Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification.

Fungi play essential roles in many ecological processes, and taxonomic classification is fundamental for microbial community characterization and vital for the study and preservation of fungal biodiversity. To cope with massive fungal barcode data, tools that can implement extensive volumes of barcode sequences, especially the internal transcribed spacer (ITS) region, are necessary. However, high variation in the ITS region and computational requirements for processing high-dimensional features remain challenging for existing predictors. In this study, we developed Its2vec, a bioinformatics tool for the classification of fungal ITS barcodes to the species level. An ITS database covering more than 25,000 species in a broad range of fungal taxa was assembled. For dimensionality reduction, a word embedding algorithm was used to represent an ITS sequence as a dense low-dimensional vector. A random forest-based classifier was built for species identification. Benchmarking results showed that our model achieved an accuracy comparable to that of several state-of-the-art predictors, and more importantly, it could implement large datasets and greatly reduce dimensionality. We expect the Its2vec model to be helpful for fungal species identification and, thus, for revealing microbial community structures and in deepening our understanding of their functional mechanisms.

[Do the new molecular assays-microarray and realtime polymerase chain reaction-for dermatophyte detection keep what they promise?] / Halten die neuen molekularen Teste ­ Microarray und Realtime-Polymerasekettenreaktion ­ zum Dermatophytennachweis das, was sie versprechen?

In this study, a novel real-time polymerase chain reaction (PCR) assay (DermaGenius®2.0, PathoNostics BV, Maastricht, The Netherlands) and a recently developed microarray test (EUROArray Dermatomycosis, Euroimmun, Lübeck, Germany) were evaluated regarding their diagnostic specificity to identify dermatophyte DNA. The tests were compared to conventional methods and sequencing. The microarray Dermatomycosis test allows the detection of 50 dermatophytes and definitive identification of 23 dermatophyte species, 6 yeasts and moulds combined in one test. In comparison, real-time PCR is able to identify 11 dermatophytes and one yeast at the species level. Using the EUROArray, 22 out of 24 dermatophyte species were correctly identified. Using real-time PCR, 9 out of the 11 different dermatophytes included in the test kit were correctly identified. Both molecular tests for detection and differentiation of dermatophytes are useful tools for daily clinical practice. The real-time PCR test does not detect as many species, and specificity is slightly lower. However, real-time PCR is a very fast and easy to perform test, especially since no post-PCR step is necessary. Real-time PCR detects the most frequent dermatophytes like T. rubrum, T. interdigitale, and M. canis without any problems. The EUROArray is more elaborate to perform in the lab, due to the hybridization step. However, the EUROArray shows higher specificity and can detect a much broader range of causative agents, including rare species, in dermatomycology.

Molecular and pathological characterization of Fusarium solani species complex infection in the head and lateral line system of Sphyrna lewini.

A severe fungal infection affecting the head and lateral line system was diagnosed in 7 captive scalloped hammerhead sharks Sphyrna lewini in an aquarium in Thailand. Extensive and severe necrotizing cellulitis was consistently observed microscopically along the cephalic and lateral line canals in conjunction with positive fungal cultures for Fusarium sp. Molecular phylogenetic analysis was performed from 3 isolates based on the nucleotide sequences containing internally transcribed spacer (ITS) and a portion of 5.8S and 28S rDNA. The fungus was highly homologous (100%) and closely related to F. solani species complex 2 (FSSC 2), which belongs to Clade 3 of the FSSC. Our results illustrate the histopathological findings and expand upon our knowledge of the prevalence of invasive fusariosis in the head and lateral line system of hammerhead sharks.

Species composition of Malassezia yeasts in dogs in Slovakia.

Malassezia (M.) pachydermatis is the lipophilic yeast, which is normally present on the skin and in the ear canal of dogs but under certain conditions it may cause dermatitis and otitis. There is less known about the occurrence of lipid-dependent Malassezia species in dogs. The aim of this study was to detect whether lipid-dependent yeasts are part of the normal microflora in dogs. Two groups of animals were selected for comparison. The group of healthy dogs contained samples of 118 individuals and the group of dogs with cutaneous lesions or otitis externa comprised 328 dogs. The isolates of Malassezia were identified by using genotypic methods that allow the precise identification. M. pachydermatis was the most frequently isolated species in this study (121 isolates). Only four isolates were identified as M. furfur and one isolate was identified as M. nana.

