The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

https://cbs.umn.edu/sites/cbs.umn.edu/files/public/downloads/Nguyenetal2015b.pdf

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

https://www.ruhr-uni-bochum.de/imperia/md/content/geobot/2007/hibbett_2007-a_higher-level-phylogenetic.pdf

A higher-level phylogenetic classification of the Fungi

Arbuscular mycorrhiza (AM), a symbiosis between plants and members of an ancient phylum of fungi, the Glomeromycota, improves the supply of water and nutrients, such as phosphate and nitrogen, to the host plant. In return, up to 20% of plant-fixed carbon is transferred to the fungus. Nutrient transport occurs through symbiotic structures inside plant root cells known as arbuscules. AM development is accompanied by an exchange of signalling molecules between the symbionts. A novel class of plant hormones known as strigolactones are exuded by the plant roots. On the one hand, strigolactones stimulate fungal metabolism and branching. On the other hand, they also trigger seed germination of parasitic plants. Fungi release signalling molecules, in the form of 'Myc factors' that trigger symbiotic root responses. Plant genes required for AM development have been characterized. During evolution, the genetic programme for AM has been recruited for other plant root symbioses: functional adaptation of a plant receptor kinase that is essential for AM symbiosis paved the way for nitrogen-fixing bacteria to form intracellular symbioses with plant cells.

Arbuscular mycorrhiza: the mother of plant root endosymbioses.

The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.

Living in a fungal world: impact of fungi on soil bacterial niche development⋆

There is a need to quantify and qualify the ability of ectomycorrhizae to improve tree growth and nutrition and, in particular, to define criteria to classify ectomycorrhizae with respect to ecologically relevant features. Whereas the numbers of ectomycorrhizae and morphotypes give useful information when related to root biomass, root length or soil volume, the development and differentiation of the extramatrical mycelium may represent important predicative features relevant to the ecological classification of ectomycorrhizae. Here, different exploration types of ectomycorrhizae are distinguished based on the amount of emanating hyphae or the presence and differentiation of rhizomorphs. Their putative ecological importance is discussed.

Exploration types of ectomycorrhizae

Ectomycorrhizae, the symbiotic organs of fungi and roots of needle and broad-leaved trees, create distinct anatomical features. These characters are preferentially dependent, influenced and fashioned by the fungal hyphae during the ontogeny of these essentially important structures of root systems. Without ectomycorrhizae, the trees, which are completely dependent on them, are unable to grow. Many features of the ectomycorrhizae are functionally crucial, i.e. they influence the growth of trees to a different degree due to their variable anatomical differentiation. But these symbiotic organs are not only fascinating from a functional point of view, they contribute frequently to disentangle fungal relationships, because systematically related fungi often evolve ectomycorrhizae of similar anatomy.
Currently, world-wide some 5,500 fungal species of a few Zygomycetes, several Ascomycetes and frequently of Hymenomycetes are suggested to form ectomycorrhizae, on most of the tree genera of seasonal climates and/or of nutrient-deficient soils, particularly on roots of, e.g. Abies, Alnus, Betula, Carpinus, Carya, Castanea, Castanopsis, Corylus, Cyclobalanopsis, Elaeocarpus, Engelhardtia, Eucalyptus, Fagus, Gilbertiodendron, Larix, Lithocarpus, Nothofagus, Picea, Pinus, Populus, Pseudotsuga, Quercus, Salix, Shorea, Tetraberlinia, and Tsuga. 

The Colour Atlas depicts the habit of ectomycorrhizae as well as the functionally important features of many fungal relationships and of the most important ectomycorrhizal tree genera and is going to include ectomycorrhizae from all over the world.
The Colour Atlas is meanwhile a world-wide accepted and sold standard work for determination and illustrations of ectomycorrhizae, which is continuously supplemented by pictures of and information on ectomycorrhizae of additional fungi. Many of the provided illustrations show ectomycorrhizae which are identified to fungal species level, and several plates depict unidentified ectomycorrhizae, of which the fungal component is not known yet. But these samples bear their own, internationally standardized and applicable names. 

The heart piece of the Colour Atlas are the folded, four-page plates, which can separately be arranged in any mode, whatever users prefer. The cover page of each plate is destined for four colour photos, the second page contains legends for all pictures, information on ecology and fruitbody illustrations, and frequently in addition data on ectomycorrhiza ecology. On the remaining two pages, half-tone photos depict important anatomical features. Dichotomous keys for determination of ectomycorrhizae, each based upon a tree genus, and comprehensive synoptic tables enable users to determine ectomycorrhizae. A glossary, explanations of important features, check lists as guides to prepare descriptions of ectomycorrhizae, keys and illustrations of the anatomy of main roots, comprehensive references, and lists of contributors complement the Colour Atlas. 

