Communities, populations and individuals of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi in the phylum Glomeromycota are found globally in most vegetation types, where they form a mutualistic symbiosis with plant roots. Despite their wide distribution, only relatively few species are described. The taxonomy is based on morphological characters of the asexual resting spores, but molecular approaches to community ecology have revealed a considerable unknown diversity from colonized roots. Although the lack of genetic recombination is not unique in the fungal kingdom, arbuscular mycorrhizal fungi are probably ancient asexuals. The long asexual evolution of the fungi has resulted in considerable genetic diversity within morphologically recognizable species, and challenges our concepts of individuals and populations. This review critically examines the concepts of species, communities, populations and individuals of arbuscular mycorrhizal fungi.     

Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’

Attempts to assess fungal global species richness are confounded by several problems: uncertainty about the number of described species, incomplete fungal inventories even at a high taxonomic level, high diversity of unknown, often small and elusive taxa, high levels of morphological conservation, and incomplete knowledge of their ecological and biogeographical distributions. The two main bases for estimating total fungal diversity are (1) the number of described species and their taxonomic structure, and (2) extrapolating species-area relationships. We argue that knowledge of fungal taxonomy and environmental sampling of fungi are both too incomplete for either approach to be reliable. However, it is likely that the true number of fungal species on the planet is a seven-digit number, and may even be an order of magnitude higher.     

Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’

Attempts to assess fungal global species richness are confounded by several problems: uncertainty about the number of described species, incomplete fungal inventories even at a high taxonomic level, high diversity of unknown, often small and elusive taxa, high levels of morphological conservation, and incomplete knowledge of their ecological and biogeographical distributions. The two main bases for estimating total fungal diversity are (1) the number of described species and their taxonomic structure, and (2) extrapolating species-area relationships. We argue that knowledge of fungal taxonomy and environmental sampling of fungi are both too incomplete for either approach to be reliable. However, it is likely that the true number of fungal species on the planet is a seven-digit number, and may even be an order of magnitude higher.     

Fungi from the roots of the common terrestrial orchid Gymnadenia conopsea

The fungal community associated with the terrestrial photosynthetic orchid Gymnadenia conopsea was characterized through PCR-amplification directly from root extracted DNA and cloning of the PCR products. Six populations in two geographically distinct regions in Germany were investigated. New ITS-primers amplifying a wide taxonomic range including Basidiomycetes and Ascomycetes revealed a high taxonomic and ecological diversity of fungal associates, including typical orchid mycorrhizas of the Tulasnellaceae and Ceratobasidiaceae as well as several ectomycorrhizal taxa of the Pezizales. The wide spectrum of potential mycorrhizal partners may contribute to this orchid's ability to colonize different habitat types with their characteristic microbial communities. The fungal community of G. conopsea showed a clear spatial structure. With 43 % shared taxa the species composition of the two regions showed only little overlap. Regardless of regions, populations were highly variable concerning taxon richness, varying between 5 and 14 taxa per population. The spatial structure and the continuous presence of mycorrhizal taxa on the one hand and the low specificity towards certain fungal taxa on the other hand suggest that the fungal community associated with G. conopsea is determined by multiple factors. In this context, germination as well as pronounced morphological and genetic differentiation within G. conopsea deserve attention as potential factors affecting the composition of the fungal community.     

The diversity of arbuscular mycorrhizal fungi in the subtropical forest of Huangshan (Yellow Mountain), East-Central China

