Journal of Microbiology

Full article

PhoU interaction with the PhoR PAS domain is required for repression of the pho regulon and Salmonella virulence, but not for polyphosphate accumulation: Seungwoo Baek, Soomin Choi, Yoontak Han, Eunna Choi, Shinae Park, Jung-Shin Lee, Eun-Jin Lee; J. Microbiol. 2025;63(9):e2505013. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2505013

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Abstract PDF Supplementary Material: The pho regulon plays a critical role in maintaining phosphate homeostasis in bacteria, with the PhoU protein functioning as a regulator that bridges the PhoB/PhoR two-component system and the PstSCAB₂ phosphate transporter. While PhoU is known to suppress PhoR autophosphorylation under high phosphate conditions via interaction with its PAS domain, its broader regulatory functions remain elusive. Here, we investigated the role of the PhoU Ala147 residue in Salmonella enterica serovar Typhimurium using a phoU^A147E substitution mutant. Bacterial two-hybrid and immunoprecipitation assays confirmed that Ala147 is essential for PhoU-PhoR PAS domain interaction, and its substitution leads to derepression of pho regulon genes, even in high phosphate conditions. This disruption impaired Salmonella survival inside macrophages and mouse virulence, demonstrating the importance of PhoU-PhoR interaction in Salmonella pathogenesis. However, unlike the phoU deletion mutant, the phoU^A147E mutant does not exhibit growth defects or polyphosphate accumulation, indicating that the PhoU-PhoR interaction is not involved in these phenotypes. Our findings reveal PhoU as a multifaceted regulator, coordinating phosphate uptake and pho regulon expression through distinct molecular interactions, and provide new insights into its role in bacterial physiology and virulence.

Research Article

Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition: Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang; J. Microbiol. 2025;63(2):e2411019. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411019

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Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO₃^-) as a terminal electron acceptor instead of molecular O₂. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they were observed to reduce NO₃^- and produce extracellular NH₄⁺ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO₃^- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO₃^-. Based on the phenotypic and transcriptional analyses of the NO₃^- reductions, all three of the facultative anaerobic strains reduced NO₃^- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO₃^- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.

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Biofertilizers Enhance Soil Fertility and Crop Yields Through Microbial Community Modulation
Xu Zhang, Lei Zhang, Junjie Liu, Zongzuan Shen, Zhuxiu Liu, Haidong Gu, Xiaojing Hu, Zhenhua Yu, Yansheng Li, Jian Jin, Guanghua Wang
Agronomy.2025; 15(7): 1572. CrossRef
Strategy of nitrate-enhanced natural attenuation for remediation of PAHs-contaminated subsoil
Xuyang Jiang, Zhen Mao, Zhenqi Hu, Tao Jin, Licun Zhong, Jinbiao Yu
Journal of Environmental Chemical Engineering.2025; 13(5): 118037. CrossRef

Journal Article

Thalassotalea aquiviva sp. nov., and Thalassotalea maritima sp. nov., Isolated from Seawater of the Coast in South Korea: Jina Lee, Seung-Hui Song, Kira Moon, Nakyeong Lee, Sangdon Ryu, Hye Seon Song, Sung Moon Lee, Yun Ji Kim, Se Won Chun, Kyung-Min Choi, Aslan Hwanhwi Lee; J. Microbiol. 2024;62(12):1099-1111. Published online December 10, 2024; DOI: https://doi.org/10.1007/s12275-024-00191-4

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Abstract PDF

Two novel bacterial strains, 273M-4^T and Sam97^T, were isolated from seawater in the Yellow Sea, Muan-gun, South Korea, and identified as members of the genus Thalassotalea. Both strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, non-flagellated, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains 273M-4^T and Sam97^T were most closely related to Thalassotalea ponticola KCTC 42155^T, with sequence similarities of 97.5% and 98.3%, respectively. Optimal growth for strain 273M-4^T occurred at 25-30 °C, pH 7.0, and 2% NaCl, while strain Sam97^T grew optimally at 30 °C, pH 8.0, and 2% NaCl. Genome sizes of strains 273M-4^T and Sam97^T were 3.37 and 3.31 Mb, with DNA G + C contents of 41.0 mol% and 42.9 mol%, respectively. The orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 71.6% and 24.4%, respectively, indicating that they are distinct species. Further genomic analyses of these two strains revealed OrthoANI values of < 73.5% and dDDH values of < 26.7% within the genus Thalassotalea, suggesting their distinctiveness from other Thalassotalea species. The predominate fatty acids of strains 273M-4^T and Sam97^T were summed feature 3 (consisting of C_16:1 ω7c/C_16:1 ω6c) and C_16:0. All strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids and ubiquinone-8 (Q-8) as the primary respiratory quinone. Based on phenotypic, phylogenetic, genotypic, and chemotaxonomic data, strains 273M-4^T (= KCTC 8644^T = LMG 33695^T) and Sam97^T (= KCTC 8645^T = LMG 33694^T) represent novel species of the genus Thalassotalea, named Thalassotalea aquiviva sp. nov. and Thalassotalea maritima sp. nov..

