This guide provides a comprehensive overview of the natural history of freshwater lake bacteria, focusing on their phylogenetic classification, ecological roles, and distribution. It introduces a new hierarchical classification system based on phylogenetics, unifying taxon names and providing a framework for understanding bacterial diversity in freshwater ecosystems. The guide includes detailed information on major bacterial phyla, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia, along with their ecological significance, metabolic processes, and distribution patterns. It also highlights the importance of molecular methods in studying bacterial communities and the challenges in naming and classifying freshwater bacterial taxa. The guide emphasizes the need for a consistent and robust vocabulary to inventory taxonomic units and discusses the ecological traits of different bacterial groups in freshwater lakes. It also addresses the biogeography of freshwater lake bacteria and their roles in nutrient cycling and water quality. The guide is structured to serve as a reference for researchers and students, offering insights into the diversity, ecology, and evolution of freshwater lake bacteria. It includes phylogenetic trees, ecological data, and a meta-analysis of bacterial life history patterns, providing a foundation for further research and understanding of freshwater microbial ecology.This guide provides a comprehensive overview of the natural history of freshwater lake bacteria, focusing on their phylogenetic classification, ecological roles, and distribution. It introduces a new hierarchical classification system based on phylogenetics, unifying taxon names and providing a framework for understanding bacterial diversity in freshwater ecosystems. The guide includes detailed information on major bacterial phyla, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia, along with their ecological significance, metabolic processes, and distribution patterns. It also highlights the importance of molecular methods in studying bacterial communities and the challenges in naming and classifying freshwater bacterial taxa. The guide emphasizes the need for a consistent and robust vocabulary to inventory taxonomic units and discusses the ecological traits of different bacterial groups in freshwater lakes. It also addresses the biogeography of freshwater lake bacteria and their roles in nutrient cycling and water quality. The guide is structured to serve as a reference for researchers and students, offering insights into the diversity, ecology, and evolution of freshwater lake bacteria. It includes phylogenetic trees, ecological data, and a meta-analysis of bacterial life history patterns, providing a foundation for further research and understanding of freshwater microbial ecology.