Phylogeny of the Zygomycota based on nuclear ribosomal sequence data

CIGAF-a database and interactive platform for insect-associated trichomycete fungi

Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.

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.

Phylogenetic Revision and Patterns of Host Specificity in the Fungal Subphylum Entomophthoromycotina

The Entomophthoromycotina, a subphylum close to the root of terrestrial fungi with a bias toward insects as their primary hosts, has been notoriously difficult to categorize taxonomically for decades. Here, we reassess the phylogeny of this group based on conserved genes encoding ribosomal RNA and RNA polymerase II subunits, confirming their general monophyly, but challenging previously assumed taxonomic relationships within and between particular clades. Furthermore, for the prominent, partially human-pathogenic taxon Conidiobolus, a new type species C. coronatus is proposed in order to compensate for the unclear, presumably lost previous type species C. utriculosus Brefeld 1884. We also performed an exhaustive survey of the broad host spectrum of the Entomophthoromycotina, which is not restricted to insects alone, and investigated potential patterns of co-evolution across their megadiverse host range. Our results suggest multiple independent origins of parasitism within this subphylum and no apparent co-evolutionary events with any particular host lineage. However, Pterygota (i.e., winged insects) clearly constitute the most dominantly parasitized superordinate host group. This appears to be in accordance with an increased dispersal capacity mediated by the radiation of the Pterygota during insect evolution, which has likely greatly facilitated the spread, infection opportunities, and evolutionary divergence of the Entomophthoromycotina as well.

Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi

The fungi are an enormously successful eukaryotic lineage that has colonized every aerobic habitat on Earth. This spectacular expansion is reflected in the dynamism and diversity of the fungal cell wall, a matrix of polysaccharides and glycoproteins pivotal to fungal life history strategies and a major target in the development of antifungal compounds. Cell wall polysaccharides are typically synthesized by Leloir glycosyltransferases, enzymes that are notoriously difficult to characterize, but their nucleotide-sugar substrates are well known and provide the opportunity to inspect the monosaccharides available for incorporation into cell wall polysaccharides and glycoproteins. In this work, we have used phylogenomic analyses of the enzymatic pathways that synthesize and interconvert nucleotide-sugars to predict potential cell wall monosaccharide composition across 491 fungal taxa. The results show a complex evolutionary history of these cell wall enzyme pathways and, by association, of the fungal cell wall. In particular, we see a significant reduction in monosaccharide diversity during fungal evolution, most notably in the colonization of terrestrial habitats. However, monosaccharide distribution is also shown to be varied across later-diverging fungal lineages.IMPORTANCE This study provides new insights into the complex evolutionary history of the fungal cell wall. We analyzed fungal enzymes that convert sugars acquired from the environment into the diverse sugars that make up the fundamental building blocks of the cell wall. Species-specific profiles of these nucleotide-sugar interconverting (NSI) enzymes for 491 fungi demonstrated multiple losses and gains of NSI proteins, revealing the rich diversity of cell wall architecture across the kingdom. Pragmatically, because cell walls are essential to fungi, our observations of variation in sugar diversity have important implications for the development of antifungal compounds that target the sugar profiles of specific pathogens.

Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota and a potential to switch between hosts

Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching fungi based on the SSU rRNA gene sequences of three species, their exact position within the fungal tree of live remained unclear. In this study, we describe two new species of nephridiophagids (Nephridiophaga postici and Nephridiophaga javanicae) from cockroaches. Using long-read sequencing of the nearly complete rDNA operon of numerous further species obtained from cockroaches and earwigs to improve the resolution of the phylogenetic analysis, we found a robust affiliation of nephridiophagids with the Chytridiomycota-a group of zoosporic fungi that comprises parasites of diverse host taxa, such as microphytes, plants, and amphibians. The presence of the same nephridiophagid species in two only distantly related cockroaches indicates that their host specificity is not as strict as generally assumed.

