Zoosporic Fungi Research Articles

Microbial Grazers May Aid in Controlling Infections Caused by the Aquatic Zoosporic Fungus Batrachochytrium dendrobatidis.

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 μm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d–1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (Imax) of 1.63 × 103 zoospores d–1, with a half saturation constant (k) of 5.75 × 103 zoospores ml–1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host–1). However, simulated inferior micrograzers (0.7 × Imax and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.

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.

Evidences of the Oldest Trophic Interactions in the Riphean Biota (Lakhanda Lagerstätte, Southeastern Siberia).

Evidences of perforation of organic-walled fossil eukaryotes by other organisms has been found in the Lakhanda Lagerstätte (1030-1000 Ma, southeastern Siberia). The type of perforation is most similar to the type described from the Akademikerbren (750 Ma, Spitsbergen), Chuar (780-740 Ma, United States) and Shaler Supergroups (1150-900 Ma, Arctic Canada). The biogenic origin of the perforations has been substantiated. A hypothesis of perforation of fossils by zoosporic fungi found in the same deposits has been proposed. At the same time, the taxonomic diversity of eukaryotic "prey" taxa and the primitive morphology of such perforations do not allow us to qualify the perforators as distinct protists and do not point out the absolute certainty of selective predation among eukaryotes during the Riphean (Mesoproterozoic). Thus, the hypothesis of explosive diversification of eukaryotes in the Late Proterozoic driven by selective predation cannot yet be confirmed paleontologically.

Filamentous cyanobacteria and associated microorganisms, structurally preserved in a Late Jurassic chert from Patagonia, Argentina

A new cyanobacterium, Patagonifilum jurassicum nov. gen. et sp., is structurally preserved in Late Jurassic hydrothermally influenced siliceous chert from the Deseado Massif, Patagonia, Argentina. The cyanobacterium occurs in the form of loosely to densely spaced, heteropolar filaments (up to 4.5 μm wide) that form turf-like stands, or spherical to hemispherical colonies on different substrates, usually degraded plant stems. Filaments consist of barrel-shaped cells enveloped in a non-stratified sheath, and basal cells that are distinct. The fossil is similar to certain present-day members of the Oscillatoriales (e.g., Homoeothrix), Synechococcales (e.g., Tapinothrix), and Nostocales (e.g., Rivularia, Gloeotrichia). Associated with the cyanobacteria are spheroidal to ovoid vesicles, up to 45 μm in diameter, which occur singly or clustered, mostly near the base of the filaments. They resemble certain present-day zoosporic fungi, and algae, coccoid cyanobacteria, and possibly certain arthropod eggs; however, their systematic affinities remain unresolved. This discovery is nevertheless important because it suggests that the cyanobacterial overgrowths from the Patagonian Jurassic cherts were not monospecific, but rather comprised different organisms that perhaps even interacted with each other.

ZOOSPORIC TRUE FUNGI, HETEROTROPHIC STRAMINIPILES AND PLASMODIOPHORIDS: STATUS OF KNOWLEDGE IN SOUTH AMERICA

Zoosporic true fungi and fungal-like organisms include unrelated groups in the kingdoms Fungi, Straminipila and Protozoa. There is very little information on the diversity of these organisms in many ecosystems of great biodiversity, particularly tropical or neotropicalareas. Research assessing their diversity has been mainly conducted in Argentina and Brazil using multiple baiting techniques, resulting in the discovery of many new taxa and new records. To date, 434 species in these groups have been recorded for both countries. Continuing research is necessary to provide a more comprehensive understanding of their diversity in South America. Few specialists are available to study such extensive areas, which are being degraded by deforestation, land/clearing, pollution and other anthropogenic activities that affect the habitat of these organisms, long before surveys can be carried out by mycologists and protistologists. Hence, attempts to gather information about the diversity of zoosporic organisms from South America are urgently needed, and should receive high priority.

