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Introduction: Fungi are organisms that present themselves in multicellular macroscopic and unicellular microscopic forms. They are eukaryotic, heterotrophic, reproduce asexually/sexually, cosmopolitan, achlorophyllates and are present in various climatic conditions and found in a variety of species and forms in nature. Aims: Present the emerging evolution of fungi, their underreporting, scale and parameters that show their potential as a heterotrophic organism, decomposer and pathogen. Methodology: In this review, we conducted a search emphasizing themes about fungi using the available databases and based on the scientific literature, we discussed a series of recent issues involving this wide realm and the constant controversies and expectations that guide the existence of fungi on the planet. Results: The results presented show an analysis of the action of these eukaryotic organisms and their interaction with other living beings, the constant changes in taxonomy, their pathogenic potential in plants and animals, issues related to the intrinsic resistance of some species to drugs and also the potential biotechnological for which these organisms demonstrate high plasticity. Conclusion: The expansion of fungal diseases to the fauna and flora of the planet; leads us to believe that, unless measures are taken to reinforce biosafety issues, it will be increasingly necessary to take care of the health conditions of the planet to avoid a global collapse caused by microscopic beings.

The phylum Chytridiomycota (the “chytrids”) is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.

Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi. Fungi originated in a freshwater environment and their evolution accompanied the rise of algae and land plants. In this Review, Berbee and colleagues examine the fossil and genomic record of ancient fungi and the inferences we can make about their lifestyle.

Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.

Chytrids are early-diverging fungi that share features with animals that have been lost in most other fungi. They hold promise as a system to study fungal and animal evolution, but we lack genetic tools for hypothesis testing. Here, we generated transgenic lines of the chytrid Spizellomyces punctatus, and used fluorescence microscopy to explore chytrid cell biology and development during its life cycle. We show that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’. The zoospores, akin to animal cells, crawl using actin-mediated cell migration. After forming a cell wall, polymerized actin reorganizes into fungal-like cortical patches and cables that extend into hyphal-like structures. Actin perinuclear shells form each cell cycle and polygonal territories emerge during cellularization. This work makes Spizellomyces a genetically tractable model for comparative cell biology and understanding the evolution of fungi and early eukaryotes.

We report here a giant microfossil resembling the conidium of an ascomycete fungus (cf. Alternaria alternata). The specimen is preserved in stromatolitic black chert of the Gunflint Iron Formation (Paleoproterozoic Eon, Orosirian Period, ca. 1.9-2.0 Ga) of southern Ontario, Canada, and the rock that provided the thin section may have been collected by Elso Barghoorn as part of the original discovery of the Gunflint microbiota. The large size of the fossil sets it apart from other, tiny by comparison, Gunflint microfossils. The fossil is 200 microns in length and has cross walls. Individual cells are 30-46 microns in greatest dimension. The apical ‘spore’ is cap-shaped, and has partly separated from the rest of the structure. Cloulicaria gunflintensis gen. nov. sp. nov. may provide early evidence for eukaryotes (fungi) in the fossil record, and may also represent the earliest evidence for asexual reproduction in a eukaryote by means of mitospores.

Fungi today enter into relationships with other fungi in many ways. Although this was likely also the case in the geologic past, detailed descriptions of interfungal associations and interactions based on fossils remain scarce. Sporocarps bounded by a peridium-like envelope occur singly within the lumen of large glomeromycotan spores ( Palaeomyces gordonii var. major ) from the Lower Devonian Rhynie chert. The envelope consists of multi-branched, interlacing hyphae. At the tips of hyphae extending from the envelope into the lumen are produced spheroidal to urn-shaped spores. Similar sporocarps are found in several present-day species in the Glomeraceae. Clusters of spores, superficially resembling sporocarps, may also form within dead spores from any member of the Glomeromycota, including non-sporocarpic groups such as Ambispora , Acaulospora , and the Gigasporaceae, probably because they provide a shielded or otherwise advantageous environment for sporulation. The sporocarps in P. gordonii var. major from the Rhynie chert provide important information for reconstructing the numerous levels of fungal associations and interactions that existed in early continental ecosystems.