The world heritage of Huangshan is located in the east-central China. In order to obtain a better overview of biodiversity in Huangshan, we investigated the diversity of arbuscular mycorrhizal fungi in the soil of Huangshan. Forty-two rhizosphere soil samples were collected and 989 arbuscular mycorrhizal fungal spore samples were obtained using the wet-sieving method. Twenty-five species of arbuscular mycorrhizal fungi were identified from the collections. The species were of the genera Acaulospora (6 species), Entrophospora (1 species), Glomus (16 species) and Scutellospora (2 species). Acaulospora and Glomus were dominant at the study site. The arbuscular mycorrhizal fungi spore density ranged from 45 to 3,250 per 100 g soil (average 839), and the species richness of arbuscular mycorrhizal fungi ranged from 1 to 9 (average 4.2) per soil sample. Shannon–Wiener index and Simpson’s index were calculated to evaluate the arbuscular mycorrhizal fungal diversity. The diversity of arbuscular mycorrhizal fungal community in the subtropical forest of Huangshan may be the result of mutual selection between arbuscular mycorrhizal fungi and the ecological environment.     

Mycorrhizas: Gene to Function

Substantial progress has been made toward development of molecular tools for identification and quantification of mycorrhizal fungi in roots and evaluation of the diversity of ectomycorrhizal (ECM) fungi and the phylogeny and genetic structure of arbuscular mycorrhizal (AM) fungi. rDNA analysis confirms high diversity of ECM fungi on their hosts, and for AM fungi has revealed considerable genetic variation within and among morphologically similar AM fungal species. The fungal and plant genes, regulation of their expression, and biochemical pathways for nutrient exchange between symbiotic partners are now coming under intense study and will eventually be used to define the ecological nutritional role of the fungi. While molecular biological approaches have increased understanding of the mycorrhizal symbiosis, such knowledge about these lower-scale processes has yet to influence our understanding of larger-scale responses to any great extent.     

Fungal‐host diversity among mycoheterotrophic plants increases proportionally to their fungal‐host overlap

The vast majority of plants obtain an important proportion of vital resources from soil through mycorrhizal fungi. Generally, this happens in exchange of photosynthetically fixed carbon, but occasionally the interaction is mycoheterotrophic, and plants obtain carbon from mycorrhizal fungi. This process results in an antagonistic interaction between mycoheterotrophic plants and their fungal hosts. Importantly, the fungal‐host diversity available for plants is restricted as mycoheterotrophic interactions often involve narrow lineages of fungal hosts. Unfortunately, little is known whether fungal‐host diversity may be additionally modulated by plant–plant interactions through shared hosts. Yet, this may have important implications for plant competition and coexistence. Here, we use DNA sequencing data to investigate the interaction patterns between mycoheterotrophic plants and arbuscular mycorrhizal fungi. We find no phylogenetic signal on the number of fungal hosts nor on the fungal hosts shared among mycoheterotrophic plants. However, we observe a potential trend toward increased phylogenetic diversity of fungal hosts among mycoheterotrophic plants with increasing overlap in their fungal hosts. While these patterns remain for groups of plants regardless of location, we do find higher levels of overlap and diversity among plants from the same location. These findings suggest that species coexistence cannot be fully understood without attention to the two sides of ecological interactions.     

Characterizing and handling different kinds of AM fungal spores in the rhizosphere

Spores are important propagules as well as the most reliable species-distinguishing traits of arbuscular mycorrhizal (AM) fungi. During surveys of AM fungal communities, spore enumeration and spore identification are frequently conducted, but generally little attention is given to the age and viability of the spores. In this study, AM fungal spores in the rhizosphere were characterized as live or dead by vital staining and by performing a germination assay. A considerable proportion of the spores in the rhizosphere were dead despite their intact appearance. Furthermore, morphological and molecular analyses of spores to determine species identity revealed that both viable spores and dead spores with contents were identified. The accurate identification of spores at different developmental stages on the basis of morphology requires considerable experience. Our findings suggest that surveys of AM fungal communities based on spore enumeration and morphological and molecular identification are likely to be inaccurate, primarily because of the large proportion of dead spores in the rhizosphere. A viability check is recommended prior to spore molecular identification, and the use of trap cultures would give more reliable morphological identification results. We show that the abundance and activity of AM fungi in the rhizosphere can be determined by calculating the density of viable spores and the density of spores that could germinate. The adoption of these methods should provide a more reliable basis for further AM fungal community analysis.     

Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with the roots of most plants, thereby mediating nutrient and carbon fluxes, plant performance, and ecosystem dynamics. Although considerable effort has been expended to understand the keystone ecological position of AM symbioses, most studies have been limited in scope to recording organism occurrences and identities, as determined from morphological characters and (mainly) ribosomal sequence markers. In order to overcome these restrictions and circumvent the shortcomings of culture- and phylogeny-based approaches, we propose a shift toward plant and fungal protein-encoding genes as more immediate indicators of mycorrhizal contributions to ecological processes. A number of candidate target genes, involved in the uptake of phosphorus and nitrogen, carbon cycling, and overall metabolic activity, are proposed. We discuss the advantages and disadvantages of future protein-encoding gene marker and current (phylo-) taxonomic approaches for studying the impact of AM fungi on plant growth and ecosystem functioning. Approaches based on protein-encoding genes are expected to open opportunities to advance the mechanistic understanding of ecological roles of mycorrhizas in natural and managed ecosystems.     

Consideration of the taxonomy and biodiversity of Australian ectomycorrhizal fungi

Mycorrhiza management in forestry must be predicated on an understanding of fungal biology and ecology. A fundamental building block of the biology and ecology of any organism is accurate identification and an understanding of its relationship to other organisms. The taxonomy of the larger fungi has been largely based on morphological classification of sexual structures but now Taxonomy routinely incorporates mating studies, and biochemical and molecular data. Taxonomy may not revolutionize theories on mycorrhiza but can clarify some of the inconsistencies due to misrepresentation or over-generalizations and inappropriate conclusions drawn from studies with inaccurately identified fungi. To illustrate this, we discuss and example where incorrect fungal names were repeatedly erroneously applied in morphological and physiological research reports on this fungus, e.g. Laccaria laccata. In this case subsequent taxonomic study revealed the reason for the conflicting research results reported for this fungus. We discuss the status of identifying the ectomycorrhizal fungi in various forest communities in Australia and the relationships of this process to assessing their use in forestry. Recent intensive efforts to collect, isolate and identify Australian ectomycorrhizal fungi have revealed an enormous and unique species diversity, e.g., for truffle-like fungi, over 2000 collections from the last five years alone have yielded 2 new families, 24 new genera, and about 184 new species. Nearly 95% of the described and undescribed fungi from Australia are novel, with some 22 genera and 3 families endemic. In most cases the current systematic knowledge of mycorrhizal fungi is inadequate to support clear framework for Australian taxa. This reflects the traditional Northern Hemisphere view of the world, the uniqueness of the Australian fungal flora, and how poorly it is known. For example, the genus Hymenogaster had been widely acknowledged as the most reduced member of the Cortinariaceae. However recent work on Hymenogaster species from the Southern Hemisphere has offered a number of alternative affinities to various species. We also discuss the role proper identification of the organisms involved plays in understanding the ecosystem. Emphasis should be placed on how species diversity equates with physiological and genetic diversity and how a sound taxonomic understanding of species and their systematic position is essential to properly manage them. Accurate taxonomic information will continue to be required as the basis for assessing the role of ectomycorrhizal fungi in sustained ecological development. Of particular significance is the role of ectomycorrhizal fungi in maintenance of plant diversity in natural ecosystems and those disturbed by management. In conclusion, we present some key research areas involving the use of taxonomy that need priority attention.     

