Journal of Microbiology

Journal Articles

Synthesis of pinene in the industrial strain Candida glycerinogenes by modification of its mevalonate pathway: Tengfei Ma , Hong Zong , Xinyao Lu , Bin Zhuge; J. Microbiol. 2022;60(12):1191-1200. Published online October 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2344-0

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Terpenes have many applications and are widely found in nature, but recent progress in synthetic biology has enabled the use of microorganisms as chassis cells for the synthesis of these compounds. Candida glycerinogenes (C. glycerinogenes) is an industrial strain that may be developed as a chassis for the synthesis of terpenes since it has a tolerance to hyperosmolality and high sugar, and has a complete mevalonate (MVA) pathway. However, monoterpenes such as pinene are highly toxic, and the tolerance of C. glycerinogenes to pinene was investigated. We also measured the content of mevalonate and squalene to evaluate the strength of the MVA pathway. To determine terpene synthesis capacity, a pathway for the synthesis of pinene was constructed in C. glycerinogenes. Pinene production was improved by overexpression, gene knockdown and antisense RNA inhibition. Pinene production was mainly enhanced by strengthening the upstream MVA pathway and inhibiting the production of by-products from the downstream pathway. With these strategies, yield could be increased by almost 16 times, to 6.0 mg/L. Overall, we successfully constructed a pinene synthesis pathway in C. glycerinogenes and enhanced pinene production through metabolic modification.

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Recent advances in genome mining and synthetic biology for discovery and biosynthesis of natural products
Mingpeng Wang, Lei Chen, Zhaojie Zhang, Qinhong Wang
Critical Reviews in Biotechnology.2025; 45(1): 236. CrossRef
Two-Phase Fermentation Systems for Microbial Production of Plant-Derived Terpenes
Tuo Li, Ximeng Liu, Haoyu Xiang, Hehua Zhu, Xuan Lu, Baomin Feng
Molecules.2024; 29(5): 1127. CrossRef
Acetic acid stress and utilization synergistically enhance squalene biosynthesis in Candida glycerinogenes
Zhenzhen You, Xueqing Du, Hong Zong, Xinyao Lu, Bin Zhuge
Biochemical Engineering Journal.2024; 210: 109413. CrossRef
Recent developments in enzymatic and microbial biosynthesis of flavor and fragrance molecules
Roman M. Dickey, Madan R. Gopal, Priyanka Nain, Aditya M. Kunjapur
Journal of Biotechnology.2024; 389: 43. CrossRef
Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica
Dong-Xun Li, Qi Guo, Yu-Xin Yang, Shun-Jie Jiang, Xiao-Jun Ji, Chao Ye, Yue-Tong Wang, Tian-Qiong Shi
ACS Synthetic Biology.2024; 13(6): 1647. CrossRef
Gene Editing of Candida glycerinogenes by Designed Toxin–Antitoxin Cassette
Wen Lv, Xinyao Lu, Bin Zhuge, Hong Zong
ACS Synthetic Biology.2024; 13(3): 816. CrossRef
Candida glycerinogenes-Promoted α-Pinene and Squalene Co-production Strategy Based on α-Pinene Stress
Tengfei Ma, Hong Zong, Xinyao Lu, Bin Zhuge
Journal of Agricultural and Food Chemistry.2023; 71(13): 5250. 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

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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.

The quorum sensing regulator OpaR is a repressor of polar flagellum genes in Vibrio parahaemolyticus: Renfei Lu , Junfang Sun , Yue Qiu , Miaomiao Zhang , Xingfan Xue , Xue Li , Wenhui Yang , Dongsheng Zhou , Lingfei Hu , Yiquan Zhang; J. Microbiol. 2021;59(7):651-657. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0629-3