The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project ( http://1000.fungalgenomes.org ). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

Cytochrome P450 (CYP) monooxygenase superfamily contributes a broad array of biological functions in living organisms. In fungi, CYPs play diverse and pivotal roles in versatile metabolism and fungal adaptation to specific ecological niches. In this report, CYPomes in the 47 genomes of fungi belong to the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota have been studied. The comparison of fungal CYPomes suggests that generally fungi possess abundant CYPs belonging to a variety of families with the two global families CYP51 and CYP61, indicating individuation of CYPomes during the evolution of fungi. Fungal CYPs show highly conserved characteristic motifs, but very low overall sequence similarities. The characteristic motifs of fungal CYPs are distinguishable from those of CYPs in animals, plants, and especially archaea and bacteria. The four representative motifs contribute to the general function of CYPs. Fungal CYP51s and CYP61s can be used as the models for the substrate recognition sites analysis. The CYP proteins are clustered into 15 clades and the phylogenetic analyses suggest that the wide variety of fungal CYPs has mainly arisen from gene duplication. Two large duplication events might have been associated with the booming of Ascomycota and Basidiomycota. In addition, horizontal gene transfer also contributes to the diversification of fungal CYPs. Finally, a possible evolutionary scenario for fungal CYPs along with fungal divergences is proposed. Our results provide the fundamental information for a better understanding of CYP distribution, structure and function, and new insights into the evolutionary events of fungal CYPs along with the evolution of fungi.

The manipulation of animal behavior by parasitic organisms is one of the most complex adaptations to have arisen via natural selection. Among the most impressive examples of behavioral manipulation are the zombie-ant fungi [1]. In this association, ants are controlled to leave the colony and perform a stereotyped death grip behavior, where they bite onto vegetation over foraging trails, before being killed for the post mortem fungal growth. Manipulation functions to provide a platform outside the nest, from which fungal parasites actively shoot out spores, targeting foraging ants because within colony transmission is prevented by strong social immunity exhibited by social insect societies [2, 3]. It is not clear how such complex examples of host manipulation arose. To address this, we performed a broad-scale phylogenetic reconstruction of the order Hypocreales, to which the zombie-ant fungi, Ophiocordyceps, belong. In order to understand the patterns of host association and host switching along the evolution of Ophiocordyceps, we performed ancestral character state reconstruction analysis. We found that zombie-ant fungi likely arose from an ancestor that infected beetle larvae residing in soil or decaying wood, similar to extant beetle-infecting Ophiocordyceps species. Surprisingly, the jump led to an extensive species radiation observed after the development of behavioral manipulation. We suggest that the jump from solitary beetle larva to ants within a colony exposed the fungus to the robust social immunity of ant societies.

Spherical microfossils collectively referred to as fungal “sporocarps” are widespread elements in Carboniferous coal balls and chert deposits, as well as Triassic permineralised peat from Antarctica. However, these structures are unknown in strata older than Carboniferous and younger than Triassic. This paper describes a new microfossil (

We investigated the diversity of fungal communities in 10 different deep-sea sediment samples by PCR-mediated internal transcribed spacer (ITS) regions of rRNA gene clone analysis. Although some of the amplified sequences were identified as common terrestrial fungal species, the majority were novel sequences that were not closely related to previously identified fungal ITS sequences in public databases. Phylogenetic analysis also suggested the novel phylogenetic affiliation of a group of predominant deep-sea phylotypes within the phylum Ascomycota. These phylotypes may be distributed widely in global deep-sea sediments. Another novel phylotype was placed in deep branches within the phylum Chytridiomycota with Rozella spp. as the closest related organisms. This study revealed the possible existence of previously unknown fungal components in various depths and sites of deep-sea sedimentary habitats. It is suggested that deep-sea environments are habitats hosting previously unexplored fungi, which may provide key insights into the early evolution of fungi and their ecological and physiological significance.

A new fossil microfungus, Kryphiomyces catenulatus gen. et sp. nov., occurs as an endobiotic mycelial thallus in a large spore of a glomeromycotan fungus from the Lower Devonian Rhynie chert. The thallus consists of branched (?pseudo-)septate hyphae with numerous catenulate swellings. Some hyphal tips produce spherical reproductive structures or propagules. Hyphal morphology in K. catenulatus is reminiscent of that in certain extant Hyphochytridiomycota, Chytridiomycota, and even Ascomycota, but specific diagnostic features that allow assignment of the fossil to modern groups are absent. The discovery of this interfungal association broadens our knowledge about the diversity of microfungi and their intricate associations in early continental ecosystems.

