Novel soil-inhabiting clades fill gaps in the fungal tree of life

Abstract

Background: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water.

Results: We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH.

Conclusions: This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.

Keywords: Biogeography; Kingdom Fungi; Niche modelling; Phylogenetic lineages; Random forest.

Fig. 1

Primer map indicating the construction of long 18S-ITS-28S rRNA gene sequences from 454 pyrosequencing-based ITS2 amplicons (in red) and Sanger sequencing of flanking conservative genes using taxon-specific reverse (Rev) and forward (Fwd) primers in combination with eukaryote primers (in blue). Primer information is given in Additional file 2: Table S1

Fig. 2

Phylogenetic placement of soil-inhabiting fungi among identified taxa and other sequences from the environment based on a simplified concatenated 18S and 28S rRNA gene maximum likelihood phylogram. Several branches were collapsed for clarity. Circles and triangles denote sequences from the present and other studies, respectively. Closed symbols indicate sequences belonging to the 44 defined clades and prominent branches; open symbols indicate sequences belonging to other groups. Terminal taxa without symbols represent identified collections, of which the most critical ones are shown for clarity

Fig. 3

Detrended correspondence analysis biplot indicating the relative placement of novel clades and prominent branches in the combined climatic, edaphic, and biogeographic space. Clades are supplied with abbreviations of phylogenetic affinities at the phylum level: A Ascomycota, Aph Aphelida, B Basidiomycota, Bla Blastocladiomycota, C Chytridiomycota, E Entorrhizomycota, G Glomeromycota, R Rozellomycota, Z Zygomycota s.lat., U unassigned