Journal of Microbiology

Journal Articles

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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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

Influence of dragon bamboo with different planting patterns on microbial community and physicochemical property of soil on sunny and shady slopes: Weiyi Liu , Fang Wang , Yanmei Sun , Lei Yang , Huihai Chen , Weijie Liu , Bin Zhu , Chaomao Hui , Shiwei Wang; J. Microbiol. 2020;58(11):906-914. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0082-8

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Abstract

Dragon bamboo (Dendrocalamus giganteus) is a giant sympodial bamboo species widely distributed in Asia. However, it remains unclear how dragon bamboo and soil microbes interact to affect soil properties. In this study, we investigated the planting patterns (semi-natural and artificial) on different slopes (sunny and shady) to determine the effects on soil properties and microbial community. The results showed that the soil in which dragon bamboo was grown was acidic, with a pH value of ~5. Also, the soil organic matter content, nitrogen hydrolysate concentration, total nitrogen, available potassium, and total potassium of the dragon bamboo seminatural forest significantly improved, especially on the sunny slope. In contrast, the available phosphorus level was higher in the artificial bamboo forest, probably owing to the phosphate fertilizer application. The bacterial and fungal diversity and the bacterial abundance were all higher on the sunny slope of the semi-natural forest than those in the other samples. The microbial operational taxonomic units (OTUs) shared between the shady and sunny slopes accounted for 47.8–62.2%, but the core OTUs of all samples were only 24.4– 30.4% of each sample, suggesting that the slope type had a significant effect on the microbial community. Some acidophilic microbes, such as Acidobacteria groups, Streptomyces and Mortierella, became dominant in dragon bamboo forest soil. A PICRUSt analysis of the bacterial functional groups revealed that post-translational modification, cell division, and coenzyme transport and metabolism were abundant in the semi-natural forest. However, some microorganisms with strong stress resistance might be activated in the artificial forest. Taken together, these results illustrated the influence of dragon bamboo growth on soil physicochemical property and microbial community, which might help understand the growth status of dragon bamboo under different planting patterns.

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Characteristic Analysis of the Soil Bacterial Community Structure of Dendrocalamus brandisii from Seven Geographical Provenances in Yunnan Province
Qian Chen, Manyun Zhang, Negar Omidvar, Zhihong Xu, Shahla Hosseini Bai, Chaomao Hui, Weiyi Liu
Agronomy.2024; 14(9): 2010. CrossRef
Unveiling the impacts moso bamboo invasion on litter and soil properties: A meta-analysis
Weixue Luo, Qingyu Zhang, Peng Wang, Jie Luo, Chunyan She, Xuman Guo, Jiajia Yuan, Yuhong Sun, Ruming Guo, Zongfeng Li, Jinchun Liu, Jianping Tao
Science of The Total Environment.2024; 909: 168532. CrossRef
Transport, pollution, and health risk of heavy metals in “soil-medicinal and edible plant-human” system: A case study of farmland around the Beiya mining area in Yunnan, China
Jiayi Hu, Xiaofang Yang, Huajian Chi, Xin Liu, Ning Lu, Ya Liu, Shengchun Yang, Xiaodong Wen
Microchemical Journal.2024; 207: 111958. CrossRef
Microbial control of soil DOM transformation during the vegetation restoration in the Loess Plateau
Wenxin Chen, Qianqian Gao, Huaying Hu, Tingwei Shao, Chuifan Zhou
Plant and Soil.2024; 504(1-2): 385. CrossRef
Soil Bacterial Community Response to Fire Varies with Slope Aspect at Zhenshan Mountain, East China
Ping Zhu, Wenyan Liu, Zhongyuan Sun, Xinfu Bai, Jianqiang Song, Nan Wu, Yuping Hou
Eurasian Soil Science.2023; 56(5): 599. CrossRef
Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau
Zhijia Cui, Ran Li, Fan Li, Ling Jin, Haixu Wu, Chunya Cheng, Yi Ma, Zhenheng Wang, Yuanyuan Wang
Frontiers in Microbiology.2023;[Epub] CrossRef
Effects of different planting durations of Dendrocalamus brandisii on the soil bacterial community
Shuhong Zhu, Xiuting Zhao, Chaomao Hui, Zhongfu Zhang, Ruli Zhang, Weihan Su, Weiyi Liu
Journal of Soils and Sediments.2023; 23(11): 3891. CrossRef
Correlates of Rhizosphere Soil Properties, Fungal Community Composition, and Active Secondary Metabolites in Cornus officinalis in Different Regions of China
Haoqiang Sun, Binkai Han, Xiaolin Yang, Changfen He, Ke Zhao, Ting Wang, Shujing An, Xiaochang Xue, Jiefang Kang
Journal of Soil Science and Plant Nutrition.2023; 23(1): 514. CrossRef
Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community
Pei Cao, Xuemin Wei, Gang Wang, Xiaochen Chen, Jianping Han, Yuan Li
Chinese Herbal Medicines.2022; 14(1): 58. CrossRef
Heterotrophic Bacteria Play an Important Role in Endemism of Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007, a Full-Year Shooting Woody Bamboo
Tize Xia, Lushuang Li, Bin Li, Peitong Dou, Hanqi Yang
Forests.2022; 13(1): 121. CrossRef

Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles: Federica De Lise , Francesca Mensitieri , Giulia Rusciano , Fabrizio Dal Piaz , Giovanni Forte , Flaviana Di Lorenzo , Antonio Molinaro , Armando Zarrelli , Valeria Romanucci , Valeria Cafaro , Antonio Sasso , Amelia Filippelli , Alberto Di Donato , Viviana Izzo; J. Microbiol. 2019;57(6):498-508. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8483-2

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Abstract

Outer membrane vesicles (OMVs) are nanostructures of 20– 200 nm diameter deriving from the surface of several Gramnegative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical “fingerprint”, suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.

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Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae
Fangfang Fan, Guangzhang Chen, Siqian Deng, Li Wei, Mariola J. Ferraro
Microbiology Spectrum.2024;[Epub] CrossRef
LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes
Ana Segura, Lázaro Molina
Frontiers in Microbiology.2023;[Epub] CrossRef
Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid
Aline Belmok, Felipe Marques de Almeida, Rodrigo Theodoro Rocha, Carla Simone Vizzotto, Marcos Rogério Tótola, Marcelo Henrique Soller Ramada, Ricardo Henrique Krüger, Cynthia Maria Kyaw, Georgios J. Pappas
Brazilian Journal of Microbiology.2023; 54(1): 239. CrossRef
Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer
Federica Dell’Annunziata, Carmela Dell’Aversana, Nunzianna Doti, Giuliana Donadio, Fabrizio Dal Piaz, Viviana Izzo, Anna De Filippis, Marilena Galdiero, Lucia Altucci, Giovanni Boccia, Massimiliano Galdiero, Veronica Folliero, Gianluigi Franci
International Journal of Molecular Sciences.2021; 22(16): 8732. CrossRef

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

Morphological changes in human gastric epithelial cells induced by nuclear targeting of Helicobacter pylori urease subunit A: Jung Hwa Lee , So Hyun Jun , Jung-Min Kim , Seung Chul Baik , Je Chul Lee; J. Microbiol. 2015;53(6):406-414. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5085-5

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Abstract

Nuclear targeting of bacterial proteins and their pathological effects on host cells are an emerging pathogenic mechanism in bacteria. We have previously reported that urease subunit A (UreA) of Helicobacter pylori targets the nuclei of COS-7 cells through nuclear localization signals (NLSs). This study further investigated whether UreA of H. pylori targets the nuclei of gastric epithelial cells and then induces molecular and cellular changes in the host cells. H. pylori 26695 strain produced and secreted outer membrane vesicles (OMVs). UreA was translocated into gastric epithelial AGS cells through outer membrane vesicles (OMVs) and then targeted the nuclei of AGS cells. Nuclear targeting of rUreA did not induce host cell death, but resulted in morphological changes, such as cellular elongation, in AGS cells. In contrast, AGS cells treated with rUreAΔNLS proteins did not show this morphological change. Next generation sequencing revealed that nuclear targeting of UreA differentially regulated 102 morphogenesis- related genes, of which 67 and 35 were up-regulated and down-regulated, respectively. Our results suggest that nuclear targeting of H. pylori UreA induces both molecular and cellular changes in gastric epithelial cells.

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Effects of Exosomes Derived From Helicobacter pylori Outer Membrane Vesicle-Infected Hepatocytes on Hepatic Stellate Cell Activation and Liver Fibrosis Induction
Masoumeh Ebadi Zahmatkesh, Mariyeh Jahanbakhsh, Negin Hoseini, Saina Shegefti, Amir Peymani, Hossein Dabin, Rasoul Samimi, Shahin Bolori
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Significance of Helicobacter pylori and Its Serological Typing in Gastric Cancer
碧玉张
Advances in Clinical Medicine.2022; 12(12): 11694. CrossRef
Rational Development of Bacterial Ureases Inhibitors
Saurabh Loharch, Łukasz Berlicki
The Chemical Record.2022;[Epub] CrossRef
Emerging therapeutic targets for gastric cancer from a host-Helicobacter pylori interaction perspective
Esmat Abdi, Saeid Latifi-Navid, Fatemeh Abedi Sarvestani, Mohammad Hassan Esmailnejad
Expert Opinion on Therapeutic Targets.2021; 25(8): 685. CrossRef
Non-enzymatic properties of Proteus mirabilis urease subunits
Valquiria Broll, Ana Paula A. Perin, Fernanda C. Lopes, Anne Helene S. Martinelli, Natalia R. Moyetta, Leonardo L. Fruttero, Matheus V.C. Grahl, Augusto F. Uberti, Diogo R. Demartini, Rodrigo Ligabue-Braun, Celia R. Carlini
Process Biochemistry.2021; 110: 263. CrossRef
Nuclear trafficking of bacterial effector proteins
Lena Hoang My Le, Le Ying, Richard L. Ferrero
Cellular Microbiology.2021;[Epub] CrossRef
Proteus mirabilis Urease: Unsuspected Non-Enzymatic Properties Relevant to Pathogenicity
Matheus V. C. Grahl, Augusto F. Uberti, Valquiria Broll, Paula Bacaicoa-Caruso, Evelin F. Meirelles, Celia R. Carlini
International Journal of Molecular Sciences.2021; 22(13): 7205. CrossRef
Helicobacter pylori Outer Membrane Vesicles and Extracellular Vesicles from Helicobacter pylori-Infected Cells in Gastric Disease Development
María Fernanda González, Paula Díaz, Alejandra Sandoval-Bórquez, Daniela Herrera, Andrew F. G. Quest
International Journal of Molecular Sciences.2021; 22(9): 4823. CrossRef
Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging
Stephanie K. Cohen, Marie‐Stéphanie Aschtgen, Jonathan B. Lynch, Sabrina Koehler, Fangmin Chen, Stéphane Escrig, Jean Daraspe, Edward G. Ruby, Anders Meibom, Margaret McFall‐Ngai
Cellular Microbiology.2020;[Epub] CrossRef
Role of Probiotics in Prophylaxis of Helicobacter pylori Infection
Kashyapi Chakravarty, Smriti Gaur
Current Pharmaceutical Biotechnology.2019; 20(2): 137. CrossRef
Helicobacter pylori: molecular basis for colonization and survival in gastric environment and resistance to antibiotics. A short review
Sharmila Fagoonee, Rinaldo Pellicano
Infectious Diseases.2019; 51(6): 399. CrossRef
Cross‐Reactivity of Polyclonal Antibodies against Canavalia ensiformis (Jack Bean) Urease and Helicobacter pylori Urease Subunit A Fragments
Zbigniew Jerzy Kaminski, Inga Relich, Iwona Konieczna, Wieslaw Kaca, Beata Kolesinska
Chemistry & Biodiversity.2018;[Epub] CrossRef
Ureases: Historical aspects, catalytic, and non-catalytic properties – A review
Karine Kappaun, Angela Regina Piovesan, Celia Regina Carlini, Rodrigo Ligabue-Braun
Journal of Advanced Research.2018; 13: 3. CrossRef
The Impact of Helicobacter pylori Urease upon Platelets and Consequent Contributions to Inflammation
Adriele Scopel-Guerra, Deiber Olivera-Severo, Fernanda Staniscuaski, Augusto F. Uberti, Natália Callai-Silva, Natália Jaeger, Bárbara N. Porto, Celia R. Carlini
Frontiers in Microbiology.2017;[Epub] CrossRef
A New Role for Helicobacter pylori Urease: Contributions to Angiogenesis
Deiber Olivera-Severo, Augusto F. Uberti, Miguel S. Marques, Marta T. Pinto, Maria Gomez-Lazaro, Céu Figueiredo, Marina Leite, Célia R. Carlini
Frontiers in Microbiology.2017;[Epub] CrossRef

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