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov.

During a study comparing the ectomycorrhizal root communities in a native forest with those at the Arnold Arboretum in Massachusetts (USA), the European species Tuber borchii was detected on the roots of a native red oak in the arboretum over two successive years. Since T. borchii is an economically important edible truffle native to Europe, we conducted a search of other roots in the arboretum to determine the extent of colonization. We also wanted to determine whether other non-native Tuber species had been inadvertently introduced into this 140-year-old Arboretum because many trees were imported into the site with intact soil and roots prior to the 1921 USDA ban on these horticultural practices in the USA. While T. borchii was not found on other trees, seven other native and exotic Tuber species were detected. Among the North American Tuber species detected from ectomycorrhizae, we also collected ascomata of a previously unknown species described here as Tuber arnoldianum. This new species was found colonizing both native and non-native tree roots. Other ectomycorrhizal taxa that were detected included basidiomycetes in the genera Amanita, Russula, Tomentella, and ascomycetes belonging to Pachyphlodes, Helvella, Genea, and Trichophaea. We clarify the phylogenetic relationships of each of the Tuber species detected in this study, and we discuss their distribution on both native and non-native host trees.

Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard.

Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.

Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns.

Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom.

Development of a new real-time PCR system for simultaneous detection of bacteria and fungi in pathological samples.

A novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (PCR) system. This system, designated the "multi-microbial real-time PCR", has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. All probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. The specificity and sensitivity of each probe-primer set were tested against DNA extracted from pure cultures of specific pathogens. The multi-microbial real-time PCR system revealed profiles of microorganism infection in lung samples collected at autopsy from 10 patients with acquired immunodeficiency syndrome. Staphylococcus aureus was the most common microbe detected (n=8), but with low copy numbers. High copy numbers of Pseudomonas aeruginosa were detected in the lung samples with abscess (n=6). Enterococcus faecium (n=6), Elizabethkingia meningoseptica (n=4), and Candida albicans (n=4) were also frequently detected. In addition, a latent infection of Mycobacterium tuberculosis was detected in one case of pneumonia. In conclusion, this multi-microbial real-time PCR system can be useful for detecting bacteria and fungi in pathological specimens from patients with uncertain diagnoses.

Pathogenicity of a microsporidium isolate from the diamondback moth against Noctuid moths: characterization and implications for microbiological pest management.

BACKGROUND: Due to problems with chemical control, there is increasing interest in the use of microsporidia for control of lepidopteran pests. However, there have been few studies to evaluate the susceptibility of exotic species to microsporidia from indigenous Lepidoptera. METHODOLOGY/PRINCIPAL FINDINGS: We investigated some biological characteristics of the microsporidian parasite isolated from wild Plutella xylostella (PX) and evaluated its pathogenicity on the laboratory responses of sympatric invasive and resident noctuid moths. There were significant differences in spore size and morphology between PX and Spodoptera litura (SL) isolates. Spores of PX isolate were ovocylindrical, while those of SL were oval. PX spores were 1.05 times longer than those of SL, which in turn were 1.49 times wider than those of the PX. The timing of infection peaks was much shorter in SL and resulted in earlier larval death. There were no noticeable differences in amplicon size (two DNA fragments were each about 1200 base pairs in length). Phylogenetic analysis revealed that the small subunit (SSU) rRNA gene sequences of the two isolates shared a clade with Nosema/Vairimorpha sequences. The absence of octospores in infected spodopteran tissues suggested that PX and SL spores are closely related to Nosema plutellae and N. bombycis, respectively. Both SL and S. exigua (SE) exhibited susceptibility to the PX isolate infection, but showed different infection patterns. Tissular infection was more diverse in the former and resulted in much greater spore production and larval mortality. Microsporidium-infected larvae pupated among both infected and control larvae, but adult emergence occurred only in the second group. CONCLUSION/SIGNIFICANCE: The PX isolate infection prevented completion of development of most leafworm and beet armyworm larvae. The ability of the microsporidian isolate to severely infect and kill larvae of both native and introduced spodopterans makes it a valuable candidate for biocontrol against lepidopteran pests.