An evolutionary signal to fungal succession during plant litter decay

Ecologists have frequently observed a pattern of fungal succession during litter decomposition, wherein different fungal taxa dominate different stages of decay in individual ecosystems. However, it is unclear which biological features of fungi give rise to this pattern. We tested a longstanding hypothesis that fungal succession depends on the evolutionary history of species, such that different fungal phyla prefer different decay stages. To test this hypothesis, we performed a meta-analysis across studies in 22 different ecosystem types to synthesize fungal decomposer abundances at early, middle and late stages of plant litter decay. Fungal phyla varied in relative abundance throughout decay, with fungi in the Ascomycota reaching highest relative abundance during early stages of decay (P < 0.001) and fungi in the Zygomycota reaching highest relative abundance during late stages of decay (P < 0.001). The best multiple regression model to explain variation in abundance of these fungal phyla during decay included decay stage, as well as plant litter type and climate factors. Most variation in decay-stage preference of fungal taxa was observed at basal taxonomic levels (phylum and class) rather than finer taxonomic levels (e.g. genus). For many finer-scale taxonomic groups and functional groups of fungi, plant litter type and climate factors were better correlates with relative abundance than decay stage per se, suggesting that the patchiness of fungal community composition in space is related to both resource and climate niches of different fungal taxa. Our study indicates that decomposer fungal succession is partially rooted in fungal decomposers’ deep evolutionary history, traceable to the divergence among phyla.

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.

Presence and distribution of insect-associated and entomopathogenic fungi in a temperate pine forest soil: An integrated approach

For decades entomopathogenic fungi have garnered interest as possible alternatives to chemical pesticides. However, their ecology outside of agroecosystems demands further study. We assessed the diversity and abundance of entomopathogenic and insect-associated fungi at a loblolly pine forest in North Carolina, USA using culture-dependent and next-generation sequencing libraries. Fungi were isolated using Galleriamellonella larvae, as well as from soil dilutions plated on a selective medium. Isolates were identified using Sanger sequencing of the ITS and LSU rRNA gene regions, and represented 36 OTUs including Metarhizium, Lecanicillium, and Paecilomyces. Additionally, we assessed the chitinolytic potential of isolates and found widespread, variable ability to degrade chitin within and between genera. Phylogenetic analyses resolved several isolates to genus, with some forming clades with other insect-associated taxa, as well as with fungi associated with plant tissues. Saprophytes were widely distributed in soil, while entomopathogens were less abundant and present primarily in the top two cm of the soil. The similarity between culture-dependent and next-generation sequencing results demonstrates that both methods can be used concurrently in this system to study the ecology of entomopathogenic fungi.

Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors

Fungi of the basal lineage order Mucorales are able to cause infections in animals and humans. Mucormycosis is a well-known, life-threatening disease especially in patients with a compromised immune system. The rate of mortality and morbidity caused by mucormycosis has increased rapidly during the last decades, especially in developing countries. The systematic, phylogenetic, and epidemiological distributions of mucoralean fungi are addressed in relation to infection in immunocompromised patients. The review highlights the current achievements in (i) diagnostics and management of mucormycosis, (ii) the study of the interaction of Mucorales with cells of the innate immune system, (iii) the assessment of the virulence of Mucorales in vertebrate and invertebrate infection models, and (iv) the determination of virulence factors that are key players in the infection process, for example, high-affinity iron permease (FTR1), spore coat protein (CotH), alkaline Rhizopus protease enzyme (ARP), ADP-ribosylation factor (ARF), dihydrolipoyl dehydrogenase, calcineurin (CaN), serine and aspartate proteases (SAPs). The present mini-review attempts to increase the awareness of these difficult-to-manage fungal infections and to encourage research in the detection of ligands and receptors as potential diagnostic parameters and drug targets.

Phylogenetic and morphological analyses of the mycoparasitic genus Piptocephalis

The Piptocephalidaceae (Zoopagales, Zoopagomycota) contains three genera of mycoparasitic, haustoria-forming fungi: Kuzuhaea, Piptocephalis, and Syncephalis. Although the species in this family are diverse and ubiquitous in soil and dung, they are among the least studied fungi. Co-cultures of Piptocephalis and their hosts are relatively easy to isolate from soil and dung samples across the globe, making them a good model taxon for the order Zoopagales. This study focuses on the systematics of the genus Piptocephalis. Despite the fact that there are approximately 40 described Piptocephalis species, there are no modern taxonomic or molecular phylogenetic treatments of this group. Minimal sequence data are available, and relatively little is known about the true diversity or biogeography of the genus. Our study addresses two aspects: Piptocephalis systematics and analyses of the length and inter- and infraspecific variation of the nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region. First, we generated a large subunit (28S) nuc rDNA phylogeny and evaluated several morphological characters by testing their correlation with the phylogeny using Bayesian Tip-association Significance testing (BaTS). We found monophyly of Piptocephalis species identified based on morphological traits, but morphological character states were not conserved across clades, suggesting that there have been multiple gains and losses of morphological characters. We also found that Kuzhuaea is nested within Piptocephalis. Second, we amplified the ITS from many Piptocephalis isolates, created a sequence alignment, and measured the lengths using the software ITSx. Piptocephalis species had ITS regions that were longer than the average for most Dikarya but were similar in length to those of the related genus Syncephalis.

