568. CrossRef
Non-Mitochondrial Aconitase-2 Mediates the Transcription of Nuclear-Encoded Electron Transport Chain Genes in Fission Yeast
Ho-Jung Kim, Soo-Yeon Cho, Soo-Jin Jung, Yong-Jun Cho, Jung-Hye Roe, Kyoung-Dong Kim
Journal of Microbiology.2024; 62(8): 639. CrossRef
Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress
Tatyana I. Rakhmanova, Varvara Yu. Sekova, Natalya N. Gessler, Elena P. Isakova, Yulia I. Deryabina, Tatyana N. Popova, Yevgeniya I. Shurubor, Boris F. Krasnikov
International Journal of Molecular Sciences.2023; 24(8): 7670. CrossRef

Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(12):1048-1055. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9260-y

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Abstract

A Gram-stain-negative, strictly aerobic, marine bacterium, designated GH2-2T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) in Gangwha Island, the Republic of Korea. The cells of the organism were oxidase- positive, catalase-positive, flagellated, short rods that grew at 10–40°C, pH 4–10, and 0–13% (w/v) NaCl. The predominant ubiquinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acid is C18:1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed an independent lineage at the base of the radiation encompassing members of the genus Thioclava, except for Thioclava arenosa. The closest relatives were T. nitratireducens (96.03% sequence similarity) and T. dalianensis (95.97%). The genome size and DNA G+C content were 3.77 Mbp and 59.6 mol%, respectively. Phylogenomic analysis supported phylogenetic distinctness based on 16S rRNA gene sequences. Average nucleotide identity values were 73.6–74.0% between the novel strain and members of the genus Thioclava. On the basis of data obtained from a polyphasic approach, the strain GH2-2T (= KCTC 62124T = DSM 105743T) represents a novel species of a new genus for which the name Hahyoungchilella caricis gen. nov., sp. nov. is proposed. Moreover, the transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava gen. nov. as Pseudothioclava arenosa comb. nov. is also proposed. Finally, Thioclava electrotropha Chang et al. 2018 is proposed to be a later heterosynonym of Thioclava sediminum Liu et al. 2017.

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Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat
Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai
Frontiers in Microbiology.2024;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef

Leifsonia flava sp. nov., a novel actinobacterium isolated from the rhizosphere of Aquilegia viridiflora: Ying Cai , Wen-Zhen Tao , Yu-Jun Ma , Juan Cheng , Meng-Yue Zhang , Yi-Xuan Zhang; J. Microbiol. 2018;56(8):549-555. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8061-z

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Abstract

SYP-B2174T is a yellow-pigmented, Gram-positive, non-motile, and rod-shaped actinobacterium isolated from the rhizospheric soil of Aquilegia viridiflora Pall. collected from the Xinjiang uygur autonomous region of China. The strain’s growth temperature ranges from 1 to 35°C, with an optimal growth being observed at 28°C. Growth occurs from 0 to 5% NaCl and at pH 6–8, with optimal growth being observed in 1% NaCl at pH 7. Comparative 16S rRNA gene sequencebased phylogenetic analysis placed the strain in a clade with the species Leifsonia kafniensis JCM 17021T and Leifsonia psychrotolerans DSM 22824T with similarities of 97.8 and 97.6%, respectively. The DNA-DNA hybridization values of the strain SYP-B2174T to its closest phylogenetic neighbors were significantly lower than 35.7%. The strain was identified as a novel species of the genus Leifsonia judging by the coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, principal phospholipids phosphatidylglycerol and diphosphatidylglycerol, major menaquinone MK-11, predominant fatty acids of anteiso-C15:0, anteiso-C17:0, and iso-C16:0, and a DNA G + C base composition of 68.7 mol%, for which the name Leifsonia flava sp. nov. is proposed. The type strain is SYP-B2174T (= CGMCC 1.15856T = DSM 105144T = KCTC 39963T).

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Enhancement of the germination and growth of Panicum miliaceum and Brassica juncea in Cd- and Zn-contaminated soil inoculated with heavy-metal-tolerant Leifsonia sp. ZP3
Ian Cho, Soo Yeon Lee, Kyung-Suk Cho
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Plant Growth-Promoting and Tequila Vinasse-Resistant Bacterial Strains
Alberto J. Valencia-Botín, Ismael F. Chávez-Díaz, Florentina Zurita-Martínez, Allan Tejeda-Ortega, Lily X. Zelaya-Molina
Microbiology Research.2024; 15(3): 1144. CrossRef
Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes
Anna C. Simpson, Pratyay Sengupta, Flora Zhang, Asif Hameed, Ceth W. Parker, Nitin K. Singh, Georgios Miliotis, Punchappady D. Rekha, Karthik Raman, Christopher E. Mason, Kasthuri Venkateswaran
Scientific Reports.2023;[Epub] CrossRef
Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region
HU PAN, JIE ZHOU, ZHUOMA DAWA, YANNA DAI, YIFAN ZHANG, HUI YANG, CHONG WANG, HUHU LIU, HUI ZHOU, XIANGYANG LU, YUN TIAN
Polish Journal of Microbiology.2021; 70(1): 87. CrossRef
Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems
Zobia Khatoon, Suiliang Huang, Mazhar Rafique, Ali Fakhar, Muhammad Aqeel Kamran, Gustavo Santoyo
Journal of Environmental Management.2020; 273: 111118. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2019; 69(1): 13. CrossRef