The Colour Atlas will be complemented with one delivery of 10 – 20 plates in intervals of one or two years. The frequency of the deliveries depends upon the submitted contributions, which generally have to depict ectomycorrhizae of which characerizations are already availabale.
Contemporarily, the general parts of the Colour Atlas are updated, too. Ectomycorrhizae of all forest types and of all fungal relationships around the world will be depicted as far as reserchers of ectomcorrhizal anatomy focus on such areas. 

The Colour Atlas, as actually it is available, contains 168 plates (see below) and the keys comprise now 406 species of ectomycorrhizae (Abies 6, Alnus 23, Betula 26, Carpinus 2, Castanopsis 1, Cistus 1, Corylus 6, Cyclobalanopsis 1, Elaeocarpus 1, Eucalyptus 5, Fagus 38, Fumana 2, Gnetum 1, Helianthemum 1, Larix 10, Nothofagus 19, Picea 96, Pinus 85, Pasania 1, Populus 7, Pseudotsuga 13, Quercus 43, Salix 4, Shorea 4, Tetraberlinia 3, Tilia 1, Tsuga 6).

Colour Atlas of Ectomycorrhizae

Publisher Summary This chapter discusses the characterization of ectomycorrhiza. Ectomycorrhiza structures consist of fungal tissues, the arrangement and organization of which can be used to describe fungal species in the same way as any other taxonomically suitable feature. Their characteristics are well conserved. Furthermore, it has been shown that some ectomycorrhizal fungi can grow their hyphae within the rhizomorphs and ectomycorrhiza of other fungi, suggesting that ectomycorrhizal fungi can influence each other with respect to plant nutrition and with respect to their fruit body formation. All ectomycorrhiza regarded as being of one species and one sample must be checked for homogeneity. To do this a few tips should be carefully compared both morphologically and anatomically using rhizomorph and mantle preparations. The chapter also discusses preparations of ectomycorrhiza with morphological characterization, color photography, and autofluorescence. The ectomycorrhiza are photographed in water to allow emanating hyphae and rhizomorphs to spread out into approximately their natural position. The ectomycorrhizal system can be held in forceps which in turn are held by a clamp. There is also a description of anatomical characterization in the chapter.

2 Characterization of Ectomycorrhiza

Aproximately 5,000–6,000 fungal species form ectomyorrhizae (ECM), the symbiotic organs with roots of predominantly trees. The contributing fungi are not evenly distributed over the system of fungi. Within Basidiomycota exclusively Hymenomycetes and within Ascomycota exclusively Ascomycetes contribute to the symbiosis. Hymenomycetes play a big part, Ascomycetes a minor role; Zygomycetes only form exceptionally ECM. Responsible for ascomycetous ECM are mostly Pezizales with their hypogeous derivatives, whereas Boletales, Gomphales, Thelephorales, Amanitaceae, Cantharellaceae, Cortinariaceae, Russulaceae, and Tricholomataceae are the most important ectomycorrhizal relationships within Hymenomycetes. ECM, as transmitting organs between soil and roots, are transporting carbohydrates for growth of mycelium and fruitbodies from roots and have to satisfy the tree’s demand for water and nutrients. The latter task particularly influences the structure of ECM as nutrients are patchily distributed in the soil and saprotrophic as well as ectomycorrhizal fungi can act as strong competitors for nutrients. In focusing these requirements, ECM developed variously structured hyphal sheaths around the roots, the so-called mantles, and differently organized mycelium that emanates from the mantle, the so-called extramatrical mycelium. The mantles can be plectenchymatous consisting of loosely woven, differently arranged hyphae or they are densely packed, forming a pseudoparenchyma similar to the epidermis of leaves. The extramatrical mycelium grows either as simple scattered hyphae from the mantle into the soil or it can be united to undifferentiated rhizomorphs with a small reach or to highly organized root-like organs with vessel-like hyphae for efficient water and nutrient transport from distances of decimeters. Cystidia, sterile and variously shaped hyphal ends, possibly appropriate for preventing animal attack, in addition, can cover mantles and rhizomorphs. Although only a limited number of species could be considered, some general conclusions are possible.

Fungal relationships and structural identity of their ectomycorrhizae

There is a need to quantify and qualify the ability of ectomycorrhizae to improve tree growth and nutrition and, in particular, to define criteria to classify ectomycorrhizae with respect to ecologically relevant features. Whereas the numbers of ectomycorrhizae and morphotypes give useful information when related to root biomass, root length or soil volume, the develop- ment and differentiation of the extramatrical mycelium may represent important predicative features relevant to the ecological classification of ectomycorrhizae. Here, different exploration types of ectomycorrhizae are distin- guished based on the amount of emanating hyphae or the presence and differentiation of rhizomorphs. Their puta- tive ecological importance is discussed.

Reinhard Agerer

Papers

Exploration types of ectomycorrhizae

Colour Atlas of Ectomycorrhizae

2 Characterization of Ectomycorrhiza

Fungal relationships and structural identity of their ectomycorrhizae

A proposal to classify ectomycorrhizal mycelial systems according to their patterns of differentiation and putative ecological importance