The fungi kingdom: heterogeneity of physiological-biochemical properties and closeness to plants, animals, and prokaryotes

This review analyzes the current taxonomy of fungi whose criteria are based on a range of episemantic molecules. In this context, data on the chemical composition of fungal cells (membrane lipids, cytosolic carbohydrates, etc.) are considered in comparison with their counterparts found in higher eukaryotes and prokaryotes. Modern theories explaining the origin of fungi and their similarity to plants, animals, and bacteria are discussed. The biochemical criteria used in this work supported the division of fungi into Eumycota and Neomycota. The latter division, especially Basidiomycota, are more closely related to plants. The heterogeneity of the kingdom Fungi is underlined, the existence of Oomycota as a separate entity is supported, and the theory of the primitive nature of fungal cells is criticized from the viewpoint of biochemical adaptation.     

Fungal evolution: cellular,genomic and metabolic complexity

The question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.     

Septation and cytokinesis in fungi

Cytokinesis is the ultimate step of a cell cycle resulting in the generation of two progeny. Failure of correct cell division may be lethal for both, mother and daughter cells, and thus such a process must be tightly regulated with other events of the cell cycle. Differing solutions to the same problem have been developed in bacteria and plants while cytokinesis in animal and fungal cells is highly similar and requires a contractile ring containing actomyosin. Cytokinesis in fungi can be viewed as a three-stage process: (i) selection of a division site, (ii) orderly assembly of protein complexes, and finally (iii) dynamic events that lead to a constriction of the contractile ring and septum construction. Elaborate mechanisms known as the Mitotic Exit Network (MEN) and the Septation Initiation Network (SIN) have evolved to link these events, particularly the final steps of cytokinesis, with nuclear division. The purpose of this review was to discuss the latest developments in the fungal field and to describe the central known players required for key steps on the road to cell division. Differences in the cytokinesis of yeast-like fungi that result in complete cell separation in contrast to septation which leads to the compartmentalization of fungal hyphae are highlighted.     

Isolation, characterization, and avenacin sensitivity of a diverse collection of cereal-root-colonizing fungi.

A total of 161 fungal isolates were obtained from the surface-sterilized roots of field-grown oat and wheat plants in order to investigate the nature of the root-colonizing fungi supported by these two cereals. Fungi were initially grouped according to their colony morphologies and then were further characterized by ribosomal DNA sequence analysis. The collection contained a wide range of ascomycetes and also some basidiomycete fungi. The fungi were subsequently assessed for their abilities to tolerate and degrade the antifungal oat root saponin, avenacin A-1. Nearly all the fungi obtained from oat roots were avenacin A-1 resistant, while both avenacin-sensitive and avenacin-resistant fungi were isolated from the roots of the non-saponin-producing cereal, wheat. The majority of the avenacin-resistant fungi were able to degrade avenacin A-1. These experiments suggest that avenacin A-1 is likely to influence the development of fungal communities within (and possibly also around) oat roots.     

Isolation, Characterization, and Avenacin Sensitivity of a Diverse Collection of Cereal-Root-Colonizing Fungi

A total of 161 fungal isolates were obtained from the surface-sterilized roots of field-grown oat and wheat plants in order to investigate the nature of the root-colonizing fungi supported by these two cereals. Fungi were initially grouped according to their colony morphologies and then were further characterized by ribosomal DNA sequence analysis. The collection contained a wide range of ascomycetes and also some basidiomycete fungi. The fungi were subsequently assessed for their abilities to tolerate and degrade the antifungal oat root saponin, avenacin A-1. Nearly all the fungi obtained from oat roots were avenacin A-1 resistant, while both avenacin-sensitive and avenacin-resistant fungi were isolated from the roots of the non-saponin-producing cereal, wheat. The majority of the avenacin-resistant fungi were able to degrade avenacin A-1. These experiments suggest that avenacin A-1 is likely to influence the development of fungal communities within (and possibly also around) oat roots.     

Essential,deadly, enigmatic: Polyamine metabolism and roles in fungal cells

Polyamines are essential metabolites found in all organisms. Intracellular polyamine levels are tightly maintained by biosynthesis, degradation, uptake and excretion processes that involve regulatory mechanisms – such as the antizyme inhibitory protein – that are conserved across the kingdoms of life, indicating that polyamine levels are critical to cell function. Nonetheless, the biochemical roles of polyamines and their involvement in numerous fundamental cellular processes including aging, cell cycle progression and growth only become apparent when polyamine homeostasis is perturbed. Thus, while polyamines are present in most cells and essential for cell growth, their biochemical functions are largely enigmatic. Studies in fungi have contributed to our basic understanding of polyamines, and might continue to bridge knowledge gaps regarding polyamine metabolism and cell function. Moreover, when considering the impact of fungi – directly or indirectly, for good or for ill – on human society, closing gaps in our understanding of polyamine functions in fungal physiology is an important goal in itself that might lead to the discovery of new targets for enhancing beneficial fungal interactions and diminishing those detrimental to crop and human health. To facilitate progress towards this prospect, here we appraise what is known about polyamine metabolism in fungi, how prevalent polyamines impact fungal physiology and metabolism, and how the levels of each polyamine are maintained in the fungal cell – thus pointing to how they might be perturbed.     

High spatial resolution analysis of fungal cell biochemistry--bridging the analytical gap using synchrotron FTIR spectromicroscopy.

Fungi impact humans and the environment in many ways, for good and ill. Some fungi support the growth of terrestrial plants or are used in biotechnology, and yet others are established or emerging pathogens. In some cases, the same organism may play different roles depending on the context or the circumstance. A better understanding of the relationship between fungal biochemical composition as related to the fungal growth environment is essential if we are to support or control their activities. Synchrotron FTIR (sFTIR) spectromicroscopy of fungal hyphae is a major new tool for exploring cell composition at a high spatial resolution. Brilliant synchrotron light is essential for this analysis due to the small size of fungal hyphae. sFTIR biochemical characterization of subcellular variation in hyphal composition will allow detailed exploration of fungal responses to experimental treatments and to environmental factors.     

High spatial resolution analysis of fungal cell biochemistry – bridging the analytical gap using synchrotron FTIR spectromicroscopy

Fungi impact humans and the environment in many ways, for good and ill. Some fungi support the growth of terrestrial plants or are used in biotechnology, and yet others are established or emerging pathogens. In some cases, the same organism may play different roles depending on the context or the circumstance. A better understanding of the relationship between fungal biochemical composition as related to the fungal growth environment is essential if we are to support or control their activities. Synchrotron FTIR (sFTIR) spectromicroscopy of fungal hyphae is a major new tool for exploring cell composition at a high spatial resolution. Brilliant synchrotron light is essential for this analysis due to the small size of fungal hyphae. sFTIR biochemical characterization of subcellular variation in hyphal composition will allow detailed exploration of fungal responses to experimental treatments and to environmental factors.     

Genetically Transformed Plant Roots as a Model for Studying Specific Metabolism and Symbiotic Contacts of the Root System

Genetic transformation of plants mediated by Ri plasmid ofAgrobacterium rhizogenes occupies a special place in plant cell engineering, since this technique based on a natural phenomenon allows cultivation of isolated growing plant roots on hormone-free media. Application of wild-type unmodified agrobacterial strains allows us to obtain root cultures capable of long-term growth in vitro due to an increased sensitivity of the cells to auxins while other biochemical properties remain unaltered. A collection of pRi T-DNA transformed roots of certain dicotyledons was made; some strains in it are used to study synthesis of secondary metabolites in root cells. Thein vitro cultivated roots could synthesize root-specific metabolites, which makes possible their application for large-scale biotechnological production of ecologically pure crude drugs. Cocultivation of pRi T-DNA transformed roots with arbuscular mycorrhizal fungi makes possible vital study of all stages of obligate symbiont development and interaction with plant roots. Dual axenic culture of AM fungi and pRi T-DNA transformed plants can be used to make a collection of the most valuable endomycorrhizal fungal species and to produce considerable quantities of homogeneous fungal inoculums.     

Plant Chitinases and Their Roles in Resistance to Fungal Diseases

Chitinases are enzymes that hydrolyze the N-acetylglucosamine polymer chitin, and they occur in diverse plant tissues over a broad range of crop and noncrop species. The enzymes may be expressed constitutively at low levels but are dramatically enhanced by numerous abiotic agents (ethylene, salicylic acid, salt solutions, ozone, UV light) and by biotic factors (fungi, bacteria, viruses, viroids, fungal cell wall components, and oligosaccharides). Different classes of plant chitinases are distinguishable by molecular, biochemical, and physicochemical criteria. Thus, plant chitinases may differ in substrate-binding characteristics, localization within the cell, and specific activities. Because chitin is a structural component of the cell wall of many phytopathogenic fungi, extensive research has been conducted to determine whether plant chitinases have a role in defense against fungal diseases. Plant chitinases have different degrees of antifungal activity to several fungi in vitro. In vivo, although rapid accumulation and high levels of chitinases (together with numerous other pathogenesis-related proteins) occur in resistant tissues expressing a hypersensitive reaction, high levels also can occur in susceptible tissues. Expression of cloned chitinase genes in transgenic plants has provided further evidence for their role in plant defense. The level of protection observed in these plants is variable and may be influenced by the specific activity of the enzyme, its localization and concentration within the cell, the characteristics of the fungal pathogen, and the nature of the host-pathogen interaction. The expression of chitinase in combination with one or several different antifungal proteins should have a greater effect on reducing disease development, given the complexities of fungal-plant cell interactions and resistance responses in plants. The effects of plant chitinases on nematode development in vitro and in vivo are worthy of investigation.     

