As I found when preparing the second edition of this text, advances in genetics continue to be made at an ever increasing rate, which presents something of a dilemma when writing an introductory text on the subject. In the years since the second edition was published, many new applications of gene manipulation technology have been developed, covering an increasingly diverse range of disciplines and applications. The temptation in preparing this third edition, as was the case for its predecessor, was to concentrate on the applications and ignore the fundamental principles of the technology. However, in initial preparation I was convinced that a basic technical introduction to the subject should remain the major focus of the text. Thus, some of the original methods used in gene manipulation have been kept as examples of how the technology developed, even though some of these have become little used or even obsolete. From the educational point of view, this should help the reader cope with more advanced information about the subject, as a sound grasp of the basic principles is an important part of any introduction to genetic engineering. I have again been gratified by the many positive comments about the second edition, and I hope that this new edition continues to serve a useful purpose as part of the introductory literature on this fascinating subject.

In trying to strike a balance between the methodology and the applications of gene manipulation, I have retained the division of the text into three sections.

INTRODUCTION

Bacteriophages have a long history as objects of biological study. They were discovered about 90 years ago and have engaged biologists ever since, initially for their potential in combating human disease through phage therapy. Later, phages served as arguably the most important model systems in the development of the discipline of molecular biology and the associated explosion of knowledge about the detailed workings of genes and cells. Yet it is only in very recent years that the study of phage evolution has attracted the attention of more than a handful of individuals. The primary reasons for the current increased interest in phage evolution, I would suggest, are two: discovery, over the past 20 years, of astonishingly high phage population numbers in the natural environment, and improved, low-cost methods of phage genotypic analysis, especially DNA sequencing. In this chapter I discuss the abundance and diversity of the global phage population, with an emphasis on what we are learning from comparative genomic studies about the mechanisms by which it has evolved to its current state.

Chapter 6 provides an introduction to basic evolutionary mechanisms of phage evolution. See Hendrix (2003), Casjens (2005), and Brüssow and Desiere (2006) for additional reviews of phage evolution from the perspective of genomic studies.

INTRODUCTION

Phage ecology, considering the ecological significance of native viruses in natural aquatic ecosystems, has had a momentous development since the early 1990s, when it was acknowledged that the abundance of viruses in natural aquatic ecosystems was much higher than had been anticipated. During that time new methods and approaches have been applied to the study of viral communities as well as different aspects of viral activity in natural ecosystems. It has been necessary to develop new concepts and models to interpret these new data and knowledge within the context of ecosystem structure and function. Several excellent reviews provide a comprehensive summary and analysis of the data and information that has accumulated (Fuhrman, 1999; Wilhelm and Suttle, 1999; Wommack and Colwell, 2000; Paul et al., 2002; Weinbauer, 2004; Suttle, 2005) and the reader should consult these for a more complete review of the literature. The purpose of the present chapter is to provide a brief overview of contemporary aquatic phage ecology, including a closer look at the extent to which present theory can be claimed to explain the observations now available.

Based on the numerical dominance of prokaryote over eukaryote unicellular organisms in the pelagic environment (a factor of 2–3 orders of magnitude), the usual assumption is that the population of free viruses is dominated by bacteriophages.

INTRODUCTION

From the perspective of evolutionary studies, phages offer benefits of short generation times, small genomes, and ease of propagation. These advantages apply chiefly to the use of phages in laboratory experiments, however. Although some understanding of phage evolution in a natural environment can be inferred from genome sequences, we have precious little understanding of the natural environment of any phage and are even ignorant of what constitutes the population of a phage. So when phages are used as model systems of evolution, with tight controls on host strains, host density, media, temperature, and population sizes, it must be assumed that we are hoping to discover generalities that transcend the specific context of the lab environment. It certainly cannot be pretended that our systems create miniature replicas of what a phage experiences naturally, which would have too many uncontrolled variables to do science. In this chapter I explore phage evolutionary biology from the perspective of laboratory experimentation, considering in particular a statistical fitness perspective on phage evolution rather than the more common functional perspective as considered, for example, in Part I (Phage ecology) of this monograph. See Chapter 6 for a general introduction to many of the concepts presented here.