388 Nutrition and the Ruminal Microbiome: Emerging Frontiers from an Old Friend

Abstract Rumen, a pregastric anaerobic gut ecosystem, inhabits arguably the most diverse and complex microbial community, with a mutualistic relationship with the host. The relationship is best exemplified in the utilization of lignocellulosic material and non-protein nitrogen to provide energy and protein to the host. The microbial community of the rumen is composed of bacteria, archaea, protozoa, fungi and bacteriophages. Culture- or microscopy-based procedures have identified over 200 species of bacteria, methanogens, ciliated protozoa and zoosporic fungi. The community analysis based on the genetic material of all microbial cells, called microbiome, has vastly expanded our understanding of the ruminal ecosystem. Microbiome analysis is based on sequencing of the targeted amplicons (16S rDNA variable regions for bacteria and archaea, 18S rDNA for protozoa or Internal Transcribed Regions for fungi) or whole genome shotgun metagenomics analysis. Rapid advancements in nucleic acid sequencing technologies and bioinformatics pipelines have provided unprecedented opportunities to delineate the diversity and complexity of the microbial community in relation ruminal function and dysfunctions and link ruminal microbes to host nutrition and productivity. Culture-independent methods have identified thousands of microbial species in the rumen, suggesting that a major fraction of the microbiome has not been cultured and functionally identified. A core microbiome in bacterial and archaeal populations of the rumen has been identified across a wide geographical regions, but significant variations in diversity, abundance, and individual taxa do exist because of diet and host genetics. However, there is evidence of signature microbiome among individual animals on the same diet and environment. Microbiome-wide association studies in relation to dietary changes, ruminal function and dysfunctions have begun to link and define the complexity of the host-microbe relationships. Translation of the potential of the microbiome analysis is supported by emerging evidences that specific microbiota can be linked to ruminal activity and productivity.

Where are the basal fungi? Current status on diversity, ecology, evolution, and taxonomy

To date, the majority of mycological studies are focused on Ascomycota and Basidiomycota. Research on basal fungi is rather limited with an obvious scarcity of data. Classification of basal fungi has witnessed ongoing changes in the last few decades. There have been numerous taxonomic revisions, establishment of new phyla and debates on the possibility to exclude some basal lineages from the currently circumscribed fungal groups. Zoosporic phyla such as Rozellomycota, Aphelidiomycota and Chytridiomycota are characterized by zoospores, which are motile spores with a flagellum. The position of the first two within the fungal kingdom is currently being debated. Non zoosporic phyla are collectively called zygomycetous fungi and include Mucoromycota and Zoopagomycota. Basal fungi perform important ecological roles. Some groups of basal fungi control the population density of plankton, Oomycetes, aphids, and small invertebrates, while taking part in recycling of energy and matter in food webs. A few basal fungi are known for uptaking toxic heavy metals from the environment. The earliest basal fungi emerged just after the divergence of the nucleariid line of phagotrophs. Various taxonomic studies question the monophyly of some basal phyla, such as Chytridiomycota. Depending on the life mode of the fungi and whether motile or non-motile spores are produced, the isolation methods differ. For the culture of parasitic zoosporic fungi, co-culturing the fungi with their host is recommended while for saprobes ones, baits can be used. For zygomycetous fungi, common methods include dilution plating and direct inoculation. In this review, we pinpoint research gaps and discuss the current classification schemes along with information on evolution, diversity, current methods and challenges to isolate and culture basal fungi.

Triskelia scotlandica, an enigmatic Rhynie chert microfossil revisited

The enigmatic microfossil Triskelia scotlandica from the Lower Devonian Rhynie chert is an acritarch-like, usually spheroidal to ovoid vesicle with a surface ornamentation comprised of isolated triradiate and meandering, high membranous ridges. The form has been formally described based on dispersed specimens preserved inside the remains of a land plant axis, and interpreted as the resting stage of a microscopic alga. Unusual microbial coatings on land plant axes from the Rhynie chert have recently yielded > 300 additional specimens of T. scotlandica, many of which occur in situ in prominent swellings of fungal hyphae. This discovery is a strong evidence that T. scotlandica is not algal, but rather fungal or fungus-like in nature. The swellings might be oogonia of a representative of the Oomycota (e.g., Saprolegniales), and T. scotlandica accordingly an ornamented oospore. However, specimens with a discharge tube suggest that T. scotlandica is more likely a zoosporangium or resting spore stage of an endoparasite, perhaps with affinities to the holocarpic Oomycota (e.g., Olpidiopsis), Cryptomycota (e.g., Rozella), or zoosporic fungi (e.g., Olpidium), in which case the hyphal swellings would be either dilatations resulting from the expansion of the parasite inside, or a host response (hypertrophy). The affinity of T. scotlandica remains unresolved, due in part to the uncertain diagnostic value of the surface ornamentation, and because no other stages of the life history of this organism are known. Nevertheless, the new specimens expand our knowledge of the microbial interactions that existed in early terrestrial ecosystems.

Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity

Mycoplankton are a diverse and ubiquitous component of marine environments with a suggested role in ocean biogeochemical cycling. Thus far, the patterns of their abundance, structure, and function against spatial environmental heterogeneity remains poorly understood. Based on in silico and experimental evaluation of multiple markers, we adopted the ITS1 region to determine the composition, guilds, and metabolic potential of mycoplankton communities in contrasting marine environments. The trophic status of estuarine (SB1 and SB2) and coastal (DB1 and DB2) sites, but not oceanic (OS) site, was the major factor that determined their abundances. While ascomycetous fungi dominated the estuarine and coastal sites, basidiomycetous fungi were found to dominate the oceanic site. The zoosporic fungi were relatively more abundant in SB1 and DB2 sites compared to the other sites. The relative abundances of the core fungi, namely Cystobasidium, Phlebia, Rhodotorula, Trichoderma, Alternaria, Penicillium, Malassezia, and Aspergillus varied widely across the sites. Additionally, several fungal genera unique to each site were also identified. DB2 site exhibited the lowest fungal richness while the OS site the highest. Conversely, the diversity and evenness were the lowest for the OS site but highest for the SB1 site. Temperature, pH, and chlorophyll-a were strongly associated with spatial diversity patterns. Of the 11 assigned guilds, some guilds particularly were not detected, including plant pathogen-wood saprotroph in DB2, the endophyte-plant pathogen in OS, the animal pathogen in SB1, and fungal parasite in DB1 and SB2. Within core functions—metabolism of amino acids, carbohydrates and energy, fatty acids and lipids, nitrogen, sulfur, and other compounds—several pathways showed spatial variations. Overall, this study not just broadens the taxonomic and metabolic repertoire of marine mycoplankton but also provides the first evidence of how these are shaped by site-scale environmental heterogeneity.

Biodiversity, spatial distribution and seasonality of heterotrophic straminipiles and true zoosporic fungi in two water bodies exposed to different effluents at Assiut (Upper Egypt).

Biodiversity, spatial distribution and seasonality of heterotrophic straminipiles and true zoosporic fungi in two water bodies exposed to different effluents at Assiut (Upper Egypt).

Quaeritorhiza haematococci is a new species of parasitic chytrid of the commercially grown alga, Haematococcus pluvialis

ABSTRACT Aquaculture companies grow the green alga Haematococcus pluvialis (Chlorophyta) to extract the carotenoid astaxanthin to sell, which is used as human and animal dietary supplements. We were requested to identify an unknown pathogen of H. pluvialis from an alga growing facility in the southwestern United States. To identify this zoosporic fungus and determine its phylogenetic placement among other chytrids, we isolated it into pure culture, photographed its morphology and zoospore ultrastructure, and sequenced and analyzed portions of nuc rDNA 18S and 28S genes. The organism belongs in the Chytridiomycota, but a comparison of rDNA with available representatives of the phylum did not convincingly place it in any described order. The unique zoospore ultrastructure supports its indeterminate ordinal position, and the morphology, as determined by light microscopy, did not match any described species. Consequently, we have placed this chytrid in the new genus, Quaeritorhiza, and described it as the new species Q. haematococci in the family Quaeritorhizaceae but otherwise incertae sedis in the Chytridiomycetes. This new taxon is important because it increases the known diversity of Chytridiomycota and the organism has the ability to disrupt agricultural production of an algal monoculture.

Actin guides filamentous rhizoid growth and morphogenesis in the zoosporic fungus Chytriomyces hyalinus

ABSTRACTThe advantage of filamentous growth to the fungal lifestyle is so great that it arose multiple times. Most zoosporic fungi from phylum Chytridiomycota exhibit a monocentric thallus form consisting of anucleate filamentous rhizoids that anchor reproductive sporangia to substrata and absorb nutrients. Actin function during polarized growth and cytokinesis is well documented across eukaryotes, but its role in sculpting nonhyphal, nonyeast fungal cells is unknown. We sought to provide a basis for comparing actin organization among major fungal lineages and to investigate the effects of actin disruption on morphogenesis in a monocentric thallus. Using fluorescence microscopy, we observed fixed, rhodamine phalloidin–stained actin in chemically fixed Chytriomyces hyalinus, exemplifying monocentric thallus development within the diverse, zoosporic phylum Chytridiomycota. We also compared rhizoid lengths and rhizoid branching of thalli incubated with the actin inhibitor latrunculin B to determine the effects of actin disruption on morphology. Actin was concentrated at the tips of growing rhizoids. Actin cables typically formed cortical, parallel arrays in hyphae, but in mature sporangia they were concentrated in a funnel-shaped array in the central region. Thalli treated with latrunculin B had shorter rhizoids with fewer branches than controls. In both hyphae and monocentric thalli, actin localization coincides with active, polarized growth and cytokinesis. Specific actin localization patterns are largely shared between monocentric species but differ significantly from patterns observed in hyphae. Actin integrity is critical for sustaining filamentous growth in all fungi.

