Fungal Diversity and Community Composition across Ecosystems

Abstract

Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth’s mycobiome.

Planktonic Marine Fungi: A Review

“…A review by provided an up-to-date and comprehensive summary of metabarcoding surveys of planktonic fungi. Of the 26 studies summarized by , only 11 included samples from the open ocean (Bass et al, 2007;Debeljak & Baltar, 2023;Hassett et al, 2017Hassett et al, , 2019Jeffries et al, 2016;W. Li et al, 2019;Morales et al, 2019;Orsi et al, 2022;Peng & Valentine, 2021;Tisthammer et al, 2016;X.…”

“…While meta-analysis of existing data sets has generated insights into patterns of fungal diversity in the open ocean (e.g., Debeljak & Baltar, 2023), most of the large-scale surveys (e.g., TARA Oceans) were not designed to target fungi, so the primers used were typically universal 18S rRNA gene primers that result in small numbers (e.g., tens to hundreds) of fungal reads per sample due to the low abundance of fungal cells in open ocean microbial communities and potential primer biases. The sequencing depth in these previous studies was likely insufficient for estimating the diversity of planktonic marine fungi.…”

“…Seasonal changes, in for example, water temperature, pH, and chlorophyll‐a, are mainly responsible for driving fungal community composition and for observed uneven distribution across coastal waters and time (Priest et al., 2021). Highest diversities are found closest to the shoreline, and decreased toward the open ocean (Debeljak & Baltar, 2023; Duan et al., 2021; Z. Gao et al., 2010; Gutiérrez et al., 2010; Sen et al., 2021). Close to shore, proximity and connectivity to estuaries seem to be determining factors in observed high diversity, probably due to directly linked input of fungi from the inflowing rivers (Debeljak & Baltar, 2023; Taylor & Cunliffe, 2016).…”

“…A review by Breyer and Baltar (2023) provided an up‐to‐date and comprehensive summary of metabarcoding surveys of planktonic fungi. Of the 26 studies summarized by Breyer and Baltar (2023), only 11 included samples from the open ocean (Bass et al., 2007; Debeljak & Baltar, 2023; Hassett et al., 2017, 2019; Jeffries et al., 2016; W. Li et al., 2019; Morales et al., 2019; Orsi et al., 2022; Peng & Valentine, 2021; Tisthammer et al., 2016; X. Wang et al., 2014). Most of these studies focused on one region of the global ocean during one field campaign, while TARA Oceans was the primary source of fungal diversity data providing larger coverage of the global ocean.…”

“…While Ascomycota and Basidiomycota consistently account for over two thirds (often >80%) of the fungal community in the open ocean detected using molecular approaches, there appears to be a systematic difference between studies depending on the primer set used for metabarcoding. The relative abundance of early diverging fungi, particularly Chytridiomycota and Mucoromycota, was usually very low (<1%) when a primer set targeting the ITS2 region was used (e.g., W. Li et al., 2019; Peng & Valentine, 2021), but when the V4 region of the 18S rRNA gene or the ITS1 region was the target, the relative abundance of early diverging fungi can reach >10% in the open ocean (Debeljak & Baltar, 2023; Jeffries et al., 2016; Orsi et al., 2022). Regardless of the type of primer used, the relative abundance of unclassified fungal taxa, which potentially represent novel lineages, was the highest in the open ocean when compared to coastal and estuarine environments (Debeljak & Baltar, 2023; W. Li et al., 2019; Peng & Valentine, 2021).…”