Phylogenetic relationships among the Harpellales and Kickxellales

Novel parasitic chytrids infecting snow algae in an alpine snow ecosystem in Japan

Introduction

Microbial communities are important components of glacier and snowpack ecosystems that influence biogeochemical cycles and snow/ice melt. Recent environmental DNA surveys have revealed that chytrids dominate the fungal communities in polar and alpine snowpacks. These could be parasitic chytrids that infect snow algae as observed microscopically. However, the diversity and phylogenetic position of parasitic chytrids has not been identified due to difficulties in establishing their culture and subsequent DNA sequencing. In this study, we aimed to identify the phylogenetic positions of chytrids infecting the snow algae, Chloromonas spp., bloomed on snowpacks in Japan.

Methods

By linking a microscopically picked single fungal sporangium on a snow algal cell to a subsequent sequence of ribosomal marker genes, we identified three novel lineages with distinct morphologies.

Results

All the three lineages belonged to Mesochytriales, located within "Snow Clade 1", a novel clade consisting of uncultured chytrids from snow-covered environments worldwide. Additionally, putative resting spores of chytrids attached to snow algal cells were observed.

Discussion

This suggests that chytrids may survive as resting stage in soil after snowmelt. Our study highlights the potential importance of parasitic chytrids that infect snow algal communities.

Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.

A new genus Unguispora in Kickxellales shows an intermediate lifestyle between saprobic and gut-inhabiting fungi

Kickxellomycotina encompasses two fungal groups: a saprobic group in excrement and soil and an arthropod gut-inhabiting group. The evolutionary transition between these two lifestyles is unclear due to the lack of knowledge on intermediate forms and lifestyles. Here, we describe a new species, Unguispora rhaphidophoridarum, that was isolated from the excrement of cave crickets (Rhaphidophoridae) in Japan. This species has a novel lifestyle that is intermediate between the saprobic and gut-inhabiting groups. The new genus Unguispora is a member of the Kickxellales and characterized by the sterile appendages born on the sporocladium and by the claw-like ornamentation of the sporangiole. Phylogenetic analysis based on 18S and 28S nuclear ribosomal DNA showed that this fungus is distinct from all known kickxellalean genera and is sister to Linderina. The sporangiospore of the new species germinated only in anaerobiosis and grew in a yeast-like form. The yeast-like cells, defined as "secondary spores," germinated into hyphae in aerobiosis. In the alimentary tract of cave crickets, the sporangiola are attached to the proventriculus (foregut) by the claw-like ornamentation and multiplicate in the same yeast-like form as under culture. We introduce a new term, "amphibious fungi," to describe fungi that have two life stages, one outside and the other inside the host gut, like U. rhaphidophoridarum. The discovery of an amphibious fungus in Kickxellales, which was formerly considered to be only saprobic, suggests that Kickxellomycotina has evolved in association with the animal gut.

Aphelidium parallelum, sp. nov., a new aphelid parasitic on selenastracean green algae

Aphelids (phylum Aphelida = Aphelidiomycota) are intracellular parasitoids of algae and represent one of the early-diverging or sister lineages of the kingdom Fungi. Although aphelids are a small group comprising four genera and 17 species, molecular phylogenetic analyses revealed that numerous environmental DNA sequences represent undescribed lineages, indicating their hidden diversity. Here, we investigated a novel aphelid strain, KS114, that parasitizes selenastracean green algae. KS114 exhibited a life cycle typical of aphelids and produced posteriorly uniflagellate zoospores that resembled those of Aphelidium chlorococcorum f. majus in possessing a single apical filopodium but could be distinguished by ultrastructure features. In KS114, the kinetosome and nonflagellated centriole were aligned in parallel, a unique characteristic among the known aphelids. Kinetid-associated structures, such as fibrillar root and microtubules, were not found in the zoospores of KS114. In the molecular phylogeny of nuc 18S rDNA sequences, KS114 clustered with two environmental sequences and was distinct from all other sequenced species. Based on these results, we describe this aphelid as a new species, Aphelidium parallelum.http://www.zoobank.org/urn:lsid:zoobank.org:act:3CB658DB-1F12-41EF-A57D-2CBFCDE6A49A.

Differentiation of Basidiobolus spp. Isolates: RFLP of a Diagnostic PCR Amplicon Matches Sequence-Based Classification and Growth Temperature Preferences

The genus Basidiobolus, known since 1886, is primarily associated with reptiles and amphibians. Although globally distributed, rare infections caused by members of this genus mainly occur in tropical and subtropical regions. Morphological and physiological characteristics were used in the past for the description of species. However, some of these characteristics vary depending on culture conditions. Therefore, most species names are regarded as synonyms of B. ranarum as the only pathogenic species. Yet, not all environmental isolates are necessarily pathogenic. This study aimed to analyze if environmental Basidiobolus isolates can be distinguished reliably based on morpho-physiological and molecular characteristics. Eleven isolates originally obtained from feces of south African reptiles and one type strain, Basidiobolus microsporus DSM 3120, were examined morpho-physiologically. Sequence analysis of the 18S and partial 28S rRNA gene and restriction analysis of a diagnostic amplicon (restriction fragment length polymorphism, RFLP) were performed for all 12 strains. Based on the results obtained, morphological features and the 18S rRNA sequence proved insufficient for the reliable differentiation of isolates. However, isolates were distinguishable by growth temperature profiles, which matched isolate clusters established by partial 28S rRNA gene sequence and restriction analysis of a Basidiobolus specific diagnostic PCR amplicon. Our results indicate that RFLP analysis can be used as a fast screening method to identify Basidiobolus isolates with similar physiological characteristics.

