The genus Candida in the Saccharomycotina has long reflected the historical practice of yeast classification based on phenotypic characteristics, retaining remnants of dual nomenclature even after its abandonment in 2011. Following this shift, many Candida species were reclassified into existing or newly proposed genera; yet, Candida itself remained heterogeneous and phylogenetically divergent. This heterogeneity is also true for genera like Ogataea, Starmerella, and Wickerhamomyces. While this heterogeneity has been demonstrated in previous studies, including several recent proposals for new genera, the inclusion of reclassified Candida species in these genera will make them more phylogenetically diverse. Despite widespread recognition of the polyphyletic nature of Candida, confusion persists due to the continued use of this single generic name for species belonging to lineages distantly related to that of the generic type species, Candida vulgaris, a current synonym under Candida tropicalis. In this study, we aim to reduce the genetic heterogeneity of the genus Candida by (i) focusing on lineages distantly related to its nomenclature type and (ii) assessing the diversity and composition of genera into which former Candida species have been reassigned. Phylogenomic analyses were conducted to determine the positions of Candida species and several genomic metrics, including average amino acid identity (AAI), percentage of conserved proteins (POCP), and presence-absence patterns of orthologs (PAPO), in order to quantify genetic divergence in genera and clades, were calculated to assist the reclassification decisions as complementary approaches. In addition to phylogenomic analyses, comprehensive phylogenetic analyses using ITS and LSU D1/D2 rDNA sequence data were performed to include species that are not represented in the genome-scale analyses and to assist species recognition in future studies. This framework led to an updated classification of Candida species and related taxa, proposing 25 new genera to accommodate reclassified species and validating 4 genera, along with 175 new combinations and 87 newly recognized species.

Floral microbes, including bacteria and fungi, alter nectar quality, thus changing pollinator visitation. Conversely, pollinator visitation can change the floral microbial community. Most studies on dispersal of floral microbes have focused on bees, ants or hummingbirds, yet Lepidoptera are important pollinators. We asked (a) where are microbes present on the butterfly body, (b) do butterflies transfer microbes while foraging, and (c) how does butterfly foraging affect microbial abundance on different floret structures. The tarsi and proboscis had significantly more microbes than the thorax in wild‐caught Glaucopsyche lygdamus (Lepidoptera: Lycaenidae) and Speyeria mormonia (Lepidoptera: Nymphalidae). Glaucopsyche lygdamus , a smaller‐bodied species, had fewer microbes than S. mormonia. As a marker for microbes, we used a bacterium ( Rhodococcus fascians, near NCBI Y11196) isolated from a S. mormonia that was foraging for nectar, and examined its dispersal by G. lygdamus and S. mormonia visiting florets of Pyrrocoma crocea (Asteraceae). Microbial dispersal among florets correlated positively with bacterial abundance in the donor floret. Dispersal also depended on butterfly species, age, and bacterial load carried by the butterfly. Recipient florets had less bacteria than donor florets. The nectaries had more bacteria than the anthers or the stigmas, while anthers and stigmas did not differ from each other. There was no differential transmission among floral organs. Lepidoptera thus act as vectors of floral microbes. Including Lepidoptera is thus crucial to an understanding of plant–pollinator–microbe interactions. Future studies should consider the role of vectored microbes in lepidopteran ecology and fitness.

Phylogenetic studies of Laboulbeniomycetes support recognition of three orders (Herpomycetales, Laboulbeniales, Pyxidiophorales) and two unnamed clades containing conidial, arthropod-associated fungi and a poorly known perithecial genus, Subbaromyces. Herpomycetales and Laboulbeniales include obligate arthropod-associated biotrophs characterized by a parenchymatous thallus of several thousand cells. Pyxidiophorales are hyphal mycoparasites with an unusual three-morph life cycle. The two-celled ascospore with a distinctive apparatus for attachment to arthropods ties together all Laboulbeniomycetes. The complex morphologies and life histories of these fungi are described as a background for research directions that will rely heavily on molecular methods, including phylogenomics, with emphasis on host–parasite relations.

