Diversity and community composition of ectomycorrhizal fungi in a dry deciduous dipterocarp forest in Thailand

Large forest areas of South-East Asia, are dominated by the Dipterocarpaceae tree family, which contains many important timber species. Unlike many other tropical trees, Dipterocarpaceae rely on ectomycorrhizal (ECM) root symbiosis for their mineral nutrition. This study aims to document the richness and community composition of ECM fungi in a dry deciduous forest in Thailand. Combining morphological and molecular identification methods revealed 69 species of ECM fungi that belong to 17 phylogenetic lineages. The /russula-lactarius, /tomentella-thelephora, /sordariales, /sebacina and /cantharellus lineages were the most species-rich. The fungal richness is comparable to other tropical rain forest sites, but the phylogenetic community structure has elements of both tropical and temperate ecosystems. Unlike tropical rain forests, the Cenococcum geophilum complex was one of the most frequent fungal taxa that had a relatively high ITS genetic diversity over the small sampling area. This study provides the first snapshot insight into the fungal community of dry dipterocarp forests. However, it is necessary to broaden the spatial and temporal scales of sampling to improve our understanding of the below-ground relations of dry and humid tropical forests.     

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.     

Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar

Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.     

DNA-based fungal diversity in Madagascar and arrival of the ectomycorrhizal fungi to the island

Madagascar is known for its high diversity and endemism of fauna and flora. Fungi, however, have been largely overlooked in diversity and evolution studies on the island, and whether fungi exhibit the same patterns as animals and plants has yet to be further examined. We collected fungal sporocarps and ectomycorrhizal (EcM) roots during three opportunistic surveys in five forests in Madagascar and generated a dataset of fungal Internal Transcribed Spacer (ITS) DNA sequences. We analyzed them together with all publicly available fungal ITS DNA sequences and identified 620 Operational Taxonomic Units (OTUs) from Madagascar, 10% of which contained only sequences from our surveys. Two hundred and ninety-two OTUs belonged to EcM species with /russula-lactarius, /boletus, /tomentella-telephora, /cortinarius, and /amanita being the most abundant EcM lineages. Overall, 60% of all fungi and 81% of the EcM species from Madagascar appear to be endemic. We conducted a phylogenetic analysis using all the OTUs in Amanitaceae, Boletaceae, and Russulaceae families to elucidate their relative timing of arrival in Madagascar. We found that most EcM species from Madagascar in the three families diverged less than 22 million years ago (mya), long after the separation of India and Madagascar (88 mya), which is consistent with a dispersal mediated process of arrival to the island. Our study provides the first comprehensive view of the overall DNA-based fungal diversity in Madagascar and the current state of knowledge of EcM fungi based on DNA sequences, useful for further ecological and evolutionary studies. Abstract in Malagasy is available with online material.     

Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape

Non-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two host, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the fungal communities of the non-native host may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems.     

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi,Sebacinales) as revealed from comparative phylogenetic analyses

Compared with plants and animals, large‐scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45–57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.     

Fine-level mycorrhizal specificity in the Monotropoideae (Ericaceae): specificity for fungal species groups

The Monotropoideae (Ericaceae) are non-photosynthetic angiosperms that obtain fixed carbon from basidiomycete ectomycorrhizal fungi. In previous work, we showed that each plant species is associated with a single genus or a set of closely related genera of ectomycorrhizal fungi. Here we show that the level of specificity is much higher. We used a molecular phylogenetic approach to contrast specificity patterns among eight plant lineages and three fungal genera. We relied on fungal nuclear internal transcribed spacer (nrITS) sequence data obtained from 161 basidiocarps and 85 monotropoid roots representing 286 sampled plants screened using restriction length polymorphisms. From the phylogenetic placement of fungal symbionts in fungal phylograms, we found that three basal (Sarcodes, Pterospora, Pleuricospora) and one derived lineage (Allotropa) of plants target narrow clades of closely related species groups of fungi, and four derived lineages (Monotropa hypopithys species group, Pityopus) target more distant species groups. Within most plant lineages, geography and photobiont association constrain specificity. Specificity extended further in Pterospora andromedea, in which sequence haplotypes at the plastid trn L-F region of 73 plants were significantly associated with different fungal species groups even in sympatry. These results indicate that both the macro- and microevolution of the Monotropoideae are tightly coupled to their mycorrhizal symbionts.     