Batrachochytrium dendrobatidis in Germany: distribution, prevalences, and prediction of high risk areas.

In Germany, the pathogenic fungus Batrachochytrium dendrobatidis (Bd) was detected in 11 indigenous frog species, 4 newt species, and 1 salamander species in 64 out of the 181 locations (35%) investigated. Among the 3450 samples collected between 2003 and 2011, 284 (8.2%) were positive for Bd infections. The highest prevalences were observed in Alytes obstetricans (17.8% of individuals, 20% of populations), followed by Ichthyosaura alpestris (14.7%, 22.2%), Bombina variegata (13.9%, 38.5%), and water frogs comprising 2 species, Pelophylax lessonae and P. ridibundus, and their hybrid form P. esculentus (13.5%, 29.0%). Bd is widespread; areas of higher prevalence were detected in eastern, southeastern, western, and southwestern Germany. Our data indicate that drift fencing of amphibians is not a risk factor for the anthropogenic spread of Bd. Although chytridiomycosis outbreaks have never been observed in Germany, it cannot be excluded that Bd infections affect the dynamics of local amphibian populations. Among the questions still to be answered is whether juveniles are more susceptible to Bd infections than adults. Further work, especially long-term observations including capture-mark-recapture studies, is required to clarify the impact Bd has on amphibians in Germany and Central Europe.

Repeated evolution of fungal cultivar specificity in independently evolved ant-plant-fungus symbioses.

Some tropical plant species possess hollow structures (domatia) occupied by ants that protect the plant and in some cases also provide it with nutrients. Most plant-ants tend patches of chaetothyrialean fungi within domatia. In a few systems it has been shown that the ants manure the fungal patches and use them as a food source, indicating agricultural practices. However, the identity of these fungi has been investigated only in a few samples. To examine the specificity and constancy of ant-plant-fungus interactions we characterised the content of fungal patches in an extensive sampling of three ant-plant symbioses (Petalomyrmex phylax/Leonardoxa africana subsp. africana, Aphomomyrmex afer/Leonardoxa africana subsp. letouzeyi and Tetraponera aethiops/Barteria fistulosa) by sequencing the Internal Transcribed Spacers of ribosomal DNA. For each system the content of fungal patches was constant over individuals and populations. Each symbiosis was associated with a specific, dominant, primary fungal taxon, and to a lesser extent, with one or two specific secondary taxa, all of the order Chaetothyriales. A single fungal patch sometimes contained both a primary and a secondary taxon. In one system, two founding queens were found with the primary fungal taxon only, one that was shown in a previous study to be consumed preferentially. Because the different ant-plant symbioses studied have evolved independently, the high specificity and constancy we observed in the composition of the fungal patches have evolved repeatedly. Specificity and constancy also characterize other cases of agriculture by insects.

Clinical significance and molecular characterization of nonsporulating molds isolated from the respiratory tracts of bronchopulmonary mycosis patients with special reference to basidiomycetes.