Fungal endophyte diversity in tundra grasses increases by grazing

Fungal endophytes are species rich and ubiquitous, yet, apart from the genus Epichloë, their ecology is largely unknown. Here we explore how herbivores affect the diversity of fungal endophytes in tundra grasslands. We assess both hyphal morphological and taxonomic diversity in grass individuals.By microscopic examination we identified endophytes to be present in all sampled grass individuals whereas identification to taxonomic units were only achieved in a subset of the individuals using laser micro dissection pressure catapulting and culturing for endophyte isolation. Hyphal morphological diversity was significantly higher in grasses exposed to grazing, along with 45 % more taxonomic units achieved.Our results suggest that grazing is an important mediator of fungal endophyte diversity in tundra grasslands. Furthermore, we suggest laser dissection of stained endophytes as a method for further exploring the ecological role of fungal endophytes.     

鼓槌石斛的地理分布与菌根真菌区系组成的相关性

本文研究了兰科石斛属鼓槌石斛的地理分布与菌根真菌区系组成的相关性。采用克隆文库技术对云南省西双版纳和临沧市两个地区的8份野生鼓槌石斛根部样品进行了分析。结果表明,共从两个地区的鼓槌石斛根部获得了14个真菌的可操作分类单元（OTU）,主要隶属于胶膜菌科Tulasnellaceae和小纺锤菌目Atractiellales。分析鼓槌石斛对菌根真菌的专一性和偏好性发现,鼓槌石斛对菌根真菌专一性较低,每个植株都能同时与多种菌根真菌共生;不同地理分布的鼓槌石斛菌根真菌类群存在明显差异,两个地区的鼓槌石斛的菌根真菌中只有1个OTU是相同的,其余均不同。说明菌根真菌可能和鼓槌石斛的生态适应存在一定的相关性。     

山西历山珍稀药用植物AM真菌资源与土壤因子的关系

以山西历山自然保护区暴马丁香、连香树、南方红豆杉和领春木4种珍稀药用植物为材料,研究其根际土壤中丛枝菌根真菌(AMF)的菌根结构类型和种属分布,同时分析土壤因子与其侵染率和孢子密度的关系。结果表明:(1)暴马丁香菌根类型为中间型(I-型),连香树和领春木为重楼型(P-型),南方红豆杉为疆南星型(A-型);4种植物根际共鉴定AMF 27种,分别隶属于球囊霉属(Glomus)、无梗囊霉属(Acaulospora)、盾巨孢囊霉属(Scutellos-pora)、多孢囊霉属(Diversispora)和原囊霉属(Archaeospora)5属,其中Glomus为优势属。(2)pH与暴马丁香和领春木的侵染率和孢子密度呈正相关,但与连香树和南方红豆杉呈负相关;速效磷与暴马丁香、南方红豆杉和领春木的侵染率和孢子密度呈正相关,但与连香树呈负相关;碱解氮、有机质与暴马丁香、连香树和领春木的侵染率和孢子密度呈正相关,但与南方红豆杉呈负相关。(3)4种药用植物的菌根侵染率主要受其根际土壤碱解氮的影响,而根际AMF孢子密度主要受根际土壤pH制约。可见,历山自然保护区内AMF资源丰富,多样性程度也较高;宿主植物不同,土壤因子对其侵染率和孢子密度的影响也不同。     

Research on arbuscular mycorrhizae in Mexico: an historical synthesis and future prospects

This review analyzes the historical development and advances of the research on arbuscular mycorrhizal fungi (AMF) in Mexico, as well as the prospects for future research. AMF-research has been focused on studying both diversity and functionality in several ecosystems of Mexico, but mainly in the tropical dry and rainy ecosystems, and the agricultural systems. In Mexico, 95 species of AMF have been recorded, representing 41% of the known species worldwide. The functional effects of AMF colonization have been examined in approximately 10% of the known host plants, but greenhouse studies continue to dominate over those conducted under field conditions. Even though research to date has been at the organismic level, further effort is needed due to the high plant diversity in Mexico. Studies on AMF biomass under field conditions and more taxonomic determination are required based on morphological features, biochemical determinations (fatty acids) and molecular tools. In addition, ecophysiological and ecological in situ studies would help in understanding the relationships among AMF, soil fauna, nutrients, and host plants. The contribution of AMF to ecosystemic processes is a priority line of research that requires an integrated approach (inter- and multidisciplinary) in order to define the role of AM symbioses for biogeochemical models. The creation of a Mexican mycorrhizal research network has and will help to identify the main challenges. Generating similar research protocols, and sharing databases and experience will assist mycorrhizologists working under the diverse financial and ecological contexts that is to be found in Mexico and Latin America.     