Diversity and community structure of ectomycorrhizal fungi in <Emphasis Type="Italic">Pinus thunbergii</Emphasis> coastal forests in the eastern region of Korea

We investigated the diversity and community structure of ectomycorrhizal (EcM) fungi in Pinus thunbergii stands on the eastern coast of Korea. We established two 10 × 10-m plots in six forest stands and sampled soil blocks containing rootlets of mature P. thunbergii trees. EcM roots were classified into morphological groups, and the fungal taxa associated with each morphotype were identified by sequencing the nuclear rDNA internal transcribed spacer region. Cenococcum geophilum and the Atheliales, Clavulinaceae, Russulaceae and Thelephoraceae species were the main members of the EcM fungal community, which included a total of 68 observed fungal taxa. As a whole, the community consisted of a few dominant fungal taxa, such as C. geophilum (28.6% relative abundance), and a large number of rare fungal taxa that showed low abundances and local distributions. Colonization patterns at the local site scale and at the scale of the study plots greatly differed among the EcM fungal taxa; C. geophilum was distributed extensively and was dominant in several study sites, whereas a certain Lactarius sp. was distributed locally but dominated in a given study site. We conclude with a discussion of the relationship between colonization patterns of EcM fungi and soil and environmental conditions.     

Ectomycorrhizal fungi diversity in a white sand forest in western Amazonia

The genera Dicymbe and Aldina (Fabaceae) host ectomycorrhizal fungi (EcM) and are common in white sand forests (WSFs), a highly specialized habitat with a high level of plant endemism compared with terra-firme forests. In this study, we visited four times a 1-ha permanent plot established in a small patch of a WSF in the south of Colombia Amazonia. Forty-eight species of EcM fungi were recovered from sporocarps and 15 ITS species-level were detected from root tips. Seventeen species were new reports to Colombia and seven corresponded to undescribed species. These results confirm that this WSF supports a significant EcM fungal diversity. Most of the species found in this study have been previously reported to be associated with other legume and/or dipterocarp species from geographically distant forests. The long-distance occurrence combined with low host specificity, suggest the possibility of gene flow between geographically distant populations of EcM fungi in neotropical lowland rainforests.     

Molecular phylogeny of the Entomophthoromycota

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.     

AM fungal communities inhabiting the roots of submerged aquatic plant <Emphasis Type="Italic">Lobelia dortmanna</Emphasis> are diverse and include a high proportion of novel taxa

While the arbuscular mycorrhizal (AM) symbiosis is known to be widespread in terrestrial ecosystems, there is growing evidence that aquatic plants also form the symbiosis. It has been suggested that symbiosis with AM fungi may represent an important adaptation for isoëtid plants growing on nutrient-poor sediments in oligotrophic lakes. In this study, we address AM fungal root colonization intensity, richness and community composition (based on small subunit (SSU) ribosomal RNA (rRNA) gene sequencing) in five populations of the isoëtid plant species Lobelia dortmanna inhabiting oligotrophic lakes in Southern Sweden. We found that the roots of L. dortmanna hosted rich AM fungal communities and about 15 % of the detected molecular taxa were previously unrecorded. AM fungal root colonization intensity and taxon richness varied along an environmental gradient, being higher in oligotrophic and lower in mesotrophic lakes. The overall phylogenetic structure of this aquatic fungal community differed from that described in terrestrial systems: The roots of L. dortmanna hosted more Archaeosporaceae and fewer Glomeraceae taxa than would be expected based on global data from terrestrial AM fungal communities.     

