Priority effects in microbiome assembly

• Published in: Nature reviews. Microbiology Vol. 20; no. 2; pp. 109 - 121
• Main Authors: Debray, Reena, Herbert, Robin A., Jaffe, Alexander L., Crits-Christoph, Alexander, Power, Mary E., Koskella, Britt
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.02.2022; Nature Publishing Group
• Subjects: 631/158/855; 631/326/2565/2134; 631/326/2565/855; Assembly; Bacteria; Bacteria - classification; Bacteria - genetics; Biology; Biomedical and Life Sciences; Community composition; Competition; Composition; Contingency; Ecological function; Ecosystem biology; Fresh water; Gastrointestinal Tract - microbiology; Infectious Diseases; Life Sciences; Medical Microbiology; Microbiology; Microbiomes; Microbiota - genetics; Microorganisms; New species; Next-generation sequencing; Nutrients; Oceans; Parasitology; Phyllosphere; Review Article; Rhizosphere; RNA, Ribosomal, 16S - genetics; Virology
• ISSN: 1740-1526; 1740-1534
• DOI: 10.1038/s41579-021-00604-w

Advances in next-generation sequencing have enabled the widespread measurement of microbiome composition across systems and over the course of microbiome assembly. Despite substantial progress in understanding the deterministic drivers of community composition, the role of historical contingency remains poorly understood. The establishment of new species in a community can depend on the order and/or timing of their arrival, a phenomenon known as a priority effect. Here, we review the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere, soil, freshwaters and oceans. We describe approaches for the direct testing and prediction of priority effects in complex microbial communities and illustrate these with re-analysis of publicly available plant and animal microbiome datasets. Finally, we discuss the shared principles that emerge across study systems, focusing on eco-evolutionary dynamics and the importance of scale. Overall, we argue that predicting when and how current community state impacts the success of newly arriving microbial taxa is crucial for the management of microbiomes to sustain ecological function and host health. We conclude by discussing outstanding conceptual and practical challenges that are faced when measuring priority effects in microbiomes. The order and timing of the arrival (priority effects) of members of a microbiome can influence microbiome composition and function. In this Review, Debray and colleagues provide an overview of the mechanisms of priority effects, highlight examples in host-associated and environmental communities, and discuss methods to detect priority effects in microbial communities.