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Biofilms /

Biofilms, Volume 53 in the ongoing Methods in Microbiology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of timely topics, including Monospecies and polymicrobial biofilms in static and flow environment, Methods used to study biofilms,...

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Bibliographic Details
Corporate Author: ScienceDirect (Online service)
Other Authors: Gurtler, Volker (Editor), Patrauchan, Marianna (Editor)
Format: eBook
Language:English
Published: London ; San Diego, CA : Academic Press, 2023.
Edition:First edition.
Series:Methods in microbiology ; v. 53.
Subjects:
Biofilms.
Biofilms > Environmental aspects.
Microbiology > Microbiology.
Biofilms > Aspect de l'environnement.
Microbiologie > Microbiologie.
Biofilms
Electronic books.
Online Access:Connect to the full text of this electronic book
Table of Contents:
  • Intro
  • Biofilms
  • Copyright
  • Contents
  • Contributors
  • Preface
  • References
  • Section 1: Plant biofilms
  • Chapter 1: Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions
  • 1. Introduction
  • 2. Rhizosphere-A microbial habitat shaped by root exudates
  • 3. Experimental approaches for studying rhizosphere biofilms
  • 3.1. Growing biofilms in the presence of root exudates
  • 3.2. The use of microfluidics in the rhizosphere biofilm research
  • 3.3. Integration of rhizosphere biofilm research with microscopy
  • 3.4. Other emerging approaches for mapping rhizosphere biofilms
  • 4. Sensing the plant host: Bacterial chemotaxis towards plant roots exudates
  • 5. Colonizing the plant root
  • 5.1. Attachment to plant roots
  • 5.2. The rhizosphere biofilm matrix
  • 5.3. Regulatory mechanisms that govern the biofilm lifestyle
  • 6. The importance of rhizosphere biofilms
  • 7. Conclusions
  • Acknowledgements
  • References
  • Section 2: Mixed species
  • Chapter 2: Monospecies and polymicrobial biofilms in static and flow environment
  • 1. Introduction
  • 2. Biofilm and flow environment
  • 3. Key resources table
  • 4. Materials and equipment
  • 5. Step-by-step method details
  • 5.1. Growth of microorganisms
  • 5.2. Static biofilm formation
  • 5.3. Crystal violet assay
  • 5.4. XTT reduction assay
  • 5.5. Flow cell preparation
  • 5.6. Flow-cell biofilm formation
  • 5.7. Flow-cell gel acrylamide preparation
  • 5.8. In situ hybridization (FISH) staining
  • 5.9. Confocal laser scanning microscopy and image analysis
  • 5.9.1. Expected outcomes
  • 6. Quantification and statistical analysis
  • 6.1. Advantages
  • 6.2. Limitations
  • 7. Optimization and troubleshooting
  • 7.1. Potential Solution to optimize the procedure
  • 8. Safety considerations and standards
  • 9. Alternative methods/procedures
  • References.