Morphology, Ultrastructure, and Molecular Phylogeny of Aphelidium collabens sp. nov. (Aphelida), a Parasitoid of a Green Alga Coccomyxa sp

Aphelids (Aphelida) are intracellular parasitoids of algae and represent one of the early diverging or sister lineages of the kingdom Fungi. Although Aphelida is a small group, molecular phylogenetic analyses revealed that many environmental sequences belong to Aphelida, suggesting that aphelids are distributed worldwide; however, the extent of their diversity is unclear. Here, we investigated a novel aphelid culture APH2 that parasitizes the green alga Coccomyxa sp. APH2 produced posteriorly uniflagellate zoospores, a defining character of the genus Aphelidium. The residual body of APH2 was spherical in the mature plasmodium, but became amorphous during zoospore formation and collapsed after zoospore discharge, which has not been described for other Aphelidium species. Zoospores of APH2 possessed a striated rhizoplast that extended anteriorly from the kinetosome to the posterior end of the nucleus, and a microtubular root arising from the side of the kinetosome and lying almost parallel to the rhizoplast, both of which are unique among aphelid taxa. A molecular phylogenetic analysis based on the 18S rDNA sequences placed APH2 as sister lineage to all other known aphelid sequences. Based on these results, we describe this aphelid as a new species, Aphelidium collabens.

Genera of Inocybaceae: New skin for the old ceremony

A six-gene phylogeny of the Inocybaceae is presented to address classification of major clades within the family. Seven genera are recognized that establish a global overview of phylogenetic relationships in the Inocybaceae. Two genera-Nothocybe and Pseudosperma-are described as new. Two subgenera of Inocybe-subg. Inosperma and subg. Mallocybe-are elevated to generic rank. These four new genera, together with the previously described Auritella, Tubariomyces, and now Inocybe sensu stricto, constitute the Inocybaceae, an ectomycorrhizal lineage of Agaricales that associates with at least 23 plant families worldwide. Pseudosperma, Nothocybe, and Inocybe are recovered as a strongly supported inclusive clade within the family. The genus Nothocybe, represented by a single species from tropical India, is strongly supported as the sister lineage to Inocybe, a hyperdiverse genus containing hundreds of species and global distribution. Two additional inclusive clades, including Inosperma, Tubariomyces, Auritella, and Mallocybe, and a nested grouping of Auritella, Mallocybe, and Tubariomyces, are recovered but with marginal statistical support. Overall, the six-gene data set provides a more robust phylogenetic estimate of relationships within the family than do single-gene and single-gene-region estimates. In addition, Africa, India, and Australia are characterized by the most genera in the family, with South America containing the fewest number of genera. A total of 180 names are recombined or proposed as new in Inosperma, Mallocybe, and Pseudosperma. A key to genera of Inocybaceae is provided.

Diversity of cytosine methylation across the fungal tree of life

The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.

Development of merosporangia in Linderina pennispora (Kickxellales, Kickxellaceae)

The vegetative and sporulating structures of Linderina pennispora are described using scanning and transmission electron microscopy. The vegetative hyphae and sporangiophores were regularly septate, possessed a two-layered wall, and coated with rod-shaped, 0.2–0.7 μm long, 0.15–0.25 μm wide ornamentations. The sporangiophore was erect, cylindrical, and narrower (4–8 μm) than the vegetative mycelium (8–12 μm). The mature sporocladium was ovoid to dome-shaped, sessile, non-septate, 18–24 μm diam, possessed a two-layered wall, and coated with rod-shaped ornamentations. Mature pseudophialides were ellipsoid, 2.0–2.5 μm wide, 4–7 μm long, possessed a two-layered wall, and formed in a series of concentric groups radiating from the “apex” of the sporocladium. The pseudophialides had a round, ca. 1.5 μm diam, base with a narrower, 0.7–0.8 μm diam lobed, cylindrical neck structure in the distal region which extended to the pseudophialide neck. The merosporangia were obovate, 3–4 μm wide near the base, and narrowed distally to 2.0–2.5 μm wide, 18–23 μm long, possessed a three-layered wall, with regular surface annulation with interconnecting ridges, but lacked rod-shaped ornamentations. The merosporangia contained a single, obovate, 2.3–2.5 μm diam merosporangiospore, with a ca. 1 μm diam papilla-like base, that possessed a four-layered wall. Detached merosporangia had a single, acicular, unbranched, 3–5 μm long, ca. 0.1 μm diam “appendage” that was attached to the merosporangiospore inner cell wall layer and passed through the septum plug to the pseudophialide.

