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Dergham Y, Le Coq D, Bridier A, Sanchez-Vizuete P, Jbara H, Deschamps J, Hamze K, Yoshida KI, Noirot-Gros MF, Briandet R. Bacillus subtilis NDmed, a model strain for biofilm genetic studies. Biofilm 2023; 6:100152. [PMID: 37694162 PMCID: PMC10485040 DOI: 10.1016/j.bioflm.2023.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/20/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.
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Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hadi Jbara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Chen Y, Liu Y, Li X, He Y, Li W, Peng Y, Zheng J. Recent Advances in Mass Spectrometry-Based Spatially Resolved Molecular Imaging of Drug Disposition and Metabolomics. Drug Metab Dispos 2023; 51:1273-1283. [PMID: 37295949 DOI: 10.1124/dmd.122.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/04/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Mass spectrometric imaging is a nontargeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables qualitative and quantitative analyses of biologic tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization mass spectrometry, secondary ion mass spectrometry, desorption electrospray ionization mass spectrometry, laser ablation electrospray ionization mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. SIGNIFICANCE STATEMENT: The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge may benefit the development of new drugs and provide a better understanding of biochemical processes related to physiology and diseases.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ximei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Yan He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
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Nayana RUK, Nakkeeran S, Saranya N, Saravanan R, Mahendra K, Ashraf S, Perveen K, Alshaikh NA, Sayyed RZ, Show PL. Triamcinolone Acetonide Produced by Bacillus velezensis YEBBR6 Exerts Antagonistic Activity Against Fusarium oxysporum f. sp. Cubense: A Computational Analysis. Mol Biotechnol 2023:10.1007/s12033-023-00797-w. [PMID: 37556108 DOI: 10.1007/s12033-023-00797-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/10/2023]
Abstract
Fusarium oxysporum f. sp. cubense is one of the most severe and threatening pathogens of bananas, causing "Panama wilt" worldwide. Confrontation assay of Foc antagonistic bacterial endophyte, Bacillus velezensis YEBBR6, with the Foc and GC-MS profiling of excised agar from the zone of inhibition, led to the unveiling of secondary metabolites produced by the endophyte. To refine the probable antifungal compounds among the numerous biomolecules formed during their di-trophic interaction with the pathogen, fungal protein targets were modeled, and docking studies (AutoDock Vina module of the PyRx 0.8 server) were done with all the compounds. Triamcinolone acetonide exhibited the most excellent affinity for the protein targets among the compounds studied. It had a maximum binding affinity of 11.2 kcal/mol for XRN2 (5' → 3'). Further, the protein-ligand complex formation kinetics was done through Molecular Dynamic Simulation studies. Graphs for the RMSD, RMSF, Rg, potential energy, and SASA were generated, and the values during the simulation period suggested the stability of the biomolecule as a complex with the protein. This indicated Triamcinolone acetonide's potential ability to act as a functional disrupter of the target protein and likely an antifungal molecule. Further, the biomolecule was tested for its activity against Foc by screening in the wet lab through the poisoned plate technique, and it was found to be fully inhibitory to the growth of the pathogen at 1000 ppm.
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Affiliation(s)
- R U Krishna Nayana
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - S Nakkeeran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - N Saranya
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Saravanan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - K Mahendra
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Suhail Ashraf
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Kahkashan Perveen
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box-22452, Riyadh, 11495, Saudi Arabia
| | - Najla A Alshaikh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box-22452, Riyadh, 11495, Saudi Arabia
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, S. I. Patil Arts, G.B. Patel Science and STKV Sangh Commerce College, Shahada, 425409, India.
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia.
| | - Pau Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
- Department of Chemical Engineering, Khalifa University, Shakhbout Bin Sultan St - Zone 1, Abu Dhabi, United Arab Emirates.
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
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4
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Yu YY, Zhang YY, Wang T, Huang TX, Tang SY, Jin Y, Mi DD, Zheng Y, Niu DD, Guo JH, Jiang CH. Kurstakin Triggers Multicellular Behaviors in Bacillus cereus AR156 and Enhances Disease Control Efficacy Against Rice Sheath Blight. PLANT DISEASE 2023:PDIS01220078RE. [PMID: 36205689 DOI: 10.1094/pdis-01-22-0078-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Kurstakin is the latest discovered family of lipopeptides secreted by Bacillus spp. In this study, the effects of kurstakin on the direct antagonism, multicellularity, and disease control ability of Bacillus cereus AR156 were explored. An insertion mutation in the nonribosomal peptide synthase responsible for kurstakin synthesis led to a significant reduction of antagonistic ability of AR156 against the plant-pathogenic fungi Rhizoctonia solani, Ascochyta citrullina, Fusarium graminearum, and F. oxysporum f. sp. cubense. The loss of kurstakin synthesis ability significantly impaired the swarming motility of AR156 and reduced biofilm formation and amyloid protein accumulation. Although the loss of kurstakin synthesis ability did not reduce the competitiveness of AR156 under laboratory conditions, the colonization and environmental adaptability of the mutant was significantly weaker than that of wild-type AR156 on rice leaves. The cell surface of wild-type AR156 colonizing the leaf surface was covered by a thick biofilm matrix under a scanning electron microscope, but not the mutant. The colonization ability on rice roots and control efficacy against rice sheath blight disease of the mutant were also impaired. Thus, kurstakin participates in the control of plant diseases by B. cereus AR156 through directly inhibiting the growth of pathogenic fungi and improving long-term environmental adaptability and colonization of AR156 on the host surface by triggering multicellularity. This study explored the multiple functions of kurstakin in plant disease control by B. cereus.
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Affiliation(s)
- Yi-Yang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Yi-Yuan Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ting Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Tao-Xiang Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Shu-Ya Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Yu Jin
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Dan-Dan Mi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Dong-Dong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
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Di Giácomo AL, Azcurra LN, García GR, Dogi CA, González Pereyra ML. Safety assessment of surfactin-producing Bacillus strains and their lipopeptides extracts in vitro and in vivo. J Basic Microbiol 2023. [PMID: 37154196 DOI: 10.1002/jobm.202300008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/14/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023]
Abstract
Beneficial Bacillus strains can be administered to livestock as probiotics to improve animal health. Cyclic lipopeptides produced by Bacillus such as surfactins may be responsible for some of the beneficial effects due to their anti-inflammatory and immunomodulatory activity. The aim of the present study was to isolate and evaluate the biocompatibility of native Bacillus spp. strains and their surfactin-like lipopeptides in vitro and in vivo to determine their potential to be used on animals. Biocompatibility of endospore suspensions (108 UFC/mL), and different dilutions (1:10; 1:50; 1:100; 1:500, and 1:1000) of Bacillus lipopeptide extracts containing surfactin was tested on Caco-2 cells by microculture tetrazolium-based colorimetric assay. Genotoxicity was tested on BALB/c mice (n = 6) administered 0.2 mL of endospore suspensions by the bone marrow erythrocyte micronuclei assay. All the isolates tested produced between 26.96 and 239.97 µg mL- 1 of surfactin. The lipopeptide extract (LPE) from isolate MFF1.11 demonstrated significant cytotoxicity in vitro. In contrast, LPE from MFF 2.2; MFF 2.7, TL1.11, TL 2.5, and TC12 had no cytotoxic effect (V% > 70%) on Caco-2 cells, not affecting cell viability signifficantly in most treatments. Similarly, none of the endospore suspensions affected cell viability (V% > 80%). Likewise, endospores did not cause genotoxicity on BALB/c mice. This study was elementary as a first step for a new line of research, since it allowed us to choose the safest isolates to keep working on the search of new potentially probiotic strains destined to production animals to improve their performance and health.