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Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater
Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho
Journal of Microbiology.2025; 63(8): e2504017. CrossRef

Review

Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater—A Review: Sua Lee , Min Cho , Michael J. Sadowsky , Jeonghwan Jang; J. Microbiol. 2023;61(9):791-805. Published online August 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00067-z

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Abstract

Nitrate ( NO3 −) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3 − have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas ( N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3 −-removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3 − in several field studies. NO3 − removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3 − to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3 − pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3 − from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3 − in WBR, and perspectives to enhance WBR performance in the future.

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Complete genome sequence of Neobacillus sp. strain OS1-2, a denitrifying bacterium isolated from apple orchard soil
Jinwoo Ahn, Jeonghwan Jang, Elinne Becket
Microbiology Resource Announcements.2025;[Epub] CrossRef
Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition
Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang
Journal of Microbiology.2025; 63(2): e2411019. CrossRef
Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater
Xinyue Gong, Qin Peng, Ruixin Jiang, Na Yang, Cijun Xing, Rui Wang
Journal of Hazardous Materials.2025; 488: 137383. CrossRef
Impact of projective soil cover with post-harvest residues on soil microbiological indicators in the conditions of the Left-Bank Forest-Steppe of Ukraine
Z. O. Dehtiarova, A. A. Dyomkin
Man and Environment. Issues of Neoecology.2025; (43): 147. CrossRef

Journal Articles

Weigela florida inhibits the expression of inflammatory mediators induced by Pseudomonas aeruginosa and Staphylococcus aureus infection: Hyo Bin Kim , Soomin Cho , Yeji Lee , Weihui Wu , Un-Hwan Ha; J. Microbiol. 2022;60(6):649-656. Published online April 30, 2022; DOI: https://doi.org/10.1007/s12275-022-1638-6

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Abstract

Inflammatory responses involve the action of inflammatory mediators that are necessary for the clearance of invading bacterial pathogens. However, excessive production of inflammatory mediators can damage tissues, thereby impairing bacterial clearance. Here, we examined the effects of Weigela florida on the expression of inflammatory cytokines induced by Pseudomonas aeruginosa or Staphylococcus aureus infection in macrophages. The results showed that pre-treatment with W. florida markedly downregulated the bacterial infectionmediated expression of cytokines. Additionally, post-treatment also triggered anti-inflammatory effects in cells infected with S. aureus to a greater extent than in those infected with P. aeruginosa. Bacterial infection activated inflammation-associated AKT (Thr308 and Ser473)/NF-κB and MAPK (p38, JNK, and ERK) signaling pathways, whereas W. florida treatment typically inhibited the phosphorylation of AKT/NF‐κB and p38/JNK, supporting the anti‐inflammatory effects of W. florida. The present results suggest that W. florida decreases the infection-mediated expression of inflammatory mediators by inhibiting the AKT/NF-κB and MAPK signaling pathways, implying that it may have potential use as an inhibitory agent of excessive inflammatory responses.

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Multifunctional fluorescence probe for simultaneous detection of viscosity, polarity, and ONOO− and its bioimaging in vitro and vivo
Yuan-Yuan Li, Jia-Ling Hu, Ji-Rou Wu, Yi-Ru Wang, Ai-Hong Zhang, Yu-Wei Tan, Ya-Jing Shang, Ting Liang, Min Li, Ya-Li Meng, Yan-Fei Kang
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Mesorhizobium denitrificans sp. nov., a novel denitrifying bacterium isolated from sludge: Muhammad Zubair Siddiqi , Ngo Thi Phuong Thao , Gyumin Choi , Dae-Cheol Kim , Young-Woo Lee , Sang Young Kim , Ji-Hyang Wee , Wan-Taek Im; J. Microbiol. 2019;57(4):238-242. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8590-0

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Abstract

A Gram-stain-negative, non-spore-forming, facultative, rodshaped bacterium (designated LA-28T) was isolated from a sludge sample from a wastewater treatment plant in Hanam city, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-28T clustered with species of the genus Mesorhizobium and appeared closely related to M. jarvisii LMG 28313T (96.8%), M. waimense ICMP 19557T (96.7%), and M. huakuii LMG 14107T (96.7%). Growth occurs at 18– 40°C on R2A medium in the presence of 1–4% NaCl (w/v) and at pH 6–8. The DNA G+C content was 61.2 mol%, and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (> 5%) were C16:0, C19:0 ω8c cyclo, C18:1 ω7c 11-methyl, and C18:1 ω7c and/or C18:1 ω6c (summed feature 8). Major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidyl-N-methylethanolamine (PME), and phosphatidylcholine (PC). Physiological and biochemical characteristics indicated that strain LA-28T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium denitrificans sp. nov. is proposed. The type strain is LA-28T (= KACC 19675T = LMG 30806T).

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