Polyploidy (whole-genome duplication) has played a pervasive role in the evolution of fungi and animals, and is particularly prominent in plants (Wendel & Doyle, 2005; Cui et al., 2006; Otto, 2007; Wood et al., 2009). This important evolutionary phenomenon has attracted renewed and growing interest from the scientific community in the last decade since it was discovered that even the smallest plant genomes considered to be ‘diploid' (e.g. Arabidopsis thaliana, reviewed in Henry et al., 2006) have incurred at least one round of whole-genome duplication, possibly predating the origins of the angiosperms (Soltis et al., 2009). Polyploidy is an important speciation mechanism for all eukaryotes and has profound impacts on biodiversity dynamics and ecosystem functioning. Newly formed polyploids, and particularly those of hybrid origin (allopolyploids), frequently exhibit rapid range expansion (Ainouche et al., 2009), and over long periods of evolutionary time, polyploidy has increased morphological complexity and probably reduced the risk of species extinction (Fawcett et al., 2009). Last, but not least, genome duplication has often provided the raw material for plant domestication (e.g. wheat, Dubkovsky & Dvorak, 2007) and thus has had a major impact on human societies and the development of an agrarian lifestyle.

Fungi are one of the most important components in ecosystems and they occupy a wide variety of environments by virtue of their highly versatile physiology function. Recently, the presence of fungi in one of the extreme environments, deep-sea, has started to be recognized. In this article, recent scientific findings through the investigation of fungal diversity in deep-sea sediments collected from several deep-sea environments, including water depths of 10,000 m and methane cold-seep sites were described. PCR-mediated analysis revealed the presence of diverse highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum of Chytridiomycota with Rozella spp. as the closest related organisms, which may provide key insights into the early evolution of fungi.

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

In the last 20 years, studies on the early evolution of fungi have made significant developments with the assistance of molecular clock dating methods and new fossil evidence. The origin of fungi probably dates back over 800 million years ago. The evolution of major fungal phyla is also reviewed. New archaeological discoveries and new analytic technologies developed in the last four decades enable us to date the artifacts related to using fungi from preliterate periods of human beings. At present, utilization of fungi by humans can be traced back to prehistorical periods. The production of alcoholic drinks and fermented foods and usage of medicinal microfungi in human history are discussed and updated.

With the advancement of molecular techniques in the last two decades, cultures of marine fungi have been sequenced, and several new lineages of marine fungi have been revealed, suggesting multiple evolution of fungi into the marine environment. High-throughput sequencing has also allowed discovery of unculturable marine fungi, such as the Cryptomycota. Traditionally, marine fungi are known to belong mostly to the Ascomycota and asexual morphs with few basidiomycetes and chytrids. In this chapter, we will introduce the phylogenetic diversity of these groups with the emphasis on the ascomycetous classes Dothideomycetes and Sordariomycetes, where most marine ascomycetes are referred to. We will also summarize the current knowledge on the marine taxa at the basal lineages of fungi including the phyla Aphelida, Cryptomycota, and Microsporidia, currently classified in the superphylum Opisthosporidia.

Glomeromycotan spores from the Lower Devonian Rhynie chert provide the first evidence for germination shields in fossil fungi and demonstrate that this complex mode of germination was in place in some fungi at least 400 million years ago. Moreover, they represent the first direct marker relative to the precise systematic position of an Early Devonian endomycorrhizal fungus. In extant fungi, germination shields occur exclusively in the genus Scutellospora (Glomeromycota: Diversisporales, Gigasporaceae). These structures are regarded as a derived feature within the phylum Glomeromycota, and hence their presence in the Rhynie chert suggests that major diversification within this group of fungi occurred before the Early Devonian.

Several new gametophytes are described from the Early Devonian Rhynie chert. The new monotypic genus Remyophyton, being the gametophyte of Rhynia, is represented by a dense stand of in situ preserved gametophytes with antheridia- and archegonia-bearing axes. The gametophytes are remarkably small in comparison to those of other Rhynie chert plants. The generic diagnoses of Lyonophyton and Langiophyton are emended to include archegonia- and antheridiabearing axes. All essential stages of the reproductive cycle, i.e. sporophytes, and male and female gametophytes, can now be demonstrated for three of the six land plants from the Rhynie chert, i.e. Rhynia gwynne-vaughanii, Aglaophyton major and Horneophyton lignieri.

Molecular markers have facilitated a better understanding of the evolution of fungi. Molecular phylogenetics determined the closest relatives of fungi and defined natural groups within the true fungi. The impact of molecular markers on the population biology of fungi has been enormous, helping to define cryptic species and elucidating fungal breeding biology. The interaction between molecular phylogenetics and the fungal fossil record is discussed.