Nonsporulating molds (NSMs), especially basidiomycetes, have predominantly been reported as human pathogens responsible for allergic and invasive disease. Their conventional identification is problematic, as many isolates remain sterile in culture. Thus, inconclusive culture reports might adversely affect treatment decisions. The clinical significance of NSMs in pulmonary mycoses is poorly understood. We sequenced the internal transcribed spacer (ITS) region and D1/D2 domain of the larger subunit (LSU) of 52 NSMs isolated from respiratory specimens. The basidiomycetes were the predominant NSMs, of which Schizophyllum commune was the most common agent in allergic bronchopulmonary mycosis (ABPM), followed by Ceriporia lacerata in invasive fungal disease. Porostereum spadiceum, Phanaerochaete stereoides, Neosartorya fischeri, and Marasmiellus palmivorus were the other molds observed. Application of ITS and LSU region sequencing identified 92% of the isolates. The antifungal susceptibility data revealed that all basidiomycetes tested were susceptible to amphotericin B and resistant to caspofungin, fluconazole, and flucytosine. Except for 3 isolates of S. commune and a solitary isolate of M. palmivorus, all basidiomycetes had low MICs for itraconazole, posaconazole, and voriconazole. Basidiomycetes were isolated from patients with ABPM, invasive pulmonary mycosis/pneumonia, or fungal balls. In addition, the majority of the basidiomycetes were isolated from patients with chronic respiratory disorders who were sensitized to one of the basidiomycetous fungi and demonstrated precipitating antibodies against the incriminating fungi, indicating an indolent tissue reaction. Thus, isolation of basidiomycetes from the lower respiratory tract could be significant, and it is important to monitor these patients in order to prevent subsequent lung damage.

Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum.

Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the understanding of the functions and evolution of fungal mitochondrial DNA.

Epidemiological characteristics of Malassezia folliculitis and use of the May-Grünwald-Giemsa stain to diagnose the infection.

Various bacterial, fungal, parasitic, and viral pathogens can cause folliculitis, which is often mistakenly treated with antibiotics for months or even years. A laboratory diagnosis is required before therapy can be planned. Here, we describe the prevalence and risk factors, as well as the clinical, cytological, and mycological characteristics, of patients with Malassezia folliculitis (MF) in Adana, Turkey. We also report the treatment responses of the MF patients and describe the Malassezia spp. using culture-based molecular methods. Cytological examinations were performed in 264 folliculitis patients, 49 of whom (18.5%) were diagnosed with MF. The positivity of the May-Grünwald-Giemsa (MGG) smear was higher (100%) than that of the potassium hydroxide test (81.6%). Using Wood's light, yellow-green fluorescence was observed in 66.7% of the MF patients. Identification using the rDNA internal transcribed spacer region revealed that Malassezia globosa was the most common species, followed by Malassezia sympodialis, Malassezia restricta, and Malassezia furfur. The MF patients were treated with itraconazole capsules (200 mg/d) for 2 weeks. Complete recovery was observed in 79.6% of the patients. These novel findings help improve our current understanding of the epidemiological characteristics of MF and establish MGG as a practical tool for the diagnosis of MF.

Phylogenetic structure of ectomycorrhizal fungal communities of western hemlock changes with forest age and stand type.

On Vancouver Island, British Columbia, fertilization with nitrogen (N) and phosphorus (P) following clearcutting increases growth of western hemlock. To explore whether fertilization also resulted in ectomycorrhizal fungal communities that were more or less similar to neighboring unlogged stands, we sampled roots from western hemlock from three replicate plots from each of five different, well-characterized, forest stand types that differed in site type, and in logging and fertilization history. We harvested four samples of 100 ectomycorrhizal root tips from each plot, a total of 60 samples per stand type. From each sample, we analyzed fungal ribosomal internal transcribed spacers and 28S DNA, sequencing 15-29 clones per sample and 60-116 clones per plot. We detected 147 fungal operational taxonomic units among a total of 1435 sequences. Craterellus tubaeformis was frequently present and resulted in a pattern of phylogenetic overdispersion in the fungal communities. Fungal species composition was strongly correlated with foliar nitrogen concentration. However, other site quality factors were also important because the fertilized regenerating hemlock and mature hemlock-amabilis fir forests had similar foliar nitrogen content but little overlap in fungal species. Compared with unfertilized regenerating forests, fungal communities in N + P-fertilized regenerating forests had significantly more species overlap with old growth forests. However, the fungal communities of all regenerating forest were similar to one another and all differed significantly from older forests. By correlating fungal clades with habitats, this research improves understanding of how forest management can contribute to maintaining diverse ectomycorrhizal fungal communities across a landscape.