Fungi: individuals, populations, and speciation

Under considerations are specific features of the fungal individuals associated with their mycelial life mode and affecting their population structure and speciation. Special attention is paid to the sympatric speciation which can be caused by trophic niche segregation, by use of different host plants, by invasion to the plants at different stage of their ontogeny, and by differences in the weather requirements. Decrease of genetic interchanges in subdivided populations promoting speciation without spatial isolation is achieved by homotallism and pseudohomotallism, by a cassette mechanism of switching among various breeding systems, and by complete lost of sexual process. Recombination reduction in agamic fungi is achieved by means of vegetative incompatibility. As the latter is similar functionally to the immune system (recognition of an alien culture and death of conjugated cells), it is possible that the fungi were the first to have developed mechanisms of sympatric speciation on the basis of the simpliest immune system.     

Specificity of assemblage,not fungal partner species,explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants

Mycoheterotrophic plants (MHPs) growing on arbuscular mycorrhizal fungi (AMF) usually maintain specialized mycorrhizal associations. The level of specificity varies between MHPs, although it remains largely unknown whether interactions with mycorrhizal fungi differ by plant lineage, species, and/or by population. Here, we investigate the mycorrhizal interactions among Burmannia species (Burmanniaceae) with different trophic modes using high-throughput DNA sequencing. We characterized the inter- and intraspecific dynamics of the fungal communities by assessing the composition and diversity of fungi among sites. We found that fully mycoheterotrophic species are more specialized in their fungal associations than chlorophyllous species, and that this specialization possibly results from the gradual loss of some fungal groups. In particular, although many fungal species were shared by different Burmannia species, fully MHP species typically host species-specific fungal assemblages, suggesting that they have a preference for the selected fungi. Although no apparent cophylogenetic relationship was detected between fungi and plants, we observe that evolutionarily closely related plants tend to have a greater proportion of shared or closely related fungal partners. Our findings suggest a host preference and specialization toward fungal assemblages in Burmannia, improving understanding of interactions between MHPs and fungi.Subject terms: Fungi, Plant sciences, Evolution     

Novel Symbiotic Protoplasts Formed by Endophytic Fungi Explain Their Hidden Existence,Lifestyle Switching,and Diversity within the Plant Kingdom

Diverse fungi live all or part of their life cycle inside plants as asymptomatic endophytes. While endophytic fungi are increasingly recognized as significant components of plant fitness, it is unclear how they interact with plant cells; why they occur throughout the fungal kingdom; and why they are associated with most fungal lifestyles. Here we evaluate the diversity of endophytic fungi that are able to form novel protoplasts called mycosomes. We found that mycosomes cultured from plants and phylogenetically diverse endophytic fungi have common morphological characteristics, express similar developmental patterns, and can revert back to the free-living walled state. Observed with electron microscopy, mycosome ontogeny within Aureobasidium pullulans may involve two organelles: double membrane-bounded promycosome organelles (PMOs) that form mycosomes, and multivesicular bodies that may form plastid-infecting vesicles. Cultured mycosomes also contain a double membrane-bounded organelle, which may be homologous to the A. pullulans PMO. The mycosome PMO is often expressed as a vacuole-like organelle, which alternatively may contain a lipoid body or a starch grain. Mycosome reversion to walled cells occurs within the PMO, and by budding from lipid or starch-containing mycosomes. Mycosomes discovered in chicken egg yolk provided a plant-independent source for analysis: they formed typical protoplast stages, contained fungal ITS sequences and reverted to walled cells, suggesting mycosome symbiosis with animals as well as plants. Our results suggest that diverse endophytic fungi express a novel protoplast phase that can explain their hidden existence, lifestyle switching, and diversity within the plant kingdom. Importantly, our findings outline “what, where, when and how”, opening the way for cell and organelle-specific tests using in situ DNA hybridization and fluorescent labels. We discuss developmental, ecological and evolutionary contexts that provide a robust framework for continued tests of the mycosome phase hypothesis.     

