Journal of Microbiology

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

387 View
24 Download

Abstract PDF Supplementary Material: 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.

Journal Articles

Description of Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. isolated from the Intestines of Aegosoma sinicum Larvae: Hae-In Joe , Jee-Won Choi , June-Young Lee , Hojun Sung , Su-Won Jeong , Yun-Seok Jeong , Jae-Yun Lee , Jin-Woo Bae; J. Microbiol. 2023;61(6):603-613. Published online May 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00051-7

71 View
0 Download
3 Web of Science
2 Crossref

Three novel bacterial strains, 321T, 335T, and 353T, were isolated from the intestines of Aegosoma sinicum larvae collected from Paju-Si, South Korea. The strains were Gram-negative, obligate aerobe and had rod-shaped cells with a single flagellum. The three strains belonged to the genus Luteibacter in the family Rhodanobacteraceae and shared < 99.2% similarity in their 16S rRNA gene sequence and < 83.56% similarity in thier whole genome sequence. Strains 321T, 335T, and 353T formed a monophyletic clade with Luteibacter yeojuensis KACC 11405T, L. anthropi KACC 17855T, and L. rhizovicinus KACC 12830T, with sequence similarities of 98.77–98.91%, 98.44–98.58%, and 97.88–98.02%, respectively. Further genomic analyses, including the construction of the Up-to-date Bacterial Core Gene (UBCG) tree and assessment of other genome-related indices, indicated that these strains were novel species belonging to the genus Luteibacter. All three strains contained ubiquinone Q8 as their major isoprenoid quinone and iso-C15:0 and summed feature 9 ( C16:0 10-methyl and/or iso-C17:1 ω9c) as their major cellular fatty acids. Phosphatidylethanolamine and diphosphatidylglycerol were the major polar lipids in all the strains. The genomic DNA G + C contents of strains 321T, 335T, and 353T were 66.0, 64.5, and 64.5 mol%, respectively. Based on multiphasic classification, strains 321T, 335T, and 353T were classified into the genus Luteibacter as the type strains of novel species, for which the names Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. are proposed, respectively.

Citations

Citations to this article as recorded by

Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome
Gagandeep Jaiswal, Rekha Rana, Praveen Kumar Nayak, Rekha Chouhan, Sumit G. Gandhi, Hitendra K. Patel, Prabhu B. Patil
Current Microbiology.2024;[Epub] CrossRef
Validation List no. 215. 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

Fus3 and Tpk2 protein kinases regulate the phosphorylation-dependent functions of RNA helicase Dhh1 in yeast mating and Ste12 protein expression: Jaehee Hwang , Daehee Jung , Jinmi Kim; J. Microbiol. 2022;60(8):843-848. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2213-x

41 View
0 Download

Abstract: Decapping of mRNA is a key regulatory step for mRNA decay and translation. The RNA helicase, Dhh1, is known as a decapping activator and translation repressor in yeast Saccharomyces cerevisiae. Dhh1 also functions as a gene-specific positive regulator in the expression of Ste12, a mating-specific transcription factor. A previous study showed that the Nerminal phosphorylation of Dhh1 regulates its association with the mRNA-binding protein, Puf6, to affect the protein translation of Ste12. Here, we investigated the roles of the phosphorylated residues of Dhh1 in yeast mating process and Ste12 expression. The phospho-deficient mutation, DHH1- T10A, was associated with decreased diploid formation during mating and decreased level of the Ste12 protein in response to α-mating pheromone. A kinase overexpression analysis revealed that Ste12 protein expression was affected by overexpression of Fus3 MAP kinase or Tpk2 kinase. Tpk2 was shown to be responsible for phosphorylation of Dhh1 at Thr10. Our study shows that overexpression of Fus3 or Tpk2 alters the Dhh1-Puf6 protein interaction and thereby affects Ste12 protein expression.