Achromobacter panacis sp. nov., isolated from rhizosphere of Panax ginseng: Priyanka Singh , Yeon Ju Kim , Hina Singh , Mohamed El-Agamy Farh , Deok-Chun Yang; J. Microbiol. 2017;55(6):428-434. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6612-3

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Abstract

A novel strain DCY105T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Re-public of Korea. Strain DCY105T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5–7.0 and in the absence of NaCl. Phylogenetically, strain DCY105T is most closely related to Achromobacter marplatensis LMG 26219T (96.81%). The DNA G+C content of strain DCY105T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and dipho-sphatidylglycerol were amongst the major polar lipids. C16:00, C8:03OH and iso-C17:03OH were identified as the major fatty acids present in DCY105T. The results of physiological and biochemical tests allowed strain DCY105T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105T (=CCTCCAB 2015193T =KCTC 42751T).

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Zwartia vadi sp. nov., a Novel Species of the GKS98 Cluster Isolated from a Stream, and the Reclassification of ‘Achromobacter Panacis’ as Zwartia panacis comb. nov
Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Microorganisms.2023; 11(9): 2150. CrossRef
Achromobacter spp. prevalence and adaptation in cystic fibrosis lung infection
Laura Veschetti, Marzia Boaretti, Giulia Maria Saitta, Rebeca Passarelli Mantovani, Maria M. Lleò, Angela Sandri, Giovanni Malerba
Microbiological Research.2022; 263: 127140. CrossRef
Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster
Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Ulrike Koll, Jacqueline Wolf, William B. Whitman, Paul L. E. Bodelier, Meina Neumann-Schaal
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Strong Antimicrobial Activity of Silver Nanoparticles Obtained by the Green Synthesis in Viridibacillus sp. Extracts
Priyanka Singh, Ivan Mijakovic
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Silver nanoparticles produced from Cedecea sp. exhibit antibiofilm activity and remarkable stability
Priyanka Singh, Santosh Pandit, Carsten Jers, Abhayraj S. Joshi, Jørgen Garnæs, Ivan Mijakovic
Scientific Reports.2021;[Epub] CrossRef
A Sustainable Approach for the Green Synthesis of Silver Nanoparticles from Solibacillus isronensis sp. and Their Application in Biofilm Inhibition
Priyanka Singh, Santosh Pandit, VRSS Mokkapati, Jørgen Garnæs, Ivan Mijakovic
Molecules.2020; 25(12): 2783. CrossRef
Emerging Gram-negative bacteria
Heather Green, Andrew M. Jones
Current Opinion in Pulmonary Medicine.2018; 24(6): 592. CrossRef

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches: Shin Ae Lee , Jiyoung Park , Bora Chu , Jeong Myeong Kim , Jae-Ho Joa , Mee Kyung Sang , Jaekyeong Song , Hang-Yeon Weon; J. Microbiol. 2016;54(12):823-831. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6410-3

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Abstract

The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culturedependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These
results
showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.

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Characterization of Nitrogen-Fixing Bacteria Isolated from Field-Grown Barley, Oat, and Wheat: Anastasia Venieraki , Maria Dimou , Eleni Vezyri , Io Kefalogianni , Nikolaos Argyris , Georgia Liara , Panagiotis Pergalis , Iordanis Chatzipavlidis , Panagiotis Katinakis; J. Microbiol. 2011;49(4):525-534. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0457-y

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Abstract: Diazotrophic bacteria were isolated from the rhizosphere of field-grown Triticum aestivum, Hordeum vulgare, and Avena sativa grown in various regions of Greece. One isolate, with the highest nitrogen-fixation ability from each of the eleven rhizospheres, was selected for further characterisation. Diazotrophic strains were assessed for plant-growth-promoting traits such as indoleacetic acid production and phosphate solubilisation. The phylogenies of 16S rRNA gene of the selected isolates were compared with those based on dnaK and nifH genes. The constructed trees indicated that the isolates were members of the species Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. Furthermore, the ipdC gene was detected in all A. brasilence and one A. zeae isolates. The work presented here provides the first molecular genetic evidence for the presence of culturable nitrogen-fixing P. stutzeri and A. zeae associated with field-grown A. sativa and H. vulgare in Greece.

