Leveraging genomics to understand the broader role of fungal small secreted proteins in niche colonization and nutrition

The last few years have seen significant advances in the breadth of fungi for which we have genomic resources and our understanding of the biological mechanisms evolved to enable fungi to interact with their environment and other organisms. One field of research that has seen a paradigm shift in our understanding concerns the role of fungal small secreted proteins (SSPs) classified as effectors. Classically thought to be a class of proteins utilized by pathogenic microbes to manipulate host physiology in support of colonization, comparative genomic studies have demonstrated that mutualistic fungi and fungi not associated with a living host (i.e., saprotrophic fungi) also encode inducible effector and candidate effector gene sequences. In this review, we discuss the latest advances in understanding how fungi utilize these secreted proteins to colonize a particular niche and affect nutrition and nutrient cycles. Recent studies show that candidate effector SSPs in fungi may have just as significant a role in modulating hyphosphere microbiomes and in orchestrating fungal growth as they do in supporting colonization of a living host. We conclude with suggestions on how comparative genomics may direct future studies seeking to characterize and differentiate effector from other more generalized functions of these enigmatic secreted proteins across all fungal lifestyles.