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Affiliation(s)
- Ana L Di Giácomo
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- Departamento de Microbiología e Inmunología, Instituto de Ciencias Veterinarias (INCIVET-CONICET-UNRC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - Lorena N Azcurra
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Gisela R García
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- Departamento de Microbiología e Inmunología, Instituto de Ciencias Veterinarias (INCIVET-CONICET-UNRC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - Cecilia A Dogi
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- Departamento de Microbiología e Inmunología, Instituto de Ciencias Veterinarias (INCIVET-CONICET-UNRC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - María L González Pereyra
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- Departamento de Microbiología e Inmunología, Instituto de Ciencias Veterinarias (INCIVET-CONICET-UNRC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
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6
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Robertson SN, Soukarieh F, White TM, Camara M, Romero M, Griffiths RL. Probing Interkingdom Signaling Molecules via Liquid Extraction Surface Analysis-Mass Spectrometry. Anal Chem 2023; 95:5079-5086. [PMID: 36881460 PMCID: PMC10034741 DOI: 10.1021/acs.analchem.2c05703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Previously, metabolites diffused or secreted from microbial samples have been analyzed via liquid chromatography-mass spectrometry (LC-MS) approaches following lengthy extraction protocols. Here, we present a model system for growing biofilms on discs before utilizing rapid and direct surface sampling MS, namely, liquid extraction surface analysis, to study the microbial exometabolome. One of the benefits of this approach is its surface-specific nature, enabling mimicking biofilm formation in a way that the study of planktonic liquid cultures cannot imitate. Even though Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Candida albicans (C. albicans) have been studied previously in isolation, very few studies consider the complexity of the interplay between these pathogens, which are commonly combined causative agents of infection. Our model system provides a route to investigate changes in the exometabolome, such as metabolites that become circulatory in the presence of multiple pathogens. Our results agree with previous reports showing that 2-alkyl-4(1H)-quinolone signal molecules produced by P. aeruginosa are important markers of infection and suggest that methods for monitoring levels of 2-heptyl-4-hydroxyquinoline and 2,4-dihydroxyquinoline, as well as pyocyanin, could be beneficial in the determination of causative agents in interkingdom infection including P. aeruginosa. Furthermore, studying changes in exometabolome metabolites between pqs quorum sensing antagonists in treated and nontreated samples suggests suppression of phenazine production by P. aeruginosa. Hence, our model provides a rapid analytical approach to gaining a mechanistic understanding of bacterial signaling.
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Affiliation(s)
- Shaun N Robertson
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Fadi Soukarieh
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Thomas M White
- Faculty of Science, School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Miguel Camara
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Manuel Romero
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rian L Griffiths
- Faculty of Science, School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, U.K
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Ferrarini E, Špacapan M, Lam VB, McCann A, Cesa-Luna C, Marahatta BP, De Pauw E, De Mot R, Venturi V, Höfte M. Versatile role of Pseudomonas fuscovaginae cyclic lipopeptides in plant and microbial interactions. FRONTIERS IN PLANT SCIENCE 2022; 13:1008980. [PMID: 36426159 PMCID: PMC9679282 DOI: 10.3389/fpls.2022.1008980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Pseudomonas fuscovaginae is the most prominent bacterial sheath rot pathogen, causing sheath brown rot disease in rice. This disease occurs worldwide and it is characterized by typical necrotic lesions on the sheath, as well as a reduction in the number of emitted panicles and filled grains. P. fuscovaginae has been shown to produce syringotoxin and fuscopeptin cyclic lipopeptides (CLPs), which have been linked to pathogenicity. In this study, we investigated the role of P. fuscovaginae UPB0736 CLPs in plant pathogenicity, antifungal activity and swarming motility. To do so, we sequenced the strain to obtain a single-contig genome and we constructed deletion mutants in the biosynthetic gene clusters responsible for the synthesis of CLPs. We show that UPB0736 produces a third CLP of 13 amino acids, now named asplenin, and we link this CLP with the swarming activity of the strain. We could then show that syringotoxin is particularly active against Rhizoctonia solani in vitro. By testing the mutants in planta we investigated the role of both fuscopeptin and syringotoxin in causing sheath rot lesions. We proved that the presence of these two CLPs considerably affected the number of emitted panicles, although their number was still significantly affected in the mutants deficient in both fuscopeptin and syringotoxin. These results reveal the importance of CLPs in P. fuscovaginae pathogenicity, but also suggest that other pathogenicity factors may be involved.
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Affiliation(s)
- Enrico Ferrarini
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Mihael Špacapan
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Van Bach Lam
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Andrea McCann
- Department of Chemistry, Faculty of Sciences, University of Liège, Liège, Belgium
| | - Catherine Cesa-Luna
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Bishnu Prasad Marahatta
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Edwin De Pauw
- Department of Chemistry, Faculty of Sciences, University of Liège, Liège, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Monica Höfte
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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9
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Lee Y, Balaraju K, Kim SY, Jeon Y. Occurrence of phenotypic variation in Paenibacillus polymyxa E681 associated with sporulation and carbohydrate metabolism. BIOTECHNOLOGY REPORTS 2022; 34:e00719. [PMID: 35686012 PMCID: PMC9171445 DOI: 10.1016/j.btre.2022.e00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/12/2022] [Indexed: 12/02/2022]
Abstract
We report phenotypic variation in P. polymyxa E681 occurred when grown on media. F-type exhibited faster cell growth than B-type after utilization of carbon sources. 2-DE identified proteins involved in various metabolic activities. The motility is mediated via the downregulation of sporulation and flagella production.
We report the phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR) isolated from a winter barley root in Korea. Phenotypic variation (F-type) occurred when E681 (B-type) was grown in the media, and F-type was generated from B-type. B- and F-types were characterized by their morphological, Biolog, and GC-MIDI analyses. F-type cells altered the original biological capacity of B-type cells on endospore and flagella formation, changes in pH in culture, and carbon utilization. In growth curve analysis, B-type variants recovered bacterial growth as the variation occurred after the decline phase, but F-type variants did not. To determine this cause, we conducted comparative proteome analysis between B- and F-types using two-dimensional gel electrophoresis (2-DE). Of the identified proteins, 47% were involved in glycolysis and other metabolic pathways associated with carbohydrate metabolism. Therefore, our findings provide new knowledge on the mechanism of phenotypic variation and insights into agricultural biotechnology.
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10
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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11
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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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12
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Rahman FB, Sarkar B, Moni R, Rahman MS. Molecular genetics of surfactin and its effects on different sub-populations of Bacillus subtilis. ACTA ACUST UNITED AC 2021; 32:e00686. [PMID: 34786355 PMCID: PMC8578018 DOI: 10.1016/j.btre.2021.e00686] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/28/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022]
Abstract
Insight into the role of surfactin on B. subtilis cell differentiation. Insight into the molecular genetics of surfactin and its production. Graphical presentation of surfactin mediated signaling cascades via quorum sensing.
Surfactin is a biosurfactant produced by Bacillus subtilis. The srfA operon, Sfp gene, and two quorum sensing systems are required for its production. The master regulator spo0A also plays an indispensable role in proper surfactin synthesis. Upon production, surfactin itself acts as a signaling molecule and triggers the activation of Spo0A gene which in turn regulates cell differentiation. Interestingly, surfactin producing cells are immune to the action of surfactin but trigger other cells to differentiate into non-motile cells, matrix producing cells, cannibals, and spores. In case of competent cell differentiation, comS, which resides within the srfA operon, is co-expressed along with surfactin and plays a vital role in competent cell differentiation in response to quorum sensing signal. Surfactin inhibits the motility of certain cell subpopulations, although it helps the non-motile cells to swarm. Thus, surfactin plays significant roles in the differentiation of different subpopulations of specialized cell types of B. subtilis.
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Affiliation(s)
- Faisal Bin Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
- Wazed Miah Science Research Center (WMSRC), Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Ripa Moni
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mohammad Shahedur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
- Wazed Miah Science Research Center (WMSRC), Jahangirnagar University, Savar, Dhaka, Bangladesh
- Corresponding author.
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13
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Griffiths RL. Surface‐sampling mass spectrometry and imaging: Direct analysis of bacterial species. SURF INTERFACE ANAL 2020. [DOI: 10.1002/sia.6907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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14
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Lee Y, Kim YS, Balaraju K, Seo YS, Park J, Ryu CM, Park SH, Kim JF, Kang S, Jeon Y. Molecular changes associated with spontaneous phenotypic variation of Paenibacillus polymyxa, a commonly used biocontrol agent, and temperature-dependent control of variation. Sci Rep 2020; 10:16586. [PMID: 33024195 PMCID: PMC7538429 DOI: 10.1038/s41598-020-73716-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/21/2020] [Indexed: 11/19/2022] Open
Abstract
There has been a growing interest in deploying plant growth-promoting rhizobacteria (PGPR) as a biological control agent (BCA) to reduce the use of agrochemicals. Spontaneous phenotypic variation of PGPR, which causes the loss of traits crucial for biocontrol, presents a large obstacle in producing commercial biocontrol products. Here, we report molecular changes associated with phenotypic variation in Paenibacillus polymyxa, a PGPR widely used for biocontrol worldwide, and a simple cultural change that can prevent the variation. Compared to B-type (non-variant) cells of P. polymyxa strain E681, its phenotypic variant, termed as F-type, fails to form spores, does not confer plant growth-promoting effect, and displays altered colony and cell morphology, motility, antagonism against other microbes, and biofilm formation. This variation was observed in all tested strains of P. polymyxa, but the frequency varied among them. RNA-seq analysis revealed differential regulation of many genes involved in sporulation, flagella synthesis, carbohydrate metabolism, and antimicrobial production in F-type cells, consistent with their pleiotropic phenotypic changes. F-type cells's sporulation was arrested at stage 0, and the key sporulation gene spo0A was upregulated only in B-type cells. The phenotypic variation could be prevented by altering the temperature for growth. When E681 was cultured at 20 °C or lower, it exhibited no variation for 7 days and still reached ~ 108 cfu/mL, the level sufficient for commercial-scale production of biocontrol products.
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Affiliation(s)
- Younmi Lee
- Department of Plant Medicals, Andong National University, Andong, 36729, Republic of Korea.,Agricultural Science and Technology Research Institute, Andong National University, Andong, 36729, Republic of Korea
| | - Young Soo Kim
- Department of Plant Medicals, Andong National University, Andong, 36729, Republic of Korea
| | - Kotnala Balaraju
- Agricultural Science and Technology Research Institute, Andong National University, Andong, 36729, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Pusan, 46241, Republic of Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Pusan, 46241, Republic of Korea
| | - Choong-Min Ryu
- Infectious Disease Research Centre, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Seung-Hwan Park
- Infectious Disease Research Centre, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Strategic Initiative for Microbiomes in Agriculture and Food (iMAF), Yonsei University, Seoul, 03722, Republic of Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yongho Jeon
- Department of Plant Medicals, Andong National University, Andong, 36729, Republic of Korea.
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15
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Penha RO, Vandenberghe LPS, Faulds C, Soccol VT, Soccol CR. Bacillus lipopeptides as powerful pest control agents for a more sustainable and healthy agriculture: recent studies and innovations. PLANTA 2020; 251:70. [PMID: 32086615 DOI: 10.1007/s00425-020-03357-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/05/2020] [Indexed: 05/27/2023]
Abstract
Lipopeptides could help to overcome a large concern in agriculture: resistance against chemical pesticides. These molecules have activity against various phytopathogens and a potential to be transformed by genetic engineering. The exponential rise of pest resistances to different chemical pesticides and the global appeal of consumers for a sustainable agriculture and healthy nutrition have led to the search of new solutions for pest control. Furthermore, new laws require a different stance of producers. Based on that, bacteria of the genus Bacillus present a great agricultural potential, producing lipopeptides (LPs) that have high activity against insects, mites, nematodes, and/or phytopathogens that are harmful to plant cultures. Biopesticide activity can be found mainly in three families of Bacillus lipopeptides: surfactin, iturin, and fengycin. These molecules have an amphiphilic nature, interfering with biological membrane structures. Their antimicrobial properties include activity against bacteria, fungi, oomycetes, and viruses. Recent studies also highlight the ability of these compounds to stimulate defense mechanisms of plants and biofilm formation, which is a key factor for the successful colonization of biocontrol organisms. The use of molecular biology has also recently been researched for continuous advances and discoveries of new LPs, avoiding possible future problems of resistance against these molecules. As a consequence of the properties and possibilities of LPs, numerous studies and developments as well as the attention of large companies in the field is expected in the near future.
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Affiliation(s)
- Rafaela O Penha
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Luciana P S Vandenberghe
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Craig Faulds
- Aix-Marseille Université, POLYTECH Marseille, UMR 1163 Biotechnologie Des Champignons Filamenteux, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Vanete T Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Carlos R Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil.
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16
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Cameron SJ, Takáts Z. Mass spectrometry approaches to metabolic profiling of microbial communities within the human gastrointestinal tract. Methods 2018; 149:13-24. [DOI: 10.1016/j.ymeth.2018.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022] Open
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17
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Besset-Manzoni Y, Rieusset L, Joly P, Comte G, Prigent-Combaret C. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29953-29970. [PMID: 29313197 DOI: 10.1007/s11356-017-1152-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/26/2017] [Indexed: 05/23/2023]
Abstract
The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell-cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe-microbe and microbe-plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.
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Affiliation(s)
- Yoann Besset-Manzoni
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Laura Rieusset
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Pierre Joly
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Gilles Comte
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Claire Prigent-Combaret
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France.
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18
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Thongkongkaew T, Ding W, Bratovanov E, Oueis E, Garcı́a-Altares M, Zaburannyi N, Harmrolfs K, Zhang Y, Scherlach K, Müller R, Hertweck C. Two Types of Threonine-Tagged Lipopeptides Synergize in Host Colonization by Pathogenic Burkholderia Species. ACS Chem Biol 2018; 13:1370-1379. [PMID: 29669203 DOI: 10.1021/acschembio.8b00221] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial infections of agriculturally important mushrooms and plants pose a major threat to human food sources worldwide. However, structures of chemical mediators required by the pathogen for host colonization and infection remain elusive in most cases. Here, we report two types of threonine-tagged lipopeptides conserved among mushroom and rice pathogenic Burkholderia species that facilitate bacterial infection of hosts. Genome mining, metabolic profiling of infected mushrooms, and heterologous expression of orphan gene clusters allowed the discovery of these unprecedented metabolites in the mushroom pathogen Burkholderia gladioli (haereogladin, burriogladin) and the plant pathogen Burkholderia glumae (haereoglumin and burrioglumin). Through targeted gene deletions, the molecular basis of lipopeptide biosynthesis by nonribosomal peptide synthetases was revealed. Surprisingly, both types of lipopeptides feature unusual threonine tags, which yield longer peptide backbones than one would expect based on the canonical colinearity of the NRPS assembly lines. Both peptides play an indirect role in host infection as biosurfactants that enable host colonization by mediating swarming and biofilm formation abilities. Moreover, MALDI imaging mass spectrometry was applied to investigate the biological role of the lipopeptides. Our results shed light on conserved mechanisms that mushroom and plant pathogenic bacteria utilize for host infection and expand current knowledge on bacterial virulence factors that may represent a new starting point for the targeted development of crop protection measures in the future.
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Affiliation(s)
- Tawatchai Thongkongkaew
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Wei Ding
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Evgeni Bratovanov
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Emilia Oueis
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Marı́a Garcı́a-Altares
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nestor Zaburannyi
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Kirsten Harmrolfs
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
- Chair for Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
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19
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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20
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Dunham SJB, Ellis JF, Baig NF, Morales-Soto N, Cao T, Shrout JD, Bohn PW, Sweedler JV. Quantitative SIMS Imaging of Agar-Based Microbial Communities. Anal Chem 2018; 90:5654-5663. [PMID: 29623707 PMCID: PMC5930052 DOI: 10.1021/acs.analchem.7b05180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Joseph F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Nameera F. Baig
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
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21
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Vallet M, Vanbellingen QP, Fu T, Le Caer JP, Della-Negra S, Touboul D, Duncan KR, Nay B, Brunelle A, Prado S. An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2863-2873. [PMID: 29139291 DOI: 10.1021/acs.jnatprod.6b01185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An integrative approach combining traditional natural products chemistry, molecular networking, and mass spectrometry imaging has been undertaken to decipher the molecular dialogue between the fungus Paraconiothyrium variabile and the bacterium Bacillus subtilis, which were isolated as endophytes from the conifer Cephalotaxus harringtonia and are characterized by a strong and mutual antibiosis. From this study, we highlight that bacterial surfactins and a fungal tetronic acid are involved in such competition and that the fungus is able to hydrolyze surfactins to fight against the bacterial partner.
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Affiliation(s)
- Marine Vallet
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Quentin P Vanbellingen
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Tingting Fu
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Pierre Le Caer
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Serge Della-Negra
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, Université Paris-Saclay , 91406, Orsay, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, HW608, University of Strathclyde , 161 Cathedral Street, Glasgow G4 ORE, U.K
| | - Bastien Nay
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
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22
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Pollitt EJG, Diggle SP. Defining motility in the Staphylococci. Cell Mol Life Sci 2017; 74:2943-2958. [PMID: 28378043 PMCID: PMC5501909 DOI: 10.1007/s00018-017-2507-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/16/2017] [Accepted: 03/14/2017] [Indexed: 01/17/2023]
Abstract
The ability of bacteria to move is critical for their survival in diverse environments and multiple ways have evolved to achieve this. Two forms of motility have recently been described for Staphylococcus aureus, an organism previously considered to be non-motile. One form is called spreading, which is a type of sliding motility and the second form involves comet formation, which has many observable characteristics associated with gliding motility. Darting motility has also been observed in Staphylococcus epidermidis. This review describes how motility is defined and how we distinguish between passive and active motility. We discuss the characteristics of the various forms of Staphylococci motility, the molecular mechanisms involved and the potential future research directions.
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Affiliation(s)
- Eric J G Pollitt
- Department of Biomedical Science, Western Bank, University of Sheffield, Sheffield, UK
| | - Stephen P Diggle
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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23
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Active depinning of bacterial droplets: The collective surfing of Bacillus subtilis. Proc Natl Acad Sci U S A 2017; 114:5958-5963. [PMID: 28536199 DOI: 10.1073/pnas.1703997114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How systems are endowed with migration capacity is a fascinating question with implications ranging from the design of novel active systems to the control of microbial populations. Bacteria, which can be found in a variety of environments, have developed among the richest set of locomotion mechanisms both at the microscopic and collective levels. Here, we uncover, experimentally, a mode of collective bacterial motility in humid environment through the depinning of bacterial droplets. Although capillary forces are notoriously enormous at the bacterial scale, even capable of pinning water droplets of millimetric size on inclined surfaces, we show that bacteria are able to harness a variety of mechanisms to unpin contact lines, hence inducing a collective slipping of the colony across the surface. Contrary to flagella-dependent migration modes like swarming, we show that this much faster "colony surfing" still occurs in mutant strains of Bacillus subtilis lacking flagella. The active unpinning seen in our experiments relies on a variety of microscopic mechanisms, which could each play an important role in the migration of microorganisms in humid environment.
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24
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Bacillus subtilis Swarmer Cells Lead the Swarm, Multiply, and Generate a Trail of Quiescent Descendants. mBio 2017; 8:mBio.02102-16. [PMID: 28174308 PMCID: PMC5296600 DOI: 10.1128/mbio.02102-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacteria adopt social behavior to expand into new territory, led by specialized swarmers, before forming a biofilm. Such mass migration of Bacillus subtilis on a synthetic medium produces hyperbranching dendrites that transiently (equivalent to 4 to 5 generations of growth) maintain a cellular monolayer over long distances, greatly facilitating single-cell gene expression analysis. Paradoxically, while cells in the dendrites (nonswarmers) might be expected to grow exponentially, the rate of swarm expansion is constant, suggesting that some cells are not multiplying. Little attention has been paid to which cells in a swarm are actually multiplying and contributing to the overall biomass. Here, we show in situ that DNA replication, protein translation and peptidoglycan synthesis are primarily restricted to the swarmer cells at dendrite tips. Thus, these specialized cells not only lead the population forward but are apparently the source of all cells in the stems of early dendrites. We developed a simple mathematical model that supports this conclusion. Swarming motility enables rapid coordinated surface translocation of a microbial community, preceding the formation of a biofilm. This movement occurs in thin films and involves specialized swarmer cells localized to a narrow zone at the extreme swarm edge. In the B. subtilis system, using a synthetic medium, the swarm front remains as a cellular monolayer for up to 1.5 cm. Swarmers display high-velocity whirls and vortexing and are often assumed to drive community expansion at the expense of cell growth. Surprisingly, little attention has been paid to which cells in a swarm are actually growing and contributing to the overall biomass. Here, we show that swarmers not only lead the population forward but continue to multiply as a source of all cells in the community. We present a model that explains how exponential growth of only a few cells is compatible with the linear expansion rate of the swarm.
