Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi

Robust species delimitations provide a foundation for investigating speciation, phylogeography, and conservation. Here we attempted to elucidate species boundaries in the cosmopolitan lichen-forming fungal taxon Lecanora polytropa. This nominal taxon is morphologically variable, with distinct populations occurring on all seven continents. To delimit candidate species, we compiled ITS sequence data from populations worldwide. For a subset of the samples, we also generated alignments for 1209 single-copy nuclear genes and an alignment spanning most of the mitochondrial genome to assess concordance among the ITS, nuclear, and mitochondrial inferences. Species partitions were empirically delimited from the ITS alignment using ASAP and bPTP. We also inferred a phylogeny for the L. polytropa clade using a four-marker dataset. ASAP species delimitations revealed up to 103 species in the L. polytropa clade, with 75 corresponding to the nominal taxon L. polytropa. Inferences from phylogenomic alignments generally supported that these represent evolutionarily independent lineages or species. Less than 10% of the candidate species were comprised of specimens from multiple continents. High levels of candidate species were recovered at local scales but generally with limited overlap across regions. Lecanora polytropa likely ranks as one of the largest species complexes of lichen-forming fungi known to date.

Molecular Phylogenetics, Speciation, and Long Distance Dispersal in Tardigrade Evolution: A case study of the genusMilnesium

Microorganisms (sensu lato, i.e., including micrometazoans) are thought to have cosmopolitan geographic distributions due to their theoretically unlimited dispersal capabilities, a consequence of their tiny size, population dynamics, and resistant forms. However, several molecular studies of microorganisms have identified biogeographic patterns indicating cryptic speciation and/or weak species definitions. Using a multi-locus approach with the genus Milnesium (Tardigrada), we aimed to determine the genetic structure of populations worldwide and the effects of long distance dispersal (LDD) on genetic connectivity and relationships across the six continents. Our results on this micrometazoan's genetic structure and LDD at global and micro-local scales indicate contrasting patterns not easily explained by a unique or simple phenomenon. Overall, we report three key findings: (i) confirmation of long distance dispersal for tardigrades, (ii) populations with globally-shared or endemic micro-local haplotypes, and (iii) a supported genetic structure instead of the homogeneous genetic distribution hypothesized for microorganisms with LDD capabilities. Moreover, incongruences between our morphological and molecular results suggest that species delimitation within the genus Milnesium could be problematic due to homoplasy. Duality found for Milnesium populations at the global scale, namely, a molecular phylogenetic structure mixed with widely distributed haplotypes (but without any apparent biogeographic structure), is similar to patterns observed for some unicellular, prokaryotic and eukaryotic, microorganisms. Factors influencing these patterns are discussed within an evolutionary framework.

Threshold effects of soil pH on microbial co-occurrence structure in acidic and alkaline arable lands

Soil pH plays a pivotal role in shaping microbial diversity and community composition in terrestrial ecosystems. Soil microbes clearly do not exist independently and instead form complex interaction networks, but little is known about the effect of soil pH upon those microbial co-occurrence networks. In this study, 62 alkaline and 61 acidic soil samples were collected from the North China Plain to investigate the effect of soil pH on microbial co-occurrence structure. Most bacterial and fungal OTUs in acidic soils were maximally abundant at soil pH of ~5.5, while in alkaline soils the corresponding OTU abundance attainted its maximum at pH ~8.3. Unlike those OTU abundance distributions, the relationship between soil pH and the number of links between OTUs in the co-occurrence network was best fitted by convex curves, with the pH thresholds found at 5.39 for bacteria and 5.60 for fungi in acidic soils. In alkaline soils, a dip in the relationship (only for fungi) between soil pH and the links was also observed, with a pH threshold at 8.04 for bacteria and 8.28 for fungi. From the co-occurrence analysis we identified 37 core bacterial species (mainly in Actinobacteria and Proteobacteria) and 24 core fungal species (mainly in Ascomycota). Together, this study revealed the threshold effects of soil pH upon microbial co-occurrence structure and identified the core microbial species in the North China Plain. These findings provide baseline information in mediating soil microbial co-occurrence structure by adjusting soil pH and core species in croplands.

Multi-Locus Phylogeny and Taxonomy of the Fungal Complex Associated With Rusty Root Rot of Panax ginseng in China

Panax ginseng rusty root rot caused by the Ilyonectria species complex is a devastating disease, and it is one of the main factors contributing to the difficulty in continual cropping. Rusty root rot occurs in all ginseng fields, but little is known about the taxonomy of the fungal pathogen complex, especially Ilyonectria and Ilyonectria-like species. Rusty root rot samples were collected from commercial ginseng cultivation areas of China, and the pathogens were isolated and purified as single spores. Based on the combination analysis of multiple loci (rDNA-ITS, TUB, HIS3, TEF, ACT, LSU, RPB1, RPB2, and SSU) and morphological characteristics, the pathogens causing ginseng rusty root rot were determined. Fungal isolates were obtained from infected roots in 56 locations within main cultivation areas in China. A total of 766 strains were identified as Ilyonectria, Ilyonectria-like and Rhexocercosporidium species, including I. robusta (55.0%), I. communis (21.7%), I. mors-panacis (10.9%), I. pseudodestructans (2.0%), I. changbaiensis (1.3%), I. qitaiheensis (1.3%), Neonectria obtusispora (2.0%), Dactylonectria torresensis (0.5%), D. sp. (0.5%), and R. panacis (1.5%), and four novel species, Thelonectria ginsengicola (1.0%), T. jixiensis (1.0%), T. mulanensis (0.8%) and T. fusongensis (0.5%), with a total of 14 species. As the pathogen present in the highest proportion, I. robusta was the most prevalent and damaging species, unlike the pathogens reported previously. All of the examined strains were proven to cause ginseng rusty root rot. Our results indicate that the taxonomy of the fungal complex associated with ginseng rusty root rot includes Ilyonectria, Ilyonectria-like genera (Dactylonectria, Neonectria, and Thelonectria) and Rhexocercosporidium.