What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious effect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus. Plants have been important in the evolution of fungi, and the rapid nature of co-evolutionary change might partially explain the lack of obvious, global characters uniting all plant pathogens.

Basal lineages of the kingdom Fungi comprise terrestrial and aquatic fungi, which are traditionally summarized to the Chytridiomycota and the Zygomycota in a colloquial sense. Advances in next-generation sequencing allow a new layer of knowledge to be gained, which is invaluable for understanding not only the evolution of fungi but also their adaptation to the environment and development of pathogenic traits. Recent revisions using large-scale multigene phylogenies suggested a polyphyletic origin of both the Chytridiomycota and the Zygomycota, which were therefore separated into three distinct phyla and five subphyla, respectively. However, because of the recent appearance of the genomic sequences of basal fungi, a comprehensive genome analysis is in progress for these basal groups. Large-scale genome projects produced a total of 51 genomes of basal fungi and 32 genomes from the Microsporidia. First insights suggest a revision of our understanding of the genome evolution and architecture, revealing fascinating novelties that qualify the basal fungi as an outstanding and unique fungal group deserving much more attention from the scientific community.

Reconstructing the early evolution of fungi and metazoans, two of the kingdoms of multicellular eukaryotes thriving on earth, is a challenging task for biologists. Among extant organisms having characters intermediate between fungi and hypothetical protistan ancestors, from which both fungi and metazoans are believed to have evolved, aphelids are unfairly neglected. The phylogenetic position of these microalgal endoparasites remained uncertain, since no nucleotide sequence data have been reported to date. Aphelids resemble some primitive zoosporic fungi in life cycle, but, unlike fungi, they live by phagotrophy. Here we present a phylogeny, in which a cultured aphelid species, Amoeboaphelidium protococcarum, forms a monophyletic group with Rozella and microsporidia as a sister group to Fungi. We also report a non-canonical nuclear genetic code in A. protococcarum.

The morphological, distributional and host range data of the species of the largest Harpellales genera, Stachylina and Smittium, published up to mid 2010 are consolidated from the available literature, including species that occur in India. Keys for identifi cation of the species of the two genera are provided, and the need for having a uniform pattern for describing a species and, where possible, integrating the molecular data of a species with that of its morphology has been emphasized for future studies. INTRODUCTION Trichomycetes, an ecological group of cryptic fungi, currently is comprised of only two orders, Harpellales and Asellariales, and three families (Lichtwardt, 1986; Lichtwardt et al., 2001a). During the last few years the investigations relating to this group have gained momentum. European and American Fungi-ch-6.indd-14-02-2011.indd 115 30-10-2011 11:14:17 116 Systematics and Evolution of Fungi researchers have discovered many new genera and species within the order Harpellales. Unfortunately, there are only a few recent reports from Asian regions (Misra and Tiwari, 2002, 2008; Strongman and Xu, 2006; Strongman et al., 2010; Wang et al., 2010). Harpellales is the biggest order of the Trichomycetes consisting of 39 genera and more than 222 species. Th e two genera, Stachylina (Harpellaceae) and Smittium (Legeriomycetaceae) have the largest number of species, 30 and 79 respectively, including one variety. Th is chapter embodies the salient morphological details of the species of two genera, and their hosts and geographical records. Keys for their species are provided. Since there is a lack of uniformity in describing the species of these frequently encountered genera, a suggestion is made to describe all details of a species whether they are seen or not in a particular collection, so that any future investigator may know whether a specifi c morphological character has been seen/not seen or ignored by the past discoverer. Stachylina Leger & Gauthier, 1932 Th alli unbranched, cylindrical to fusiform, attached to peritrophic matrix of the host either by a small secreted holdfast or by penetrating the membrane. Trichospores oval to biconical, with or without a collar, with a single appendage. Zygospores known for only one species (St. refl exa) Type species: Stachylina macrospora Leger & Gauthier – C. R. Acad. Sci. Paris 194: 2262-2265, 1932. (=Stachylina intermedia Poisson, 1936, nom. nud., in Melanges dedies au Professeur Lucien Daniel. Universite de Rennes, pp. 75-86, Figs. 1, 2) Key to species 1a. Th allus base penetrating the peritrophic matrix of the host 2 1b. Th allus base not penetrating the peritrophic matrix of the host 7 2a. Trichospores up to 20 μm long 3 2b. Trichospores more than 20 μm long 4 3a. Trichospores with a short appendage St.. minuta 3b. Trichospores without appendage St. minima 4a. Trichospores up to 30 μm long 5 4b. Trichospores more than 30 μm long 6 5a. Penetrating base of the thallus foot-like St. pedifer 5b. Penetrating base of the thallus bulbous St. queenslandiae 6a. Trichospores 30-50 μm long St. penetralis Fungi-ch-6.indd-14-02-2011.indd 116 30-10-2011 11:14:18