Biosynthesis of adipic acid in metabolically engineered Saccharomyces cerevisiae: Xi Zhang , Yingli Liu , Jing Wang , Yunying Zhao , Yu Deng; J. Microbiol. 2020;58(12):1065-1075. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0261-7

49 View
0 Download
13 Web of Science
13 Crossref

Abstract

Adipic Acid (AA) is a valued platform chemical compound, which can be used as a precursor of nylon-6,6. Due to the generation of an enormous amount of nitric oxide metabolites and the growing depletion of oil resources as a result of AA production from a mixture of cyclohexanol and cyclohexanone, the microbial methods for synthesizing AA have attracted significant attention. Of the several AA-producing pathways, the reverse adipate degradation pathway in Thermobifida fusca (Tfu RADP) is reported to be the most efficient, which has been confirmed in Escherichia coli. In this study, the heterologous Tfu RADP was constructed for producing AA in S. cerevisiae by co-expressing genes of Tfu_ 0875, Tfu_2399, Tfu_0067, Tfu_1647, Tfu_2576, and Tfu_ 2576. The AA titer combined with biomass, cofactors and other by-products was all determined after fermentation. During batch fermentation in a shake flask, the maximum AA titer was 3.83 mg/L, while the titer increased to 10.09 mg/L during fed-batch fermentation in a 5-L bioreactor after fermentation modification.

Citations

Citations to this article as recorded by

Experimental, modeling and optimisation of adipic acid reactive extraction using ionic liquids
Elena Niculina Dragoi, Alexandra Cristina Blaga, Dan Cascaval, Anca Irina Galaction
Journal of Molecular Liquids.2024; 410: 125564. CrossRef
Structure sensitivity of the electrochemical hydrogenation of cis,cis-muconic acid to hexenedioic acid and adipic acid
Deep M. Patel, Prathamesh T. Prabhu, Geet Gupta, Marco Nazareno Dell'Anna, Samantha Kling, Huy T. Nguyen, Jean-Philippe Tessonnier, Luke T. Roling
Green Chemistry.2024; 26(8): 4506. CrossRef
Exploring the Potential of Bio-plasticizers: Functions, Advantages, and Challenges in Polymer Science
Felipe Martins de Souza, Ram K. Gupta
Journal of Polymers and the Environment.2024; 32(11): 5499. CrossRef
Poly (Butylene Adipate‐Co‐Terephthalate) (PBAT) – Based Biocomposites: A Comprehensive Review
Blessing E. Itabana, Amar K. Mohanty, Phil Dick, Mohini Sain, Atul Bali, Mike Tiessen, Loong‐Tak Lim, Manjusri Misra
Macromolecular Materials and Engineering.2024;[Epub] CrossRef
Comparative analysis of biotechnological and catalytic approaches to the production of organic acids
K. N. Sorokina, Y. V. Samoylova, V. N. Parmon
Kataliz v promyshlennosti.2024; 24(3): 73. CrossRef
Mid–Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects
Shanna Gu, Fuzhou Zhu, Lin Zhang, Jianping Wen
Journal of Agricultural and Food Chemistry.2024; 72(11): 5555. CrossRef
Toward the use of mixed microbial cultures for the biological production of adipic and levulinic acid
Fernanda Pinto-Ibieta, Mara Cea, Antonio Serrano, Fernando E. Felissia, María Cristina Area, Francisco Cabrera, Gustavo Ciudad
Frontiers in Microbiology.2023;[Epub] CrossRef
Producing malonate in Saccharomyces cerevisiae via the β-alanine pathway
Shiyun Li, Wenxuan Fu, Ruifang Su, Yunying Zhao, Yu Deng
Systems Microbiology and Biomanufacturing.2023; 3(2): 328. CrossRef
Engineering yeast cell factories to produce biodegradable plastics and their monomers: Current status and prospects
Feng-Li Zhang, Lin Zhang, Du-Wen Zeng, Sha Liao, Yachao Fan, Verawat Champreda, Weerawat Runguphan, Xin-Qing Zhao
Biotechnology Advances.2023; 68: 108222. CrossRef
Sustainable Routes for the Synthesis of Renewable Adipic Acid from Biomass Derivatives
Man Lang, Hao Li
ChemSusChem.2022;[Epub] CrossRef
Research Progress on the Construction of Artificial Pathways for the Biosynthesis of Adipic Acid by Engineered Microbes
Yuchen Ning, Huan Liu, Renwei Zhang, Yuhan Jin, Yue Yu, Li Deng, Fang Wang
Fermentation.2022; 8(8): 393. CrossRef
Opportunities in the microbial valorization of sugar industrial organic waste to biodegradable smart food packaging materials
Sandhya Jayasekara, Lakshika Dissanayake, Lahiru N. Jayakody
International Journal of Food Microbiology.2022; 377: 109785. CrossRef
Implementation of Synthetic Pathways to Foster Microbe-Based Production of Non-Naturally Occurring Carboxylic Acids and Derivatives
Ana Vila-Santa, Fernão C. Mendes, Frederico C. Ferreira, Kristala L. J. Prather, Nuno P. Mira
Journal of Fungi.2021; 7(12): 1020. CrossRef