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Paenibacillus pini sp. nov., a Cellulolytic Bacterium Isolated from the Rhizosphere of Pine Tree: Byung-Chun Kim , Kang Hyun Lee , Mi Na Kim , Eun-Mi Kim , Sung Ran Min , Hyun Soon Kim , Kee-Sun Shin; J. Microbiol. 2009;47(6):699-704. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0343-z

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Abstract: Strain S22T, a novel cellulolytic bacterium was isolated from the rhizosphere of pine trees. This isolate was Gram-reaction positive, motile and rods, and formed terminal or subterminal ellipsoidal spores. S22T represented positive activity for catalase, oxidase, esterase (C4), esterase lipase (C8), β-galactosidase, leucine arylamidase, and hydrolysis of esculin. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall. The predominant isoprenoid quinone was menaquinone 7 (MK-7), and the major cellular fatty acids were anteiso-C15:0 (52.9%), iso-C16:0 (11.3%), and iso-C15:0 (10.0%). The DNA G+C content was 43.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate belonged to the family Paenibacillaceae. S22T exhibited less than 97.0% 16S rRNA gene similarity with all relative type strains in the genus Paenibacillus, and the most closely related strains were Paenibacillus anaericanus MH21T and Paenibacillus ginsengisoli Gsoil 1638T, with equal similarities of 95.8%. This polyphasic evidence suggested that strain S22T should be considered a novel species in the genus Paenibacillus, for which the name, Paenibacillus pini sp. nov., is proposed. The type strain is S22T (=KCTC 13694T =KACC 14198T =JCM 16418T)

Paenibacillus pinihumi sp. nov., a Cellulolytic Bacterium Isolated from the Rhizosphere of Pinus densiflora: Byung-Chun Kim , Kang Hyun Lee , Mi Na Kim , Eun-Mi Kim , Moon-Soo Rhee , O-Yu Kwon , Kee-Sun Shin; J. Microbiol. 2009;47(5):530-535. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0270-z

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Abstract: A novel cellulolytic bacterium, strain S23T, was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase- positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, α-galactosidase, and β-galactosidase activities. The DNA G+C content was 49.5mol%. The main cellular fatty acids were anteiso-C15:0 (51.9%), iso-C16:0 (14.7%), and iso-C15:0 (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23T and other Paenibacillus species were between 89.9% and 95.9%, and S23T was most closely related to Paenibacillus tarimensis SA-7-6T. On the basis of phylogenetic and phenotypic properties of strain S23T, the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23T (=KCTC 13695T =KACC 14199T =JCM 16419T)

Paenibacillus filicis sp. nov., Isolated from the Rhizosphere of the Fern: Byung-Chun Kim , Mi Na Kim , Kang Hyun Lee , Sun Beom Kwon , Kyung Sook Bae , Kee-Sun Shin; J. Microbiol. 2009;47(5):524-529. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0266-8

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Abstract

A Gram-positive and endospore-forming bacterial strain, designated S4T, was isolated from the rhizosphere of ferns in Daejeon, Republic of Korea. This isolate is strictly aerobic, motile, and rod-like in shape, and it is positive for catalase, oxidase, esterase lipase, and β-galactosidase activities. In addition, this strain grows when cultured at temperatures between 15 and 37°C and at pH values ranging from 5.5 to 9.0. The DNA G+C content was determined to be 53.2 mol%. Strain S4T has meso-diaminopimelic acid in the cell-wall peptidoglycan; it also contains menaquinone 7 (MK-7) as the predominant isoprenoid quinone and anteiso-C15:0 (57.5%), iso-C16:0 (11.3%), and C16:0 (9.4%) as the major cellular fatty acids. Phylogenetic analysis based on alignments of the 16S rRNA gene sequence showed that S4T is affiliated with a cluster of strains within the genus Paenibacillaceae and is most closely related to Paenibacillus chinjuensis WN9T, with 96.8% similarity. Based on the phylogenetic and phenotypic characteristics of strain S4T, we believe that this isolate should be distinguished from all type species of the genus Paenibacillus and should thus represent a novel taxon within the genus Paenibacillus. We propose naming this type species Paenibacillus filicis sp. nov. for the rhizosphere isolate; the type strain will be known as S4T (=KCTC 13693T =KACC 14197T =JCM 16417T).

