Navigating complexity: key considerations for studying fungal-bacterial interactions

Fungal-bacterial interactions are widespread phenomena that are currently gaining attention across diverse research fields. But what are interactions, how do we identify them, and why should we adopt ecological theory when studying them? While microbial interactions are often conceptualized and characterized as static properties, these relationships are dynamic and complex. They are shaped by the interplay of numerous variables, which themselves fluctuate over space and time, that scale from molecules to ecosystems. In this perspective, we discuss the theoretical and practical challenges of studying the interactions between these two ubiquitous and diverse groups of microorganisms and propose a framework grounded on mechanistic and systems approaches rather than relying on correlations or fragmented practices. We hope to inspire efforts to build and integrate a more comprehensive understanding of this fascinating and quickly growing subdiscipline of microbial ecology.