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25
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Abstract
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In the two decades since mass spectrometry imaging (MSI) was first
applied to visualize the distribution of peptides across biological
tissues and cells, the technique has become increasingly effective
and reliable. MSI excels at providing complementary information to
existing methods for molecular analysis—such as genomics, transcriptomics,
and metabolomics—and stands apart from other chemical imaging
modalities through its capability to generate information that is
simultaneously multiplexed and chemically specific. Today a diverse
family of MSI approaches are applied throughout the scientific community
to study the distribution of proteins, peptides, and small-molecule
metabolites across many biological models. The inherent strengths
of MSI make the technique valuable for studying
microbial systems. Many microbes reside in surface-attached multicellular
and multispecies communities, such as biofilms and motile colonies,
where they work together to harness surrounding nutrients, fend off
hostile organisms, and shield one another from adverse environmental
conditions. These processes, as well as many others essential for
microbial survival, are mediated through the production and utilization
of a diverse assortment of chemicals. Although bacterial cells are
generally only a few microns in diameter, the ecologies they influence
can encompass entire ecosystems, and the chemical changes that they
bring about can occur over time scales ranging from milliseconds to
decades. Because of their incredible complexity, our understanding
of and influence over microbial systems requires detailed scientific
evaluations that yield both chemical and spatial information. MSI
is well-positioned to fulfill these requirements. With small adaptations
to existing methods, the technique can be applied to study a wide
variety of chemical interactions, including those that occur inside
single-species microbial communities, between cohabitating microbes,
and between microbes and their hosts. In recognition of this
potential for scientific advancement, researchers
have adapted MSI methodologies for the specific needs of the microbiology
research community. As a result, workflows exist for imaging microbial
systems with many of the common MSI ionization methods. Despite this
progress, there is substantial room for improvements in instrumentation,
sample preparation, and data interpretation. This Account provides
a brief overview of the state of technology in microbial MSI, illuminates
selected applications that demonstrate the potential of the technique,
and highlights a series of development challenges that are needed
to move the field forward. In the coming years, as microbial MSI becomes
easier to use and more universally applicable, the technique will
evolve into a fundamental tool widely applied throughout many divisions
of science, medicine, and industry.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joanna F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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26
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Nguyen SN, Liyu AV, Chu RK, Anderton CR, Laskin J. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography. Anal Chem 2016; 89:1131-1137. [PMID: 27973782 DOI: 10.1021/acs.analchem.6b03293] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.
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Affiliation(s)
- Son N Nguyen
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Andrey V Liyu
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Rosalie K Chu
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Christopher R Anderton
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Julia Laskin
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
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27
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Li B, Comi TJ, Si T, Dunham SJB, Sweedler JV. A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1030-1035. [PMID: 27476992 PMCID: PMC5297451 DOI: 10.1002/jms.3827] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 05/03/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging of biofilms cultured on agar plates is challenging because of problems related to matrix deposition onto agar. We describe a one-step, spray-based application of a 2,5-dihydroxybenzoic acid solution for direct matrix-assisted laser desorption/ionization imaging of hydrated Bacillus subtilis biofilms on agar. Using both an optimized airbrush and a home-built automatic sprayer, region-specific distributions of signaling metabolites and cannibalistic factors were visualized from B. subtilis cells cultivated on biofilm-promoting medium. The approach provides a homogeneous, relatively dry coating on hydrated samples, improving spot to spot signal repeatability compared with sieved matrix application, and is easily adapted for imaging a range of agar-based biofilms. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Troy J Comi
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Si
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sage J B Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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28
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Li H, Balan P, Vertes A. Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2016; 55:15035-15039. [DOI: 10.1002/anie.201607751] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Hang Li
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
| | - Pranav Balan
- Thomas Jefferson High School for Science and Technology; Alexandria VA 22312 USA
| | - Akos Vertes
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
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29
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Li H, Balan P, Vertes A. Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hang Li
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
| | - Pranav Balan
- Thomas Jefferson High School for Science and Technology; Alexandria VA 22312 USA
| | - Akos Vertes
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
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30
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Wehrli PM, Angerer TB, Farewell A, Fletcher JS, Gottfries J. Investigating the Role of the Stringent Response in Lipid Modifications during the Stationary Phase in E. coli by Direct Analysis with Time-of-Flight-Secondary Ion Mass Spectrometry. Anal Chem 2016; 88:8680-8. [DOI: 10.1021/acs.analchem.6b01981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Patrick M. Wehrli
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Tina B. Angerer
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Anne Farewell
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
| | - John S. Fletcher
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Johan Gottfries
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
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31
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Si T, Li B, Zhang K, Xu Y, Zhao H, Sweedler JV. Characterization of Bacillus subtilis Colony Biofilms via Mass Spectrometry and Fluorescence Imaging. J Proteome Res 2016; 15:1955-62. [PMID: 27136705 PMCID: PMC4895246 DOI: 10.1021/acs.jproteome.6b00127] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Colony
biofilms of Bacillus subtilis are a widely
used model for studying cellular differentiation. Here, we applied
matrix-assisted laser desorption/ionization (MALDI) mass spectrometry
imaging (MSI) to examine cellular and molecular heterogeneity in B. subtilis colony biofilms. From B. subtilis cells cultivated on a biofilm-promoting medium, we detected two
cannibalistic factors not found in previous MALDI MSI studies of the
same strain under different culturing conditions. Given the importance
of cannibalism in matrix formation of B. subtilis biofilms, we employed a transcriptional reporter to monitor matrix-producing
cell subpopulations using fluorescence imaging. These two complementary
imaging approaches were used to characterize three B. subtilis strains, the wild type isolate NCIB3610, and two mutants, Δspo0A and ΔabrB, with defective and
enhanced biofilm phenotypes, respectively. Upon deletion of key transcriptional
factors, correlated changes were observed in biofilm morphology, signaling,
cannibalistic factor distribution, and matrix-related gene expression,
providing new insights on cannibalism in biofilm development. This
work underscores the advantages of using multimodal imaging to compare
spatial patterns of selected molecules with the associated protein
expression patterns, obtaining information on cellular heterogeneity
and function not obtainable when using a single method to characterize
biofilm formation.
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Affiliation(s)
- Tong Si
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Bin Li
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ke Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yiran Xu
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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32
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Abstract
The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species: Myxococcus xanthus, Bacillus subtilis, and Pseudomonas aeruginosa. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is M. xanthus, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.
