Bridging the scales: what can microbial ecologists learn from classic ecology?

Luca Beldi, Alyssa Henderson, Megan N. Y. Lee, Julien S Luneau, Florent Mazel, Thomas E Miller, Prajwal Padmanabha, Benjamin Raach, Simon van Vliet, Anna S Weiss, Oliver J Meacock , Margaret A Vogel

The fields of ecology and microbiology have historically developed independently of one another, resulting in each having unique methods, terminology, and concepts. Microbial ecology aims to synthesise these perspectives, merging the molecular and reductionist strengths of the microbiologist with the systems-level viewpoint of the ecologist. However, unifying disciplines with independent histories is not a straightforward task. Ecology is characterised by a series of concepts that aim to explain the diversity and composition of macroscopic ecosystems. Many of these concepts are associated with longstanding controversies surrounding their definitions and application, and these must be taken into consideration when applying them to new, microbial contexts. These concepts and theories from classic ecology also need to be critically evaluated and adjusted to account for the unique characteristics of microbes. Nonetheless, provided that the distinctions between microbial and macroscopic settings are taken into consideration, microbial systems are ideal experimental systems for many of the concepts from classic ecology. Here, we provide a concise and practical guide for microbiologists to five key frameworks from classic ecology—Niche theory, Trophic levels, Keystone species, Succession, and Metacommunities. We discuss the historical context and use of each framework, assess their applications to microbial systems and associated limitations, and offer suggestions for future research to help bridge the gap between the two fields.