Bacteriophage Ecology

Abstract

Ecology is the study of the interactions of organisms with their environments. Environments consist of biotic components (e.g., cellular organisms such as bacterial hosts) and abiotic components (e.g., temperature, pH, or ultraviolet radiation). Bacteriophage ecology thus is the study of the interactions of bacteriophages (phages) with biotic as well as abiotic aspects of their environments. The fundamental focus of ecology tends to be on populations, that is, genetically coherent groupings of organisms (species). Often this also involves considerations of the ecology of communities (interactions among multiple species in the same area) as well as the ecology of ecosystems (which include, conceptually, both communities and abiotic aspects of environments). Also within the purview of ecology are evolutionarily relevant interactions between organisms such as antagonistic coevolution, which here would be “arms races” between phages and bacteria. Ecology can be studied either observationally or empirically. Metagenomics, the study of the collective genetic material acquired from environmental samples, currently is the most prominent means of observational study in environmental microbiology, the latter an aspect of microbial ecology and thus (especially as viromics) of phage ecology as well. Empirical studies, by contrast, commonly use “models” to explore ecology, including ones exploring phage ecology. These models range from broth culture-based experiments in the laboratory to experimental microcosms located in situ, the latter such as in a pond but still separated from the pond. Particularly as theoretical studies, models also can be mathematical or computer-based. All of these approaches can be combined toward comprehending how individual organisms, groups of organisms, ecosystems, or even groups of ecosystems function in nature. In this chapter, we consider the ecology of phages as well as the ecological aspects of their evolutionary biology. As what is addressed can be considered to be the bulk of phage biology as found outside of well-controlled laboratory systems, the chapter covers substantial ground. As complementary material in this volume, we point the reader to the biology of phage productive infections, lysogeny, bacterial resistance to phages, and, as a form of applied phage ecology, phage therapy pharmacology.