Extreme specificity in epiparasitic Monotropoideae (Ericaceae): widespread phylogenetic and geographical structure

The Monotropoideae (Ericaceae) are nonphotosynthetic plants that obtain fixed carbon from their fungal mycorrhizal associates. To infer the evolutionary history of this symbiosis we identified both the plant and fungal lineages involved using a molecular phylogenetic approach to screen 331 plants, representing 10 of the 12 described species. For five species no prior molecular data were available; for three species we confirmed prior studies which used limited samples; for five species all previous reports are in conflict with our results, which are supported by sequence analysis of multiple samples and are consistent with the phylogenetic patterns of host plants. The phylogenetic patterns observed indicate that: (i) each of the 13 plant phylogenetic lineages identified is specialized to a different genus or species group within five families of ectomycorrhizal Basidiomycetes; (ii) mycorrhizal specificity is correlated with phylogeny; (iii) in sympatry, there is no overlap in mature plant fungal symbionts even if the fungi and the plants are closely related; and (iv) there are geographical patterns to specificity.     

分室培养装置在丛枝菌根真菌研究中的应用及其发展

重点围绕玻璃珠分室培养系统、H形分室培养系统、根排斥室培养系统、供体自养植物的双分室体外培养系统、丛枝菌根(AM)真菌与普通植物根器官的双重培养系统、AM真菌与Ri T-DNA转型根的双重单胞无菌培养系统、AM真菌与Ri T-DNA转型根双重培养的改良分室单胞培养系统等7个不同的分室培养装置, 对AM真菌的培养类型及其应用进行了系统的评述。其中, 采用玻璃珠分室培养装置易于将AM真菌与培养基质分开, 能获得大量纯净的AM真菌繁殖体, 用于研究AM真菌对矿质元素和微量元素的吸收, 具有不可替代的作用。H形分室培养系统和根排斥室(RECs)培养系统均能够获得连续的、可切断的共生菌根网络(CMNs), 可用于研究植物-植物、植物-昆虫之间化感作用产生的信息交流。供体自养植物的双分室培养系统有益于研究AM真菌对宿主植物在单作和混作条件下生长效应的影响。AM真菌与植物根器官的双重培养系统为研究AM真菌的侵染过程及生理、生化特性提供了极大的方便, 同时为纯培养研究提供了重要的理论依据。AM真菌与Ri T-DNA转型根的双重单胞无菌培养体系可以获得AM真菌纯净菌体, 是研究AM真菌遗传、生理、生化等特性的理想方法。以AM真菌与Ri T-DNA转型根的双重单胞无菌培养系统为基础, 可以在菌丝生长室置换培养基、在根室中补充适量碳源, 并多次收获AM真菌繁殖体。转型根改良双重培养系统是提高AM真菌孢子接种剂产量的有效方法。综上所述, AM真菌的分室培养系统已经取得显著进展, 为开展个体、种群、群落等不同层次的菌根生态学研究提供了依据。     

Diversity and Spatial Structure of Belowground Plant–Fungal Symbiosis in a Mixed Subtropical Forest of Ectomycorrhizal and Arbuscular Mycorrhizal Plants

Plant–mycorrhizal fungal interactions are ubiquitous in forest ecosystems. While ectomycorrhizal plants and their fungi generally dominate temperate forests, arbuscular mycorrhizal symbiosis is common in the tropics. In subtropical regions, however, ectomycorrhizal and arbuscular mycorrhizal plants co-occur at comparable abundances in single forests, presumably generating complex community structures of root-associated fungi. To reveal root-associated fungal community structure in a mixed forest of ectomycorrhizal and arbuscular mycorrhizal plants, we conducted a massively-parallel pyrosequencing analysis, targeting fungi in the roots of 36 plant species that co-occur in a subtropical forest. In total, 580 fungal operational taxonomic units were detected, of which 132 and 58 were probably ectomycorrhizal and arbuscular mycorrhizal, respectively. As expected, the composition of fungal symbionts differed between fagaceous (ectomycorrhizal) and non-fagaceous (possibly arbuscular mycorrhizal) plants. However, non-fagaceous plants were associated with not only arbuscular mycorrhizal fungi but also several clades of ectomycorrhizal (e.g., Russula) and root-endophytic ascomycete fungi. Many of the ectomycorrhizal and root-endophytic fungi were detected from both fagaceous and non-fagaceous plants in the community. Interestingly, ectomycorrhizal and arbuscular mycorrhizal fungi were concurrently detected from tiny root fragments of non-fagaceous plants. The plant–fungal associations in the forest were spatially structured, and non-fagaceous plant roots hosted ectomycorrhizal fungi more often in the proximity of ectomycorrhizal plant roots. Overall, this study suggests that belowground plant–fungal symbiosis in subtropical forests is complex in that it includes “non-typical” plant–fungal combinations (e.g., ectomycorrhizal fungi on possibly arbuscular mycorrhizal plants) that do not fall within the conventional classification of mycorrhizal symbioses, and in that associations with multiple functional (or phylogenetic) groups of fungi are ubiquitous among plants. Moreover, ectomycorrhizal fungal symbionts of fagaceous plants may “invade” the roots of neighboring non-fagaceous plants, potentially influencing the interactions between non-fagaceous plants and their arbuscular-mycorrhizal fungal symbionts at a fine spatial scale.     