Mobile DNA distributions refine the phylogeny of "matsutake" mushrooms, Tricholoma sect. Caligata.

"Matsutake" mushrooms are formed by several species of Tricholoma sect. Caligata distributed across the northern hemisphere. A phylogenetic analysis of matsutake based on virtually neutral mutations in DNA sequences resolved robust relationships among Tricholoma anatolicum, Tricholoma bakamatsutake, Tricholoma magnivelare, Tricholoma matsutake, and Tricholoma sp. from Mexico (=Tricholoma sp. Mex). However, relationships among these matsutake and other species, such as Tricholoma caligatum and Tricholoma fulvocastaneum, were ambiguous. We, therefore, analyzed genomic copy numbers of σ marY1 , marY1, and marY2N retrotransposons by comparing them with the single-copy mobile DNA megB1 using real-time polymerase chain reaction (PCR) to clarify matsutake phylogeny. We also examined types of megB1-associated domains, composed of a number of poly (A) and poly (T) reminiscent of RNA-derived DNA elements among these species. Both datasets resolved two distinct groups, one composed of T. bakamatsutake, T. fulvocastaneum, and T. caligatum that could have diverged earlier and the other comprising T. magnivelare, Tricholoma sp. Mex, T. anatolicum, and T. matsutake that could have evolved later. In the first group, T. caligatum was the closest to the second group, followed by T. fulvocastaneum and T. bakamatsutake. Within the second group, T. magnivelare was clearly differentiated from the other species. The data suggest that matsutake underwent substantial evolution between the first group, mostly composed of Fagaceae symbionts, and the second group, comprised only of Pinaceae symbionts, but diverged little within each groups. Mobile DNA markers could be useful in resolving difficult phylogenies due to, for example, closely spaced speciation events.

Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy.

The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.

Detection of invasive fungal pathogens by real-time PCR and high-resolution melting analysis.

BACKGROUND/AIM: Causative agents most frequently encountered in systemic infections are bacteria, although fungi that cause invasive infections have also emerged, mostly in immune-compromised patients. The early detection and adequate treatment of bloodstream infections are critical for successful treatment. The aim of this study was to develop a rapid and efficient method for the detection and differentiation of the most common fungal pathogens. MATERIALS AND METHODS: Real-time Polymerase chain reaction (PCR) and consecutive high-resolution melting analysis was used for the detection and differentiation of fungal pathogens. RESULTS: The developed analysis procedure proved appropriate for discrimination of the ten most relevant Candida species, four Aspergillus species, and Cryptococcus neoformans. The sensitivity of the PCR reaction was 5, which is suitable for the detection of these fungi in blood. CONCLUSION: This technique is not adaptable as a general identification method, but it is highly useful when certain fungal species are to be expected in clinical samples.

Preliminary insights into the phylogeography of six aquatic hyphomycete species.

Aquatic hyphomycetes occur worldwide on a wide range of plant substrates decomposing in freshwaters, and are known to play a key role in organic matter turnover. The presumed worldwide distribution of many aquatic hyphomycete species has been based on morphology-based taxonomy and identification, which may overlook cryptic species, and mask global-scale biogeographical patterns. This might be circumvented by using DNA sequence data. The internal transcribed spacer (ITS) region from rDNA was recently designated as the most suitable barcode for fungal identification. In this study, we generated ITS barcodes of 130 isolates belonging to 6 aquatic hyphomycete species (Anguillospora filiformis, Flagellospora penicillioides, Geniculospora grandis, Lunulospora curvula, Tetrachaetum elegans and Tricladium chaetocladium), and collected from streams of Southwest Europe (86 isolates) and East Australia (44 isolates). European and Australian populations of 4 species (A. filiformis, F. penicillioides, G. grandis and T. elegans) grouped into different clades, and molecular diversity indices supported significant differentiation. Continents did not share haplotypes, except for T. chaetocladium. Overall results show substantial population diversity for all tested species and suggests that the biogeography of aquatic hyphomycetes may be species-specific.