The article discusses the role of ecological theory in microbial ecology, emphasizing the rapid accumulation of molecular data and the need for theoretical frameworks to organize and interpret these data. It highlights the importance of bacteria and archaea in Earth's systems, their vast diversity, and their essential roles in biogeochemical cycles. The authors argue that the application of ecological theory to microbial systems is crucial for advancing understanding and practical applications, such as wastewater treatment and climate change mitigation. They identify challenges in applying existing ecological theory to microorganisms, including the lack of data, cultural barriers, and the unique characteristics of microorganisms. The article explores various aspects of ecological theory, such as species concepts, diversity estimation, spatial and temporal scales, and competitive strategies, and suggests that microbial ecology can benefit from adapting and developing new theoretical approaches. The authors conclude that advances in microbial ecology require collaboration with other disciplines and a theoretical foundation to address fundamental questions and practical challenges.The article discusses the role of ecological theory in microbial ecology, emphasizing the rapid accumulation of molecular data and the need for theoretical frameworks to organize and interpret these data. It highlights the importance of bacteria and archaea in Earth's systems, their vast diversity, and their essential roles in biogeochemical cycles. The authors argue that the application of ecological theory to microbial systems is crucial for advancing understanding and practical applications, such as wastewater treatment and climate change mitigation. They identify challenges in applying existing ecological theory to microorganisms, including the lack of data, cultural barriers, and the unique characteristics of microorganisms. The article explores various aspects of ecological theory, such as species concepts, diversity estimation, spatial and temporal scales, and competitive strategies, and suggests that microbial ecology can benefit from adapting and developing new theoretical approaches. The authors conclude that advances in microbial ecology require collaboration with other disciplines and a theoretical foundation to address fundamental questions and practical challenges.