Kinetid Structure of Aphelidium and Paraphelidium (Aphelida) Suggests the Features of the Common Ancestor of Fungi and Opisthosporidia.

The aphelids (phylum Aphelida) are phagotrophic parasitoids of algae and represent the most basal branch in superphylum Opisthosporidia, which contains the Microsporidia, Rozellosporidia and Aphelida. Being the closest group to traditional fungi, the aphelids should have ancestral features of both phyla. As in chytrids and other zoosporic fungi, the structure of zoospores is the most informative and important morphological feature for the phylogeny and taxonomy of aphelids. Though a general zoospore description exists for some aphelid species, their flagellar apparatus (kinetid) structure, which contains pivotal taxonomic and phylogenetic characters, has not been studied. Here we represent the kinetid structure in two genera, Aphelidium and Paraphelidium, and demonstrate independent reduction in the kinetid in each genus. The kinetid-mitochondrion connection found in Aphelidium and Paraphelidium is rare for opisthokonts in general, but present in the most basal branches of Fungi and Opisthosporidia. We suggest, therefore, that this connection represents an ancestral character for both these phyla.

Copper (II), Lead (ll) and Zinc (ll) reduce the rate of attachment in three zoosporic true fungi from soils of NSW, Australia

Copper (II), Lead (ll) and Zinc (ll) reduce the rate of attachment in three zoosporic true fungi from soils of NSW, Australia

Identification and characterization of GH11 xylanase and GH43 xylosidase from the chytridiomycetous fungus, Rhizophlyctis rosea

The early-lineage, aerobic, zoosporic fungi from the Chytridiomycota constitute less than 1% of the described fungi and can use diverse sources of nutrition from plant or animal products. One of the ancestral sources of fungal nutrition could be products following enzymatic degradation of plant material. However, carbohydrate-active enzymes from these ancient fungi have been less studied. A GH11 xylanase (RrXyn11A) (EC 3.2.1.8) and a GH43 xylosidase (RrXyl43A) (EC 3.2.1.37) were identified from an early-lineage aerobic zoosporic fungus, Rhizophlyctis rosea NBRC 105426. Both genes were heterologously expressed in Pichia pastoris and the recombinant enzymes were purified and characterized. The optimal pH for recombinant RrXyn11A and RrXyl43A was pH 7. RrXyn11A had high stability over a wide range of pH (4–8) and temperature (25–70 °C). RrXyn11A also showed high substrate specificity on both azurine-cross-linked (AZCL) arabinoxylan and AZCL xylan. RrXyl43A had β-xylosidase and minor α-l-arabinofuranosidase activity. This enzyme showed low product inhibition and retained 51% activity in the presence of 100 mM xylose. A combination of RrXyn11A and RrXyl43A exhibited significantly higher hydrolytic and polymer degradation capability and xylose release on wheat bran and beechwood xylan compared to treatment with commercial enzymes. This study was the first to heterologously express and characterize the GH11 xylanase (RrXyn11A) and GH43 xylosidase (RrXyl43A) from the ancient fungus, R. rosea. Meanwhile, this study also demonstrated that the enzymes from the ancient fungus R. rosea can be easily handled and heterologously expressed in Pichia, which presents a promising path to a new source of enzymes for biomass degradation.

Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae.

Chytrids are zoosporic fungi that play an important, but yet understudied, ecological role in aquatic ecosystems. Many chytrid species have been morphologically described as parasites on phytoplankton. However, the majority of them have rarely been isolated and lack DNA sequence data. In this study we isolated and cultivated three parasitic chytrids, infecting a common volvocacean host species, Yamagishiella unicocca. To identify the chytrids, we characterized morphology and life cycle, and analyzed phylogenetic relationships based on 18S and 28S rDNA genes. Host range and specificity of the chytrids was determined by cross-infection assays with host strains, characterized by rbcL and ITS markers. We were able to confirm the identity of two chytrid strains as Endocoenobium eudorinae Ingold and Dangeardia mamillata Schröder and described the third chytrid strain as Algomyces stechlinensis gen. et sp. nov. The three chytrids were assigned to novel and phylogenetically distant clades within the phylum Chytridiomycota, each exhibiting different host specificities. By integrating morphological and molecular data of both the parasitic chytrids and their respective host species, we unveiled cryptic host-parasite associations. This study highlights that a high prevalence of (pseudo)cryptic diversity requires molecular characterization of both phytoplankton host and parasitic chytrid to accurately identify and compare host range and specificity, and to study phytoplankton-chytrid interactions in general.

