The book will cover the role of viruses, bacteria, archaea, protists, and fungi in the environment. The book will not be limited by taxonomic coverage; rather, it aims to provide a perspective on and an introduction to understanding the ecology of microscopic organisms, and how they interact with the rest of the system. This book treats ecology from a community structure, food web, ecosystem, and biogeography perspective. Interactions among bacteria, protists, fungi, their micro-invertebrate grazers, and their interactions with plants and animals will be considered. Applications are dealt with at the end. An outline is provided below.

One recurring aspect in the text will be to lay out ecological theory and concepts at the beginning of each chapter, then to explain, with examples, how these concepts pertain to microbial ecology. Some ecological concepts are obviously less important to microbial ecology, while others gain in importance in this context. A second recurring theme will be to consider topics from different scales, from the sub-millimetre to the ecosystem.