Integrating Morphological and Molecular Data in Fungal Systematics, David L. Hawksworth The Systematics and Evolutionary Perspectives of Fossil Fungi, S.K.M. Tripathi From Zoospores to Molecules: The Evolution and Systematics of Chytridiomycota, Martha J. Powell and Peter M. Letcher Current Systematics of Zygomycotan Fungi with Brief Review on their Biology, Gerald L. Benny Evolution of Trichomycetes, Robert W. Lichtwardt Systematics of Stachylina and Smittium-The Two Largest Genera of Harpellales, Zygomycota, J.K. Misra Phylogentic Analysis within Genera Morchella (Ascomycota, Pezizales) and Macrolepiota (Basidiomycota, Agaricales) Inferred from rDNAITS and EF-1a Sequences, Gayane S. Barseghyan, Anush Kosakyan, Omoanghe S. Isikhuemhen, Maryna Didukh and Solomon P. Wasser Phylogenetic Conundrum of the Mushroom-forming Fungi (Agaricomycetes), Ivan V. Zmitrovich and Solomon P. Wasser Phylogenetic Analyses of Phellinus s.l., and Inonotus s.l. (Hymenochaetales) Inferred From rDNA ITS Sequences and Morphological Data, Daniel Tura, Ivan V. Zmitrovich, Solomon P. Wasser, Dina Raats and Eviatar Nevo Morphological and Molecular Taxonomy of Highly Toxigenic Fusarium Species From Small Cereal Grains in Northern Europe and Asia, Tapani Yli-Mattila Understanding the Phylogeny of the Alternarioid Hyphomycetes, What can the Consequences be in Taxonomy? Philipp B. Gannibal Biomarker Discovery for Rapid Diagnosis of Invasive Candidiasis through Protein Profiling, A Review, Jalpa P. Tewari, Sanjiv Tewari and William G. Gardner Comparative Methods in Fungal Evolutionary Biology, Theory, Examples and Potential Applications, Laszlo Nagy, Tamas Papp and Csaba Vagvolgyi

The importance of fungi found in deep-sea extreme environments is becoming increasingly recognized. In this chapter, current scientific findings on the fungal diversity in several deep-sea environments by conventional culture and culture-independent methods are reviewed and discussed, primarily focused on culture-independent approaches. Fungal species detected by conventional culture methods mostly belonged to Ascomycota and Basidiomycota phyla. Culture-independent approaches have revealed the presence of highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum Chytridiomycota and unknown ancient fungal groups. Future attempts to culture these unknown fungal groups may provide key insights into the early evolution of fungi and their ecological and physiological significance in deep-sea environments.

The oxidative phosphorylation (OXPHOS) pathway plays a central role in the energetic metabolism of aerobic organisms. Despite such centrality, this pathway has not remained unaltered through evolution, and variations of it, including its complete loss, can be found in organisms adapted to different ecological niches. Fungi, a eukaryotic group of species with a high metabolic diversity, represent an ideal phylum in which to study the evolutionary plasticity of the OXPHOS pathway from a phylogenomics perspective. With more than 100 completely sequenced genomes, and thanks to recent progress in elucidating their evolutionary relationships, fungal species have served to reveal the evolutionary mechanisms that underlie the evolution of the core respiratory pathways. In this chapter, we review recent progress toward the characterization of OXPHOS components in fungi and in understanding their evolution. A special focus is devoted to the history of duplications that the multi-protein complexes in OXPHOS have experienced.