  • Further reading
  • Chapter 3: Optimization of protocol for quantification of biofilm formed by pathogenic rapidly-growing nontuberculous mycobac
  • 1. Introduction
  • 1.1. Biofilm
  • 1.1.1. Factors influencing biofilm formation
  • 1.1.2. Quorum sensing
  • 1.2. The nontuberculous mycobacteria (NTM)
  • 1.2.1. Transmission of NTM
  • 1.2.2. Mycobacterium fortuitum
  • 1.2.3. Mycobacterium chelonae
  • 1.2.4. Mycobacterium abscessus
  • 1.3. NTM biofilm
  • 1.4. Biofilm estimation methods
  • 1.4.1. Crystal violet assay
  • 1.4.2. Viable plate count method (CFU counting)
  • 1.4.3. Microscopy
  • 1.4.3.1. Light icroscopy
  • 1.4.3.2. Scanning electron microscopy (SEM)
  • 1.4.3.3. Confocal scanning laser microscopy (CSLM)
  • 1.4.3.4. Atomic force microscopy (AFM)
  • 1.4.4. Congo red agar method
  • 1.4.5. Fluorescent dyes and proteins
  • 1.4.6. Next-generation sequencing
  • 1.5. Outline of the chapter
  • 1.5.1. Notes
  • 2. Biofilm culture of the NTM strain
  • 2.1. Materials, equipment, and reagents
  • 2.2. Protocols
  • 2.2.1. Growth of planktonic NTM culture
  • 2.2.2. Ziehl-Neelsen staining
  • 2.2.3. NTM biofilm formation protocol
  • 2.3. Safety considerations and standards
  • 2.4. Analysis and statistics
  • 2.5. Pros and cons
  • 2.6. Troubleshooting and optimization
  • 3. Crystal violet assay of the NTM biofilm
  • 3.1. Materials, equipment, and reagents
  • 3.2. Protocol
  • 3.3. Safety considerations and standards
  • 3.4. Analysis and statistics
  • 3.5. Pros and cons
  • 3.6. Troubleshooting and optimization
  • 4. Response surface methodology based optimization of culture conditions favouring maximum biofilm formation by NTM
  • 4.1. Materials, equipment, and reagents
  • 4.2. Protocol
  • 4.2.1. RSM design of experiment (DoE)
  • 4.2.2. RSM experimental runs
  • 4.2.3. RSM ANOVA, regression, and graphical analysis
  • 4.2.4. RSM numerical optimization.
  • 4.3. Safety considerations and standards
  • 4.4. Analysis and statistics
  • 4.5. Pros and cons
  • 4.6. Troubleshooting and optimization
  • 5. Sonication and colony forming unit (CFU) count of NTM biofilm
  • 5.1. Materials, equipment, and reagents
  • 5.2. Protocols
  • 5.2.1. Sonication of NTM biofilm
  • 5.2.2. Serial dilution and plating
  • 5.3. Safety considerations and standards
  • 5.4. Analysis and statistics
  • 5.5. Pros and cons
  • 5.6. Troubleshooting and optimization
  • 6. Determination of the number of days required for NTM biofilm formation
  • 6.1. Materials, equipment, and reagents
  • 6.2. Protocols
  • 6.2.1. Crystal violet assay of the NTM biofilm
  • 6.2.2. Sonication and CFU count of NTM biofilm
  • 6.3. Safety considerations and standards
  • 6.4. Analysis and statistics
  • 6.5. Pros and cons
  • 6.6. Troubleshooting and optimization
  • 7. Basic fuchsin staining of biofilm-forming cells of the pathogenic NTM strain
  • 7.1. Materials, equipment, and reagents
  • 7.2. Protocol
  • 7.3. Safety considerations and standards
  • 7.4. Analysis and statistics
  • 7.5. Pros and cons
  • 7.6. Troubleshooting and optimization
  • 8. Scanning electron microscopy (SEM) of NTM planktonic and biofilm-forming cells
  • 8.1. Materials, equipment, and reagents
  • 8.2. Protocols
  • 8.2.1. Culture and growth of NTM biofilm
  • 8.2.2. Preparation of 1L 0.1M phosphate buffered saline (PBS) (pH 7.4)
  • 8.2.3. NTM biofilm cell-fixation
  • 8.2.4. Dehydration of NTM biofilm-forming cells using ethanol gradient
  • 8.2.5. FEGSEM of NTM biofilm-forming cells
  • 8.2.6. SEM of planktonic NTM cells
  • 8.3. Safety considerations and standards
  • 8.4. Analysis and statistics
  • 8.5. Pros and cons
  • 8.6. Troubleshooting and optimization
  • 9. Conclusion
  • Acknowledgement
  • References.
