Journal of Microbiology

Journal Articles

Enhancing Seed Germination of Cremastra appendiculata: Screening and Identification of Four New Symbiotic Fungi in the Psathyrellaceae Family: Zhangneng Pan, Jing Wang, Shanshan He, Haiyang Zhao, Xinyue Dong, Tao Feng, Yanyan Meng, Xiaojun Li; J. Microbiol. 2024;62(8):671-682. Published online June 28, 2024; DOI: https://doi.org/10.1007/s12275-024-00148-7

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Abstract: Several coprinoid fungi have been identified as promotors of Cremastra appendiculata seed germination, while others appear ineffective. This study aimed to discern which genera within the Psathyrellaceae family exhibit this capability and to identify the most effective coprinoid fungi for the cultivation of C. appendiculata. We collected 21 coprinoid fungi from diverse sources and symbiotically cultured them with C. appendiculata seeds. 9 fungi were found to induce seed germination and support seed development, specifically within the genera Coprinellus, Tulosesus, and Candolleomyces. In contrast, fungi that failed to promote germination predominantly belonged to the genera Coprinopsis and Parasola. Notably, four fungi-Coprinellus xanthothrix, Coprinellus pseudodisseminatus, Psathyrella singeri, and Psathyrella candolleana-were documented for the first time as capable of enhancing C. appendiculata seed germination. Strain 218LXJ-10, identified as Coprinellus radians, demonstrated the most significant effect and has been implemented in large-scale production, underscoring its considerable practical value. These findings contribute vital scientific insights for the conservation and sustainable use of C. appendiculata resources.

Crystal Structures of Plk1 Polo‑Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2‑Derived Peptide: Sujin Jung , Hye Seon Lee , Ho-Chul Shin , Joon Sig Choi , Seung Jun Kim , Bonsu Ku; J. Microbiol. 2023;61(8):755-764. Published online September 8, 2023; DOI: https://doi.org/10.1007/s12275-023-00071-3

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Abstract: Human papillomaviruses (HPVs) can increase the proliferation of infected cells during HPV-driven abnormalities, such as cervical cancer or benign warts. To date, more than 200 HPV genotypes have been identified, most of which are classified into three major genera: Alphapapillomavirus, Betapapillomavirus, and Gammapapillomavirus. HPV genomes commonly encode two structural (L1 and L2) and seven functional (E1, E2, E4–E7, and E8) proteins. L2, the minor structural protein of HPVs, not only serves as a viral capsid component but also interacts with various human proteins during viral infection. A recent report revealed that L2 of HPV16 recruits polo-like kinase 1 (Plk1), a master regulator of eukaryotic mitosis and cell cycle progression, for the delivery of viral DNA to mitotic chromatin during HPV16 infection. In this study, we verified the direct and potent interactions between the polo-box domain (PBD) of Plk1 and PBD-binding motif (S–S–pT–P)-containing phosphopeptides derived from L2 of HPV16/HPV18 (high-risk alphapapillomaviruses), HPV5b (low-risk betapapillomavirus), and HPV4 (low-risk gammapapillomavirus). Subsequent structural determination of the Plk1 PBD bound to the HPV18 or HPV4 L2-derived phosphopeptide demonstrated that they interact with each other in a canonical manner, in which electrostatic interactions and hydrogen bonds play key roles in sustaining the complex. Therefore, our structural and biochemical data imply that Plk1 is a broad binding target of L2 of various HPV genotypes belonging to the Alpha-, Beta-, and Gammapapillomavirus genera.

Review

Prions in Microbes: The Least in the Most: Moonil Son , Sia Han , Seyeon Lee; J. Microbiol. 2023;61(10):881-889. Published online September 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00070-4

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Abstract

Prions are infectious proteins that mostly replicate in self-propagating amyloid conformations (filamentous protein polymers) and consist of structurally altered normal soluble proteins. Prions can arise spontaneously in the cell without any clear reason and are generally considered fatal disease-causing agents that are only present in mammals. However, after the seminal discovery of two prions, [PSI+] and [URE3], in the eukaryotic model microorganism Saccharomyces cerevisiae, at least ten more prions have been discovered, and their biological and pathological effects on the host, molecular structure, and the relationship between prions and cellular components have been studied. In a filamentous fungus model, Podospora anserina, a vegetative incomparability-related [Het-s] prion that directly triggers cell death during anastomosis (hyphal fusion) was discovered. These prions in eukaryotic microbes have extended our understanding to overcome most fatal human prion/amyloid diseases. A prokaryotic microorganism (Clostridium botulinum) was reported to have a prion analog. The transcriptional regulators of C. botulinum-Rho can be converted into the self-replicating prion form ([RHO-X-C+]), which may affect global transcription. Here, we outline the major issues with prions in microbes and the lessons learned from the relatively uncovered microbial prion world.

