Journal of Microbiology

Journal Articles

Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyung Park , Shin Nam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(2):189-197. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00017-9

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Indoor fungi obtain carbon sources from natural sources and even recalcitrant biodegradable materials, such as plastics and synthetic dye. Their vigorous activity may have negative consequences, such as structural damage to building materials or the destruction of precious cultural materials. The animal specimen room of the Seoul National University stocked 36,000 animal resources that had been well-maintained for over 80 years. Due to abandonment without the management of temperature and humidity during the rainy summer season, many stuffed animal specimens had been heavily colonized by fungi. To investigate the fungal species responsible for the destruction of the historical specimens, we isolated fungi from the stuffed animal specimens and identified them at the species level based on morphology and molecular analysis of the β-tubulin (BenA) gene. A total of 365 strains were isolated and identified as 26 species in Aspergillus (10 spp.), Penicillium (14 spp.), and Talaromyces (2 spp.). Penicillium brocae and Aspergillus sydowii were isolated from most sections of the animal specimens and have damaged the feathers and beaks of valuable specimens. Our findings indicate that within a week of mismanagement, it takes only a few fungal species to wipe out the decades of history of animal diversity. The important lesson here is to prevent this catastrophe from occurring again through a continued interest, not to put all previous efforts to waste.

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Investigating the Role of Microclimate and Microorganisms in the Deterioration of Stone Heritage: The Case of Rupestrian Church from Jac, Romania
Dorina Camelia Ilieș, Andrei-Ionuț Apopei, Cristina Mircea, Alexandru Ilieș, Tudor Caciora, Berdenov Zharas, Lucian Barbu-Tudoran, Nicolaie Hodor, Alexandru Turza, Ana Cornelia Pereș, Thowayeb H. Hassan, Bahodirhon Safarov, Ioan-Cristian Noje
Applied Sciences.2024; 14(18): 8136. CrossRef
Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation
Geoffrey Michael Gadd, Marina Fomina, Flavia Pinzari, Mark D. Rose
Microbiology and Molecular Biology Reviews.2024;[Epub] CrossRef

Microbial metabolic responses and CO2 emissions differentiated by soil water content variation in subarctic tundra soils: Dockyu Kim , Namyi Chae , Mincheol Kim , Sungjin Nam , Tai Kyoung Kim , Ki-Tea Park , Bang Yong Lee , Eungbin Kim , Hyoungseok Lee; J. Microbiol. 2022;60(12):1130-1138. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2378-3

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Abstract

Recent rapid air temperature increases across the northernlatitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature (Ts) and volumetric soil water content (SWC). Under prolonged soil warming at 8°C, Alaskan tundra soils were incubated in a microcosm system and examined for the SWC differential influence on the microbial decomposition activity of large molecular weight (MW) humic substances (HS). When one microcosm soil (AKC1-1) was incubated at a constant SWC of 41% for 90 days (T = 90) and then SWC was gradually decreased from 41% to 29% for another T = 90, the initial HS was partly depolymerized. In contrast, in AKC1-2 incubated at a gradually decreasing SWC from the initial 32% to 10% for T = 90 and then increasing to 27% for another T = 90, HS depolymerization was undetected. Overall, the microbial communities in AKC1-1 could maintain metabolic activity at sufficient and constant SWC during the initial T = 90 incubation. In contrast, AKC1-2 microbes may have been damaged by drought stress during the drying SWC regimen, possibly resulting in the loss of HS decomposition activity, which did not recover even after re-wetting to an optimal SWC range (20–40%). After T = 90, the CO2 production in both treatments was attributed to the increased decomposition of small-MW organic compounds (including aerobic HS-degradative products) within an optimal SWC range. We expect this study to provide new insights into the early effects of warming- and topography-induced SWC variations on the microbial contribution to CO2 emissions via HS decomposition in northern-latitude tundra soil.

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Unidirectional freeze–thaw redistributes water and amplifies soil microbial heterogeneity in a mecrocosm experiment
Huimin Liu, Yaxian Hu, Yuan Song, Xianwen Li, Xiaorong Wei
Geoderma.2025; 453: 117126. CrossRef
Analysis of CO2 Emission from Urban Soils of the Kola Peninsula (European Arctic)
M. V. Korneykova, V. I. Vasenev, N. V. Saltan, M. V. Slukovskaya, A. S. Soshina, M. S. Zavodskikh, Yu. L. Sotnikova, A. V. Dolgikh
Eurasian Soil Science.2023; 56(11): 1653. CrossRef
Analysis of CO₂ Emission by Urban Soils under the Conditions of the Kola North
M. V. Korneykova, V. I. Vasenev, N. V. Saltan, M. V. Slukovskaya, A. S. Soshina, M. S. Zavodskikh, Y. L. Sotnikova, A. V. Dolgikh
Почвоведение.2023; (11): 1385. CrossRef

Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.: Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh; J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1581-6

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Abstract

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C, respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of β-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T = JCM 34760T), respectively.

