Biofouling Methods.

Intro -- Biofouling Methods -- Copyright -- Contents -- List of contributors -- Introduction -- Guide to methods -- Part I Methods for Microfouling -- Chapter 1 Microscopy of biofilms -- Section 1: Traditional light and epifluorescent microscopy -- 1.1 Introduction -- 1.2 Determination of bacterial abundance -- 1.3 Catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) -- 1.4 Suggestions, with examples, for data analysis and presentation -- Acknowledgements -- References -- Chapter 2 Traditional and bulk methods for biofilms -- Section 1: Traditional microbiological methods -- 2.1 Introduction -- 2.2 Enrichment culture, isolation of microbes -- 2.3 Counting methods -- 2.4 Troubleshooting hints and tips -- References -- Section 2 Bulk methods -- 2.5 Introduction -- 2.6 Measurement of biofilm thickness -- 2.7 Biofilm dry weight determination -- 2.8 Biofilm ATP content -- 2.9 Troubleshooting hints and tips -- Acknowledgements -- References -- Chapter 3 Biocide testing against microbes -- Section 1: Testing biocides in solution: flow cytometry for planktonic stages -- 3.1 Introduction -- 3.2 Method introductions -- 3.3 Pros and cons -- 3.4 Materials and equipment -- 3.5 Methods -- 3.6 Troubleshooting hints and tips -- 3.7 Suggestions -- References -- Section 2 Biocide testing using single and multispecies biofilms -- 3.8 Introduction -- 3.9 Questions to answer when applying biocides -- 3.10 Laboratory methods for testing biocide effect -- 3.11 Field methods for testing biocide effect -- 3.12 Troubleshooting hints and tips -- Acknowledgements -- References -- Chapter 4 Molecular methods for biofilms -- Section 1: Isolation of nucleic acids -- 4.1 Introduction -- 4.2 Materials -- 4.3 Isolation of DNA from a biofilm -- 4.4 Troubleshooting hints and tips -- References -- Section 2 PCR and DNA sequencing.

4.5 PCR and DNA sequencing: General introduction -- 4.6 PCR -- 4.7 Microbial marker genes - 16S -- 4.8 DNA sequencing -- 4.9 454 16S amplicon pyrotag sequencing -- 4.10 Protocol 1: DNA extraction using the Qiagen DNeasy Plant Mini Kit -- 4.11 Protocol 2: Full-length 16S PCR using the Qiagen Multiplex Kit -- 4.12 Protocol 3: Analysis of full-length 16S genes -- 4.13 Protocol 4: 16S amplicon PCR for 454 sequencing using the Qiagen Multiplex Kit -- 4.14 Protocol 5: Trimming and filtering of 454 16S pyrotag sequencing -- 4.15 Protocol 6: Taxon-based analyses -- 4.16 Protocol 7: Phylogeny-based analyses -- References -- Section 3 Community comparison by genetic fingerprinting techniques -- 4.17 Introduction -- 4.18 History and principles of the methods -- 4.19 Advantages and limitations of fingerprinting techniques -- 4.20 Materials and equipment -- 4.21 Suggestions for data analysis and presentation -- 4.22 Troubleshooting hints and tips -- Acknowledgements -- References -- Section 4 Metagenomics -- 4.23 Introduction and brief summary of methods -- 4.24 Overview of metagenomics methods -- 4.25 Method introduction -- 4.26 Overview of DNA handling for BAC library construction -- 4.27 BAC and Fosmid library construction -- 4.28 Library handling, archiving, and databasing -- 4.29 Facilitating library screening -- 4.30 Time frame considerations -- 4.31 Materials and equipment -- 4.32 Detailed methods: DNA handling and BAC library construction -- 4.33 Troubleshooting tips -- 4.34 Suggestions for data analysis -- 4.35 Suggestions for presentation of data -- Acknowledgements -- References -- Chapter 5 Methods for biofilm constituents and turnover -- Section 1: Destructive and nondestructive methods -- 5.1 Introduction -- 5.2 Pros and cons of destructive and nondestructive M-LSM methods for biofilm analysis.