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A Story Between s and S: [Het-s] Prion of the Fungus Podospora anserina
Moonil Son
Mycobiology.2024; 52(2): 85. CrossRef

Journal Articles

Tubulysins are Essential for the Preying of Ciliates by Myxobacteria: Uisang Yu , Jiha Kim , Seohui Park , Kyungyun Cho; J. Microbiol. 2023;61(6):627-632. Published online June 14, 2023; DOI: https://doi.org/10.1007/s12275-023-00056-2

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Abstract

Tubulysins are bioactive secondary metabolites produced by myxobacteria that promote microtubule disassembly. Microtubules are required for protozoa such as Tetrahymena to form cilia and flagella. To study the role of tubulysins in myxobacteria, we co-cultured myxobacteria and Tetrahymena. When 4000 Tetrahymena thermophila and 5.0 × 108 myxobacteria were added to 1 ml of CYSE medium and co-cultured for 48 h, the population of T. thermophila increased to more than 75,000. However, co-culturing tubulysin-producing myxobacteria, including Archangium gephyra KYC5002, with T. thermophila caused the population of T. thermophila to decrease from 4000 to less than 83 within 48 h. Almost no dead bodies of T. thermophila were observed in the culture medium. Co-culturing of T. thermophila and the A. gephyra KYC5002 strain with inactivation of the tubulysin biosynthesis gene led to the population of T. thermophila increasing to 46,667. These results show that in nature, most myxobacteria are preyed upon by T. thermophila, but some myxobacteria prey on and kill T. thermophila using tubulysins. Adding purified tubulysin A to T. thermophila changed the cell shape from ovoid to spherical and caused cell surface cilia to disappear.

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Tubulysin Production by the Dead Cells of Archangium gephyra KYC5002
Seohui Park, Chaehyeon Park, Yujin Ka, Kyungyun Cho
Journal of Microbiology.2024; 62(6): 463. CrossRef
Two reasons to kill: predation and kin discrimination in myxobacteria
Christine Kaimer, Michael L. Weltzer, Daniel Wall
Microbiology .2023;[Epub] CrossRef

Effects of Continuous Straw Returning on Soil Functional Microorganisms and Microbial Communities: Yunpeng Guan , Meikang Wu , Songhao Che , Shuai Yuan , Xue Yang , Siyuan Li , Ping Tian , Lei Wu , Meiying Yang , Zhihai Wu; J. Microbiol. 2023;61(1):49-62. Published online January 26, 2023; DOI: https://doi.org/10.1007/s12275-022-00004-6

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Abstract

This study examined the changes in soil enzymatic activity, microbial carbon source metabolic diversity, and straw decomposition rates in paddy fields treated with 1, 2, or 3 years of straw returning (SR1–SR3). The soil’s ability to decompose straw and cellulolytic bacteria increased with the number of treatment years (1: 31.9% vs. 2: 43.9% vs. 3: 51.9%, P < 0.05). The numbers of Azotobacter, Nitrobacteria, cellulolytic bacteria, and inorganic phosphate bacteria increased progressively with the numbers of straw returning years. Cellulolytic bacteria and inorganic phosphate bacteria were significantly positively correlated with the decomposition rate (r = 0.783 and r = 0.375, P < 0.05). Based on 16S sequencing results, straw returning improved the microbial diversity of paddy soils by increasing unclassified bacteria and keeping dominant soil microorganism populations unchanged. The relative importance of individual microbial taxa was compared using random forest models. Proteobacteria, ammoniating bacteria, and potassium dissolving bacteria contributed to peroxidase activity. The significant contributors to phosphate monoesterase were Acidobacteriota, Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria. Proteobacteria, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to urease activity. Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to the neutral invertase activity. In conclusion, soil microbial community structure and function were affected within 2 years of straw returning, which was driven by the combined effects of soil organic carbon, available nitrogen, available potassium, and pH. With elapsing straw returning years, soil properties interacted with soil microbial communities, and a healthier soil micro-ecological environment would form.