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.

Introducing ribosomal tandem repeat barcoding for fungi

Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.

Leveraging single-cell genomics to expand the fungal tree of life

Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.

Human Pathogenic Entomophthorales

The pathogenic entomophthoralean fungi cause infection in insects and mammalian hosts. Basidiobolus and Conidiobolus species can be found in soil and insect, reptile, and amphibian droppings in tropical and subtropical areas. The life cycles of these fungi occur in these environments where infecting sticky conidia are developed. The infection is acquired by insect bite or contact with contaminated environments through open skin. Conidiobolus coronatus typically causes chronic rhinofacial disease in immunocompetent hosts, whereas some Conidiobolus species can be found in immunocompromised patients. Basidiobolus ranarum infection is restricted to subcutaneous tissues but may be involved in intestinal and disseminated infections. Its early diagnosis remains challenging due to clinical similarities to other intestinal diseases. Infected tissues characteristically display eosinophilic granulomas with the Splendore-Höeppli phenomenon. However, in immunocompromised patients, the above-mentioned inflammatory reaction is absent. Laboratory diagnosis includes wet mount, culture serological assays, and molecular methodologies. The management of entomophthoralean fungi relies on traditional antifungal therapies, such as potassium iodide (KI), amphotericin B, itraconazole, and ketoconazole, and surgery. These species are intrinsically resistant to some antifungals, prompting physicians to experiment with combinations of therapies. Research is needed to investigate the immunology of entomophthoralean fungi in infected hosts. The absence of an animal model and lack of funding severely limit research on these fungi.

Sleeping Beauties: Horizontal Transmission via Resting Spores of Species in the Entomophthoromycotina

Many of the almost 300 species of arthropod-pathogenic fungi in the Entomophthoromycotina (Zoopagomycota) are known for being quite host-specific and are able to cause epizootics. Most species produce two main types of spores, conidia and resting spores. Here, we present a review of the epizootiology of species of Entomophthoromycotina, focusing on their resting spores, and how this stage leads to horizontal transmission and persistence. Cadavers in which resting spores are produced can often be found in different locations than cadavers of the same host producing conidia. Resting spores generally are dormant directly after production and require specific conditions for germination. Fungal reproduction resulting from infections initiated by Entomophaga maimaiga resting spores can differ from reproduction resulting from conidial infections, although we do not know how commonly this occurs. Reservoirs of resting spores can germinate for variable lengths of time, including up to several months, providing primary infections to initiate secondary cycling based on conidial infections, and not all resting spores germinate every year. Molecular methods have been developed to improve environmental quantification of resting spores, which can exist at high titers after epizootics. Ecological studies of biological communities have demonstrated that this source of these spores providing primary inoculum in the environment can decrease not only because of germination, but also because of the activity of mycopathogens.

Classification and infection mechanism of entomopathogenic fungi

ABSTRACT: Entomopathogenic fungi are important biological control agents throughout the world, have been the subject of intensive research for more than 100 years, and can occur at epizootic or enzootic levels in their host populations. Their mode of action against insects involves attaching a spore to the insect cuticle, followed by germination, penetration of the cuticle, and dissemination inside the insect. Strains of entomopathogenic fungi are concentrated in the following orders: Hypocreales (various genera), Onygenales (Ascosphaera genus), Entomophthorales, and Neozygitales (Entomophthoromycota).

Preliminary phylogeny of Coemansia (Kickxellales), with descriptions of four new species from Taiwan

Four new species of Coemansia from Taiwan are described. Three produce spirally twisted sporangiophores, and these new taxa increase the number of species in the Coemansia spiralis complex from three to six. Each new taxon is morphologically unique. Coemansia biformis, sp. nov., has two different asexual reproductive types on the same thallus; one is straight and the other has a spiral fertile region. Coemansia helicoidea, sp. nov., has stoloniferous sporangiophores with a helicoid fertile region. Coemansia pennisetoides, sp. nov., has a sporangiophore with a fertile region that resembles the inflorescence of the plant genus Pennisetum. Coemansia umbellata, sp. nov., has an umbellate sporangiophore branching pattern and a spirally twisted fertile region on the lowest branches. A dichotomous key was provided to identify the 23 accepted Coemansia species. Phylogenetic analysis based on a combined data set of D1-D2 domains of nuc 28S ribosomal RNA (rDNA) and partial nuc 18S rDNA identifies several independent evolutionary lineages within Coemansia and suggests that Spirodactylon aureum and Kickxella alabastrina may be nested within the genus Coemansia. Sequences of nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) are also used to support the description of these new species of Coemansia.