Studies on the diversity of the distinct phylogenetic lineage encompassing Glomus claroideum and Glomus etunicatum

Morphological and molecular characters were analysed to investigate diversity within isolates of the Glomus claroideum/Glomus etunicatum species group in the genus Glomus. The inter- and intra-isolate sequence diversity of the large subunit (LSU) rRNA gene D2 region of eight isolates of G. claroideum and G. etunicatum was studied using PCR-single strand conformational polymorphism (SSCP)-sequencing. In addition, two isolates recently obtained from Southern China were included in the analysis to allow for a wider geographic screening. Single spore DNA isolation confirmed the magnitude of gene diversity found in multispore DNA extractions. An apparent overlap of spore morphological characters was found between G. claroideum and G. etunicatum in some isolates. Analysis of the sequence frequencies in all G. etunicatum and G. claroideum isolates (ten) showed that four LSU D2 sequences, representing 32.1% of the clones analysed for multispore extraction (564) were found to be common to both species, and those sequences were the most abundant in four of the ten isolates analysed. The frequency of these sequences ranged between 23.2% and 87.5% of the clones analysed in each isolate. The implications for the use of phenotypic characters to define species in arbuscular mycorrhizal fungi are discussed. The current position of G. claroideum/G.etunicatum in the taxonomy of the Glomeromycota is also discussed.     

Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.     

Ecological aspect in the systematics of fungi

The main morphological features of fungi representing different evolutionary lines are discussed.Environmental situations which stimulate morphological changes are regarded.It is suggested to define ecological significance of fungal morphological characters,dividing them to the ecologically inert(the main characters determining evolutionary line) and ecologically active-characters which submerged to the changes with the changing of environmental conditions.Two main strategies for fungi in nature are described:raising competitive ability to win conquer for substratum,for the place in ecosystem,and the second way for less competitive species-to adapt to more stressful natural conditions and to occupy ecological niches becoming free.Some examples of analysis of adaptation to substrata and climatic zones by fungi are shown.     

Untangling above‐ and belowground mycorrhizal fungal networks in tropical orchids

Orchids typically depend on fungi for establishment from seeds, forming mycorrhizal associations with basidiomycete fungal partners in the polyphyletic group rhizoctonia from early stages of germination, sometimes with very high specificity. This has raised important questions about the roles of plant and fungal phylogenetics, and their habitat preferences, in controlling which fungi associate with which plants. In this issue of Molecular Ecology, Martos et al. (2012) report the largest network analysis to date for orchids and their mycorrhizal fungi, sampling a total of over 450 plants from nearly half the 150 tropical orchid species on Reunion Island, encompassing its main terrestrial and epiphytic orchid genera. The authors found a total of 95 operational taxonomic units of mycorrhizal fungi and investigated the architecture and nestedness of their bipartite networks with 73 orchid species. The most striking finding was a major ecological barrier between above‐ and belowground mycorrhizal fungal networks, despite both epiphytic and terrestrial orchids often associating with closely related taxa across all three major lineages of rhizoctonia fungi. The fungal partnerships of the epiphytes and terrestrial species involved a diversity of fungal taxa in a modular network architecture, with only about one in ten mycorrhizal fungi partnering orchids in both groups. In contrast, plant and fungal phylogenetics had weak or no effects on the network. This highlights the power of recently developed ecological network analyses to give new insights into controls on plant–fungal symbioses and raises exciting new hypotheses about the differences in properties and functioning of mycorrhiza in epiphytic and terrestrial orchids.