The textbook "Environmental Microbiology: Methods and Protocols" provides a comprehensive overview of modern molecular mechanisms for studying microbial communities and their biological activities. The second edition of this work highlights current advances in environmental microbiology, including innovative technologies such as metagenomics, NanoSIMS, and stable isotope sampling. The book is divided into four main parts: the first part addresses methods for sampling environmental microbes, the second part examines the diversity and composition of microbial communities, the third part focuses on techniques for analyzing biological activities in situ, and the final part is dedicated to high-throughput 'Omics' approaches for characterizing environmental microbes. Each chapter includes an introduction to the respective topic, a list of required materials and reagents, as well as step-by-step, reproducible laboratory protocols that highlight best practices and potential pitfalls. This comprehensive and authoritative resource aims to provide a deep understanding of the structure, composition, and activity of microbial communities in various environments and to illuminate their impact on global ecological processes.