Is There Truly Hidden Diversity Among Environmental Yeasts—and Can In Situ Cultivation Help Reveal It?

Yeasts, as unicellular fungi spanning Ascomycota and Basidiomycota, inhabit diverse ecosystems and drive essential processes like nutrient cycling, fermentation, symbiosis, and pathogenesis. Despite their ubiquity and significance, the vast majority of environmental yeasts remain uncultured, constrained by methodological limitations such as inadequate media, lack of key growth factors, and unoptimized conditions, alongside physiological barriers including the viable-but-nonculturable (VBNC) state and ecological dependencies. Culture-independent approaches, including ITS metabarcoding and metagenomics, consistently uncover extensive “fungal dark matter,” with estimates suggesting substantial yeast diversity undetected in standard isolations, often inflated by artifacts like primer bias and non-viable DNA. This commentary examines the evidence for hidden yeast diversity, asks whether cultivation discrepancies reflect artifacts or genuine unaccessed taxa, and evaluates how in situ cultivation—adapted from bacterial strategies like diffusion chambers and iChip—can bridge this gap through ecologically realistic workflows. We synthesize yeast ecological roles (e.g., decomposers, symbionts) and biotechnological prospects (e.g., biofuels, bioremediation), propose a tailored yeast-centric protocol emphasizing substrate preconditioning, semi-permeable incubation, and conservative VBNC resuscitation (e.g., catalase, pyruvate, cAMP; limited co-culture), and discuss implications for uncovering novel taxa, metabolites, and functions in ecology, biotechnology, and clinical mycology. By rethinking cultivation toward native microhabitat simulation, this approach aims to illuminate uncultured lineages, advancing functional insights and applications amid biodiversity loss.