Isolation and Characterization of Three Zygomycetous Fungi in Korea: Backusella circina, Circinella muscae, and Mucor ramosissimus

While surveying undiscovered fungal taxa in Korea, three rare zygomycetous fungal strains, CNUFC-PTF2-1, CNUFC-TF3-1, and CNUFC-ESAF3-1, were isolated from soil, leaf, and freshwater samples, respectively. The strains were analyzed morphologically as well as phylogenetically based on the internal transcribed spacer region and 28S rDNA sequences. Sequence analysis of the two loci revealed that the isolates, CNUFC-PTF2-1, CNUFC-TF3-1, and CNUFC-ESAF3-1, were identified as Backusella circina, Circinella muscae, and Mucor ramosissimus, respectively. These species have not yet been previously described in Korea.

New insights from molecular phylogenetics of amoebophagous fungi (Zoopagomycota, Zoopagales)

Amoebophagous fungi are represented in all fungal groups: Basidiomycota, Ascomycota, Zygomycota, and Chytridiomycota. The amoebophagous fungi, within the zygomycota (Zoopagales, Zoopagomycota), mainly affect naked amoebae as ectoparasites or endoparasites. It is rather difficult to isolate members of the Zoopagales, because of their parasitic lifestyle, and to bring them into culture. Consequently, gene sequences of this group are undersampled, and its species composition and phylogeny are relatively unknown. In the present study, we were able to isolate amoebophagous fungi together with their amoeba hosts from various habitats (moss, pond, bark, and soil). Altogether, four fungal strains belonging to the genera Acaulopage and Stylopage plus one unidentified isolate were detected. Sequences of the 18S rDNA and the complete ITS region and partial 28S (LSU) rDNA were generated. Subsequent phylogenetic analyses showed that all new isolates diverge at one branch together with two environmental clonal sequences within the Zoopagomycota. Here, we provide the first molecular characterization of the genus Stylopage. Stylopage is closely related to the genus Acaulopage. In addition, taxonomy and phylogeny of amoebophagous fungi and their ecological importance are reviewed based on new sequence data, which includes environmental clonal sequences.

Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites

We examined phylogenetic relationships among species of the mycoparasite genus Syncephalis using sequences from three nuclear ribsosomal DNA genes (18S, 5.8S, and 28S nuc rDNA) and a gene encoding the largest subunit of RNA polymerase II (RPB1). Our data set included 88 Syncephalis isolates comprising 23 named species and several unnamed taxa. We also revived a culturing technique using beef liver and cellophane to grow several Syncephalis isolates without their host fungi to obtain pure parasite DNA. Most isolates, however, were grown in co-cultures with their host fungi, so we designed Syncephalis-specific primers to obtain sequence data. Individual and combined data sets were analyzed by maximum likelihood (ML) and Bayesian methods. We recovered 20 well-supported lineages and 38 operational taxonomic units (OTUs). Most major clades contained isolates from distant localities on multiple continents. There were taxonomic and nomenclature issues within several clades, probably due to high phenotypic plasticity or species dimorphism. We also conducted an analysis of Syncephalis nuc rDNA internal transcribed spacer (ITS) sequences for 31 phylogenetically diverse isolates, and we determined that most Syncephalis species have long ITS sequences relative to other fungi. Although commonly employed eukaryotic and fungal primers are compatible with diverse Syncephalis species, the ITS sequences of Syncepahlis are nonetheless rarely recovered in environmental molecular diversity surveys.

Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.