Behind the veil - exploring the diversity in Phallus indusiatus s.l. (Phallomycetidae, Basidiomycota)

Studies have demonstrated that many cosmopolitan species actually consist of divergent clades that present high levels of morphological stasis throughout their evolutionary histories. Phallusindusiatus s.l. has been described as a circum-tropical species. However, this distribution may actually reflect the lack of taxonomic resolution due to the small number of diagnostic morphological characters, which leads to the identification of new records as populations of P.indusiatus. Here, we examine the diversity of P.indusiatus-like species in Brazilian Amazonia. We show a clear congruence between detailed morphological data and ITS, nuc-LSU and atp6 based phylogenetic analyses and three new species are described within the Brazilian indusiate clade. These results highlight the importance of more detailed investigation, with the inclusion of molecular information, in Neotropical fungi.

Host availability drives distributions of fungal endophytes in the imperilled boreal realm

Boreal forests represent the world's largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth's greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.

Fungal species boundaries in the genomics era

Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.

Addressing the diversity of Xylodon raduloides complex through integrative taxonomy

In this study, the taxonomic diversity of the Xylodon raduloides species complex (Hymenochaetales, Basidiomycota) is examined. Specimens were studied using an integrative taxonomic approach that includes molecular phylogenetic and morphological analyses, and environmental niche comparisons. Four different species were found inside the Xylodon raduloides complex, with a biogeographic distribution pattern bound by geographic regions: Europe, North America, Patagonia, and Australia-New Zealand. Molecular, morphological, and environmental evidences delimit two lineages within this complex: a Northern Hemisphere clade with longer basidiospores and wider ranges in temperature and precipitation tolerance, and a Southern Hemisphere clade with smaller and more spherical basidiospores, and an isothermal and more humid climate preference. The integrative taxonomic approach used in this study demonstrates congruence between data sets and shows how morphological and environmental characteristics contribute to the differentiation of fungal species complexes. By combining various sources of taxonomic information, three new species are described: Xylodon laurentianus, X. novozelandicus, and X. patagonicus.

Hyphoderma paramacaronesicum sp. nov. (Meruliaceae, Polyporales, Basidiomycota), a cryptic lineage to H. macaronesicum

This article re-evaluates the taxonomy of Hyphoderma macaronesicum based on various strategies, including the cohesion species recognition method through haplotype networks, multilocus genetic analyses using the genealogical concordance phylogenetic concept, as well as species tree reconstruction. The following loci were examined: the internal transcribed spacers of nuclear ribosomal DNA (ITS nrDNA), the intergenic spacers of nuclear ribosomal DNA (IGS nrDNA), two fragments of the protein-coding RNA polymerase II subunit 2 (RPB2), and two fragments of the translation elongation factor 1-α (EF1-α). Our results indicate that the name H. macaronesicum includes at least two separate species, one of which is newly described as Hyphoderma paramacaronesicum. The two species are readily distinguished based on the various loci analysed, namely ITS, IGS, RPB2 and EF1-α.

Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation

Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities.

More than one fungus in the pepper pot: Integrative taxonomy unmasks hidden species within Myriostoma coliforme (Geastraceae, Basidiomycota)

Since the nineteenth century, Myriostoma has been regarded as a monotypic genus with a widespread distribution in north temperate and subtropical regions. However, on the basis of morphological characters and phylogenetic evidence of DNA sequences of the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), four species are now delimited: M. areolatum comb. & stat. nov., M. calongei sp. nov., M. capillisporum comb. & stat. nov., and M. coliforme. Myriostoma coliforme is typified by selecting a lectotype (iconotype) and a modern sequenced collection as an epitype. The four species can be discriminated by a combination of morphological characters, such as stomatal form, endoperidial surface texture, and basidiospore size and ornamentation.

Pleiocarpon gen. nov. and a new species of Ilyonectria causing basal rot of Strelitzia reginae in Italy

During 2015, a new basal rot disease was observed on potted plants of Strelitzia reginae in an ornamental nursery located in eastern Sicily. Isolations from symptomatic parts of these diseased plants consistently yielded cylindrocarpon-like isolates. Multigene analyses of the partial gene regions of 28S large subunit nrDNA, β-tubulin, histone H3, translation elongation factor 1-alpha, internal transcribed spacer region and intervening 5.8S nrRNA gene, and RNA polymerase II second largest subunit genes, supported by morphological characters supported the recognition of a new genus, Pleiocarpon based on P. strelitziae sp. nov., and a new Ilyonectria species, described here as I. strelitziae sp. nov. The pathogenicity of both I. strelitziae and P. strelitziae were confirmed on young plants cultivated under controlled conditions in a growth chamber. Both cylindrocarpon-like fungi were pathogenic to S. reginae and reproduced symptoms similar to those observed in the nursery. Of the two species, P. strelitziae was more aggressive than I. strelitziae, resulting in the death of all inoculated plants.

Dimensions of biodiversity in the Earth mycobiome

Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.

A fungal perspective on conservation biology

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.