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Abstract

Vibrio parahaemolyticus possesses two types of flagella: a single polar flagellum (Pof) for swimming and the peritrichous lateral flagella (Laf) for swarming. Expression of Laf genes has previously been reported to be regulated by the quorum sensing (QS) regulators AphA and OpaR. In the present study, we showed that OpaR, the QS regulator at high cell density (HCD), acted as a negative regulator of swimming motility and the transcription of Pof genes in V. parahaemolyticus. OpaR bound to the promoter-proximal DNA regions of flgAMN, flgMN, and flgBCDEFGHIJ within the Pof gene loci to repress their transcription, whereas it negatively regulates the transcription of flgKL-flaC in an indirect manner. Thus, this work investigated how QS regulated the swimming motility via direct action of its master regulator OpaR on the transcription of Pof genes in V. parahaemolyticus.

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H-NS-Mediated Regulation of Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus
Yue Zhou, Jingyang Chang, Feng Li, Mei He, Rui Li, Yaqin Hou, Yiquan Zhang, Renfei Lu, Ming Yang
Current Microbiology.2025;[Epub] CrossRef
GefB, a GGDEF domain-containing protein, affects motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing regulators
Yining Zhou, Jingyang Chang, Miaomiao Zhang, Xue Li, Xi Luo, Wanpeng Li, Zhukang Tian, Nan Zhang, Bin Ni, Yiquan Zhang, Renfei Lu
Gene.2025; 933: 148968. CrossRef
The effect of environmental calcium on gene expression, biofilm formation and virulence of Vibrio parahaemolyticus
Xue Li, Jingyang Chang, Miaomiao Zhang, Yining Zhou, Tingting Zhang, Yiquan Zhang, Renfei Lu
Frontiers in Microbiology.2024;[Epub] CrossRef
VPA0198, a GGDEF domain-containing protein, affects the motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing associated regulators
Yining Zhou, Jingyang Chang, Miaomiao Zhang, Xue Li, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bin Ni, Renfei Lu, Yiquan Zhang
Microbial Pathogenesis.2024; 195: 106882. CrossRef
Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus
F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, A. Alexis Lopez-Zavala
F1000Research.2024; 12: 1256. CrossRef
Environmental magnesium ion affects global gene expression, motility, biofilm formation and virulence of Vibrio parahaemolyticus
Xue Li, Xiaobai Zhang, Miaomiao Zhang, Xi Luo, Tingting Zhang, Xianjin Liu, Renfei Lu, Yiquan Zhang
Biofilm.2024; 7: 100194. CrossRef
The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842
Baiyuan Li, Songwei Ni, Yabo Liu, Jianzhong Lin, Xiaoxue Wang
Microbiological Research.2024; 286: 127817. CrossRef
The Impact of Vp-Porin, an Outer Membrane Protein, on the Biological Characteristics and Virulence of Vibrio Parahaemolyticus
Jinyuan Che, Qitong Fang, Shaojie Hu, Binghong Liu, Lei Wang, Xiu Fang, Lekang Li, Tuyan Luo, Baolong Bao
Biology.2024; 13(7): 485. CrossRef
Phenotypic changes and gene expression profiles of Vibrio parahaemolyticus in response to low concentrations of ampicillin
Xi Luo, Miaomiao Zhang, Yiquan Zhang, Xue Li, Renfei Lu
The Journal of Antibiotics.2024; 77(12): 823. CrossRef
Bioprospecting and Exploration of Phytochemicals as Quorum Sensing Inhibitors against Cariogenic Dental Biofilm
S. Arya, R. Usha
Journal of Pure and Applied Microbiology.2024; 18(1): 100. CrossRef
Identification of an LysR family transcriptional regulator that activates motility and flagellar gene expression in Vibrio parahaemolyticus
Jingyang Chang, Yining Zhou, Xue Li, Miaomiao Zhang, Yiquan Zhang, Bin Ni, Renfei Lu
Letters in Applied Microbiology.2024;[Epub] CrossRef
The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces