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Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef
Validation List no. 208. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Complete Genome Sequence of Brachybacterium sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef

Improved tolerance of recombinant Chlamydomonas rainhardtii with putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pyropia yezoensis to nitrogen starvation: Seo-jeong Park , Joon Woo Ahn , Jong-il Choi; J. Microbiol. 2022;60(1):63-69. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1491-7

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Abstract

In a previous study, a putative 2-amino-3-carboxymuconate- 6-semialdehyde decarboxylase (ACMSD) was highly expressed in a mutant strain of Pyropia yezoensis, which exhibited an improved growth rate compared to its wild strain. To investigate the functional role of the putative ACMSD (Pyacmsd) of P. yezoensis, the putative Pyacmsd was cloned and expressed in Chlamydomonas reinhardtii. Recombinant C. reinhardtii cells with Pyacmsd (Cr_Pyacmsd) exhibited enhanced tolerance compared to control C. reinhardtii cells (Cr_control) under nitrogen starvation. Notably, Cr_Pyacmsd cells showed accumulation of lipids in nitrogen-enriched conditions. These
results
demonstrate the role of Pyacmsd in the generation of acetyl-coenzyme A. Thus, it can be used to enhance the production of biofuel using microalgae such as C. reinhardtii and increase the tolerance of other biological systems to nitrogendeficient conditions.

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Characteristics of Recombinant Chlamydomonas reinhardtii Expressing Putative Germin-Like Protein from Neopyropia yezoensis
Jiae Kim, Jong-il Choi
Journal of Microbiology and Biotechnology.2024; 34(10): 2132. CrossRef
Overexpression of putative glutathione peroxidase from Neopyropia-associated microorganisms in Chlamydomonas to respond to abiotic stress
Jeong Hyeon Kim, Eun-Jeong Park, Jong-il Choi
Archives of Microbiology.2023;[Epub] CrossRef
Overexpression of S-Adenosylmethionine Synthetase in Recombinant Chlamydomonas for Enhanced Lipid Production
Jeong Hyeon Kim, Joon Woo Ahn, Eun-Jeong Park, Jong-il Choi
Journal of Microbiology and Biotechnology.2023; 33(3): 310. CrossRef

Amino acid residues in the Ler protein critical for derepression of the LEE5 promoter in enteropathogenic E. coli: Su-Mi Choi , Jae-Ho Jeong , Hyon E. Choy , Minsang Shin; J. Microbiol. 2016;54(8):559-564. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6027-6

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Abstract

Enteropathogenic E. coli causes attaching and effacing (A/E) intestinal lesions. The genes involved in the formation of A/E lesions are encoded within a chromosomal island comprising of five major operons, LEE1-5. The global regulator H-NS represses the expression of these operons. Ler, a H-NS homologue, counteracts the H-NS–mediated repression. Using a novel genetic approach, we identified the amino acid residues in Ler that are involved in the interaction with H-NS: I20 and L23 in the C-terminal portion of α-helix 3, and I42 in the following unstructured linker region.

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Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens
R. Christopher D. Furniss, Abigail Clements, William Margolin
Journal of Bacteriology.2018;[Epub] CrossRef

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

Note] Identification of High-Specificity H-NS Binding Site in LEE5 Promoter of Enteropathogenic Esherichia coli (EPEC): Abhay Prasad Bhat , Minsang Shin , Hyon E. Choy; J. Microbiol. 2014;52(7):626-629. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3562-x

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Abstract

Histone-like nucleoid structuring protein (H-NS) is a small but abundant protein present in enteric bacteria and is involved in compaction of the DNA and regulation of the transcription. Recent reports have suggested that H-NS binds to a specific AT rich DNA sequence than to intrinsically curved DNA in sequence independent manner. We detected two high-specificity H-NS binding sites in LEE5 promoter of EPEC centered at -110 and -138, which were close to the proposed consensus H-NS binding motif. To identify H-NS binding sequence in LEE5 promoter, we took a random mutagenesis approach and found the mutations at around -138 were specifically defective in the regulation byH-NS. It was concluded that H-NS exertsmaximumrepression via the specific sequence at around -138 and ubsequently contacts α subunit of RNAP through oligomerization.

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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands
Alejandro Piña-Iturbe, Isidora D. Suazo, Guillermo Hoppe-Elsholz, Diego Ulloa-Allendes, Pablo A. González, Alexis M. Kalergis, Susan M. Bueno
Genes.2020; 11(2): 142. CrossRef
Recent advances in genetic engineering tools based on synthetic biology
Jun Ren, Jingyu Lee, Dokyun Na
Journal of Microbiology.2020; 58(1): 1. CrossRef
Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens
R. Christopher D. Furniss, Abigail Clements, William Margolin
Journal of Bacteriology.2018;[Epub] CrossRef
Bacterial-Chromatin Structural Proteins Regulate the Bimodal Expression of the Locus of Enterocyte Effacement (LEE) Pathogenicity Island in Enteropathogenic Escherichia coli
Hervé Leh, Ahmad Khodr, Marie-Christine Bouger, Bianca Sclavi, Sylvie Rimsky, Stéphanie Bury-Moné, Susan Gottesman
mBio.2017;[Epub] CrossRef
Alternative Synthesis Route of Biocompatible Polyvinylpyrrolidone Nanoparticles and Their Effect on Pathogenic Microorganisms
Vedran Milosavljevic, Pavlina Jelinkova, Ana Maria Jimenez Jimenez, Amitava Moulick, Yazan Haddad, Hana Buchtelova, Sona Krizkova, Zbynek Heger, Lukas Kalina, Lukas Richtera, Pavel Kopel, Vojtech Adam
Molecular Pharmaceutics.2017; 14(1): 221. CrossRef
H-NS and RNA polymerase: a love–hate relationship?
Robert Landick, Joseph T Wade, David C Grainger
Current Opinion in Microbiology.2015; 24: 53. CrossRef
Effect of promoter-upstream sequence on σ38-dependent stationary phase gene transcription
Hyung-Ju Lim, Kwangsoo Kim, Minsang Shin, Jae-Ho Jeong, Phil Youl Ryu, Hyon E. Choy
Journal of Microbiology.2015; 53(4): 250. CrossRef

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