Evolutionary Roots of Fungi 1 The Protistan Origins of Animals and FungiMartin Carr, Sandra L. Baldauf 2 Microsporidia -- Highly Reduced and Derived Relatives of FungiBryony A. P. Williams, Patrick J. Keeling 3 Environmental DNA Analysis and the Expansion of the Fungal Tree of Life Meredith D. M. Jones, Thomas A. Richards Evolution of Signalling in Fungi and Fungal-Like Organisms 4 Evolution of Signalling and Morphogenesis in the DictyostelidsPauline Schaap 5 Function and Evolution of Pheromones and Pheromone Receptors in Filamentous AscomycetesStefanie Poggeler 6 Mating Type in Basidiomycetes: Unipolar, Bipolar, and Tetrapolar Patterns of SexualityUrsula Kues, Timothy Y. James, Joseph Heitman Evolution of Mutualistic Systems and Metabolism in Fungi 7 Evolution of the 'Plant-Symbiotic' Fungal Phylum, GlomeromycotaArthur Schussler, Christopher Walker 8 Fruiting Body Evolution in the Ascomycota: a Molecular Perspective Integrating Lichenized and Non-Lichenized GroupsImke Schmitt 9 Genomic and Comparative Analysis of the Class DothideomycetesJames K. Hane, Angela H. Williams, Richard P. Oliver 10 Evolution of Genes for Secondary Metabolism in FungiInes Teichert, Minou Nowrousian 11 Carbonic Anhydrases in Fungi and Fungal-Like Organisms -- Functional Distribution and Evolution of a Gene FamilySkander Elleuche Evolutionary Mechanisms and Trends 12 Evolution of Mating-Type Loci and Mating-Type Chromosomes in Model Species of Filamentous AscomycetesCarrie A. Whittle, Hanna Johannesson 13 Evolution of Special Metabolism in Fungi: Concepts, Mechanisms, and PathwaysChristine Schimek

Intenzivnim bavljenjem filogenijom gljiva, znanstvenici su došli do brojnih otkrića. Tako su Paquin i suradnici, korištenjem mitohondrijskih gena koji kodiraju podjedinice 1 – 3 i citokrom b, na temelju rezultata istraživanja pružili snažnu potporu teoriji gljiva i životinja kao sestrinskih grupa, te su predložili postavljanje Spizellomycetales kao bazu gljiva rađe nego Blastocladiales. Još jedna snažna potpora gljivama i životinjama kao sestrinskim grupama dolazi iz istraživanja Baldaufa i Palmera koji su koristili konzervirane gene jezgre za aktin, α i β – tubulin, histone i translacijski, elongacijski faktor Ef - 1α. Dollittle i suradnici su proveli istraživanje bazirano na 53 različita gena koji kodiraju enzime, te su rezultati pokazali kako su gljive divergirale od životinja prije oko 965 milijuna godina. Bowen i suradnici su sekvencionirali gene hitin sintaze, pripadaju trima genskim obiteljima, te su izveli stablo sekvenci u kojem gljive dijele na 3 razreda. Seifert i suradnici, te Kuhls i suradnici, koristeći sekvence 18S i 28S ribosomskih gena, utvrđuju filogenetske odnose između spolnih i nespolnih gljiva koje su prije bile smatrane različitim vrstama. Provedeno je i istraživanje temeljeno na genima β podjedinice F1 – ATP – aze koje je pokazalo prisustvo vertikalnog prijenosa gena (sa pretka na potomke) kod mrkve i krušne plijesni. Za mnoga filogenetska pitanja sekvence ribosomskih gena ne nude jasne odgovore, te su sekvence drugih gena i razne karakteristike poželjne i dobrodošle. Red, rad, disciplina, nove spoznaje, nove ideje, novi tehnološki napreci, povećanje svote novca namijenjene znanosti, što bolja povezanost i suradnja znanstvenika cijelog svijeta, mogu nam pomoći i olakšati put približavanja istinitoj evoluciji koja je bitna cjelokupnom čovječanstvu i koja će, bar djelomično, ponuditi odgovor na čovjekova vječna pitanja njegovog postanka, razvoja, srodstvenih odnosa i konačno svrhovitosti života. Working intensively on the phylogeny of fungi, scientists have come up with a number of discoveries. Thus, Paquin et al, using the mitochondrial genes encoding subunits 1-3 and cytochrome b, provided strong support for the theory of fungi and animals as sister groups, and proposed setting Spizellomycetales as fungi base rather than Blastocladiales. Another strong support for fungi and animals as sister groups comes from Baldauf`s and Palmer`s studies who used conserved nucleus genes for actin, α and β - tubulin, histones, and the translation, elongation factor Ef - 1α. Dollittle et al. conducted a study based on 53 different genes that encode enzymes, and the results showed that the fungi have divergated from animals less than about 965 million years ago. Bowen et al. sequenced chitin synthase genes, belong to three gene families, and they performed tree in which the fungi are divided into 3 classes. Seifert et al., and Kuhls et al, using a sequence of 18S and 28S ribosomal genes, determined phylogenetic relationships between sexual and asexual fungi that have previously been regarded as different species. The study with carrots and bread mold, based on genes of β subunits of F1 - ATP – ase, showed the presence of vertical gene transfer. For many phylogenetic questions ribosomal gene sequences do not offer clear answers. The sequences of other genes and different characteristics are wanted and welcome. Order, work, discipline, new knowledge, new ideas, new technological advances, increasing amounts of money intended for science, better linkages and cooperation of scientists around the world, can help us and also alleviate our way of approaching the true evolution that is essential to all of humanity and will, at least in part, offer an answer to man's eternal questions of his origin, development, relationships and ultimately purposefulness of life.