Arthropod-fungus interactions involving the Laboulbeniomycetes have been pondered for several hundred years. Early studies of Laboulbeniomycetes faced several uncertainties. Were they parasitic worms, red algal relatives, or fungi? If they were fungi, to which group did they belong? What was the nature of their interactions with their arthropod hosts? The historical misperceptions resulted from the extraordinary morphological features of these oddly constructed ectoparasitic fungi. More recently, molecular phylogenetic studies, in combination with a better understanding of life histories, have clearly placed these fungi among filamentous Ascomycota (subphylum Pezizomycotina). Species discovery and research on the classification of the group continue today as arthropods, and especially insects, are routinely collected and examined for the presence of Laboulbeniomycetes. Newly armed with molecular methods, mycologists are poised to use Laboulbeniomycetes-insect associations as models for the study of a variety of basic evolutionary and ecological questions involving host-parasite relationships, modes of nutrient intake, population biology, host specificity, biological control, and invasion biology. Collaboration between mycologists and entomologists is essential to successfully advance knowledge of Laboulbeniomycetes and their intimate association with their hosts.

Historically, thallus-forming Laboulbeniomycetes, including the orders Laboulbeniales and Herpomycetales, were set apart because of their distinctive morphology and ecology. Although some biologists correctly interpreted these arthropod ectoparasites as fungi, even ascomycetes, others thought they were worms, red algae, or members of taxa described especially for them. Speculation on the evolution of the group involving red algae, the morphology-based Floridean Hypothesis, persisted deep into the 20th century, in part because valid alternatives were not presented. Although the distinctive features of Laboulbeniales clearly set them apart from other fungi, the difficulty was in the absence of characters grouping them among the fungi. Thaxter considered the Laboulbeniales to be ascomycetes, but he avoided phylogenetic discussions involved in the Floridean Hypothesis all of his life. Eventually, developmental studies of the life history of Pyxidiophora species, hyphal perithecial ascomycetes with 2-celled ascospores, revealed characters connecting Laboulbeniales to other ascomycetes. The distinctive morphological features of Laboulbeniales (absence of mycelium, a thallus developed from 2-celled ascospores by cell divisions in several planes, arthropod parasitism) can be best understood by comparison with Pyxidiophora. The development of a 3-dimensional thallus composed of true parenchyma occurs not only in Laboulbeniales, but also in Pyxidiophora species. The life history of arthropod ectoparasitism of Laboulbeniales as well as mycoparasitism and phoretic dispersal by arthropods of Pyxidiophora species can be explained by Tranzschel's Law, originally applied to rust fungi. Molecular analyses including other arthropod-associated fungi have contributed to a better understanding of an enlarged class, Laboulbeniomycetes, which now includes a clade comprising Chantransiopsis, Tetrameronycha, and Subbaromyces. A two-locus phylogenetic tree highlights evolutionary and life history questions with regard to the placement of Herpomycetales as the first diverging lineage of the Laboulbeniomycetes. The sister group for all the Laboulbeniomycetes remains to be discovered.

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

Nothing is sterile. Insects, plants, and fungi, highly speciose groups of organisms, conceal a vast fungal biodiversity. An approximation of the total number of fungal species on Earth remains an elusive goal, but estimates should include fungal species hidden in associations with other organisms. Some specific roles have been discovered for the fungi hidden within other life forms, including contributions to nutrition, detoxification of foodstuffs, and production of volatile organic compounds. Fungi rely on associates for dispersal to fresh habitats and, under some conditions, provide them with competitive advantages. New methods are available to discover microscopic fungi that previously have been overlooked. In fungal conservation efforts, it is essential not only to discover hidden fungi but also to determine if they are rare or actually endangered.