Francis J. Santoriello, Bonnie L. Bassler, Ankur B. Dalia
PLOS Genetics.2024; 20(7): e1011243. CrossRef
Evaluation of Therapeutic Efficiency of Stylicin against Vibrio parahaemolyticus Infection in Shrimp Penaeus vannamei through Comparative Proteomic Approach
Saranya Chakrapani, Akshaya Panigrahi, Esakkiraj Palanichamy, Sathish Kumar Thangaraj, Naveenkumar Radhakrishnan, Puspamitra Panigrahi, Radhakrishnan Nagarathnam
Probiotics and Antimicrobial Proteins.2024; 16(1): 76. CrossRef
CalR Inhibits the Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus
Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Haisheng Wu, Renfei Lu, Yiquan Zhang
Journal of Microbiology.2024; 62(12): 1125. CrossRef
Quorum sensing: An emerging role for Vibrio infection and host defense
Hao-Nan Lin, Xian-Hui Huang, Xin-Jun Miao, Wei-Lin Hu, Yong-Liang Lou, Dan-Li Xie
Infectious Microbes and Diseases.2024;[Epub] CrossRef
QsvR and OpaR coordinately repress biofilm formation by Vibrio parahaemolyticus
Miaomiao Zhang, Xingfan Xue, Xue Li, Qimin Wu, Tingting Zhang, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Renfei Lu, Yiquan Zhang
Frontiers in Microbiology.2023;[Epub] CrossRef
Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation
Yiquan Zhang, Tingting Zhang, Yue Qiu, Miaomiao Zhang, Xiuhui Lu, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bo Gao, Renfei Lu
Current Microbiology.2023;[Epub] CrossRef
Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus
F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, A. Alexis Lopez-Zavala
F1000Research.2023; 12: 1256. CrossRef
Effect of sublethal dose of chloramphenicol on biofilm formation and virulence in Vibrio parahaemolyticus
Miaomiao Zhang, Liyan Cai, Xi Luo, Xue Li, Tingting Zhang, Fei Wu, Yiquan Zhang, Renfei Lu
Frontiers in Microbiology.2023;[Epub] CrossRef
Quorum sensing and QsvR tightly control the transcription of vpa0607 encoding an active RNase II-type protein in Vibrio parahaemolyticus
Yiquan Zhang, Xingfan Xue, Fengjun Sun, Xue Li, Miaomiao Zhang, Qimin Wu, Tingting Zhang, Xi Luo, Renfei Lu
Frontiers in Microbiology.2023;[Epub] CrossRef
QsvR represses the transcription of polar flagellum genes in Vibrio parahaemolyticus
Miaomiao Zhang, Xingfan Xue, Xue Li, Xi Luo, Qimin Wu, Tingting Zhang, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Renfei Lu, Yiquan Zhang
Microbial Pathogenesis.2023; 174: 105947. CrossRef
Transcriptomic Analysis of Vibrio parahaemolyticus Underlying the Wrinkly and Smooth Phenotypes
Qimin Wu, Xue Li, Tingting Zhang, Miaomiao Zhang, Xingfan Xue, Wenhui Yang, Lingfei Hu, Zhe Yin, Dongsheng Zhou, Yuyu Sun, Renfei Lu, Yiquan Zhang, Sébastien P. Faucher
Microbiology Spectrum.2022;[Epub] CrossRef
Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains
Masa-aki Yoshida, Takuma Tanabe, Hideo Akiyoshi, Makoto Kawamukai
Scientific Reports.2022;[Epub] CrossRef
Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus
Nur Afiqah Md Yusof, Siti Aisyah Razali, Azyyati Mohd Padzil, Benjamin Yii Chung Lau, Syarul Nataqain Baharum, Nor Azlan Nor Muhammad, Nurul Hanun Ahmad Raston, Chou Min Chong, Natrah Fatin Mohd Ikhsan, Magdalena Lenny Situmorang, Low Chen Fei
Biology.2022; 11(11): 1600. CrossRef
An Increase of Seawater Temperature Upregulates the Expression of Vibrio parahaemolyticus Virulence Factors Implicated in Adhesion and Biofilm Formation
Mélanie Billaud, François Seneca, Eric Tambutté, Dorota Czerucka
Frontiers in Microbiology.2022;[Epub] CrossRef
Characterization of the RpoN regulon reveals the regulation of motility, T6SS2 and metabolism in Vibrio parahaemolyticus
Dan Gu, Youkun Zhang, Kangru Wang, Mingzhu Li, Xinan Jiao
Frontiers in Microbiology.2022;[Epub] CrossRef

Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities: Edmond Kuete Yimagou , Jean-Pierre Baudoin , Rita Abou Abdallah , Fabrizio Di Pinto , Jacques Yaacoub Bou Khalil , Didier Raoult; J. Microbiol. 2020;58(5):377-386. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9365-3

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Abstract

The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the “microscomics” approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our cultureindependent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect “minimicrobes” Candidate Phyla Radiation (CPR) for the first time in human stool samples. This “microscomics” approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease
Sabrina Naud, Ahmad Ibrahim, Camille Valles, Mohamad Maatouk, Fadi Bittar, Maryam Tidjani Alou, Didier Raoult
Clinical Microbiology Reviews.2022;[Epub] CrossRef
Radiotherapy and the gut microbiome: facts and fiction
Jing Liu, Chao Liu, Jinbo Yue
Radiation Oncology.2021;[Epub] CrossRef
Host–microbiota maladaptation in colorectal cancer
Alina Janney, Fiona Powrie, Elizabeth H. Mann
Nature.2020; 585(7826): 509. CrossRef

Improved tolerance of Escherichia coli to oxidative stress by expressing putative response regulator homologs from Antarctic bacteria: Seo-jeong Park , Sangyong Lim , Jong-il Choi; J. Microbiol. 2020;58(2):131-141. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9290-5

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Abstract

Response regulator (RR) is known a protein that mediates cell’s response to environmental changes. The effect of RR from extremophiles was still under investigation. In this study, response regulator homologs were mined from NGS data of Antarctic bacteria and overexpressed in Escherichia coli. Sixteen amino acid sequences were annotated corresponding to response regulators related to the two-component regulatory systems; of these, 3 amino acid sequences (DRH632, DRH1601 and DRH577) with high homology were selected. These genes were cloned in pRadGro and expressed in E. coli. The transformant strains were subjected to various abiotic stresses including oxidative, osmotic, thermal stress, and acidic stress. There was found that the robustness of E. coli to abiotic stress was increased in the presence of these response regulator homologs. Especially, recombinant E. coli overexpressing drh632 had the highest survival rate in oxidative, hypothermic, osmotic, and acidic conditions. Recombinant E. coli overexpressing drh1601 showed the highest tolerance level to osmotic stress. These results will be applicable for development of recombinant strains with high tolerance to abiotic stress.

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Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
Seul-Ki Yang, Soyoung Jeong, Inwoo Baek, Jong-il Choi, Sangyong Lim, Jong-Hyun Jung
Microorganisms.2023; 11(9): 2135. CrossRef
Bacterial redox response factors in the management of environmental oxidative stress
Sudharsan M, Rajendra Prasad N, Saravanan Rajendrasozhan
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef
Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli
Sadika Dkhili, Miguel Ribeiro, Salma Ghariani, Houssem Ben Yahia, Mélanie Hillion, Patricia Poeta, Karim Ben Slama, Michel Hébraud, Gilberto Igrejas
OMICS: A Journal of Integrative Biology.2021; 25(10): 626. CrossRef
Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. 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

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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.

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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

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes: Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul; J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9217-1

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Abstract

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.