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The role of tillage practices in wheat straw decomposition and shaping the associated microbial communities in Endocalcaric– Epigleyic Cambisol soil
Arman Shamshitov, Gražina Kadžienė, Francesco Pini, Skaidrė Supronienė
Biology and Fertility of Soils.2025; 61(2): 211. CrossRef
Impact of straw returning on soil ecology and crop yield: A review
Vincent Ninkuu, Zhixin Liu, Aizhi Qin, Yajie Xie, Xiao Song, Xuwu Sun
Heliyon.2025; 11(2): e41651. CrossRef
The different pathways of microbial regulation of organic carbon turnover in the topsoil and subsoil of coastal saline soil after long-term stubble return and subsoiling
Xunya Su, Le Zhang, Hao Meng, Jiaxue Zhao, Han Wang, Lunxiao Shang, Qiyuan Guo, Yupeng Xing, Xianliang Song, Xuezhen Sun, Xiaopei Zhang, Xiaoli Tian, Lili Mao
Applied Soil Ecology.2025; 208: 105970. CrossRef
Long-Term Effects of Potassium Fertilization and Wheat Straw Return on Cropland Soil Fertility and Microorganisms in the Qinghai–Tibet Plateau
Tingting Xu, Rong Zhang, Yang Zhang, Xiaojun Wang, Zhengpeng Li, Yajun Gao
Agronomy.2025; 15(3): 742. CrossRef
Synergistic Effects of Rice Straw Return and Nitrogen Fertilizer on Rhizosphere Bacterial Communities and Soil Fertility
Nasita Rahman Borny, Golam Mohammod Mostakim, Asif Raihan, Md Shoaibur Rahman
Journal of Soil, Plant and Environment.2024; : 41. CrossRef
Vertical differences in carbon metabolic diversity and dominant flora of soil bacterial communities in farmlands
Bufan Zheng, Zhipeng Xiao, Jiaqi Liu, Yi Zhu, Kaifeng Shuai, Xiaye Chen, Yongjun Liu, Ruiwen Hu, Guangjue Peng, Junlin Li, Yichao Hu, Zan Su, Ming Fang, Juan Li
Scientific Reports.2024;[Epub] CrossRef
Microbial Network Complexity Helps to Reduce the Deep Migration of Chemical Fertilizer Nitrogen Under the Combined Application of Varying Irrigation Amounts and Multiple Nitrogen Sources
Taotao Chen, Erping Cui, Yanbo Zhang, Ge Gao, Hao You, Yurun Tian, Chao Hu, Yuan Liu, Tao Fan, Xiangyang Fan
Agriculture.2024; 14(12): 2311. CrossRef
Effects of Combined Peanut Shell and Biochar Application on Soil Nutrient Content, CO2 Emission, and Bacterial Community in Dryland Red Soil of Southern China
Xinyi Yu, Qian Wei, Meng Na, Chunjie Tian, Shangqi Xu, Jihai Zhou
Journal of Soil Science and Plant Nutrition.2024; 24(1): 219. CrossRef
Long-term in situ straw returning increased soil aggregation and aggregate associated organic carbon fractions in a paddy soil
Jiaren Liu, Xuehai Wang, Hu Zhang, Yifei Lu, Yusef Kianpoor Kalkhajeh, Hongxiang Hu, Jieying Huang
Heliyon.2024; 10(11): e32392. CrossRef
Agricultural ecosystems rather than fertilization strategies drives structure and composition of the ureolytic microbial functional guilds
Na Lv, Ping Gong, Hao Sun, Xiangxin Sun, Zhiguang Liu, Xueshi Xie, Yan Xue, Yuchao Song, Kaikuo Wu, Tingting Wang, Zhijie Wu, Lili Zhang
Journal of Environmental Management.2024; 372: 123148. CrossRef
Effects of Burial Furrow Parameters on Soil Water Movement under Subsurface Stalk Composite Pipe Irrigation
Feng Wu, Xuefang Feng, Xuemei Liu, Di Wu, Songmei Zai, Linbao Liu
Agriculture.2024; 14(2): 287. CrossRef
Improving Soil Quality and Crop Yields Using Enhancing Sustainable Rice Straw Management Through Microbial Enzyme Treatments
Van-Phuc Dinh, Hoai-An Tran-Vu, Thanh Tran, Bich-Ngoc Duong, Ngoc-Mai Dang-Thi, Hoai-Luan Phan-Van, Tuan-Kiet Tran, Van-Hieu Huynh, Thi-Phuong-Tu Nguyen, Thanh Q Nguyen
Environmental Health Insights.2024;[Epub] CrossRef
Improvement of Saline–Alkali Soil and Straw Degradation Efficiency in Cold and Arid Areas Using Klebsiella sp. and Pseudomonas sp.
Xiaoyu Zhao, Xiaofang Yu, Julin Gao, Jiawei Qu, Qinggeer Borjigin, Tiantian Meng, Dongbo Li
Agronomy.2024; 14(11): 2499. CrossRef
Successive Years of Rice Straw Return Increased the Rice Yield and Soil Nutrients While Decreasing the Greenhouse Gas Intensity
Meikang Wu, Min Nuo, Zixian Jiang, Ruiyao Xu, Hongcheng Zhang, Xiao Lu, Liqun Yao, Man Dou, Xu Xing, Xin Meng, Dongchao Wang, Xiaoshuang Wei, Ping Tian, Guan Wang, Zhihai Wu, Meiying Yang
Plants.2024; 13(17): 2446. CrossRef
The effects of straw return on soil bacterial diversity and functional profiles: A meta-analysis
Miaomiao Zhang, Pengfei Dang, Bart Haegeman, Xiaoqing Han, Xiaofan Wang, Xuan Pu, Xiaoliang Qin, Kadambot H.M. Siddique
Soil Biology and Biochemistry.2024; 195: 109484. CrossRef
Dissolved Organic Matters, an Intermediary of the Microbial Community and Potassium Fertilizers in A. carmichaeli rhizosphere Soil
Fei Xia, Meng Fu, Chen Liu, Yulong Li, Yi Qiang, Ding He, Guoyan Zhang, Langjun Cui
Journal of Soil Science and Plant Nutrition.2024; 24(3): 5472. CrossRef
Effects of Straw and Nitrogenous Fertilizers on the Soil Aggregate Stability and Quality in Subtropical Regions of China
Jia Yi Yang, Shahbaz Atta Tung, Jin Ting Xu, Yan Qiong Pan, Li Yang, Xun Bo Zhou
Journal of Soil Science and Plant Nutrition.2024; 24(3): 5988. CrossRef
Improved Straw Decomposition Products Promote Peanut Growth by Changing Soil Chemical Properties and Microbial Diversity
Yaxin Liu, Meng Wu, Jia Liu, Daming Li, Xiaoli Liu, Ling Chen, Xi Guo, Ming Liu
Sustainability.2024; 16(16): 7096. CrossRef
Effects of Different Tillage Measures Combined with Straw Returning on Soil Enzyme Activity and Microbial Community Structure and Diversity
Sa Xiao, Bing Li, Tingting Zhang, Jianzhu Luo, Jie Wang, Xiangqian Zhang, Juan Li, Dejian Zhang
Agriculture.2024; 15(1): 56. CrossRef
Straw Returning Measures Enhance Soil Moisture and Nutrients and Promote Cotton Growth
Min Tang, Rui Liu, Zhenhai Luo, Chao Zhang, Jiying Kong, Shaoyuan Feng
Agronomy.2023; 13(7): 1850. CrossRef