Hyphal tip cytoplasmic organization in four zygomycetous fungi

We have examined the hyphal tip structure in four zygomycetous fungi: Mortierella verticillata (Mortierellales), Coemansia reversa (Kickxellales), Mucor indicus and Gilbertella persicaria (Mucorales) using both light and transmission electron microscopy. We have used cryofixation and freeze-substitution methods to preserve fungal hyphae for transmission electron microscopy, which yielded improved preservation of ultrastructural details. Our research has confirmed studies that described the accumulation of secretory vesicles as a crescent at the hyphal apex (i.e. the apical vesicle crescent [AVC]) and provided a more detailed understanding of the vesicle populations. In addition, we have been able to observe the behavior of the AVC during hyphal growth in M. indicus and G. persicaria.

Phylogenomics and evolution of secondary metabolism in plant-associated fungi

Fungi produce a myriad of secondary metabolites, compounds that are not required for basic cellular processes, but are thought to be central to ecological functions. Genomic sequencing of fungi has revealed a greater diversity of secondary metabolism than previously realized, including novel taxonomic distributions of known compounds and uncharacterized gene clusters in well-studied organisms. Here we provide an overview of the major groups of metabolites, their ecological functions, the genetic systems that produce them, and the patterns and processes associated with evolutionary diversification of secondary metabolism in plant-associated filamentous ascomycetes.

Evolution of zygomycetous spindle pole bodies: Evidence from Coemansia reversa mitosis

PREMISE OF THE STUDY

The earliest eukaryotes were likely flagellates with a centriole that nucleates the centrosome, the microtubule-organizing center (MTOC) for nuclear division. The MTOC in higher fungi, which lack flagella, is the spindle pole body (SPB). Can we detect stages in centrosome evolution leading to the diversity of SPB forms observed in terrestrial fungi? Zygomycetous fungi, which consist of saprobes, symbionts, and parasites of animals and plants, are critical in answering the question, but nuclear division has been studied in only two of six clades.

METHODS

Ultrastructure of mitosis was studied in Coemansia reversa (Kickxellomycotina) germlings using cryofixation or chemical fixation. Character evolution was assessed by parsimony analysis, using a phylogenetic tree assembled from multigene analyses.

KEY RESULTS

At interphase the SPB consisted of two components: a cytoplasmic, electron-dense sphere containing a cylindrical structure with microtubules oriented nearly perpendicular to the nucleus and an intranuclear component appressed to the nuclear envelope. Markham's rotation was used to reinforce the image of the cylindrical structure and determine the probable number of microtubules as nine. The SPB duplicated early in mitosis and separated on the intact nuclear envelope. Nuclear division appears to be intranuclear with spindle and kinetochore microtubules interspersed with condensed chromatin.

CONCLUSIONS

This is the sixth type of zygomycetous SPB, and the third type that suggests a modified centriolar component. Coemansia reversa retains SPB character states from an ancestral centriole intermediate between those of fungi with motile cells and other zygomycetous fungi and Dikarya.

Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi

The evolution of filamentous hyphae underlies an astounding diversity of fungal form and function. We studied the cellular structure and evolutionary origins of the filamentous form in the Monoblepharidomycetes (Chytridiomycota), an early-diverging fungal lineage that displays an exceptional range of body types, from crescent-shaped single cells to sprawling hyphae. To do so, we combined light and transmission electron microscopic analyses of hyphal cytoplasm with molecular phylogenetic reconstructions. Hyphae of Monoblepharidomycetes lack a complex aggregation of secretory vesicles at the hyphal apex (i.e. Spitzenkörper), have centrosomes as primary microtubule organizing centers and have stacked Golgi cisternae instead of tubular/fenestrated Golgi equivalents. The cytoplasmic distribution of actin in Monoblepharidomycetes is comparable to the arrangement observed previously in other filamentous fungi. To discern the origins of Monoblepharidomycetes hyphae, we inferred a phylogeny of the fungi based on 18S and 28S ribosomal DNA sequence data with maximum likelihood and Bayesian inference methods. We focused sampling on Monoblepharidomycetes to infer intergeneric relationships within the class and determined 78 new sequences. Analyses showed class Monoblepharidomycetes to be monophyletic and nested within Chytridiomycota. Hyphal Monoblepharidomycetes formed a clade sister to the genera without hyphae, Harpochytrium and Oedogoniomyces. A likelihood ancestral state reconstruction indicated that hyphae arose independently within the Monoblepharidomycetes lineage and in at least two other lineages. Cytological differences among monoblepharidalean and other fungal hyphae are consistent with these convergent origins.

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.

