Biofouling Methods

Biofouling Methods provides a "cook book" for
both established workers and those new to the field. The methods
included in this important new book range from tried and tested
techniques to those at the cutting edge, encompassing the full
diversity of this multidisciplinary field.

The book covers methods for microbial and macrofouling, coatings
and biocides, and ranges from methods for fundamental studies to
methods relevant for industrial applications. There is an emphasis
on answering questions and each chapter provides technical methods
and problem-solving hints and tips.

Bringing together a wealth of international contributions and
edited by three internationally known and respected experts in the
subject Biofouling Methods is the essential methodology
reference in the field for all those working in the antifouling
industry including those involved in formulation of antifouling
products such as paints and other coatings. Aquatic biologists,
ecologists, environmental scientists and lawyers, marine engineers,
aquaculture personnel, chemists, and medical researchers will all
find much of interest within this book. All universities and
research establishments where these subjects are studied and taught
should have copies of this important work on their shelves.

Autorentext

Dr. Sergey Dobretsov has worked for more than 20 years on
biofouling, is widely published, and is the co-inventor on four
international antifouling patents. He trained as a biologist in St
Petersburg State University, Russia, and has worked in leading
biofouling research centers in Russia, Hong Kong, Germany, and the
USA. He is currently an Assistant Professor at Sultan Qaboos
University, Oman. He is on the editorial boards of the journals
Marine Ecology Progress Series and Biofouling.

Dr. David N. Williams is the RD&I Director for
AkzoNobel Marine & Protective Coatings. Based in the North East
of England he originally trained as a chemist at Durham University
and at Lausanne University, Switzerland. His specific expertise is
in the area of nonbiocidal antifouling technologies and he is the
co-inventor on a number of patents on silicone foul-release
coatings and applications.

Dr. Jeremy C. Thomason is a marine biologist, a former
academic at a British University and Royal Society Industrial
Research Fellow, and now runs a scientific and technical
consultancy, Ecoteknica, from the Yucatán, México. He has
worked in the field of biofouling for more than 20 years, is
co-inventor on several patents, and is a co-editor of the book
Biofouling also published by Wiley Blackwell in 2010.

Zusammenfassung

Biofouling Methods provides a cook book for both established workers and those new to the field. The methods included in this important new book range from tried and tested techniques to those at the cutting edge, encompassing the full diversity of this multidisciplinary field.

The book covers methods for microbial and macrofouling, coatings and biocides, and ranges from methods for fundamental studies to methods relevant for industrial applications. There is an emphasis on answering questions and each chapter provides technical methods and problem-solving hints and tips.

Bringing together a wealth of international contributions and edited by three internationally known and respected experts in the subject Biofouling Methods is the essential methodology reference in the field for all those working in the antifouling industry including those involved in formulation of antifouling products such as paints and other coatings. Aquatic biologists, ecologists, environmental scientists and lawyers, marine engineers, aquaculture personnel, chemists, and medical researchers will all find much of interest within this book. All universities and research establishments where these subjects are studied and taught should have copies of this important work on their shelves.

Inhalt
List of Contributors xii Introduction xvi

Guide to Methods xviii

Part I Methods for Microfouling 1

Part Editor: Sergey Dobretsov

1 Microscopy of biofilms 3

Section 1 Traditional light and epifluorescent microscopy 4
Sergey Dobretsov and Raeid M.M. Abed

1.1 Introduction 4

1.2 Determination of bacterial abundance 8

1.3 Catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) 9

1.4 Suggestions, with examples, for data analysis and presentation 12

Acknowledgements 13

References 13

Section 2 Confocal laser scanning microscopy 15
Koty Sharp

1.5 Introduction 15

1.6 Materials, equipment, and method 18

1.7 Image acquisition 21

1.8 Presentation 21

1.9 Troubleshooting hints and tips 21

1.10 Notes 23

References 23

Section 3 Electron microscopy 26
Omar Skalli, Lou G. Boykins, and Lewis Coons

1.11 Introduction 26

1.12 Transmission electron microscopy (TEM) 27

1.13 Scanning electron microscopy (SEM) 35

References 40

2 Traditional and bulk methods for biofilms 44

Section 1 Traditional microbiological methods 45
Hans-Uwe Dahms

2.1 Introduction 45

2.2 Enrichment culture, isolation of microbes 45

2.3 Counting methods 48

2.4 Troubleshooting hints and tips 49

References 50

Section 2 Bulk methods 52
Sergey Dobretsov

2.5 Introduction 52

2.6 Measurement of biofilm thickness 53

2.7 Biofilm dry weight determination 54

2.8 Biofilm ATP content 55

2.9 Troubleshooting hints and tips 56

Acknowledgements 57

References 57

3 Biocide testing against microbes 58

Section 1 Testing biocides in solution: flow cytometry for planktonic stages 59
Tristan Biggs, Tom Vance, and Glen Tarran

3.1 Introduction 59

3.2 Method introductions 60

3.3 Pros and cons 66

3.4 Materials and equipment 67

3.5 Methods 68

3.6 Troubleshooting hints and tips 70

3.7 Suggestions 71

References 72

Section 2 Biocide testing using single and multispecies biofilms 76
Torben Lund Skovhus

3.8 Introduction 76

3.9 Questions to answer when applying biocides 76

3.10 Laboratory methods for testing biocide effect 78

3.11 Field methods for testing biocide effect 81

3.12 Troubleshooting hints and tips 83

Acknowledgements 84

References 84

4 Molecular methods for biofilms 87

Section 1 Isolation of nucleic acids 88
Isabel Ferrera and Vanessa Balagué

4.1 Introduction 88

4.2 Materials 89

4.3 Isolation of DNA from a biofilm 90

4.4 Troubleshooting hints and tips 91

References 91

Section 2 PCR and DNA sequencing 93
Christian R. Voolstra, Manuel Aranda, and Till Bayer

4.5 PCR and DNA sequencing: General introduction 93

4.6 PCR 93

4.7 Microbial marker genes 16S 94

4.8 DNA sequencing 95

4.9 454 16S amplicon pyrotag sequencing 95

4.10 Protocol 1: DNA extraction using the Qiagen DNeasy Plant Mini Kit 96

4.11 Protocol 2: Full-length 16S PCR using the Qiagen Multiplex Kit 98

4.12 Protocol 3: Analysis of full-length 16S genes 100

4.13 Protocol 4: 16S amplicon PCR for 454 sequencing using the Qiagen Multiplex Kit 102

4.14 Protocol 5: Trimming and filtering of 454 16S pyrotag sequencing 106 4.15 Protocol 6: Taxon-based ana...