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Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil
Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
Journal of Microbiology and Biotechnology.2024; 34(8): 1636. CrossRef
Paenibacillus puerhi sp. nov., isolated from the rhizosphere soil of Pu-erh tea plants (Camellia sinensis var. assamica)
Rui-Juan Yang, De Zhou, Qiao-Mei Wang, Xing-Hua Wang, Wen-Jie Zhang, Li Zhuang, Xuan-Jun Wang, Liang Yan, Jie Lv, Jun Sheng
Archives of Microbiology.2021; 203(4): 1375. CrossRef
Paenibacillus konkukensis sp. nov., isolated from animal feed
Wan-Taek Im, Kwon-Jung Yi, Sang-Suk Lee, Hyung In Moon, Che Ok Jeon, Dong-Woon Kim, Soo-Ki Kim
International Journal of Systematic and Evolutionary Microbiology.2017; 67(7): 2343. CrossRef
Paenibacillus cucumis sp. nov. isolated from greenhouse soil
Jae-Hyung Ahn, Byoung-chan Kim, Byung-Yong Kim, Soo-Jin Kim, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
Journal of Microbiology.2014; 52(6): 460. CrossRef
Paenibacillus vulneris sp. nov., isolated from a necrotic wound
Stefanie P. Glaeser, Enevold Falsen, Hans-Jürgen Busse, Peter Kämpfer
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_2): 777. CrossRef
Identification and Characterization of Psychrotolerant Sporeformers Associated with Fluid Milk Production and Processing
Reid A. Ivy, Matthew L. Ranieri, Nicole H. Martin, Henk C. den Bakker, Bruno M. Xavier, Martin Wiedmann, Kathryn J. Boor
Applied and Environmental Microbiology.2012; 78(6): 1853. CrossRef
List of new names and new combinations previously effectively, but not validly, published

International Journal of Systematic and Evolutionary Microbiology .2010; 60(1): 1. CrossRef
Paenibacillus pini sp. nov., a cellulolytic bacterium isolated from the rhizosphere of pine tree
Byung-Chun Kim, Kang Hyun Lee, Mi Na Kim, Eun-Mi Kim, Sung Ran Min, Hyun Soon Kim, Kee-Sun Shin
The Journal of Microbiology.2009; 47(6): 699. CrossRef

Evaluation of the Diversity of Cyclodextrin-Producing Paenibacillus graminis Strains Isolated from Roots and Rhizospheres of Different Plants by Molecular Methods: Renata Estebanez Vollu , Rafael Fogel , Silvia Cristina Cunha dos Santos , Fabio Faria da Mota , Lucy Seldin; J. Microbiol. 2006;44(6):591-599.; DOI: https://doi.org/2469 [pii]

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Abstract: To address the diversity of cyclodextrin-producing P. graminis strains isolated from wheat roots and rhizospheres of maize and sorghum sown in Australia, Brazil, and France, restriction fragment length polymorphism analysis of part of genes encoding RNA polymerase (rpoB-RFLP) and DNA gyrase subunit B (gyrB-RFLP) was used to produce genetic fingerprints. A phylogenetic tree based on rpoB gene sequences was also constructed. The isolates originated from Brazil could be separated from those from Australia and France, when data from the rpoB-based phylogenetic tree or gyrB-RFLP were considered. These analyses also allowed the separation of all P. graminis strains studied here into four clusters; one group formed by the strains GJK201 and RSA19T, second group formed by the strains MC22.02 and MC04.21, third group formed by the strains TOD61, TOD 221, TOD302, and TOD111, and forth group formed by all strains isolated from plants sown in Cerrado soil, Brazil. As this last group was formed by strains isolated from sorghum and maize sown in the same soil (Cerrado) in Brazil, our results suggest that the diversity of these P. graminis strains is more affected by the soil type than the plant from where they <br>have been isolated.

Diversity of Yeasts Associated with Panax ginseng: Soon Gyu Hong , Kang Hyun Lee , Jangyul Kwak , Kyung Sook Bae; J. Microbiol. 2006;44(6):674-679.; DOI: https://doi.org/2457 [pii]

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Abstract: Biodiversity of yeasts was investigated in the ginseng cultivation field. Among 34 isolates tested in this study, 26 isolates belonged to the hymenomycetous yeast group. These 26 strains were classified into 12 species including four new-species candidates that did not have clear affiliation to any established species. Seven isolates among the remaining strains were classified into three ascomycetous yeast species, and one isolate was identified as a urediniomycetous yeast species.

Molecular Detection of Catabolic Genes for Polycyclic Aromatic Hydrocarbons in the Reed Rhizosphere of Sunchon Bay: Hyung-Yeel Kahng , Kye-Heon Oh; J. Microbiol. 2005;43(6):572-576.; DOI: https://doi.org/2287 [pii]

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Abstract: This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.

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