Biofouling Methods -  - ebook

Biofouling Methods ebook

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Opis

Biofouling Methods provides a "cook book" forboth established workers and those new to the field. The methodsincluded in this important new book range from tried and testedtechniques to those at the cutting edge, encompassing the fulldiversity of this multidisciplinary field. The book covers methods for microbial and macrofouling, coatingsand biocides, and ranges from methods for fundamental studies tomethods relevant for industrial applications. There is an emphasison answering questions and each chapter provides technical methodsand problem-solving hints and tips. Bringing together a wealth of international contributions andedited by three internationally known and respected experts in thesubject Biofouling Methods is the essential methodologyreference in the field for all those working in the antifoulingindustry including those involved in formulation of antifoulingproducts such as paints and other coatings. Aquatic biologists,ecologists, environmental scientists and lawyers, marine engineers,aquaculture personnel, chemists, and medical researchers will allfind much of interest within this book. All universities andresearch establishments where these subjects are studied and taughtshould have copies of this important work on their shelves.

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Liczba stron: 821




CONTENTS

Cover

Title page

Copyright page

List of contributors

Introduction

Guide to methods

Part I: Methods for Microfouling

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

Section 2: Confocal laser scanning microscopy

1.5 Introduction

1.6 Materials, equipment, and method

1.7 Image acquisition

1.8 Presentation

1.9 Troubleshooting hints and tips

1.10 Notes

References

Section 3: Electron microscopy

1.11 Introduction

1.12 Transmission electron microscopy (TEM)

1.13 Scanning electron microscopy (SEM)

References

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

3 Biocide testing against microbes

Section 1: Testing biocides in solution

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

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

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

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

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

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

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

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

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

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

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

End User License Agreement

List of Tables

Chapter 01

Table 1.1 Pros and cons of light and epifluorescent microscopy.

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