The diversity of ant-associated black yeasts: insights into a newly discovered world of symbiotic interactions

Based on pure culture studies and DNA phylogenetic analyses, black yeasts (Chaetothyriales, Ascomycota) are shown to be widely distributed and important components of numerous plant-ant-fungus networks, independently acquired by several ant lineages in the Old and New World. Data from ITS and LSU nu rDNA demonstrate that a high biodiversity of fungal species is involved. There are two common ant-fungus symbioses involving black yeasts: (1) on the carton walls of ant nests and galleries, and (2) the fungal mats growing within non-pathogenic naturally hollow structures (so-called domatia) provided by myrmecophytic plants as nesting space for ants (ant-plant symbiosis). Most carton- and domatia-inhabiting fungi stem from different phylogenetic lineages within Chaetothyriales, and almost all of the fungi isolated are still undescribed. Despite being closely related, carton and domatia fungi are shown to differ markedly in their morphology and ecology, indicating that they play different roles in these associations. The carton fungi appear to improve the stability of the carton, and several species are commonly observed to co-occur on the same carton. Carton fungi commonly have dark-walled monilioid hyphae, colouring the carton blackish and apparently preventing other fungi from invading the carton. Despite the simultaneous presence of usually several species of fungi, forming complex associations on the carton, little?overlap is observed between carton fungi from different ant species, even those that co-occur in nature, indicating at least some host specificity of fungi. Most fungi present on carton belong to Chaetothyriales, but in a few samples, Capnodiales are also an important component. Carton fungi are difficult to assign to anamorph genera, as most lack conidiation. The domatia fungi are more specific. In domatia, usually only one or two fungal species co-occur, producing a dense layer on living host plant tissue in domatia. They have hyaline or light brown thin-walled hyphae, and are commonly sporulating. In both carton and domatia, the fungal species seem to be specific to each ant-plant symbiosis. Representative examples of carton and domatia ant-fungus symbioses are illustrated. We discuss hypotheses on the ecological significance of the Chaetothyriales associated with ants.     

Ectomycorrhizal root tips harbor distinctive fungal associates along a soil nitrogen gradient

A diverse range of fungi associate with ectomycorrhizal (EcM) root tips, however, their identity and the biotic and abiotic filters structuring these communities remain unknown. We employed a metabarcoding approach to characterize fungal communities associating with the EcM root tips of Quercus rubra along a natural soil nitrogen gradient. EcM communities and ectomycorrhizal associated fungi (EcAF) were tightly linked across the breadth of the soil gradient. Notably, EcAF communities were primarily shaped by the morphological attributes of EcM communities, particularly the relative abundance of EcM taxa forming rhizomorphic hyphae. Edaphic properties (soil C:N and net N mineralization) exerted minimal influence, suggesting a strong role of biotic interactions in EcAF community assembly. The presence of plants forming ericoid mycorrhizal associations also shapes the prevalence of ericoid mycorrhizal fungi associating with EcM root tips. Overall, EcAF communities were dominated by helotialean fungi, ericoid mycorrhizal fungi, dark septate endophytes, and the white-rot fungi Mycena.     

Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest

? The ectomycorrhizal (ECM) symbiosis was historically considered restricted to the temperate zones, but recent studies have shown the importance of this symbiosis across the tropics. We examined ECM fungal diversity, host plant phylogeny and ECM host preferences in a rainforest dominated by the leguminous host plants Dicymbe corymbosa, Dicymbe altsonii and Aldina insignis. ? Ectomycorrhizal fungi were identified by internal transcribed spacer rDNA sequencing and host species were verified with chloroplast trnL sequencing. To test whether Dicymbe and Aldina represent independent gains of the ECM symbiosis, we constructed a Fabaceae phylogeny using MatK and trnL. We identified four independent ECM lineages within the Fabaceae. ? We detected a diverse community of 118 ECM species dominated by the /clavulina, /russula-lactarius, /boletus, and /tomentella-thelephora lineages. Ectomycorrhizal species in Agaricales, Atheliales and Polyporales may represent previously unrecognized tropical-endemic ECM lineages. Previous studies suggested that ECM fungi did not diversify in the tropics, but the /clavulina lineage appears to have a center of diversity in tropical South America. ? Dicymbe and Aldina represent independent gains of the ECM symbiosis in Fabaceae but their fungal symbionts showed no host preferences. Spatial factors are more important than hosts in structuring the ECM fungal community in this ecosystem.     

