Sphaerocreas pubescens is a member of the Mucoromycotina closely related to fungi associated with liverworts and hornworts

Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes)

Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophosporakesseensis, Hoforsarebekkae, Kahvenarebeccae, Kelottijaerviashannonae, Kungsaengenashadiae, Langduoadianae, Lehetuaindrekii, Lokrumastenii, Moosteastephanieae, Nikkaluoktamahdiehiae, Parniguacraigii, Riederbergasylviae, Ruuacoralieae, Tammsaareavivikae and Unemaeeanathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversisporabareae, Diversisporanevadensis, Fuscutatacerradensis, Fuscutatareticulata, Viscosporadeserticola and Parvocarpumbadium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the "dark matter fungi".

Taxonomic study of Endogonaceae in the Japanese islands: New species of Endogone, Jimgerdemannia, and Vinositunica, gen. nov

Species of Endogonaceae (Endogonales, Mucoromycotina) are characterized by the formation of relatively large sporocarps and zygosporangia. Numerous species in this family remain undescribed or have unclear phylogenetic positions. In Asia specifically, the species diversity of this family is almost completely unknown. However, many mycobionts of bryophytes belonging to several novel clades in Endogonaceae have recently been identified phylogenetically. Therefore, establishing a robust taxonomic system for this family is essential. We obtained numerous sporocarps of undescribed Endogonaceae-like species from the Japanese islands. Morphological observation and multilocus phylogenetic analysis of nuc 18S rDNA (18S), nuc 28S rDNA (28S), and portions of two nuclear protein-coding regions-translation elongation factor 1-alpha (tef1) and RNA polymerase II large subunit (rpb1)-from these species resulted in the description of one new species each of Endogone and Jimgerdemannia and two new species of Vinositunica, gen. nov. Because Vinositunica is characterized by purplish sporocarps and red-wine-colored chlamydospores up to 700 μm in diameter, we emended the definition of Endogonaceae.

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a 'Third Kingdom', embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.

Dual colonization of Mucoromycotina and Glomeromycotina fungi in the basal liverwort, Haplomitrium mnioides (Haplomitriopsida)

In general, Glomeromycotina was thought to be the earliest fungi forming mycorrhiza-like structure (MLS) in land plant evolution. In contrast, because the earliest divergent lineage of extant land plants, i.e. Haplomitriopsida liverworts, associates only with Mucoromycotina mycobionts, recent studies suggested that those fungi are novel candidates for the earliest mycobionts. Therefore, Mucoromycotina-Haplomitriopsida association currently attracts attention as an ancient mycorrhiza-like association. However, mycobionts were identified in only 7 of 16 Haplomitriopsida species and the mycobionts diversity of this lineage is largely unclarified. To clarify the taxonomic composition of mycobionts in Haplomitriopsida, we observed MLSs in the rhizome of Haplomitrium mnioides (Haplomitriopsida), the Asian representative Haplomitriopsida species, and conducted molecular identification of mycobionts. It was recorded for the first time that Glomeromycotina and Mucoromycotina co-occur in Haplomitriopsida as mycobionts. Significantly, the arbuscule-like branching (ALB) of Glomeromycotina was newly described. As the Mucoromycotina fungi forming MLSs in H. mnioides, Endogonaceae and Densosporaceae were detected, in which size differences of hyphal swelling (HS) were found between the fungal families. This study provides a novel evidence in the MLS of Haplomitriopsida, i.e. the existence of Glomeromycotina association as well as the dominant Mucoromycotina association. In addition, since hyphal characteristics of the HS-type MLS were quite similar to those of fine endophytes (FE) of Endogonales in other bryophytes and vascular plants previously described, this MLS is suggested to be included in FE. These results suggest that Glomeromycotina and Mucoromycotina were acquired concurrently as the mycobionts by the earliest land plants evolved into arbuscular mycorrhizae and FE. Therefore, dual association of Haplomitriopsida, with Endogonales and Glomeromycotina will provide us novel insight on how the earliest land plants adapted to terrestrial habitats with fungi.

Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota

Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.

Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants

Endogonales is a lineage of early diverging fungi within Mucoromycota. Many species in this order produce small sporophores (“sporocarps”) containing a large number of zygospores, and many species form symbioses with plants. However, due to limited collections, subtle morphological differentiation, difficulties in growing these organisms in vitro, and idiosyncrasies in their rDNA that make PCR amplification difficult, the systematics and character evolution of these fungi have been challenging to resolve. To overcome these challenges we generated a multigene phylogeny of Endogonales using sporophores collected over the past three decades from four continents. Our results show that Endogonales harbour significant undescribed diversity and form two deeply divergent and well-supported phylogenetic clades, which we delimit as the families Endogonaceae and Densosporaceae fam. nov. The family Densosporaceae consists of the genus Densospora,Sphaerocreas pubescens, and many diverse lineages known only from environmental DNA sequences of plant-endosymbiotic fungi. Within Endogonaceae there are two clades. One corresponds to Endogone and includes the type species, E. pisiformis. Species of Endogone are characterized by above- and below-ground sporophores, a hollow and infolded sporophore form, a loose zygosporangial hyphal mantle, homogeneous gametangia, and an enigmatic trophic mode with no evidence of ectomycorrhizal association for most species. For the other clade we introduce a new generic name, Jimgerdemannia gen. nov. Members of that genus (J. flammicorona and J. lactiflua species complexes, and an undescribed species) are characterized by hypogeous sporophores with a solid gleba, a well-developed zygosporangial hyphal mantle, heterogeneous gametangia, and an ectomycorrhizal trophic mode. Future studies on Densosporaceae and Endogonaceae will be important for understanding fungal innovations including evolution of macroscopic sporophores and symbioses with plants.

Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats

Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences). Phylogenetic and maximum likelihood phylogenomic reconstructions revealed that the taxon represents a novel lineage in Mucoromycotina, only preceded by Calcarisporiella, the earliest diverging lineage in the subphylum. Sequences for the novel taxon are frequently detected in environmental sequencing studies, and it is currently part of UNITE's dynamic list of most wanted fungi. The fungus is dimorphic, grows best at room temperature, and is associated with a wide variety of bacteria. Here, a new monotypic genus, Bifiguratus, is proposed, typified by Bifiguratus adelaidae.

First detection of Endogone ectomycorrhizas in natural oak forests

The order Endogonales in Mucoromycotina, an early divergent lineage of fungi, includes ectomycorrhizal (EM) fungi. This order is therefore considered a key taxon for elucidation of the evolution of EM associations. Recent studies have revealed high diversity of EM lineages of Basidiomycota and Ascomycota; however, EM associations of Endogonales and its relatives remain largely unknown. In this study, EM root tips with a unique fungal sheath, with aseptate and highly branched hyphae of variable widths, were identified in Quercus acutissima and Quercus crispula forests in the temperate zone of Japan. The mycobionts were confirmed as Endogone sp., which were placed as a sister clade of Endogone pisiformis, based on phylogenetic analyses of the small and large subunits of the nuclear ribosomal RNA and elongation factor-1α genes. This is the first report of EM of Endogone in natural forests of the Northern Hemisphere and the first finding on Quercus.