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33
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Bellin DL, Sakhtah H, Rosenstein JK, Levine PM, Thimot J, Emmett K, Dietrich LEP, Shepard KL. Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms. Nat Commun 2015; 5:3256. [PMID: 24510163 PMCID: PMC3969851 DOI: 10.1038/ncomms4256] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/14/2014] [Indexed: 12/20/2022] Open
Abstract
Despite advances in monitoring spatiotemporal expression patterns of genes and proteins with fluorescent probes, direct detection of metabolites and small molecules remains challenging. A technique for spatially resolved detection of small molecules would benefit the study of redox-active metabolites produced by microbial biofilms, which can drastically affect colony development. Here we present an integrated circuit-based electrochemical sensing platform featuring an array of working electrodes and parallel potentiostat channels. “Images” over a 3.25 × 0.9 mm area can be captured with a diffusion-limited spatial resolution of 750 μm. We demonstrate that square wave voltammetry can be used to detect, identify, and quantify (for concentrations as low as 2.6 μM) four distinct redox-active metabolites called phenazines. We characterize phenazine production in both wild-type and mutant Pseudomonas aeruginosa PA14 colony biofilms, and find correlations with fluorescent reporter imaging of phenazine biosynthetic gene expression.
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Affiliation(s)
- Daniel L Bellin
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
| | - Hassan Sakhtah
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jacob K Rosenstein
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Peter M Levine
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jordan Thimot
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
| | - Kevin Emmett
- Department of Physics, Columbia University, New York, New York 10027, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Kenneth L Shepard
- 1] Department of Electrical Engineering, Columbia University, New York, New York 10027, USA [2] Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
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34
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Production and characterization of surfactin-type lipopeptides as bioemulsifiers produced by a Pinctada martensii-derived Bacillus mojavensis B0621A. Appl Biochem Biotechnol 2015; 177:1520-9. [PMID: 26373943 DOI: 10.1007/s12010-015-1832-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 09/03/2015] [Indexed: 10/23/2022]
Abstract
Bacillus mojavensis B0621A was isolated from the mantle of a pearl oyster Pinctada martensii collected from South China Sea. Semi-purified surfactins (225 mg L(-1)) were obtained by acid precipitation and vacuum flash chromatography. The component of the semi-purified surfactins was preliminarily analyzed by liquid chromatography mass spectrometer system, and the results showed that all these surfactins could be a group of homologues. Eight surfactin homologues were isolated and afforded by reversed phase high-performance liquid chromatography. Furthermore, their structure was characterized by mass spectrometry analysis combined with nuclear magnetic resonance spectroscopy techniques. These surfactins shared seven amino acids as peptide backbone and a saturated β-hydroxy fatty acid chain residue (from C13 to C15), differed each other from peptide sequence in the position of Leu7 or Val7. All these surfactins had significant activity and stability of emulsification under various pH (from 7.0 to 12.0), temperature range (from 20 to 115 °C) and sodium chloride concentration (from 2.5 to 20.0 %, w/v). Taken all together, these results indicated that B. mojavensis B0621A have potential to be an alternative source as a biological-derived emulsifying agent.
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Vanbellingen QP, Elie N, Eller MJ, Della-Negra S, Touboul D, Brunelle A. Time-of-flight secondary ion mass spectrometry imaging of biological samples with delayed extraction for high mass and high spatial resolutions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1187-95. [PMID: 26395603 PMCID: PMC5033000 DOI: 10.1002/rcm.7210] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 05/10/2023]
Abstract
RATIONALE In Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS), pulsed and focused primary ion beams enable mass spectrometry imaging, a method which is particularly useful to map various small molecules such as lipids at the surface of biological samples. When using TOF-SIMS instruments, the focusing modes of the primary ion beam delivered by liquid metal ion guns can provide either a mass resolution of several thousand or a sub-µm lateral resolution, but the combination of both is generally not possible. METHODS With a TOF-SIMS setup, a delayed extraction applied to secondary ions has been studied extensively on rat cerebellum sections in order to compensate for the effect of long primary ion bunches. RESULTS The use of a delayed extraction has been proven to be an efficient solution leading to unique features, i.e. a mass resolution up to 10000 at m/z 385.4 combined with a lateral resolution of about 400 nm. Simulations of ion trajectories confirm the experimental determination of optimal delayed extraction and allow understanding of the behavior of ions as a function of their mass-to-charge ratio. CONCLUSIONS Although the use of a delayed extraction has been well known for many years and is very popular in MALDI, it is much less used in TOF-SIMS. Its full characterization now enables secondary ion images to be recorded in a single run with a submicron spatial resolution and with a mass resolution of several thousand. This improvement is very useful when analyzing lipids on tissue sections, or rare, precious, or very small size samples.
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Affiliation(s)
- Quentin P Vanbellingen
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Nicolas Elie
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Michael J Eller
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, 91406, Orsay, France
| | - Serge Della-Negra
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, 91406, Orsay, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
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Floyd KA, Moore JL, Eberly AR, Good JAD, Shaffer CL, Zaver H, Almqvist F, Skaar EP, Caprioli RM, Hadjifrangiskou M. Adhesive fiber stratification in uropathogenic Escherichia coli biofilms unveils oxygen-mediated control of type 1 pili. PLoS Pathog 2015; 11:e1004697. [PMID: 25738819 PMCID: PMC4349694 DOI: 10.1371/journal.ppat.1004697] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/22/2015] [Indexed: 12/02/2022] Open
Abstract
Bacterial biofilms account for a significant number of hospital-acquired infections and complicate treatment options, because bacteria within biofilms are generally more tolerant to antibiotic treatment. This resilience is attributed to transient bacterial subpopulations that arise in response to variations in the microenvironment surrounding the biofilm. Here, we probed the spatial proteome of surface-associated single-species biofilms formed by uropathogenic Escherichia coli (UPEC), the major causative agent of community-acquired and catheter-associated urinary tract infections. We used matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) to analyze the spatial proteome of intact biofilms in situ. MALDI-TOF IMS revealed protein species exhibiting distinct localizations within surface-associated UPEC biofilms, including two adhesive fibers critical for UPEC biofilm formation and virulence: type 1 pili (Fim) localized exclusively to the air-exposed region, while curli amyloid fibers localized to the air-liquid interface. Comparison of cells grown aerobically, fermentatively, or utilizing an alternative terminal electron acceptor showed that the phase-variable fim promoter switched to the “OFF” orientation under oxygen-deplete conditions, leading to marked reduction of type 1 pili on the bacterial cell surface. Conversely, S pili whose expression is inversely related to fim expression were up-regulated under anoxic conditions. Tethering the fim promoter in the “ON” orientation in anaerobically grown cells only restored type 1 pili production in the presence of an alternative terminal electron acceptor beyond oxygen. Together these data support the presence of at least two regulatory mechanisms controlling fim expression in response to oxygen availability and may contribute to the stratification of extracellular matrix components within the biofilm. MALDI IMS facilitated the discovery of these mechanisms, and we have demonstrated that this technology can be used to interrogate subpopulations within bacterial biofilms. Bacteria are commonly found in multicellular communities known as biofilms. Biofilms can form on a variety of surfaces, both outside and within living things, and can have detrimental effects on human health. The characteristics of bacteria occupying different areas within biofilms are not well understood, and such knowledge is critical for understanding how biofilms form and for developing strategies to treat biofilm-related infections. Here, we adapted a technique to sample how proteins cluster within bacterial biofilms as a means to identify the location of bacteria with differential protein expression within the community. We observed that with uropathogenic E. coli, which is the major cause of urinary tract and catheter-associated urinary tract infections, bacteria close to the air-exposed region of the biofilm expressed different adhesive fibers compared to those at the liquid interface. We went on to show that lack of oxygen shuts down the production of fibers known to be critical for adherence to host bladder cells and to catheter material. This discovery was enabled by a new application of an existing technology that allowed us to gain insights into the spatial regulation of proteins within bacterial biofilms and to elucidate pathways that could be targeted to inhibit bacterial adherence.
