Search

Bacteriophage viruses (phages) are seemingly ubiquitous across all niches on earth occupied by their bacterial hosts. These phages can either integrate into the genomes of bacterial hosts or reproduce within, and then lyse their host cells. In both cases phages are able to shape the evolution and ecology of bacterial populations, often with important consequences for other interacting species or ecological and biogeochemical processes that depend on microbial organisms. This article explores the process and impact of bacteria–phage coevolution as evidenced from both controlled laboratory experiments and studies of natural populations.

Bacteriophages (phages) are the viruses of bacteria and the study of phage biology can be differentiated, roughly, into molecular, environmental, evolutionary, ecological, and applied aspects. While for much of the past fifty-plus years molecular and then applied aspects have dominated the field, more recently environmental concerns, especially the phage impact on biogeochemical cycles, have driven an increase in the appreciation of phage ecology. Over approximately the same time frame, decreasing sequencing costs have combined with phage molecular characterization to give rise to an inescapable consideration of phage comparative genomics. That, along with environmental metagenomics, has stimulated, especially among molecular biologists, a more general interest in phage evolutionary biology. However, while reviews of phage ecology have become exceedingly common, overviews of phage evolutionary biology are comparatively rare, and broad considerations of phage evolutionary biology drawn from an ecological perspective rarer still. In this chapter I jump into this latter void, providing an overview of phage evolutionary biology as viewed from the perspective of phage-environment interactions, that is, from the perspective of phage ecology. This I do over five sections constituting (1) an introduction to phages and how, phenotypically, they can be differentiated into three basics types that correlate, more or less, with genomic size, that is, tailed (generally larger genomes), lipid-containing (medium-sized genomes), and single-stranded (small genomes); (2) a brief introduction to phage ecology as considered particularly from a classical ecological perspective; (3) an extended introduction to evolutionary biology as viewed from a phage and phage-ecological standpoint; (4) phage evolutionary ecology, that is, consideration of phage adaptations from the vantage of why, in terms of phage fitness, those adaptations may have evolved; and (5) phage evolutionary biology, including evolutionary ecology, as viewed from the perspective of phage genomics.

Publisher Summary This chapter emphasizes the importance of using island systems to test and apply ecological principles so as to better understand bacterial community assembly, and bacterial spatial and temporal scaling. Bacteria comprise one of the three domains of life the [other two are Archaea and Eukaryota (which includes all of the animals and plants)] and are ubiquitous in the environment, living in every conceivable habitat on Earth. Although invisible to the naked eye, bacteria and their communities are central to health, agriculture, sustainable cities, and play key roles in many of the Earth's geochemical cycles. Patterns in bacterial diversity will give us a better understanding on how bacteria are distributed spatially and temporally. The studies of biogeography and spatial scaling are outlined in this chapter. In time, this will in turn provide important information about the underlying mechanisms that regulate microbial diversity and the complexity of the ecosystems they inhabit; this can be achieved by utilizing, testing and adapting theories and principles developed in general ecology.

Bacteriophage are viruses of bacteria. An enormous number of bacteriophages are found the world over, on the order of 1030 or more. This article first presents an overview of techniques employed to characterize phage existence in natural environments, including by direct microscopic count, viable count, and various molecular means of phage in situ characterization. Then it provides an overview of the science of phage ecology. This overview is followed by four sections in which four subdisciplines of phage ecology – phage organismal ecology, phage population ecology, phage community ecology, and phage ecosystem ecology – are discussed in detail. These represent, respectively, (1) the impact of phage growth parameters (such as latent period, burst size, and virion resistance to decay) on phage ecological success, (2) phage population growth and intraspecific interaction, (3) the phage impact especially on bacterial communities, and (4) the phage impact on environmental energy flow and nutrient cycling. Note that these various means of looking at phage ecology build upon one another.

Bacteriophages were discovered in 1915 (Twort) and 1917 (d’Herelle). During the early period (1939–40), the viral nature of phages was questioned and finally proven by electron microscopy. Phage therapy started in 1919 and is still practiced. Phages were used for epidemiology of bacterial diseases (phage typing). The intermediate (1939–62) period is associated with the development of molecular biology. Phage research inspired techniques and concepts of general virology, notably the concept of latency. Lysogenic phages have a dual nature with a vegetative and a lysogenic cycle. Latent phage genomes (prophages) often carry bacterial virulence genes (e.g., for toxins). Phage typing became widespread. The present period (1965–today) is characterized by diversification of phage research, discovery of new phages and phage families, and development of phage taxonomy. At least 5500 phages are presently known, including phages for cyanobacteria and archaea. The most important research fields are phage morphology, assembly, and three-dimensional structure; genome sequencing and genomics; phage evolution; role of phages in bacterial pathogenesis; role of phages in the dairy industry; practical applications (as indicators of fecal pollution; for bacterial detection, biotechnology, ‘phage display’, phage therapy); and phage ecology.

Phenotypic characterization will be a pivotal aspect of future research in understanding the biofilm mode of growth. We hope that the concepts and techniques presented in this chapter will benefit other investigators in this field. Although initial studies will necessarily involve monocultures, eventually mixed culture work will have to be performed to understand biofilm growth in the natural environment. As the study of biofilm-phage interactions is new, there is considerable fundamental work that needs to be addressed. Here, we anticipate that some phage are better adapted to growth in biofilms, some are adept in growing in mixed culture biofilms, and others are better adapted to infecting planktonic organisms. Whereas biofilms are now widely accepted as a fundamental aspect of microbial growth in nature, the field of phage ecology is quite new and an exciting challenge for the future.