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Mario Fernández, Salvador Barahona, Fernando Gutierrez, Jennifer Alcaíno, Víctor Cifuentes, Marcelo Baeza
Current Issues in Molecular Biology.2024; 46(11): 13165. CrossRef
Cold adaptation and response genes of Antarctic Cryobacterium sp. SO2 from the Fildes Peninsula, King George Island
Chui Peng Teoh, Marcelo González‑Aravena, Paris Lavin, Clemente Michael Vui Ling Wong
Polar Biology.2024; 47(2): 135. CrossRef
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Célica Cagide, Juan José Marizcurrena, Diego Vallés, Beatriz Alvarez, Susana Castro-Sowinski
Applied Microbiology and Biotechnology.2023; 107(5-6): 1707. CrossRef
Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review
Ninian Prem Prashanth Pabbathi, Aditya Velidandi, Tanvi Tavarna, Shreyash Gupta, Ram Sarvesh Raj, Pradeep Kumar Gandam, Rama Raju Baadhe
Biomass Conversion and Biorefinery.2023; 13(2): 1371. CrossRef
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Yanhong Yuan, Lan Chen, Jieying Wang, Yanfang Liu, Chengjie Ren, Yaoxin Guo, Jun Wang, Ninglian Wang, Fazhu Zhao, Wenying Wang
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Investigation of cold-active and mesophilic cellulases: opportunities awaited
Sambhaji Chavan, Ashvini Shete, Yasmin Mirza, Mahesh S. Dharne
Biomass Conversion and Biorefinery.2023; 13(10): 8829. CrossRef
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Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef
Reclamation of abandoned saline-alkali soil increased soil microbial diversity and degradation potential
Fating Yin, Fenghua Zhang
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Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass
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Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni: Jae-Bong Lee , Seon Hwa Jeon , Seok-Gwan Choi , Hee-Young Jung , Myung Kyum Kim , Sathiyaraj Srinivasan; J. Microbiol. 2016;54(12):809-813. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6473-1

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Abstract

In this paper, a new bacterial strain designated as 16MFT21T is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21T is a Gram-staining-positive, catalase- oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21T revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21T is with Bacillus licheniformis ATCC 14580T (96.6%) and Bacillus sonorensis NBRC 101234T (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH􍾘from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone- 7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21T (=KCTC 18866T =JCM 31664T) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

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

Antioxidant Capacity of Novel Pigments from an Antarctic Bacterium: Daniela N. Correa-Llantén , Maximiliano J. Amenábar , Jenny M. Blamey; J. Microbiol. 2012;50(3):374-379. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2029-1

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Abstract: In Antarctica microorganisms are exposed to several conditions that trigger the generation of reactive oxygen species, such as high UV radiation. Under these conditions they must have an important antioxidant defense system in order to prevent oxidative damage. One of these defenses are pigments which are part of the non-enzymatic antioxidant mechanisms. In this work we focused on the antioxidant capacity of pigments from an Antarctic microorganism belonging to Pedobacter genus. This microorganism produces different types of pigments which belong to the carotenoids group. The antioxidant capacity of a mix of pigments was analyzed by three different methods: 1,1-diphenyl-2-picrylhydrazyl, ROS detection and oxygen electrode. The results obtained from these approaches indicate that the mix of pigments has a strong antioxidant capacity. The oxidative damage induced by UVB exposure to liposomes was also analyzed. Intercalated pigments within the liposomes improved its resistance to lipid peroxidation. Based on the analysis carried out along this research we conclude that the antioxidant properties of the mix of pigments protect this bacterium against oxidative damage. These properties make this mix of pigments a powerful antioxidant mixture with potential biotechnological applications.