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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Abstract

The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

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Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production
Lufeng Chen, Guoyi Cheng, Zhengwen Zhou, Yong Liang, Zhijia Ci, Yongguang Yin, Guangliang Liu, Yong Cai, Yanbin Li
Water Research.2024; 258: 121792. CrossRef
Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef
Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples
Agata Anna Cisek, Iwona Bąk, Bożena Cukrowska
Microorganisms.2023; 11(3): 660. CrossRef

Helicobacter pylori-mediated gastric pathogenesis is attenuated by treatment of 2-deoxyglucose and metformin: Hanfu Su , Eun-Jung Bak , Aeryun Kim , Kavinda Tissera , Jeong-Heon Cha , Sungil Jang; J. Microbiol. 2022;60(8):849-858. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2130-z

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Abstract

Helicobacter pylori infection causes chronic inflammation in the stomach, which is linked to the development of gastric cancer. The anti-inflammatory and anticancer effects of a glycolysis inhibitor 2-deoxyglucose (2DG) and an antidiabetic medication metformin (Met) have gotten attention. Using a Mongolian gerbil animal model, we investigated H. pylorimediated gastric pathogenesis and how this pathogenesis is influenced by 2DG and Met. Five-week-old male gerbils were infected with H. pylori strain 7.13. After 2 weeks of infection, gerbils were fed 2DG-containing food (0.03% w/w), Met-containing water (0.5% w/v), or both (Combi) for 2 (short-term) or 10 weeks (long-term). Gastric pathogenesis and host response to H. pylori infection were examined by macroscopic and histopathologic analysis of gerbils’ stomach. As a result, indicators of gastric pathogenesis by H. pylori infection including infiltration of polymorphonuclear neutrophils and lymphocytes, intestinal metaplasia, atrophy, and proliferation of gastric epithelial cells were attenuated by short-term administration of 2DG, Met, or Combi. When the infection was sustained for long-term, gastric pathogenesis in drug-treated gerbils was equivalent to that in untreated gerbils, with the exception that the infiltration of neutrophil was reduced by 2DG. Colonization of H. pylori in stomach was unaffected by both short- and long-term treatments. Our findings demonstrate that the progression of gastric pathogenesis induced by H. pylori infection can be attenuated by the shortterm individual or combinational treatment of 2DG and Met, implying that 2DG or Met could be considered as a treatment option for gastric diseases in the early stages of infection.