Mucormycosis caused by unusual mucormycetes, non-Rhizopus, -Mucor, and -Lichtheimia species

Rhizopus, Mucor, and Lichtheimia (formerly Absidia) species are the most common members of the order Mucorales that cause mucormycosis, accounting for 70 to 80% of all cases. In contrast, Cunninghamella, Apophysomyces, Saksenaea, Rhizomucor, Cokeromyces, Actinomucor, and Syncephalastrum species individually are responsible for fewer than 1 to 5% of reported cases of mucormycosis. In this review, we provide an overview of the epidemiology, clinical manifestations, diagnosis of, treatment of, and prognosis for unusual Mucormycetes infections (non-Rhizopus, -Mucor, and -Lichtheimia species). The infections caused by these less frequent members of the order Mucorales frequently differ in their epidemiology, geographic distribution, and disease manifestations. Cunninghamella bertholletiae and Rhizomucor pusillus affect primarily immunocompromised hosts, mostly resulting from spore inhalation, causing pulmonary and disseminated infections with high mortality rates. R. pusillus infections are nosocomial or health care related in a large proportion of cases. While Apophysomyces elegans and Saksenaea vasiformis are occasionally responsible for infections in immunocompromised individuals, most cases are encountered in immunocompetent individuals as a result of trauma, leading to soft tissue infections with relatively low mortality rates. Increased knowledge of the epidemiology and clinical presentations of these unusual Mucormycetes infections may improve early diagnosis and treatment.

The fungi: 1, 2, 3 ... 5.1 million species?

PREMISE OF THE STUDY

Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist.

METHODS

Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa.

KEY RESULTS

Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered.

CONCLUSIONS

Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.

A molecular survey of ectomycorrhizal hyphae in a California Quercus-Pinus woodland

Ectomycorrhizal (ECM) hyphal communities have not been well characterized. Furthermore, there have been few studies where the ECM hyphal community is compared to fungi detected as sporocarps or ECM-colonized root tips. We investigated fungi present as hyphae in a well-studied California Quercus-Pinus woodland. Hyphal species present were compared to those found as sporocarps and ECM root tips at the same site. Hyphae were extracted from root-restrictive nylon mesh in-growth bags buried in the soil near mature Quercus douglasii, Quercus wislizeni, and Pinus sabiniana. Taxa were identified using PCR, cloning, and DNA sequencing of internal transcribed spacer and 28s rDNA. Among the 33 species detected, rhizomorph-forming ECM fungi dominated the hyphal community, especially species of Thelephoraceae and Boletales. Most fungi in soils near Quercus spp. and P. sabiniana were ECM basidiomycetes, but we detected two ECM ascomycetes and three non-mycorrhizal fungi. Many ECM species present as hyphae were also previously detected at this site as sporocarps (18%) or on ECM root tips (58%). However, the hyphal community was mostly dominated by different taxa than either the sporocarp or ECM root communities.

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

The ectomycorrhizal (EcM) symbiosis involves a large number of plant and fungal taxa worldwide. During studies on EcM diversity, numerous misidentifications, and contradictory reports on EcM status have been published. This review aims to: (1) critically assess the current knowledge of the fungi involved in the EcM by integrating data from axenic synthesis trials, anatomical, molecular, and isotope studies; (2) group these taxa into monophyletic lineages based on molecular sequence data and published phylogenies; (3) investigate the trophic status of sister taxa to EcM lineages; (4) highlight other potentially EcM taxa that lack both information on EcM status and DNA sequence data; (5) recover the main distribution patterns of the EcM fungal lineages in the world. Based on critically examining original reports, EcM lifestyle is proven in 162 fungal genera that are supplemented by two genera based on isotopic evidence and 52 genera based on phylogenetic data. Additionally, 33 genera are highlighted as potentially EcM based on habitat, although their EcM records and DNA sequence data are lacking. Molecular phylogenetic and identification studies suggest that EcM symbiosis has arisen independently and persisted at least 66 times in fungi, in the Basidiomycota, Ascomycota, and Zygomycota. The orders Pezizales, Agaricales, Helotiales, Boletales, and Cantharellales include the largest number of EcM fungal lineages. Regular updates of the EcM lineages and genera therein can be found at the UNITE homepage http://unite.ut.ee/EcM_lineages . The vast majority of EcM fungi evolved from humus and wood saprotrophic ancestors without any obvious reversals. Herbarium records from 11 major biogeographic regions revealed three main patterns in distribution of EcM lineages: (1) Austral; (2) Panglobal; (3) Holarctic (with or without some reports from the Austral or tropical realms). The holarctic regions host the largest number of EcM lineages; none are restricted to a tropical distribution with Dipterocarpaceae and Caesalpiniaceae hosts. We caution that EcM-dominated habitats and hosts in South America, Southeast Asia, Africa, and Australia remain undersampled relative to the north temperate regions. In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures. Due to great risk of contamination, future reports on EcM status of previously unstudied taxa should integrate molecular identification tools with axenic synthesis experiments, detailed morphological descriptions, and/or stable isotope investigations. We believe that the introduced lineage concept facilitates design of biogeographical studies and improves our understanding about phylogenetic structure of EcM fungal communities.