Journal Article

Psychroflexus lacisalsi sp. nov., a Moderate Halophilic Bacterium Isolated from a Hypersaline Lake (Hunazoko-Ike) in Antarctica: Hongyan Zhang , Shoko Hosoi-Tanabe , Syuhei Ban , Satoshi Imura; J. Microbiol. 2010;48(2):160-164. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-0018-9

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Abstract: A novel Gram-negative, aerobic, moderate halophilic, and psychrotolerant bacterium, designated as strain H7T, was isolated from a hypersaline lake located in Skarvsnes, Antarctica. Cells were filaments with varying lengths. Coccoid bodies developed in old cultures. Growth occurred with 0.5-15% (w/v) NaCl (optimum, 5.8-7.0%), at pH 6.0-10.0 (optimum, pH 7.0-8.0), and at 10-28°C (optimum, 25°C). The strain had a G+C content of 34.9 mol%, which is within the range of 32-36 mol% reported for the genus Psychroflexus. Chemotaxonomic data (major respiratory quinone: MK-6; major fatty acids: aC15:0, iC16:0 3-OH, and aC15: 1 A) supported the classification of strain H7T within the genus Psychroflexus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H7T should be assigned to the genus Psychroflexus and has a homology with Psychroflexus salinarum (98.2%), P. sediminis (96.1%), P. torquis (95.2%), P. tropicus (95.8%), and P. gondwanense (92.2%). Strain H7 is not identified as P. salinarum because that DNA-DNA hybridization data were 8.5% between strain H7T and P. salinarum. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics, and chemotaxonomic differences supported the view that strain H7T represents a novel species of the genus Psychroflexus. The name Psychroflexus lacisalsi is proposed, and the type strain is H7T (=JCM 16231T =KACC 14089T).

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

Antarcticimonas flava gen. nov., sp. nov., Isolated from Antarctic Coastal Seawater: Seung-Jo Yang , Hyun-Myung Oh , Sangyun Chung , Jang-Cheon Cho; J. Microbiol. 2009;47(5):517-523. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0225-4

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9 Scopus

Abstract: A marine bacterium, designated IMCC3175T, was isolated from a seawater sample collected off the Antarctic coast. The strain was Gram-negative, obligately aerobic, carotenoid pigment-containing, and rod-shaped bacterium that divided by binary fission. As determined by 16S rRNA gene sequence comparisons, the most closely related genera were Formosa (92.9~93.3%), Bizionia (91.6~93.2%), Gaetbulibacter (91.5~92.8%), Sediminibacter (92.7%), Yeosuana (92.6%), Subsaximicrobium (92.1~92.2%), and Gillisia (89.5~92.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a monophyletic clade together with the genera Sediminibacter and Subsaximicrobium but represented an independent phyletic line in this clade of the family Flavobacteriaceae. The DNA G+C content of the strain was 37.3 mol%. The major respiratory quinone was MK-6 and the predominant cellular fatty acids were C16:1 ω7c and/or iso-C15:0 2-OH (12.8%), anteiso-C15:0 (9.4%), and iso-C16:1 (9.4%). Low 16S rRNA gene sequence similarity, formation of a distinct phylogenetic branch, and several phenotypic characteristics, including a narrow range of temperature and salinity for growth, differentiated strain IMCC3175T from other related genera in the family Flavobacteriaceae. Therefore the name Antarcticimonas flava gen. nov., sp. nov. is proposed, with strain IMCC3175T (=KCCM 42713T =NBRC 103398T) as the type strain.

Lichen Flora around the Korean Antarctic Scientific Station, King George Island, Antarctic: Ji Hee Kim , In-Young Ahn , Soon Gyu Hong , Mikhail Andreev , Kwang-Mi Lim , Mi Jin Oh , Young Jin Koh , Jae-Seoun Hur; J. Microbiol. 2006;44(5):480-491.; DOI: https://doi.org/2450 [pii]

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Abstract: As part of the long-term monitoring projects on Antarctic terrestrial vegetation in relation to global climate change, a lichen floristical survey was conducted around the Korean Antarctic Station (King Sejong Station), which is located on Barton Peninsula, King George Island, in January and February of 2006. Two hundred and twenty-five lichen specimens were collected and sixty-two lichen species in 38 genera were identified by morphological characteristics, chemical constituents, TLC analysis and ITS nucleotide sequence analysis.

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