Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems

ABSTRACT Understanding the extraordinary environmental adaptability of prokaryotes is crucial for manipulating microbial communities, as their adaptive mechanisms drive community dynamics, resilience and functional responses to interventions like bioremediation. Microbial adaptation to the environment is shaped not only by their intrinsic characteristics but also by interactions with other microorganisms. Among them, temperate phages, which reside alongside cellular microorganisms across diverse ecosystems, are emerging as key players in microbial adaptation. This review delves into the contribution of temperate phages to microbial adaptation across multiple levels. It begins with a survey of culture‐dependent studies that reveal the complex mechanisms by which temperate phages facilitate adaptation at the individual and population levels. The review then explores how temperate phage–host symbioses interact with selection pressures in complex environments, assessing both the influence of these pressures on lysogeny at the community level and how prophages respond. Finally, building on established concepts and recent scientific advances, this review outlines the potential for harnessing temperate phages to help address major societal challenges. This synthesis underscores the importance of temperate phages and encourages further exploration in phage ecology.