India is rich in biodiversity. One-third of fungal diversity of the globe exists in India. The early fossil record of the fungi is poor, as unlike other organisms, fungal structures do not fossilize well. Thus, theories on phylogeny of fungi are based on the morphological features of the extant fungi. From the beginning of the 20th century fungi were proposed to be monophyletic, assuming that all the fungi were derived from an algal ancestor that lost its ability to photosynthesize. This gave rise to the flagellate fungi, from which rest of the fungi evolved. The loss of flagella and the evolution of zygospore gave rise to the Zygomycotina. The uninucleate zygospores of the Edogonales gave rise to the Ascomycota. The link between them being a fungus resembling Dipodascopsis (Ascomycota). The unicellular yeasts and complex filamentous Ascomycota members having extended dikaryotic stage evolved from it, believed to be similar to modern day Taphrina. This Taphrina-like ancestor was believed to have given rise to the ancestral Basidiomycota.

Several different chytridiomycetes are described from the Lower Devonian (Siegenian) Rhynie chert. Included are both eucarpic and apparently holocarpic forms that occur in Palaeonitel/a, Aglaophyton, Lyonophyton, Horneophyton, and clusters of algal cells, as well as in the surrounding chert matrix. Holocarpic types consist of endobiotic sporangia, each characterized by one discharge tube. Sporangia can be traced from the thallus stage to the discharge of zoospores. Monocentric and polycentric eucarpic chytrids are associated with the miospores of Aglaophyton and various thick-walled fungal spores. In these forms the sporangia are variable in size and shape ranging up to 30 jum. Most appear to be inoperculate and there is evidence that the sporangium ruptured on the distal surface. Some contain zoospores with flagella. One operculate eucarpic form had parasitized the cellular gametophyte emerging from the proximal surface of an Aglaophyton spore. Several of the Rhynie chert chytrids are comparable with a number of extant forms (e.g., Olpidiaceae and Spizellomycetaceae), while others possess features that encompass several groups. These fossil fungi are discussed in the context of their interactions with other organisms in this Lower Devonian freshwater paleoecosystem.

Proteins of the SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein receptor) family are key factors in all vesicle-fusion steps in the endocytic and secretory pathways. SNAREs can assemble into a tight four-helix bundle complex between opposing membranes, a process that is thought to pull the two membranes into close proximity. The complex-forming domains are highly conserved, not only between different species, but also between different vesicular trafficking steps. SNARE protein sequences can be classified into four main types (Qa, Qb, Qc and R), each reflecting their position in the four-helix bundle. Further refinement of these main types resulted in the identification of 20 distinct conserved groups, which probably reflect the original repertoire of a proto-eukaryotic cell. We analysed the evolution of the SNARE repertoires in metazoa and fungi and unveiled remarkable differences in both lineages. In metazoa, the SNARE repertoire appears to have undergone a substantial expansion, particularly in the endosomal pathways. This expansion probably occurred during the transition from a unicellular to a multicellular lifestyle. We also observed another expansion that led to a major increase of the secretory SNAREs in the vertebrate lineage. Interestingly, fungi developed multicellularity independently, but in contrast with plants and metazoa, this change was not accompanied by an expansion of the SNARE set. Our findings suggest that the rise of multicellularity is not generally linked to an expansion of the SNARE set. The structural and functional diversity that exists between fungi and metazoa might offer a simple explanation for the distinct evolutionary history of their SNARE repertoires.

Both flagellated and nonflagellated fungi have an extensive fossil record, which is, however, unevenly documented and often difficult to interpret. Recent work on Silurian, Devonian and Carboniferous terrestrial assemblages has provided plausible evidence for all major groups of extant fungi in the Paleozoic. Key events in fungal macroevolution thus probably took place in the early Paleozoic or the late Precambrian, and the likelihood of finding definitive fossil evidence for them is small. The fossil record also provides evidence for morphological conservatism and early establishment of a spectrum of intimate associations between fungi and vascular plants. A model for the origin of terrestrial fungi involving two distinct lines of biotrophs in lichen-like symbioses with algae is proposed.