基因组学时代的真菌分类学:机遇与挑战

真菌物种的形态特征有限,加之形态滞后和形态可塑性,仅靠外部形态、内部结构及生理生化指标,很难把握真菌的系统亲缘。应用DNA测序、基因组测序、比较基因组学及生物信息学等技术,研究人员可以快速识别真菌演化中出现的数量众多的单系支系,为建立各分类等级的新分类单元提供有力证据,为真菌分类学研究带来了新的希望和活力。自2000年以来,在真菌界至少发表了1新亚界、4新门、7新亚门、19新纲、9新亚纲、40余新目等高级分类单元。近3年来,我国发表了20余个真菌新属,其中绝大多数属的建立都有分子证据支持。可以预见,大量的新种、新属、新科乃至更高级分类单元将会在今后10年内持续发现和建立。这必将大大促进真菌分类学的发展,完善现有的真菌分类系统。我们应该顺势而上,利用我国丰富的真菌资源,为真菌分类学的发展做出应有贡献。与此同时,真菌分类学也面临着十分严峻的挑战。挑战主要来自3个方面,一是研究变得越来越综合,不但需要有相应的研究经费支持,而且要求从事该领域的研究人员技术更全面、知识更广博及知识更新速度更快捷;二是新物种描述进度偏慢,远远不能满足人们对物种认识和利用的日益增长的需要;三是研究人员亟需创新研究模式,以新技术、新思路、新机制来构建新的真菌分类学,加速新物种的发现和描述进度,最终为社会进步和科学发展服务。     

Relatedness, phylogeny, and evolution of the fungi

Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi includingBasidiobolus, 3) detection of a major new lineage “Archiascomycetes,” comprisingTaphrina, Protomyces andSaitoella, Schizosaccharomyces, andPneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genusGeosmithia, and 5) phylogenetic placement ofMixia osmundae, species correctly and incorrectly assigned to the genusTaphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated. “Traditional studies of evolution have amply demonstrated that evolution at the phenotypic level is characterized by adaptation and opportunism, irregularity in pace, and inequality of rates among lineages. In contrast, studies of molecular evolution have revealed quite different features characterized by changes that are conservative in nature, random in pattern (independent of phenotypic characters), and quite regular in pace with equal rates among diverge [sic] lineages for a given protein”. (Kimura, M. 1983. The neutral theory of molecular evolution, pp. 308–309, Cambridge University Press, Cambridge.) Recipient of the 2nd Mycological Society of Japan's Excellent Achievement Award, 1998; the awarding lecture was given at the 42nd Annual Meeting of the Mycological Society of Japan, 16 May, 1998, Kyoto University, Kyoto. This review is based mainly on the publications intended for the Award.     

Towards global patterns in the diversity and community structure of ectomycorrhizal fungi

Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.     

Complex host-pathogen coevolution in the Apterostigma fungus-growing ant-microbe symbiosis

Background  

The fungus-growing ant-microbe symbiosis consists of coevolving microbial mutualists and pathogens. The diverse fungal lineages that these ants cultivate are attacked by parasitic microfungi of the genus Escovopsis. Previous molecular analyses have demonstrated strong phylogenetic congruence between the ants, the ants-cultivated fungi and the garden pathogen Escovopsis at ancient phylogenetic levels, suggesting coevolution of these symbionts. However, few studies have explored cophylogenetic patterns between these symbionts at the recent phylogenetic levels necessary to address whether these parasites are occasionally switching to novel hosts or whether they are diversifying with their hosts as a consequence of long-term host fidelity.