H2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica: Zhifeng Yang , Yu Zhang , Yongxin Lv , Wenkai Yan , Xiang Xiao , Bo Sun , Hongmei Ma; J. Microbiol. 2019;57(12):1095-1104. Published online November 22, 2019; DOI: https://doi.org/10.1007/s12275-019-9366-2

43 View
0 Download
11 Web of Science
10 Crossref

Abstract

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]- hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.

Citations

Citations to this article as recorded by

Microbial genetic potential differs among cryospheric habitats of the Damma glacier
Maomao Feng, Serina Robinson, Weihong Qi, Arwyn Edwards, Beat Stierli, Marcel van der Heijden, Beat Frey, Gilda Varliero
Microbial Genomics .2024;[Epub] CrossRef
Inorganic carbon metabolism enhanced hydrogen-driven denitrification: Evaluation of carbon fixation pathways and microbial traits
Puchun Wang, Yang Wu, Lan Yang, Xiong Zheng, Min Long, Yinguang Chen
Chemical Engineering Journal.2024; 497: 154528. CrossRef
The response of C/N/S cycling functional microbial communities to redox conditions in shallow aquifers using in-situ sediment as bio-trap matrix
Cui Li, Rong Chen, Weiwei Ouyang, Chen Xue, Minghui Liu, Hui Liu
Environmental Technology.2024; 45(18): 3666. CrossRef
Glacial Water: A Dynamic Microbial Medium
Gilda Varliero, Pedro H. Lebre, Beat Frey, Andrew G. Fountain, Alexandre M. Anesio, Don A. Cowan
Microorganisms.2023; 11(5): 1153. CrossRef
Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard
Chen Tian, Yongxin Lv, Zhifeng Yang, Ruifeng Zhang, Zhuoyi Zhu, Hongmei Ma, Jing Li, Yu Zhang
Microbial Ecology.2023; 86(2): 933. CrossRef
Aerobic hydrogen-oxidizing bacteria in soil: from cells to ecosystems
Xinyun Fan, Xuemeng Zhang, Guohua Zhao, Xin Zhang, Lei Dong, Yinguang Chen
Reviews in Environmental Science and Bio/Technology.2022; 21(4): 877. CrossRef
Prokaryotic community and diversity in coastal surface waters along the Western Antarctic Peninsula
Rafet Cagri Ozturk, Ali Muzaffer Feyzioglu, Ilhan Altinok
Polar Science.2022; 31: 100764. CrossRef
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)
Carla Perez-Mon, Weihong Qi, Surendra Vikram, Aline Frossard, Thulani Makhalanyane, Don Cowan, Beat Frey
Microbial Genomics .2021;[Epub] CrossRef
Global modeling of hydrogen using GFDL-AM4.1: Sensitivity of soil removal and radiative forcing
Fabien Paulot, David Paynter, Vaishali Naik, Sergey Malyshev, Raymond Menzel, Larry W. Horowitz
International Journal of Hydrogen Energy.2021; 46(24): 13446. CrossRef
Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments
Eric C. Dunham, John E. Dore, Mark L. Skidmore, Eric E. Roden, Eric S. Boyd
Proceedings of the National Academy of Sciences.2021;[Epub] CrossRef

First
Prev
Page of 1
Next
Last

Search