171 The fungi contain possibly as many as 1.5 million species (Hawksworth 1991, 2001), ranging from organisms that are microscopic and unicellular to multicellular colonies that can be as large as the largest animals and plants (Alexopoulos et al. 1996). Phylogenetic analyses of nuclear small subunit (nSSU) ribosomal DNA (rDNA) put fungi and animals as sister clades that diverged 0.9 to 1.6 billion years ago (Wainright et al. 1993, Berbee and Taylor 2001, Heckman et al. 2001). The grouping of fungi and animals as sister taxa is controversial, with some protein-coding genes supporting the association and others not (Wang et al. 1999, Loytynoja and Milinkovitch 2001, Lang et al. 2002). Assuming that fungi and animals are sister taxa, a comparison of basal fungi (Chytridiomycota) with basal animals and associated groups (e.g., choanoflagellates and mesomycetozoa) should shed light on the nature of the last common ancestor of animals and fungi (fig. 12.1). It must have been unicellular and motile, indicating that multicellularity evolved independently in the two clades, and again in the several differently pigmented plant clades (M. Medina, A. C. Collins, J. W. Taylor, J. W. Valentine, J. H. Lips, L. Amaral-Zettler, and M. L. Sogin, unpubl. obs.). Fungi, like animals, are heterotrophs but, unlike animals, fungi live in their food. They do so as unicellular yeasts or as thin, filamentous tubes, termed hyphae (hypha, singular), which absorb simple molecules and export hydrolytic enzymes to make more simple molecules out of complex polymers, such as carbohydrates, lipids, proteins, and nucleic acids. Fungi have been spectacularly successful in the full range of heterotrophic interactions—decomposition, symbiosis, and parasitism. Fungi are well known to decay food stored too long in the refrigerator, wood in homes that have leaky roofs, and even jet fuel in tanks where condensation has accumulated. In nature, apart from fire, almost all biological carbon is recycled by microbes. The hyphae of filamentous fungi do the hard work in cooler climes and wherever invasive action is needed, as in the decay of wood. Fungi enter into many symbioses, three of the most widespread and enduring are with microbial algae and cyanobacteria as lichens, with plants as mycorrhizae, and again with plants as endophytes. These symbioses are anything but rare. Nearly one-fourth of all described fungi form lichens, and lichens are the last complex life forms seen as one travels to either geographic pole (Brodo et al. 2001). Almost all plant species form mycorrhizae, and there is good fossil and molecular phylogenetic evidence that the first land plants got there with fungi in their rhizomes (Smith and Read 1997). There probably is not a plant that lacks a fungal endophyte, and there is good evidence that the endophytes improve plant fitness by deterring insect and mammalian herbivores and affect plant community structure (Clay 2001). Fungi are not limited to symbioses with autotrophs. Symbioses with animals are also prevalent, with partners ranging from ants and other insects to the gut of many ruminate animals and other herbivores (Blackwell 2000). Many insects may have been able to occupy new habitats due to associations with gut yeasts that provide digestive enzymes (Suh et al. 2003). David S. Hibbett

Candida tanzawaensis clade members are now placed in Suhomyces. The group was virtually unknown until the early 2000s. Here, we review progress made on Suhomyces over the last two decades and provide data from reports of new members of the group from distant localities worldwide, their habitats and a new study of mating loci that helps explain earlier failed compatibility tests. Phylogenetic studies indicate early diverging members are mostly associated with plants, but later diverging species are usually fungus-feeding insect associates. The genome of S. tanzawaensis was known to have a heterothallic mating allele arrangement with a single MAT α idiomorph. For this review, we generate sequence data and compare the MAT gene arrangement of 30 strains from nine Suhomyces species. These varied from MAT α loci containing mating genes α1 and α2, hypothetical MAT a loci without detectable mating genes a1 and a2 to truncated, possibly completely dissociated MAT loci with intraspecific variation. The absence of a second MAT in a genome locus precludes the possibility of mating type switching. Sympatric speciation likely occurred after MAT locus deterioration began in isolated habitats. Although asexual reproduction may be an effective short-term strategy, theory predicts it will not endure over the extreme long term.

Phylogenetic taxon definitions (PTDs) are explicit, phylogeny-based statements that specify clades. PTDs are central to the system of rank-free classification that is governed by the PhyloCode, but they can also be used to clarify the meanings of ranked names. We present PTDs for four major groups: Fungi, Dikarya, Ascomycota, and Basidiomycota.