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Antibacterial and Immunoregulatory Effects of Metformin against Helicobacter pylori Infection in Rat Model
Hassan Valadbeigi, Saeed Khoshnood, Babak Negahdari, Mohd Azmuddin Abdullah, Mohammad Hossein Haddadi, Abhimanyu Abhimanyu
BioMed Research International.2023;[Epub] CrossRef
Effect of Metformin on the Prognosis of Gastric Cancer Patients with Type 2 Diabetes Mellitus: A Meta-Analysis Based on Retrospective Cohort Studies
Lingna Li, Jianing Huang, Tongmin Huang, Jie Yao, Yeyuan Zhang, Meiling Chen, Haojie Shentu, Haiying Lou, Flavia Prodam
International Journal of Endocrinology.2023; 2023: 1. CrossRef

Assessment of Cre-lox and CRISPR-Cas9 as tools for recycling of multiple-integrated selection markers in Saccharomyces cerevisiae: Hye Yun Moon† , Gyu Hun Sim† , Hyeon Jin Kim , Keunpil Kim , Hyun Ah Kang; J. Microbiol. 2022;60(1):18-30. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1580-7

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Abstract

We evaluated the Cre-lox and CRISPR-Cas9 systems as markerrecycling tools in Saccharomyces cerevisiae recombinants containing multiple-integrated expression cassettes. As an initial trial, we constructed rDNA-nontranscribed spacer- or Ty4- based multiple integration vectors containing the URA3 marker flanked by the loxP sequence. Integrants harboring multiple copies of tHMG1 and NNV-CP expression cassettes were obtained and subsequently transformed with the Cre plasmid. However, the simultaneous pop-out of the expression cassettes along with the URA3 marker hampered the use of Cre-lox as a marker-recycling tool in multiple integrants. As an alternative, we constructed a set of CRISPR-Cas9-gRNA vectors containing gRNA targeted to auxotrophic marker genes. Transformation of multiple integrants of tHMG1 and NNV-CP cassettes by the Cas9-gRNA vector in the presence of the URA3 (stop) donor DNA fragments generated the Ura- transformants retaining multiple copies of the expression cassettes. CRISPR-Cas9-based inactivation led to the recycling of the other markers, HIS3, LEU2, and TRP1, without loss of expression cassettes in the recombinants containing multiple copies of tHMG1, NNV-CP, and SfBGL1 cassettes, respectively. Reuse of the same selection marker in marker-inactivated S. cerevisiae was validated by multiple integrations of the TrEGL2 cassette into the S. cerevisiae strain expressing SfBGL1. These results demonstrate that introducing stop codons into selection marker genes using the CRISPR-Cas9 system with donor DNA fragments is an efficient strategy for markerrecycling in multiple integrants. In particular, the continual reuse of auxotrophic markers would facilitate the construction of a yeast cell factory containing multiple copies of expression cassettes without antibiotic resistance genes.

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Multiple metabolic engineering of Saccharomyces cerevisiae for the production of lycopene
Jiaheng Liu, Minxia Song, Xianhao Xu, Yaokang Wu, Yanfeng Liu, Guocheng Du, Jianghua Li, Long Liu, Xueqin Lv
Food Bioengineering.2024;[Epub] CrossRef
Biochemical and Biorefinery Platform for Second-Generation Bioethanol: Fermentative Strategies and Microorganisms
Karla D. González-Gloria, Elia Tomás-Pejó, Lorena Amaya-Delgado, Rosa M. Rodríguez-Jasso, Araceli Loredo-Treviño, Anusuiya Singh, Meenu Hans, Carlos Martín, Sachin Kumar, Héctor A. Ruiz
Fermentation.2024; 10(7): 361. CrossRef
CRISPR/Cas9-based toolkit for rapid marker recycling and combinatorial libraries in Komagataella phaffii
Wei Zhou, Yuanyi Li, Guosong Liu, Weichuang Qin, Dongzhi Wei, Fengqing Wang, Bei Gao
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef
Establishment, optimization, and application of genetic technology in Aspergillus spp.
Jing Gao, Huiqing Liu, Zhenzhen Zhang, Zhihong Liang
Frontiers in Microbiology.2023;[Epub] CrossRef
CRISPR-Cas Technology for Bioengineering Conventional and Non-Conventional Yeasts: Progress and New Challenges
Yuanyuan Xia, Yujie Li, Wei Shen, Haiquan Yang, Xianzhong Chen
International Journal of Molecular Sciences.2023; 24(20): 15310. CrossRef
Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products
Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-joo Jeon, Che Ok Jeon, Seong-il Eyun, Hyun Ah Kang
FEMS Yeast Research.2023;[Epub] CrossRef
Multiplex genome editing to construct cellulase engineered Saccharomyces cerevisiae for ethanol production from cellulosic biomass
Yatika Dixit, Preeti Yadav, Arun Kumar Sharma, Poornima Pandey, Arindam Kuila
Renewable and Sustainable Energy Reviews.2023; 187: 113772. CrossRef

Function of Rhs proteins in porcine extraintestinal pathogenic Escherichia coli PCN033: Wenjia Lu , Jia Tan , Hao Lu , Gaoyan Wang , Wenqi Dong , Chenchen Wang , Xiaodan Li , Chen Tan; J. Microbiol. 2021;59(9):854-860. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1189-2

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Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen that places severe burdens on public health and animal husbandry. There are many pathogenic factors in E. coli. The type VI secretion system (T6SS) is a nano-microbial weapon that can assemble quickly and inject toxic effectors into recipient cells when danger is encountered. T6SSs are encoded in the genomes of approximately 25% of sequenced Gram-negative bacteria. When these bacteria come into contact with eukaryotic cells or prokaryotic microbes, the T6SS assembles and secretes associated effectors. In the porcine ExPEC strain PCN033, we identified four classic rearrangement hotspot (Rhs) genes. We determined the functions of the four Rhs proteins through mutant construction and protein expression. Animal infection experiments showed that the Δrhs-1CT, Δrhs-2CT, Δrhs-3CT, and Δrhs-4CT caused a significant decrease in the multiplication ability of PCN033 in vivo. Cell infection experiments showed that the Rhs protein is involved in anti-phagocytosis activities and bacterial adhesion and invasion abilities. The results of this study demonstrated that rhs1, rhs3, and rh4 plays an important role in the interaction between PCN033 and host cell. Rhs2 has contribution to cell and mice infection. This study helps to elucidate the pathogenic mechanism governing PCN033 and may help to establish a foundation for further research seeking to identify potential T6SS effectors.

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Molecular characterization of the integrative and conjugative elements harbouring multidrug resistance genes in Glaesserella parasuis
Yongliang Che, Renjie Wu, Hongjie Li, Longbai Wang, Xuemin Wu, Qiuyong Chen, Rujing Chen, Lunjiang Zhou
Veterinary Microbiology.2024; 291: 110014. CrossRef
Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing usin
Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou, Qi Huang
Virulence.2023;[Epub] CrossRef
Dual RNA-Seq of Flavobacterium psychrophilum and Its Outer Membrane Vesicles Distinguishes Genes Associated with Susceptibility to Bacterial Cold-Water Disease in Rainbow Trout (Oncorhynchus mykiss)
Pratima Chapagain, Ali Ali, Mohamed Salem
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Distribution and diversity of type VI secretion system clusters in Enterobacter bugandensis and Enterobacter cloacae
Amy J. G. Anderson, Becca Morrell, Guillermo Lopez Campos, Miguel A. Valvano
Microbial Genomics .2023;[Epub] CrossRef

Different distribution patterns of microorganisms between aquaculture pond sediment and water: Lili Dai , Chengqing Liu , Liang Peng , Chaofeng Song , Xiaoli Li , Ling Tao; J. Microbiol. 2021;59(4):376-388. Published online February 25, 2021; DOI: https://doi.org/10.1007/s12275-021-0635-5

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Abstract

Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.

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Arcadius Martinien Agassin Ahogle, Nicholas K. Korir, Pascal Houngnandan, Lina Abu-Ghunmi, Sammy Letema
International Journal of Environmental Studies.2024; 81(4): 1836. CrossRef
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Reviews

The osmotic stress response operon betIBA is under the functional regulation of BetI and the quorum-sensing regulator AnoR in Acinetobacter nosocomialis: Bindu Subhadra , Surya Surendran , Bo Ra Lim , Jong Sung Yim , Dong Ho Kim , Kyungho Woo , Hwa-Jung Kim , Man Hwan Oh , Chul Hee Choi; J. Microbiol. 2020;58(6):519-529. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0186-1

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Abstract

Adaptation to changing environmental conditions is crucial for the survival of microorganisms. Bacteria have evolved various mechanisms to cope with osmotic stress. Here, we report the identification and functional characterization of the osmotic stress response operon, betIBA, in Acinetobacter nosocomialis. The betIBA operon encodes enzymes that are important for the conversion of choline to the osmoprotectant, glycine betaine. The betIBA operon is polycistronic and is under the regulation of the first gene, betI, of the same operon. A bioinformatics analysis revealed the presence of a BetI-binding motif upstream of the betIBA operon, and electrophoretic mobility shift assays confirmed the specific binding of BetI. An mRNA expression analysis revealed that expression of betI, betB, and betA genes is elevated in a betIeletion mutant compared with the wild type, confirming that the autorepressor BetI represses the betIBA operon in A. nosocomialis. We further found that the betIBA operon is under the transcriptional control of the quorum-sensing (QS) regulator, AnoR in, A. nosocomialis. A subsequent analysis of the impact of BetI on expression of the QS genes, anoR and anoI, demonstrated that BetI acts as a repressor of anoR and anoI. In addition, it was noticed that the osmotic stress response regulator, OmpR might play an important role in controlling the expression of betIBA operon in A. nosocomialis. Collectively, these data demonstrate that QS and osmotic stress-response systems are correlated in A. nosocomialis and that the expression of genes in both systems is finely tuned by various feedback loops depending on osmolarity conditions.

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MINIREVIEW] Fungi in salterns: Dawoon Chung† , Haryun Kim† , Hyun Seok Choi; J. Microbiol. 2019;57(9):717-724. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9195-3

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Abstract

Salterns are hypersaline extreme environments with unique physicochemical properties such as a salinity gradient. Although the investigation of microbiota in salterns has focused on archaea and bacteria, diverse fungi also thrive in the brine and soil of salterns. Fungi isolated from salterns are represented by black yeasts (Hortaea werneckii, Phaeotheca triangularis, Aureobasidium pullulans, and Trimmatostroma salinum), Cladosporium, Aspergillus, and Penicillium species. Most studies on saltern-derived fungi gave attention to black yeasts and their physiological characteristics, including growth under various culture conditions. Since then, biochemical and molecular tools have been employed to explore adaptation of these fungi to salt stress. Genome databases of several fungi in salterns are now publicly available and being used to elucidate salt tolerance mechanisms and discover the target genes for agricultural and industrial applications. Notably, the number of enzymes and novel metabolites known to be produced by diverse saltern-derived fungi has increased significantly. Therefore, fungi in salterns are not only interesting and important subjects to study fungal biodiversity and adaptive mechanisms in extreme environments, but also valuable bioresources with potential for biotechnological applications.

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Journal Articles

Screening and identification of Aspergillus activity against Xanthomonas oryzae pv. oryzae and analysis of antimicrobial components: Bei Jiang , Zhiying Wang , Chuxuan Xu , Weijia Liu , Donghua Jiang; J. Microbiol. 2019;57(7):597-605. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8330-5

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Abstract

To screen for Aspergillus activity against Xanthomonas oryzae pv. oryzae and analyse the antimicrobial components involved, 60 Aspergillus spp. were isolated and purified from fruits, soil and other habitats. As-75, an Aspergillus strain that can antagonize Xanthomonas oryzae pv. oryzae, was identified based on the zone of inhibition formed during co-culture. According to morphological, ITS rDNA gene sequencing and phylogenetic tree results, the strain showed close homology to Aspergillus sclerotiorum. The biochemical characterization tests showed that the fermentation broth of strain As-75 exhibited a high capacity for environmental adaptation. The results of the antimicrobial spectrum experiments demonstrated that As-75 exhibited fairly strong antagonistic activity against five plant pathogenic fungi and six plant pathogenic bacteria in vitro. The fermentation broth of strain As-75 displayed maximum stability under fluorescent illumination at temperatures below 60°C at pH 6.5. A substance with antagonistic activity was obtained from strain As-75 via fractional extraction, silica gel column chromatography and thinlayer chromatography. Through mass spectrometry, nuclear magnetic resonance and electrospray ionization mass spectrometry (ESI-MS) analyses, the target compound was identified as (2Z)-2-butenedioic acid-2-(1-methylethenyl)-4-methyl ester; its molecular weight of 170.06 daltons and formula of C8H10O4 identify it as a novel compound. Trials of the preventative and curative effects demonstrated that compound S1 exhibited a better control efficiency than the control against rice bacterial blight. Additionally, the M1 processing
method
was better, and the efficiency of compound S1 in preventing rice bacterial blight in six rice varieties, TN1, IR24, ZF802, Zhonghua 11, Wuyunjing 21, and Nipponbare, was 78.3%, 77.5%, 74.2%, 75.3%, 70.9%, and 72.1%, respectively.

