New taxa in Glomeromycota: Polonosporaceae fam. nov., Polonospora gen. nov., and P. polonica comb. nov

New taxa and a combination in Glomerales (Glomeromycota, Glomeromycetes)

This article presents the results of morphological studies, as well as comparisons and phylogenetic analyzes of sequences of four arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota): Dominikiaindica, Dominikiaindica strain 211, Isolate 517, and Isolate 524. Dominikiaindica strain 211 was previously characterized only by sequences of the 45S nuc rDNA region (= 18S, partial, ITS-1-5.8S-ITS2, 28S, partial) and the rpb1 gene (without any morphological data) that were deposited in GenBank under the incorrect name "Dominikiaindica strain 211". Its 45S sequences differed from the original D.indica sequences and, consequently, resulted in erroneous phylogenetic classification of this species. Isolate 517 and Isolate 524 slightly differed in morphology from Macrodominikiacompressa (formerly D.compressa) and Microkamienskiaperpusilla (formerly Kamienskiaperpusilla), respectively. Microkamienskiaperpusilla was originally found in a maritime dune site of Italy in 2009 and not yet reported from any other habitat in the world. Our sequence comparisons and analyses showed that D.indica represents a new genus, here created under the name Delicatispora gen. nov. with De.indica comb. nov., and Dominikiaindica strain 211 is a new species, described as Dominikiaparaminuta sp. nov. These analyses also indicated that Isolate 517 is conspecific to M.compressa and confirmed the correctness of the transfer of D.compressa by other AMF researchers to Macrodominikia gen. nov. with M.compressa comb. nov. Morphological studies of our M.compressa specimens grown in culture showed that the original description of this species is incomplete and, therefore, the description was emended. Phylogenetic analyses of Isolate 524 proved its conspecificity to Mk.perpusilla and thus revealed its second site of occurrence, i.e., the coastal dunes of the Hel Peninsula in northern Poland.

Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

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".

An updated LSU database and pipeline for environmental DNA identification of arbuscular mycorrhizal fungi

Recent work established a backbone reference tree and phylogenetic placement pipeline for identification of arbuscular mycorrhizal fungal (AMF) large subunit (LSU) rDNA environmental sequences. Our previously published pipeline allowed any environmental sequence to be identified as putative AMF or within one of the major families. Despite this contribution, difficulties in implementation of the pipeline remain. Here, we present an updated database and pipeline with (1) an expanded backbone tree to include four newly described genera and (2) several changes to improve ease and consistency of implementation. In particular, packages required for the pipeline are now installed as a single folder (conda environment) and the pipeline has been tested across three university computing clusters. This updated backbone tree and pipeline will enable broadened adoption by the community, advancing our understanding of these ubiquitous and ecologically important fungi.

Arbuscular Mycorrhizal Fungi as Biostimulant and Biocontrol Agents: A Review

Arbuscular mycorrhizal fungi (AMF) are soil microorganisms living in symbiosis with most terrestrial plants. They are known to improve plant tolerance to numerous abiotic and biotic stresses through the systemic induction of resistance mechanisms. With the aim of developing more sustainable agriculture, reducing the use of chemical inputs is becoming a major concern. After providing an overview on AMF history, phylogeny, development cycle and symbiosis benefits, the current review aims to explore the potential of AMF as biostimulants and/or biocontrol agents. Nowadays, AMF inoculums are already increasingly used as biostimulants, improving mineral nutrient plant acquisition. However, their role as a promising tool in the biocontrol market, as an alternative to chemical phytosanitary products, is underexplored and underdiscussed. Thus, in the current review, we will address the mechanisms of mycorrhized plant resistance to biotic stresses induced by AMF, and highlight the various factors in favor of inoculum application, but also the challenges that remain to be overcome.

Richness of Arbuscular Mycorrhizal Fungi in a Brazilian Tropical Shallow Lake: Assessing an Unexpected Assembly in the Aquatic-Terrestrial Gradient

Aquatic ecosystems are historically overlooked regarding the occurrence of Arbuscular Mycorrhizal Fungi (AMF). Tropical lakes in the southern hemisphere are generally impacted by human actions, such as those in Brazil, although they still preserve a great diversity of macrophyte species that can support AMF communities. Thus, the study aimed to test (i) whether AMF community structure (composition, richness, diversity, dominance, and evenness) differs between aquatic and terrestrial conditions, and (ii) between seasons—rainy and dry. A total of 60 AMF species, distributed in 10 families and 17 genera, were found, with a difference in AMF composition between conditions (terrestrial and aquatic) and seasons (dry and rainy). The absolute species richness differed between conditions, seasons, and interactions. The aquatic/rainy season, which retrieved the most significant number of species, had the highest absolute richness and number of glomerospores and differed significantly from the terrestrial/rainy season. The results suggest that a shallow oligotrophic lake harbors a high AMF richness. In addition, this environment has a distinct AMF community from the adjacent coastal sand plain vegetation and is affected by seasonality.

A new order, Entrophosporales, and three new Entrophospora species in Glomeromycota

As a result of phylogenomic, phylogenetic, and morphological analyses of members of the genus Claroideoglomus, four potential new glomoid spore-producing species and Entrophospora infrequens, a new order, Entrophosporales, with one family, Entrophosporaceae (=Claroideoglomeraceae), was erected in the phylum Glomeromycota. The phylogenomic analyses recovered the Entrophosporales as sister to a clade formed by Diversisporales and Glomeraceae. The strongly conserved entrophosporoid morph of E. infrequens, provided with a newly designated epitype, was shown to represent a group of cryptic species with the potential to produce different glomoid morphs. Of the four potential new species, three enriched the Entrophosporales as new Entrophospora species, E. argentinensis, E. glacialis, and E. furrazolae, which originated from Argentina, Sweden, Oman, and Poland. The fourth fungus appeared to be a glomoid morph of the E. infrequens epitype. The physical association of the E. infrequens entrophosporoid and glomoid morphs was reported and illustrated here for the first time. The phylogenetic analyses, using nuc rDNA and rpb1 concatenated sequences, confirmed the previous conclusion that the genus Albahypha in the family Entrophosporaceae sensu Oehl et al. is an unsupported taxon. Finally, the descriptions of the Glomerales, Entrophosporaceae, and Entrophospora were emended and new nomenclatural combinations were introduced.

Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere

Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.

Three new species of arbuscular mycorrhizal fungi of the genus Diversispora from maritime dunes of Poland

Three new species of arbuscular mycorrhizal fungi of the genus Diversispora (phylum Glomeromycota) were described based on their morphology and molecular phylogeny. The phylogeny was inferred from the analyses of the partial 45S rDNA sequences (18S-ITS-28S) and the largest subunit of RNA polymerase II (rpb1) gene. These species were associated in the field with plants colonizing maritime sand dunes of the Baltic Sea in Poland and formed mycorrhiza in single-species cultures.