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Affiliation(s)
- Kyle A. Floyd
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jessica L. Moore
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Allison R. Eberly
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - James A. D. Good
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Center for Microbial Research, Umeå University, Umeå, Sweden
| | - Carrie L. Shaffer
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Himesh Zaver
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Biology and Department of Chemistry, Belmont University, Nashville, Tennessee, United States of America
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Center for Microbial Research, Umeå University, Umeå, Sweden
| | - Eric P. Skaar
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Departments of Biochemistry and Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail: (RMC); (MH)
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail: (RMC); (MH)
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Tata A, Perez CJ, Ore MO, Lostun D, Passas A, Morin S, Ifa DR. Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites. RSC Adv 2015. [DOI: 10.1039/c5ra12805f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Optimized in situ screening, characterization and imaging of fungal metabolites by imprint DESI-MS.
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Affiliation(s)
| | | | | | | | | | - Sylvie Morin
- Department of Chemistry
- York University
- Toronto
- Canada
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38
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39
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Lanni EJ, Masyuko R, Driscoll CM, Aerts JT, Shrout JD, Bohn PW, Sweedler JV. MALDI-guided SIMS: multiscale imaging of metabolites in bacterial biofilms. Anal Chem 2014; 86:9139-45. [PMID: 25133532 PMCID: PMC4165220 DOI: 10.1021/ac5020222] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
Mass spectrometry imaging (MSI) is a versatile tool for visualizing molecular distributions in complex biological specimens, but locating microscopic chemical features of interest can be challenging in samples that lack a well-defined anatomy. To address this issue, we developed a correlated imaging approach that begins with performing matrix-assisted laser desorption/ionization (MALDI) MSI to obtain low-resolution molecular maps of a sample. The resulting maps are then used to direct subsequent microscopic secondary ion mass spectrometry (SIMS) imaging and tandem mass spectrometry (MS/MS) experiments to examine selected chemical regions of interest. By employing MALDI undersampling, the sample surface is left mostly unperturbed and available for the SIMS analysis, while also generating an ablation array that can be used for navigation in SIMS. We validated this MALDI-guided SIMS approach using cultured biofilms of the opportunistic pathogen Pseudomonas aeruginosa; bioactive secondary metabolites, including rhamnolipids and quinolones, were detected and visualized on both macro- and microscopic size scales. MSI mass assignments were confirmed with in situ MALDI MS/MS and capillary electrophoresis-electrospray ionization MS/MS analysis of biofilm extracts. Two strains of P. aeruginosa were compared, wild type and a quorum sensing mutant, and differences in metabolite abundance and distribution were observed.
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Affiliation(s)
- Eric J. Lanni
- Department
of Chemistry and Beckman Institute for Advanced Science
and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rachel
N. Masyuko
- Department of Chemistry and Biochemistry and Department
of Chemical
and Biomolecular Engineering, and Department of Civil and Environmental Engineering
and Earth Sciences and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Callan M. Driscoll
- Department of Chemistry and Biochemistry and Department
of Chemical
and Biomolecular Engineering, and Department of Civil and Environmental Engineering
and Earth Sciences and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jordan T. Aerts
- Department
of Chemistry and Beckman Institute for Advanced Science
and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joshua D. Shrout
- Department of Chemistry and Biochemistry and Department
of Chemical
and Biomolecular Engineering, and Department of Civil and Environmental Engineering
and Earth Sciences and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry and Department
of Chemical
and Biomolecular Engineering, and Department of Civil and Environmental Engineering
and Earth Sciences and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V. Sweedler
- Department
of Chemistry and Beckman Institute for Advanced Science
and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Bouslimani A, Sanchez LM, Garg N, Dorrestein PC. Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 2014; 31:718-29. [PMID: 24801551 PMCID: PMC4161218 DOI: 10.1039/c4np00044g] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this Highlight, we feature emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade.
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Affiliation(s)
- Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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41
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Debois D, Jourdan E, Smargiasso N, Thonart P, De Pauw E, Ongena M. Spatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging. Anal Chem 2014; 86:4431-8. [PMID: 24712753 DOI: 10.1021/ac500290s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some soil Bacilli living in association with plant roots can protect their host from infection by pathogenic microbes and are therefore being developed as biological agents to control plant diseases. The plant-protective activity of these bacteria has been correlated with the potential to secrete a wide array of antibiotic compounds upon growth as planktonic cells in isolated cultures under laboratory conditions. However, in situ expression of these antibiotics in the rhizosphere where bacterial cells naturally colonize root tissues is still poorly understood. In this work, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) to examine spatiotemporal changes in the secreted antibiome of Bacillus amyloliquefaciens developing as biofilms on roots. Nonribosomal lipopeptides such as the plant immunity elicitor surfactin or the highly fungitoxic iturins and fengycins were readily produced albeit in different time frames and quantities in the surrounding medium. Interestingly, tandem mass spectrometry (MS/MS) experiments performed directly from the gelified culture medium also allowed us to identify a new variant of surfactins released at later time points. However, no other bioactive compounds such as polyketides were detected at any time, strongly suggesting that the antibiome expressed in planta by B. amyloliquefaciens does not reflect the vast genetic arsenal devoted to the formation of such compounds. This first dynamic study reveals the power of MALDI MSI as tool to identify and map antibiotics synthesized by root-associated bacteria and, more generally, to investigate plant-microbe interactions at the molecular level.
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Affiliation(s)
- Delphine Debois
- Mass Spectrometry Laboratory, Chemistry Department, University of Liege , 4000 Liege, Belgium
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42
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Liu J, Gingras J, Ganley KP, Vismeh R, Teffera Y, Zhao Z. Whole-body tissue distribution study of drugs in neonate mice using desorption electrospray ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:185-190. [PMID: 24338966 DOI: 10.1002/rcm.6775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/25/2013] [Accepted: 10/26/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Although Desorption Electrospray Ionization (DESI) Mass Spectrometry Imaging (MSI) is uniquely suited for whole-body (WB) tissue distribution study of drugs, success in this area has been difficult. Here, we present WB tissue distribution studies using DESI-MSI and a new histological tissue-friendly solvent system. METHODS Neonate pups were dosed subcutaneously (SC) with clozapine, compound 1, compound 2, or compound 3. Following euthanization by hypothermia, neonates underwent a transcardiac perfusion (saline) to remove blood. After cryosectioning, DESI-MSI was conducted for the WB tissue slides, followed sequentially by histological staining. RESULTS Whole-body tissue imaging showed that clozapine and its N-oxide metabolite were distributed in significant amounts in the brain, spinal cord, liver, heart (ventricle), and lungs. Compound 1 was distributed mainly in the liver and muscle, and its mono-oxygenated metabolite was detected by DESI-MSI exclusively in the liver. Compound 2 was distributed mainly in the muscle and fatty tissue. Compound 3 was distributed mainly in fatty tissue and its metabolites were also mainly detected in the same tissue. CONCLUSIONS The results demonstrate the successful application of DESI-MSI in whole-body tissue distribution studies of drugs and metabolites in combination with sequential histology staining for anatomy. The results also identified lipophilicity as the driving force in the tissue distribution of the three Amgen compounds.
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Affiliation(s)
- Jingzhou Liu
- Pharmacokinetics and Drug Metabolism, Amgen Inc., 360 Binney Street, Cambridge, MA, 02142, USA
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Mangwani N, Kumari S, Shukla SK, Rao TS, Das S. Phenotypic Switching in Biofilm-Forming Marine Bacterium Paenibacillus lautus NE3B01. Curr Microbiol 2014; 68:648-56. [DOI: 10.1007/s00284-014-0525-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
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Shih CJ, Chen PY, Liaw CC, Lai YM, Yang YL. Bringing microbial interactions to light using imaging mass spectrometry. Nat Prod Rep 2014; 31:739-55. [DOI: 10.1039/c3np70091g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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45
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Kiss A, Smith DF, Jungmann JH, Heeren RMA. Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2745-2750. [PMID: 24214859 DOI: 10.1002/rcm.6719] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/23/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. METHODS In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. RESULTS The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. CONCLUSIONS We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging.
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Affiliation(s)
- András Kiss
- FOM Institute AMOLF, Science Park 104, 1098 XG, Amsterdam, The Netherlands
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46
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Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC. Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry. Anal Chem 2013; 85:10385-91. [PMID: 24047514 DOI: 10.1021/ac4023154] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.
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Affiliation(s)
- Jeramie Watrous
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California, 92037 United States
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Lanekoff I, Geydebrekht O, Pinchuk GE, Konopka AE, Laskin J. Spatially resolved analysis of glycolipids and metabolites in living Synechococcus sp. PCC 7002 using nanospray desorption electrospray ionization. Analyst 2013; 138:1971-8. [PMID: 23392077 DOI: 10.1039/c3an36716a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms release a diversity of organic compounds that couple interspecies metabolism, enable communication, or provide benefits to other microbes. Increased knowledge of microbial metabolite production will contribute to understanding of the dynamic microbial world and can potentially lead to new developments in drug discovery, biofuel production, and clinical research. Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables detailed chemical characterization of molecules from a specific location on a surface without special sample pretreatment. Due to its ambient nature, living bacterial colonies growing on agar plates can be rapidly analyzed without affecting the viability of the colony. In this study we demonstrate for the first time the utility of nano-DESI for spatial profiling of chemical gradients generated by microbial communities on agar plates. We found that despite the high salt content of the agar used in this study (~350 mM), nano-DESI analysis enables detailed characterization of metabolites produced by the Synechococcus sp. PCC 7002 colonies. High resolution mass spectrometry and MS/MS analysis of the living Synechococcus sp. PCC 7002 colonies allowed us to detect metabolites and lipids on the colony and on the surrounding agar, and confirm their identities. High sensitivity of nano-DESI enabled identification of several glycolipids that have not been previously reported by extracting the cells using conventional methods. Spatial profiling demonstrated that a majority of lipids and metabolites were localized on the colony while sucrose and glucosylglycerol, an osmoprotective compound produced by cyanobacteria, were secreted onto agar. Furthermore, we demonstrated that the chemical gradients of sucrose and glucosylglycerol on agar depend on the age of the colony. The methodology presented in this study will facilitate future studies focused on molecular-level characterization of interactions between bacterial colonies.
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Affiliation(s)
- Ingela Lanekoff
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, PO Box 999, K8-88 Richland, WA 99352, USA.
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48
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Sample preparation for mass spectrometry imaging: Small mistakes can lead to big consequences. J Proteomics 2012; 75:4893-4911. [DOI: 10.1016/j.jprot.2012.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 12/13/2022]
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49
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Vismeh R, Waldon DJ, Teffera Y, Zhao Z. Localization and Quantification of Drugs in Animal Tissues by Use of Desorption Electrospray Ionization Mass Spectrometry Imaging. Anal Chem 2012; 84:5439-45. [DOI: 10.1021/ac3011654] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramin Vismeh
- Pharmacokinetics and Drug Metabolism, Amgen Incorporated, Cambridge, Massachusetts 02142,
United States
| | - Daniel J. Waldon
- Pharmacokinetics and Drug Metabolism, Amgen Incorporated, Cambridge, Massachusetts 02142,
United States
| | - Yohannes Teffera
- Pharmacokinetics and Drug Metabolism, Amgen Incorporated, Cambridge, Massachusetts 02142,
United States
| | - Zhiyang Zhao
- Pharmacokinetics and Drug Metabolism, Amgen Incorporated, Cambridge, Massachusetts 02142,
United States
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50
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Nihorimbere V, Cawoy H, Seyer A, Brunelle A, Thonart P, Ongena M. Impact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499. FEMS Microbiol Ecol 2012; 79:176-91. [PMID: 22029651 DOI: 10.1111/j.1574-6941.2011.01208.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Cyclic lipopeptides (cLPs) of the surfactin, iturin and fengycin families synthesized by plant-associated Bacilli represent an important class of antibiotics as they may be tightly involved in the protective effect of selected strains against phytopathogens. However, their production by Bacillus cells developing on roots under rhizosphere conditions is still poorly understood. In this work, we combined electrospray and imaging mass spectrometry-based approaches to determine the detailed pattern of surfactins, iturins and fengycins produced in planta by Bacillus amyloliquefaciens S499. Very different production rates were observed for the three cLPs families. Whereas surfactin accumulated in significant amounts, much lower quantities of iturins and fengycins were detected in the environment of colonized roots in comparison with laboratory medium. In addition, the surfactin pattern produced by strain S499 evolving on roots is enriched in homologues with long fatty acid chains (C15) compared with the chains typically secreted under in vitro conditions. Additional experiments revealed that lipopeptide production by root-associated S499 cells is qualitatively and quantitatively dictated by the specific nutritional context of the rhizosphere (exudates enriched in organic acids, oxygen limitation) but also by the formation of biofilm-related structures around root hairs. As surfactins, iturins and fengycins retain specific functions and bioactivities, the biological relevance of their differential production observed in planta is discussed in the context of biocontrol of plant diseases.
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Affiliation(s)
- Venant Nihorimbere
- Walloon Center for Industrial Biology, University of Liège/Gembloux Agro-Bio Tech, Gembloux, Belgium
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