Absidia parricida plays a dominant role in biotrophic fusion parasitism among mucoralean fungi (Zygomycetes): Lentamyces, a new genus for A. parricida and A. zychae

Within the order Mucorales (Zygomycetes), the facultative parasites Parasitella parasitica, Chaetocladium brefeldii, Chaetocladium jonesii and Absidia parricida are known to initiate biotrophic fusion parasitic interactions on a wide variety of other mucoralean hosts. Their phylogenetic relationship within the Mucorales and their ability to form parasitic structures with several known host species was examined. Together with interspecific reactions between the mycoparasites, this study found: (i) no evident differences in the spectrum of non-parasitic hosts tested within the study; (ii) A. parricida parasitises all other fusion parasites; (iii) A. parricida is ancestral to all other parasites; (iv) A. parricida is reported for the first time as phylogenetically basal to all other mucoralean fungi except the Umbelopsidaceae and (v) based on phylogenetic analyses and physiological and morphological characteristics, the slow-growing species A. parricida and Absidia zychae are removed from the genus Absidia and reclassified in the newly described genus Lentamyces.

New species of Lancisporomyces, Orphella, and Paramoebidium, endosymbionts of stonefly nymphs from streams in Nova Scotia, Canada

Trichomycetes are endobionts that include both fungal and protistan species living in the guts of aquatic insects. Although widely distributed around the world, the biodiversity of these fungi in Canada is virtually unknown. We report the occurrence of 13 species of trichomycetes associated with stonefly nymphs in the families Capniidae, Leuctridae, Nemouridae, and Taeniopterygidae from collections spanning 8 years. This paper extends the geographical range for a number of known fungal species. We describe four new species of Harpellales, Lancisporomyces anguilliformis, Lancisporomyces falcatus, Lancisporomyces nemouridarum, and Orphella dalhousiensis, including both asexual and sexual features for each, as well as two new species of Paramoebidium (Amoebidiales), Paramoebidium cassidula and Paramoebidium stipula. The observations on zygospore morphology in Lancisporomyces and ontogeny of sexual spores in Orphella broaden our perspective on sexual reproduction in the Harpellales. Also highlighted are data on temporal aspects of species occurrence, asexual and sexual sporulation for some species that show host specificity as well as synchrony in maturation of the endobionts with their stonefly hosts.

Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.

Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics

The chytrids (Chytridiomycota) are morphologically simple aquatic fungi that are unified by their possession of zoospores that typically have a single, posteriorly directed flagellum. This study addresses the systematics of the chytrids by generating a phylogeny of ribosomal DNA sequences coding for the small subunit gene of 54 chytrids, with emphasis on sampling the largest order, the Chytridiales. Selected chytrid sequences were also compared with sequences from Zygomycota, Ascomycota, and Basidiomycota to derive an overall fungal phylogeny. These analyses show that the Chytridiomycota is probably not a monophyletic group; the Blastocladiales cluster with the Zygomycota. Analyses did not resolve relationships among chytrid orders, or among clades within the Chytridiales, which suggests that the divergence times of these groups may be ancient. Four clades were well supported within the Chytridiales, and each of these clades was coincident with a group previously identified by possession of a common subtype of zoospore ultrastructure. In contrast, the analyses revealed homoplasy in several developmental and zoosporangial characters.Key words: zoospore ultrastructure, Chytridiales, molecular phylogeny, Chytridiomycota, operculum.

Phylogeny and PCR identification of clinically important Zygomycetes based on nuclear ribosomal-DNA sequence data

A molecular database for all clinically important Zygomycetes was constructed from nucleotide sequences from the nuclear small-subunit (18S) ribosomal DNA and domains D1 and D2 of the nuclear large-subunit (28S) ribosomal DNA. Parsimony analysis of the aligned 18S and 28S DNA sequences was used to investigate phylogenetic relationships among 42 isolates representing species of Zygomycetes reported to cause infections in humans and other animals, together with commonly cultured contaminants, with emphasis on members of the Mucorales. The molecular phylogeny provided strong support for the monophyly of the Mucorales, exclusive of Echinosporangium transversale and Mortierella spp., which are currently misclassified within the Mucorales. Micromucor ramannianus, traditionally classified within Mortierella, and Syncephalastrum racemosum represent the basal divergences within the Mucorales. Based on the 18S gene tree topology, Absidia corymbifera and Rhizomucor variabilis appear to be misplaced taxonomically. A. corymbifera is strongly supported as a sister group of the Rhizomucor miehei-Rhizomucor pusillus clade, while R. variabilis is nested within Mucor. The aligned 28S sequences were used to design 13 taxon-specific PCR primer pairs for those taxa most commonly implicated in infections. All of the primers specifically amplified DNA of the size predicted based on the DNA sequence data from the target taxa; however, they did not cross-react with phylogenetically related species. These primers have the potential to be used in a PCR assay for the rapid and accurate identification of the etiological agents of mucormycoses and entomophthoromycoses.