5.3 Materials and equipment required for M-LSM -- 5.4 Example of questions than can be answered with the method -- 5.5 Suggestions for data analysis and presentation -- References -- Section 2: Biofilm formation and quorum sensing bioassays -- 5.6 Introduction -- 5.7 Materials and equipment -- 5.8 Methods -- Acknowledgements -- References -- Chapter 6 Sampling and experiments with biofilms in the environment -- Section 1: Field trials with biofilms -- 6.1 Introduction -- 6.2 Materials and equipment -- 6.3 Method -- 6.4 Troubleshooting hints and tips -- 6.5 Suggestions for data analysis and presentation -- References -- Section 2: Sampling from large structures such as ballast tanks -- 6.6 Introduction -- 6.7 Materials and equipment -- 6.8 Troubleshooting hints and tips -- 6.9 Analytical methods -- 6.10 Suggestions for data analysis and presentation -- References -- Section 3: Sampling from living organisms -- 6.11 Introduction -- 6.12 Historical background -- 6.13 Advantages and limitations of collection techniques -- 6.14 Protocols -- 6.15 Suggestions for data analysis -- 6.16 Troubleshooting hints and tips -- Acknowledgment -- References -- Section 4: Optical methods in the field -- 6.17 Introduction -- 6.18 Examples of the use of optical methods -- 6.19 Spectral characteristics of biofilms -- 6.20 The use of chlorophyll-a as an index of biomass of biofilm -- 6.21 Multi-versus hyperspectral measurements (CIR imagery versus field spectrometry) -- 6.22 Calibration of data to reflectance -- 6.23 Suggestions for data analysis and presentation -- 6.24 Methods -- 6.25 Troubleshooting hints and tips -- References -- Chapter 7 Laboratory experiments and cultures -- Section 1: Static, constant depth and/or flow cells -- 7.1 Introduction -- 7.2 Portable Biofouling Unit -- 7.3 Pros and cons of the method -- 7.4 Materials and equipment.

7.5 Suggestions for data analysis -- 7.6 "Benchmark" bacteria and biofilm characterization -- 7.7 Troubleshooting hints and tips -- References -- Section 2: Mixed population fermentor -- 7.8 Introduction -- 7.9 Pros and cons -- 7.10 Fermentor -- 7.11 Mixed species microfouling culture -- 7.12 Utilizing the fermentor test section -- 7.13 Troubleshooting, hints and tips -- References -- Part II Methods for Macrofouling, Coatings and Biocides -- Chapter 8 Measuring larval availability, supply and behaviour -- Section 1: Larval availability and supply -- 8.1 Introduction to measuring larval availability and supply -- 8.2 Measuring settlement and recruitment -- References -- Section 2: Larval behavior -- 8.3 Introduction -- 8.4 Method for tracking larvae -- 8.5 Troubleshooting hints and tips -- 8.6 Suggestions for data analysis and presentation -- References -- Chapter 9 Assessing macrofouling -- Section 1 Assessing fouling assemblages -- 9.1 Introduction -- 9.2 A note on taxonomy -- 9.3 Field methods -- 9.4 Digital methods -- 9.5 Functional groups -- 9.6 Predicting total richness: from the known to the unknown -- References -- Section 2 : Assessment of in-service vessels for biosecurity risk -- 9.7 Introduction -- 9.8 Surveys of vessel hulls -- 9.9 Sample and data analysis -- Acknowledgements -- References -- Section 3: Experiments on a global scale -- 9.10 Experiments in ecology: the need for scaling up -- 9.11 GAME - a program for modular experimental research in marine ecology -- 9.12 Marine macrofouling communities as model systems -- 9.13 Chronology of a GAME project -- Acknowledgements -- References -- Chapter 10 Efficacy testing of nonbiocidal and fouling-release coatings -- 10.1 Introduction -- 10.2 Test organisms -- 10.3 Test samples -- 10.4 "Antifouling" settlement assays -- 10.5 Fouling-release assays.

10.6 Adhesion assays for high-throughput screening -- 10.7 Apparatus -- Acknowledgements -- References -- Chapter 11 Contact angle measurements -- Section 1: Surface characterization by contact angle measurements -- 11.1 Introduction -- 11.2 Liquids in contact with solids -- 11.3 Reproducible contact angle measurements -- 11.4 Surface energy calculations -- References -- Section 2 Underwater contact angle measurement by the captive bubble method -- 11.5 Introduction -- 11.6 Materials and requirements -- 11.7 Method -- 11.8 Surface energy -- Acknowledgements -- References -- Chapter 12 Efficacy testing of biocides and biocidal coatings -- 12.1 Introduction -- 12.2 Laboratory assays for biocides -- 12.3 Field test methodology for biocidal coatings -- References -- Chapter 13 Commercialization -- Section 1: Processing a new marine biocide from innovation through regulatory approvals towards commercialization -- 13.1 Introduction -- 13.2 Basics about the regulatory landscape from the academic perspective -- 13.3 Risk, risk assessment and risk management -- 13.4 Future directions -- 13.5 Conclusions -- References -- Section 2: From laboratory to ship: pragmatic development of fouling control coatings in industry -- 13.6 Introduction -- 13.7 Laboratory coating development -- 13.8 Laboratory bioassay screening -- 13.9 Fitness for purpose (FFP) testing -- 13.10 Field antifouling performance testing -- 13.11 Test patch and vessel trials -- 13.12 Performance monitoring -- 13.13 Summary -- References -- Index -- Supplemental Images.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.