ABSTRACT Fungi and insects live together in the same habitats, and many species of both groups rely on each other for success. Insects, the most successful animals on Earth, cannot produce sterols, essential vitamins, and many enzymes; fungi, often yeast-like in growth form, make up for these deficits. Fungi, however, require constantly replenished substrates because they consume the previous ones, and insects, sometimes lured by volatile fungal compounds, carry fungi directly to a similar, but fresh, habitat. Yeasts associated with insects include Ascomycota (Saccharomycotina, Pezizomycotina) and a few Basidiomycota. Beetles, homopterans, and flies are important associates of fungi, and in turn the insects carry yeasts in pits, specialized external pouches, and modified gut pockets. Some yeasts undergo sexual reproduction within the insect gut, where the genetic diversity of the population is increased, while others, well suited to their stable environment, may never mate. The range of interactions extends from dispersal of yeasts on the surface of insects (e.g., cactus- Drosophila -yeast and ephemeral flower communities, ambrosia beetles, yeasts with holdfasts) to extremely specialized associations of organisms that can no longer exist independently, as in the case of yeast-like symbionts of planthoppers. In a few cases yeast-like fungus-insect associations threaten butterflies and other species with extinction. Technical advances improve discovery and identification of the fungi but also inform our understanding of the evolution of yeast-insect symbioses, although there is much more to learn.

ABSTRACT 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.

Production of fermented beverages and bread making represents a multibillion dollar worldwide industry (1) with its origins linked to the Middle East nearly 10,000 y ago (2). Despite this long history, the cause of fermentation was not discovered until the pioneering work beginning in the middle of the 19th century when Louis Pasteur demonstrated that fermentation is yeast-mediated. The long-term questions have been which yeast and where did it come from? The name selected for the wine fermentation yeast was Saccharomyces cerevisiae, but based on phenotype, it appeared that there were related fermentative species. Early studies from DNA reassociation (3) and from gene sequencing (4) verified this premise and demonstrated that additional species of Saccharomyces were involved in fermentation, such as Saccharomyces uvarum for lager beers. DNA sequence evidence supports the use of S. cerevisiae in wine making in Egypt 5,000 y ago (5). Unresolved has been an understanding of the natural habitat of Saccharomyces species. It has been proposed that S. cerevisiae evolved into a domesticated species found only in wineries and associated vineyards, but the discovery of Saccharomyces species on tree bark has raised the intriguing possibility that S. cerevisiae and related species have a natural habitat associated with forest trees (6). More recent genome sequencing revealed a new species, Saccharomyces eubayanus and, further, that it shares homologous genes with S. cerevisiae, Saccharomyces paradoxus, and S …

Production of fermented beverages and bread making represents a multibillion dollar worldwide industry (1) with its origins linked to the Middle East nearly 10,000 y ago (2). Despite this long history, the cause of fermentation was not discovered until the pioneering work beginning in the middle of the 19th century when Louis Pasteur demonstrated that fermentation is yeast-mediated. The long-term questions have been which yeast and where did it come from? The name selected for the wine fermentation yeast was Saccharomyces cerevisiae , but based on phenotype, it appeared that there were related fermentative species. Early studies from DNA reassociation (3) and from gene sequencing (4) verified this premise and demonstrated that additional species of Saccharomyces were involved in fermentation, such as Saccharomyces uvarum for lager beers. DNA sequence evidence supports the use of S. cerevisiae in wine making in Egypt 5,000 y ago (5). Unresolved has been an understanding of the natural habitat of Saccharomyces species. It has been proposed that S . cerevisiae evolved into a domesticated species found only in wineries and associated vineyards, but the discovery of Saccharomyces species on tree bark has raised the intriguing possibility that S . cerevisiae and related species have a natural habitat associated with forest trees (6). More recent genome sequencing revealed a new species, Saccharomyces eubayanus and, further, that it shares homologous genes with S . cerevisiae , Saccharomyces paradoxus , and S … [↵][1]1To whom correspondence should be addressed. Email: mblackwell{at}lsu.edu. [1]: #xref-corresp-1-1

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Ourwell-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as L-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA.