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In situ identification of environmental microorganisms with Raman spectroscopy

environmental Science and Ecotechnology 2022年第3期11卷 102-113页

作者： Dongyu Cui Lingchao Kong Yi Wang Yuanqing Zhu Chuanlun Zhang Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou511458China Department of Ocean Science and Engineering Southern University of Science and TechnologyShenzhen518055China State environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control School of Environmental Science&EngineeringSouthern University of Science and TechnologyShenzhen518055China Shenzhen Key Laboratory of Marine Archaea Geo-Omics University of Southern University of Science and TechnologyShenzhen518055China Shanghai Sheshan National Geophysical Observatory Shanghai Earthquake AgencyShanghai200062China

microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment.However,it is challenging to delineate environmental microbes'actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated.Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells.It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ.The first part of this review introduces the principles,advantages,progress,and analytical methods of Raman spectroscopy applied in environmental microbiology.The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing(SIP),fluorescence in situ hybridization(FISH),Raman-activated cell sorting and genomic sequencing,and machine learning in microbiological studies.Finally,this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms,especially for uncultured microorganisms.

关键词： Raman spectroscopy environmental microorganisms Single cells Metabolic activities

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Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines

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Chinese Herbal Medicines 2024年第2期16卷 190-203页

作者： Yue Ouyang Qiqing Cheng Chunsong Cheng Ziyu Tang Yufeng Huang Eyu Tan Shaofeng Ma Xinheng Lin Ying Xie Hua Zhou Guangdong Provincial Hospital of Chinese Medicine Guangdong Provincial Academy of Chinese Medical SciencesState Key Laboratory of Dampness Syndrome of Chinese MedicineSecond Affiliated Hospital of Guangzhou University of Chinese MedicineGuangdong-Hong Kong-Macao Joint Lab on Chinese Medicine and Immune Disease ResearchGuangzhou 510006China Faculty of Chinese Medicine Macao University of Science and TechnologyMacao 999078China School of Pharmacy Hubei University of Science and TechnologyXianning 437100China Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant Lushan Botanical GardenChinese Academy of SciencesJiujiang 332900China Jiangmen Wuyi Hospital of Traditional Chinese Medicine Jiangmen 529020China Joint Laboratory for Translational Cancer Research of Chinese Medicine Ministry of EducationGuangzhou University of Chinese MedicineGuangzhou 510006China

Microbial resource influences the life activities of medicinal plants from several perspectives.Endophytes,rhizosphere microorganisms,and other environmental microorganisms play essential roles in medicinal plant growth and development,plant yield,and clinical efficacy.The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways.They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites.microorganisms can interact with their host plants to produce long-term,targeted selection results and improve their ability to adapt to the environment.Due to the interdependence and interaction between microorganisms and medicinal plants,Chinese herbal medicines(CHMs)quality is closely related to the associated microorganisms.This review summarizes the relationship between medicinal plants and their associated microorganisms,including their species,distribution,life activities,and metabolites.microorganisms can aid in quality control,improve the efficacy of medicinal plants,and provide markers for identifying the origin and storage time of CHMs.Therefore,a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.

关键词： Chinese herbal medicines endophytes environmental microorganisms microbiota rhizosphere microorganisms

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Application of Biological Nanopore Sequencing Technology in the Detection of microorganisms

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Chinese Journal of Chemistry 2023年第23期41卷 3473-3483页

作者： Ming-Qian Zhang Xiao-Bin Huang Hai-Chen Wu Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living BiosystemsInstitute of ChemistryChinese Academy of SciencesBeijing100190 China University of Chinese Academy of Sciences Beijing100049 China

environmental pollution and the spread of pathogenic microorganisms pose a significant threat to the health of humans and the planet.Thus,understanding and detecting microorganisms is crucial for maintaining a healthy living environment.Nanopore sequencing is a single-molecule detection method developed in the 1990s that has revolutionized various research fields.It offers several advantages over traditional sequencing methods,including low cost,label-free,time-saving detection speed,long sequencing reading,real-time monitoring,convenient carrying,and other significant advantages.In this review,we summarize the technical principles and characteristics of nanopore sequencing and discuss its applications in amplicon sequencing,metagenome sequencing,and whole-genome sequencing of environmental microorganisms,as well as its in situ application under some special circumstances.We also analyze the advantages and challenges of nanopore sequencing in microbiology research.Overall,nanopore sequencing has the potential to greatly enhance the detection and understanding of microorganisms in environmental research,but further developments are needed to overcome the current challenges.

关键词： Nanopore sequencing technology environmental microorganisms Amplicon sequencing Metagenome sequencing Whole genome sequencing Gene technology Ion channels Nucleic acids

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