Morphologic and phylogenetic characterization of Conidiobolus lamprauges recovered from infected sheep

Conidiobolus lamprauges, a soil and plant entomophthoralean fungus, has been reported only in a horse and, more recently, in sheep with rhinopharyngeal entomophthoramycosis. Thus, little information is available to enable proper identification of this pathogen and its differentiation from other saprotrophic and pathogenic Conidiobolus species. Using classical mycological tools and molecular methodologies, we report for the first time the taxonomic and phylogenetic description of three C. lamprauges isolates recovered from sheep with rhinopharyngeal entomophthoramycosis. The distinctive clinical and pathological features of C. lamprauges are compared with those of other Conidiobolus spp. affecting sheep, as well as with those of the stramenopilan ovine agent Pythium insidiosum. The comparative morphological attributes of Conidiobolus spp. are also diagramed; along with the sequence data generated, they should assist laboratories in the identification of these uncommon species.

Spectrum of zygomycete species identified in clinically significant specimens in the United States

Several members of the order Mucorales (subphylum Mucoromycotina) are important agents of severe human infections. The identification of these fungi by using standard mycologic methods is often difficult and time consuming. Frequently, the etiological agent in clinical cases is reported either as a Mucor sp., which is not the most frequent genus of zygomycetes, or only as a member of the Mucorales. For this reason, the actual spectrum of species of zygomycetes and their incidences in the clinical setting is not well known. The goals of this study were to compare the results of the molecular identification of an important set of clinical isolates, received in a mycological reference center from different regions of the United States, with those obtained by using the traditional morphological methods and to determine the spectrum of species involved. We tested 190 isolates morphologically identified as zygomycetes by using sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA. Molecular identification revealed that Rhizopus oryzae represented approximately half (44.7%) of these isolates. The remainder was identified as Rhizopus microsporus (22.1%), Mucor circinelloides (9.5%), Mycocladus corymbifer (formerly Absidia corymbifera) (5.3%), Rhizomucor pusillus (3.7%), Cunninghamella bertholletiae (3.2%), Mucor indicus (2.6%), Cunninghamella echinulata (1%), and Apophysomyces elegans (0.5%). The most common anatomic sites for clinically significant zygomycetes, as determined by isolates sent to the Fungus Testing Laboratory for identification and/or susceptibility testing and included in this study, were the sinuses, lungs, and various cutaneous locations, at 25.8%, 26.8%, and 28%, respectively. These sites represented approximately 80% of the isolates evaluated. A high level of correlation (92.6%) between morphological and molecular identifications was found.

Identification of the sex genes in an early diverged fungus

Sex determination in fungi is controlled by a small, specialized region of the genome in contrast to the large sex-specific chromosomes of animals and some plants. Different gene combinations reside at these mating-type (MAT) loci and confer sexual identity; invariably they encode homeodomain, alpha-box, or high mobility group (HMG)-domain transcription factors. So far, MAT loci have been characterized from a single monophyletic clade of fungi, the Dikarya (the ascomycetes and basidiomycetes), and the ancestral state and evolutionary history of these loci have remained a mystery. Mating in the basal members of the kingdom has been less well studied, and even their precise taxonomic inter-relationships are still obscure. Here we apply bioinformatic and genetic mapping to identify the sex-determining (sex) region in Phycomyces blakesleeanus (Zygomycota), which represents an early branch within the fungi. Each sex allele contains a single gene that encodes an HMG-domain protein, implicating the HMG-domain proteins as an earlier form of fungal MAT loci. Additionally, one allele also contains a copy of a unique, chromosome-specific repetitive element, suggesting a generalized mechanism for the earliest steps in the evolution of sex determination and sex chromosome structure in eukaryotes.