Diverse fungal lineages in subtropical ponds are altered by sediment-bound copper

Ponds represent a black box for fungal ecology. Compared to terrestrial environments, the fungal ecology of aquatic environments is rarely studied, and the few published studies have tended to be of lotic habitats in the northern hemisphere. We explored fungal communities and their responses to a gradient of copper in five year old artificial, replicated ponds in Australia. Ponds were subject to natural variations in temperature, precipitation and biotic colonisation. To explore the fungal communities, we amplified the ITS1 region of rDNA from samples of the water column, the sediment and cellulose baits (analogues to leaf fall) alone and in the presence of a gradient of copper. Fungal amplicon data revealed almost 800 fungal species from these habitats within the ponds. Interestingly, no chytrids from the Cladochytriales and Rhizophlyctidales were detected on cellulose baits, instead, putatively novel zoosporic taxa in the Chytridiomycota and the Rozellomycota were observed. Given the keystone role zoosporic fungi are thought to play in aquatic food webs, along with their role as primary decomposers of plant material, improved knowledge of their diversity and distribution is vital for understanding ecosystem function in standing water habitats. In aquatic environments copper tends to be bound to sediment and is not especially mobile in the water phase. The presence of copper in our sediment samples was correlated with repeatable and profound shifts in the fungal community, with chytrid species appearing to be the most sensitive, suggesting that they may be useful indicator organisms. Indirect effects of copper on fungal communities living on leaf analogues and in the water column were also explored.

The Transcriptome of <i>Paraphelidium Tribonemae</i> Illuminates the Ancestry of Fungi and Opisthosporidia

Aphelids constitute a group of diverse, yet poorly known, parasites of algae. Their life cycle and morphology resemble those of zoosporic fungi (chytrids) and rozellids (Cryptomycota/Rozellosporidia), another specious group of parasites of fungi and oomycetes. Unlike fungi, which are osmotrophs, aphelids and rozellids are phagotrophs, feeding on the host’s cytoplasm. Combined RNA polymerase and rRNA gene trees suggested that aphelids and rozellids relate to Microsporidia, extremely reduced parasites with remnant mitochondria. Accordingly, aphelids, rozellids and Microsporidia were proposed to form a monophyletic clade sister to Fungi, called Opisthosporidia. Microsporidia would have subsequently lost the ancestral opisthosporidian phagotrophy. However, the limited phylogenetic signal of those genes combined with microsporidian fast-evolving sequences have resulted in incongruent tree topologies, showing either rozellids or aphelids as the earliestbranching lineages of Opisthosporidia, and challenging their monophyly. We have generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae. Multi-gene phylogenomic analyses clearly confirm the monophyly of Opisthosporidia, placing aphelids as the earliest branching opisthosporidian lineage. This is consistent with the rich proteome inferred for P. tribonemae, which includes cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways that were lost in the comparatively reduced Rozella allomycis genome. Contrary to recent claims suggesting a parasitic root for Fungi, our results suggest that Fungi and Opisthosporidia evolved from a free-living phagotrophic ancestor that became osmotrophic at the fungal root and evolved towards phagotrophic parasitism in the opisthosporidian line.

New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus.

Zoosporic fungi are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems. They comprise at least three phyla, of which two, Chytridiomycota and Blastocladiomycota, developed a range of thallus morphologies including branching hyphae. Here we describe Retesporangicus lyonii gen. et sp. nov., an exceptionally well preserved fossil, which is the earliest known to produce multiple sporangia on an expanded hyphal network. To better characterize the fungus we develop a new method to render surfaces from image stacks generated by confocal laser scanning microscopy. Here, the method helps to reveal thallus structure. Comparisons with cultures of living species and character state reconstructions analysed against recent molecular phylogenies of 24 modern zoosporic fungi indicate an affinity with Blastocladiomycota. We argue that in zoosporic fungi, kinds of filaments such as hyphae, rhizoids and rhizomycelium are developmentally similar structures adapted for varied functions including nutrient absorption and anchorage. The fossil is the earliest known type to develop hyphae which likely served as a saprotrophic adaptation to patchy resource availability. Evidence from the Rhynie chert provides our earliest insights into the biology of fungi and their roles in the environment. It demonstrates that zoosporic fungi were already diverse in 407 million-year-old terrestrial ecosystems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.