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Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model: Katherine D. Mueller , Hao Zhang , Christian R. Serrano , R. Blake Billmyre , Eun Young Huh , Philipp Wiemann , Nancy P. Keller , Yufeng Wang , Joseph Heitman , Soo Chan Lee; J. Microbiol. 2019;57(6):509-520. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8682-x

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Abstract

Mucor circinelloides is a pathogenic fungus and etiologic agent of mucormycosis. In 2013, cases of gastrointestinal illness after yogurt consumption were reported to the US FDA, and the producer found that its products were contaminated with Mucor. A previous study found that the Mucor strain isolated from an open contaminated yogurt exhibited virulence in a murine systemic infection model and showed that this strain is capable of surviving passage through the gastrointestinal tract of mice. In this study, we isolated another Mucor strain from an unopened yogurt that is closely related but distinct from the first Mucor strain and subsequently examined if Mucor alters the gut microbiota in a murine host model. DNA extracted from a ten-day course of stool samples was used to analyze the microbiota in the gastrointestinal tracts of mice exposed via ingestion of Mucor spores. The bacterial 16S rRNA gene and fungal ITS1 sequences obtained were used to identify taxa of each kingdom. Linear regressions revealed that there are changes in bacterial and fungal abundance in the gastrointestinal tracts of mice which ingested Mucor. Furthermore, we found an increased abundance of the bacterial genus Bacteroides and a decreased abundance of the bacteria Akkermansia muciniphila in the gastrointestinal tracts of exposed mice. Measurements of abundances show shifts in relative levels of multiple bacterial and fungal taxa between mouse groups. These findings suggest that exposure of the gastrointestinal tract to Mucor can alter the microbiota and, more importantly, illustrate an interaction between the intestinal mycobiota and bacteriota. In addition, Mucor was able to induce increased permeability in epithelial cell monolayers in vitro, which might be indicative of unstable intestinal barriers. Understanding how the gut microbiota is shaped is important to understand the basis of potential methods of treatment for gastrointestinal illness. How the gut microbiota changes in response to exposure, even by pathogens not considered to be causative agents of food-borne illness, may be important to how commercial food producers prevent and respond to contamination of products aimed at the public. This study provides evidence that the fungal microbiota, though understudied, may play an important role in diseases of the human gut.

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A Novel Resistance Pathway for Calcineurin Inhibitors in the Human-Pathogenic Mucorales Mucor circinelloides
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Transcriptome analysis of differential gene expression in Dichomitus squalens during interspecific mycelial interactions and the potential link with laccase induction: Zixuan Zhong , Nannan Li , Binghui He , Yasuo Igarashi , Feng Luo; J. Microbiol. 2019;57(2):127-137. Published online September 13, 2018; DOI: https://doi.org/10.1007/s12275-019-8398-y

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Abstract

Interspecific mycelial interactions between white rot fungi are always accompanied by an increased production of laccase. In this study, the potential of the white rot fungus Dichomitus squalens to enhance laccase production during interactions with two other white rot fungi, Trametes versicolor or Pleurotus ostreatus, was assessed. To probe the mechanism of laccase induction and the role that laccase plays during combative interaction, we analyzed the differential gene expression profile of the laccase induction response to stressful conditions during fungal interaction. We further confirmed the expression patterns of 16 selected genes by qRT-PCR analysis. We noted that many differentially expressed genes (DEGs) encoded proteins that were involved in xenobiotic detoxification and reactive oxygen species (ROS) generation or reduction, including aldo/keto reductase, glutathione S-transferases, cytochrome P450 enzymes, alcohol oxidases and dehydrogenase, manganese peroxidase and laccase. Furthermore, many DEG-encoded proteins were involved in antagonistic mechanisms of nutrient acquisition and antifungal properties, including glycoside hydrolase, glucanase, chitinase and terpenoid synthases. DEG analyses effectively revealed that laccase induction was likely caused by protective responses to oxidative stress and nutrient competition during interspecific fungal interactions.

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