Functional soil mycobiome across ecosystems

Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. Significance: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.

Automated summary

This study investigates the metaproteome of fungal communities in different ecosystems across the globe, revealing differences in protein richness, evenness, and diversity of soil fungi based on edaphic and environmental variables. Functions of fungal communities vary between forests and shrublands, shifting from metabolism to information processing and storage. Metaproteomics proves to be a useful tool in understanding the functional microbiomes in soil and highlights the importance of studying the structure and function of fungal communities in relation to ecosystem services and future climate impacts.