“The number of known species of fungi is about 69,000”, but species of the fungal world are conservatively estimated to be 1.5 million (xcHawksworth, 1991). The fungi are of great consequence agronomically, bioindustrially, medically, and biologically. In spite of their importance, their taxonomic inventory is poor, particularly for the tropical regions. In addition, very little is known about the phylogeny and evolution of fungi and between these and other organisms. As pointed out by xcBruns et al. (1991), “their simple and frequently convergent morphology, their lack of a useful fossil record, and their diversity have been major impediments to progress in this field”.

Introduction Although fungi are generally disregarded in the biogeochemical literature, they undoubtedly constitute crucial biogeochemical factors in many elemental cycles. This fact, combined with their abundance in the soil, warrants greater detailed study into their geoecological impact. The network formed by fungal filaments can represent 10 000 km of thread-like mycelia in 1 m 2 of fertile soil. Their mass is evaluated at 3500 kg ha − 1 at a depth of 20 cm in an average continental soil, i.e. taking into account all the different terrestrial environments on Earth (Gobat et al ., 2004). In comparison, bacteria and algae would represent 1500 and 10–1000 kg ha − 1 respectively, in the same virtual average soil. Fungi are not only biologically important as saprophytes in the recycling of organic matter, but also play a geological role by excreting notable amounts of organic acids, among which oxalic acid is particularly important (Gadd, 1999), contributing to continental weathering as well as to mineral neogenesis (Verrecchia & Dumont, 1996; Verrecchia, 2000; Burford et al ., 2003 a , b ). The first fossil fungi have been identified in rocks dated from the Ordovician, i.e. 460 to 455 Ma ago (Redecker et al ., 2000). However, molecular clock estimates for the evolution of fungi have suggested a Late Precambrian (600 Ma) colonization on land (Berbee & Taylor 2000). Recent molecular studies, based on protein sequence analysis, indicate that fungi were present on continents 1 billion years ago and possibly affected (together with plants) the evolution of Earth's atmosphere and climate since 700 Ma (Heckman et al ., 2001).

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

The fossil record of fungi and lichens is scarce. Here we report the discovery of lichen-like fossils, involving filamentous hyphae closely associated with coccoidal cyanobacteria or algae, preserved in marine phosphorite of the Doushantuo Formation (between 551 and 635 million years old) at Weng'an, South China. These fossils indicate that fungi developed symbiotic partnerships with photoautotrophs before the evolution of vascular plants.

Although evidence for horizontal gene transfer (HGT) in eukaryotes remains largely anecdotal, literature on HGT in fungi suggests that it may have been more important in the evolution of fungi than in other eukaryotes. Still, HGT in fungi has not been widely accepted because the mechanisms by which it may occur are unknown, because it is usually not directly observed but rather implied as an outcome, and because there are often equally plausible alternative explanations. Despite these reservations, HGT has been justifiably invoked for a variety of sequences including plasmids, introns, transposons, genes, gene clusters, and even whole chromosomes. In some instances HGT has also been confirmed under experimental conditions. It is this ability to address the phenomenon in an experimental setting that makes fungi well suited as model systems in which to study the mechanisms and consequences of HGT in eukaryotic organisms.

The colonization of land by eukaryotes probably was facilitated by a partnership (symbiosis) between a photosynthesizing organism (phototroph) and a fungus. However, the time when colonization occurred remains speculative. The first fossil land plants and fungi appeared 480 to 460 million years ago (Ma), whereas molecular clock estimates suggest an earlier colonization of land, about 600 Ma. Our protein sequence analyses indicate that green algae and major lineages of fungi were present 1000 Ma and that land plants appeared by 700 Ma, possibly affecting Earth's atmosphere, climate, and evolution of animals in the Precambrian.

Fossilized fungal hyphae and spores from the Ordovician of Wisconsin (with an age of about 460 million years) strongly resemble modern arbuscular mycorrhizal fungi (Glomales, Zygomycetes). These fossils indicate that Glomales-like fungi were present at a time when the land flora most likely only consisted of plants on the bryophytic level. Thus, these fungi may have played a crucial role in facilitating the colonization of land by plants, and the fossils support molecular estimates of fungal phylogeny that place the origin of the major groups of terrestrial fungi (Ascomycota, Basidiomycota, and Glomales) around 600 million years ago.