  • Chapter 4: Investigating inter-kingdom interaction between oral Streptococcus mutans and Candida species in mixed
  • 1. Introduction
  • 2. Materials and methods
  • 2.1. Bacterial strains, media, and growth condition
  • 2.2. Biofilm formation
  • 2.2.1. Preparing the inoculum
  • 2.2.2. Biofilm formation on coverslips
  • 2.2.3. Biofilms initiated by shear flow
  • 2.3. Staining biofilms grown on a coverslip
  • 2.4. Biofilm examination and image acquisition
  • 2.4.1. Extracellular polymeric substance (EPS) formation in the biofilm by microscopy
  • 2.4.2. Examination of the biofilms formed on coverslips by confocal microscopy
  • 2.4.3. Examination of the biofilms formed on the BioFlux plate by fluorescence microscopy
  • 2.5. Microbial growth assay
  • 2.6. pH measurement
  • 2.7. Measuring the effect of antimicrobial agents on biofilms
  • 2.8. Statistical analysis
  • 3. Results and discussions
  • 3.1. Growth of S. mutans and Candida species and experimental conditions
  • 3.2. Formation of biofilms in the microchannel of the BioFlux plate
  • 3.3. Structural examination of the mono-species and mixed-species biofilms
  • 3.4. Characteristic comparison of the bacterium-fungal mixed-species biofilms
  • 3.5. Characterization of antimicrobial activity on co-culture
  • 4. Conclusion
  • References
  • Section 3: Nano techniques
  • Chapter 5: Programming bacterial adhesion to functionalized surfaces through cellular display of recombinant nanobodies
  • 1. Introduction
  • 2. Materials
  • 2.1. Strains and plasmids
  • 2.2. Bacterial growth media
  • 2.3. Chemicals and reagents
  • 2.4. DNA and protein techniques
  • 2.5. Other laboratory material
  • 3. Methods
  • 3.1. Introducing the recombinant adhesin expression plasmid into E. coli
  • 3.1.1. Preparation of E. coli competent cells
  • 3.1.2. Plasmid transformation
  • 3.2. Testing the expression of the recombinant adhesin.
  • 3.2.1. Recombinant protein expression, purification and SDS-PAGE
  • 3.2.2. Detection of recombinant fusion proteins by western blot
  • 3.3. Assaying the display of the recombinant adhesin
  • 3.4. Evaluating the functionality of the recombinant adhesin
  • 3.4.1. Functionalization of surfaces with protein of interest
  • 3.4.2. Bacterial attachment visualization
  • 3.4.3. Bacterial attachment quantification
  • 4. Notes/troubleshooting
  • Acknowledgements
  • References
  • Chapter 6: Micro- and nanoscale techniques for studying biofilm-mineral interactions
  • 1. Introduction
  • 2. Confocal laser scanning microscopy (CLSM) to image biofilm-minerals assemblages in situ, at the submicrometer scale
  • 3. Optical coherence tomography (OCT) to in situ characterize the structure of thick biofilms at the micrometre scale ove ...
  • 4. Atomic force microscopy (AFM) to image the topography, and mechanical, electrical and chemical properties of biofilm-m ...
  • 5. Vertical scanning interferometry (VSI) to quantify dissolution rates of mineral substrates covered by biofilms
  • 6. Analyses of biofilm-mineral interactions down to the nanometre scale by scanning electron microscopy and helium ion mi ...
  • 7. Focused ion beam milling for TEM sample preparation and 3D nanoscale investigation of biofilm-mineral interactions
  • 8. Transmission electron microscopy (TEM) to study biofilm-mineral interactions
  • 9. Characterizing chemical element distribution and speciation in biofilm-mineral assemblages by spectroscopies
  • Acknowledgements
  • References
  • Section 4: Genetics and microfluidics
  • Chapter 7: Methods for studying biofilms: Microfluidics and translation in the clinical context
  • 1. Introduction
  • 2. General in vitro methods to study biofilms
  • 2.1. Static or closed models
  • 2.1.1. Classic static models
  • 2.1.2. Novel static models.