Unravelling evolutionary relationships between epifoliar Meliolaceae and angiosperms

Epifoliar fungi are a group of poorly studied fungal symbionts that coinhabit the surface of living plants. Meliolaceae is the largest group of epifoliar fungi and has been considered as obligate parasites. We investigated the taxonomy of Meliolaceae and the coevolutionary events with their host plants using time-calibrated cophylogeny based on large subunit, small subunit, and internal transcribed spacer (ITS) sequence data obtained from 17 different fungal taxa and rbcL, ITS, and trnH-psbA sequence data from their corresponding hosts. Nine new fungal species are introduced in this paper and Appendiculella is synonymized under Asteridiella. The dominant coevolutionary events during the Cretaceous and Cenozoic are cospeciation and host shift, respectively. We hypothesize that the evolutionary history of epifoliar fungi can be divided into three major periods: origins of families, formations of genera, and diversification of species. The rise of angiosperms prompted the evolution of modern epifoliar fungi and the diversification of orders of Angiospermae fostered the formation of epifoliar fungal genera. Phylogenetically, epifoliar fungal genera can be delimited according to their coevolutionary patterns and divergent periods.     

Evolutionary histories and mycorrhizal associations of mycoheterotrophic plants dependent on saprotrophic fungi

Mycoheterotrophic plants (MHPs) are leafless, achlorophyllous, and completely dependent on mycorrhizal fungi for their carbon supply. Mycorrhizal symbiosis is a mutualistic association with fungi that is undertaken by the majority of land plants, but mycoheterotrophy represents a breakdown of this mutualism in that plants parasitize fungi. Most MHPs are associated with fungi that are mycorrhizal with autotrophic plants, such as arbuscular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. Although these MHPs gain carbon via the common mycorrhizal network that links the surrounding autotrophic plants, some mycoheterotrophic lineages are associated with saprotrophic (SAP) fungi, which are free-living and decompose leaf litter and wood materials. Such MHPs are dependent on the forest carbon cycle, which involves the decomposition of wood debris and leaf litter, and have a unique biology and evolutionary history. MHPs associated with SAP fungi (SAP-MHPs) have to date been found only in the Orchidaceae and likely evolved independently at least nine times within that family. Phylogenetically divergent SAP Basidiomycota, mostly Agaricales but also Hymenochaetales, Polyporales, and others, are involved in mycoheterotrophy. The fungal specificity of SAP-MHPs varies from a highly specific association with a single fungal species to a broad range of interactions with multiple fungal orders. Establishment of symbiotic culture systems is indispensable for understanding the mechanisms underlying plant–fungus interactions and the conservation of MHPs. Symbiotic culture systems have been established for many SAP-MHP species as a pure culture of free-living SAP fungi is easier than that of biotrophic AM or ECM fungi. Culturable SAP-MHPs are useful research materials and will contribute to the advancement of plant science.

     

Programming good relations--development of the arbuscular mycorrhizal symbiosis

The majority of plants live in symbiotic associations with fungi or bacteria that improve their nutrition. Critical steps in a symbiosis are mutual recognition and subsequently the establishment of an intimate association, which involves the penetration of plant tissues and, in many cases, the invasion of individual host cells by the microbial symbiont. Recent advances revealed that in the arbuscular mycorrhizal symbiosis with soil fungi of the order Glomeromycota, plant-derived signals attract fungal hyphae and stimulate their growth. Upon physical attachment of the fungal symbiont to the root surface, an active plant developmental program prepares the epidermal cells for penetration by the fungus. Thus, plants actively help symbiotic fungi to colonize their roots rather than just tolerating them.