A culture-based survey of fungi in soil from bat hibernacula in the eastern United States and its implications for detection of Geomyces destructans, the causal agent of bat white-nose syndrome

Bat white-nose disease fungus diversity in time and space

White-nose disease (WND), caused by the psychrophilic fungus Pseudogymnoascusdestructans, represents one of the greatest threats for North American hibernating bats. Research on molecular data has significantly advanced our knowledge of various aspects of the disease, yet more studies are needed regarding patterns of P.destructans genetic diversity distribution. In the present study, we investigate three sites within the native range of the fungus in detail: two natural hibernacula (karst caves) in Bulgaria, south-eastern Europe and one artificial hibernaculum (disused cellar) in Germany, northern Europe, where we conducted intensive surveys between 2014 and 2019. Using 18 microsatellite and two mating type markers, we describe how P.destructans genetic diversity is distributed between and within sites, the latter including differentiation across years and seasons of sampling; across sampling locations within the site; and between bats and hibernaculum walls. We found significant genetic differentiation between hibernacula, but we could not detect any significant differentiation within hibernacula, based on the variables examined. This indicates that most of the pathogen's movement occurs within sites. Genotypic richness of P.destructans varied between sites within the same order of magnitude, being approximately two times higher in the natural caves (Bulgaria) compared to the disused cellar (Germany). Within all sites, the pathogen's genotypic richness was higher in samples collected from hibernaculum walls than in samples collected from bats, which corresponds with the hypothesis that hibernacula walls represent the environmental reservoir of the fungus. Multiple pathogen genotypes were commonly isolated from a single bat (i.e. from the same swab sample) in all study sites, which might be important to consider when studying disease progression.

Eight novel cave fungi in Thailand's Satun Geopark

Karst caves are unique oligotrophic ecosystems characterised by the scarcity of organic litter, darkness, low to moderate temperatures, and high humidity, supporting diverse fungal communities. Despite their importance, little is known about the fungi in karst caves in Thailand. In 2019, we explored the culturable mycobiota associated with three selected types of substrates (air, soil/sediment and organic litter samples) from two karst caves, the Le Stegodon and Phu Pha Phet Caves, in the Satun UNESCO Global Geopark in southern Thailand. Based on morphological characters and multilocus phylogenetic analyses, eight new species (Actinomortierella caverna, Hypoxylon phuphaphetense, Leptobacillium latisporum, Malbranchea phuphaphetensis, Scedosporium satunense, Sesquicillium cavernum, Thelonectria satunensis and Umbelopsis satunensis) were described, illustrated, and compared to closely related species. These new fungal taxa form independent lineages distinct from other previously described species and classified into eight different families across six orders and two phyla (Ascomycota and Mucoromycota). This paper provides additional evidence that the karst caves located within the Satun UNESCO Global Geopark, situated in the southern region of Thailand, harbour a diverse range of newly discovered species. Citation: Preedanon S, Suetrong S, Srihom C, Somrithipol S, Kobmoo N, Saengkaewsuk S, Srikitikulchai P, Klaysuban A, Nuankaew S, Chuaseeharonnachai C, Chainuwong B, Muangsong C, Zhang ZF, Cai L, Boonyuen N (2023). Eight novel cave fungi in Thailand's Satun Geopark. Fungal Systematics and Evolution 12: 1-30. doi: 10.3114/fuse.2023.12.01.

DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic

Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.

Environmental transmission of Pseudogymnoascus destructans to hibernating little brown bats

Pathogens with persistent environmental stages can have devastating effects on wildlife communities. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in bat populations of North America. In 2009, during the early stages of the WNS investigation and before molecular techniques had been developed to readily detect P. destructans in environmental samples, we initiated this study to assess whether P. destructans can persist in the hibernaculum environment in the absence of its conclusive bat host and cause infections in naive bats. We transferred little brown bats (Myotis lucifugus) from an unaffected winter colony in northwest Wisconsin to two P. destructans contaminated hibernacula in Vermont where native bats had been excluded. Infection with P. destructans was apparent on some bats within 8 weeks following the introduction of unexposed bats to these environments, and mortality from WNS was confirmed by histopathology at both sites 14 weeks following introduction. These results indicate that environmental exposure to P. destructans is sufficient to cause the infection and mortality associated with WNS in naive bats, which increases the probability of winter colony extirpation and complicates conservation efforts.

Development and Application of Loop-Mediated Isothermal Amplification (LAMP) Assays for Rapid Diagnosis of the Bat White-Nose Disease Fungus Pseudogymnoascus destructans

Pseudogymnoascus destructans (= Geomyces destructans) is a psychrophilic filamentous fungus that causes White-Nose Disease (WND; the disease associated with White-Nose Syndrome, WNS) in hibernating bats. The disease has caused considerable reductions in bat populations in the USA and Canada since 2006. Identification and detection of the pathogen in pure cultures and environmental samples is routinely based on qPCR or PCR after DNA isolation and purification. Rapid and specific direct detection of the fungus in the field would strongly improve prompt surveillance, and support control measures. Based on the genes coding for ATP citrate lyase1 (acl1) and the 28S-18S ribosomal RNA intergenic spacer (IGS) in P. destructans, two independent LAMP assays were developed for the rapid and sensitive diagnosis of the fungus. Both assays could discriminate P. destructans from 159 tested species of filamentous fungi and yeasts. Sensitivity of the assays was 2.1 picogram per reaction (pg/rxn) and 21 femtogram per reaction (fg/rxn) for the acl1 and IGS based assays, respectively. Moreover, both assays also work with spores and mycelia of P. destructans that are directly added to the master mix without prior DNA extraction. For field-diagnostics, we developed and tested a field-applicable version of the IGS-based LAMP assay. Lastly, we also developed a protocol for preparation of fungal spores and mycelia from swabs and tape liftings of contaminated surfaces or infected bats. This protocol in combination with the highly sensitive IGS-based LAMP-assay enabled sensitive detection of P. destructans from various sources.

Multifaceted DNA metabarcoding of guano to uncover multiple classes of ecological data in two different bat communities

DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next-generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed-species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White-nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto- and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain.

Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region

We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.

Description of the First Four Species of the Genus Pseudogymnoascus From Antarctica

The genus Pseudogymnoascus represents a diverse group of fungi widely distributed in different cold regions on Earth. Our current knowledge of the species of Pseudogymnoascus is still very limited. Currently, there are only 15 accepted species of Pseudogymnoascus that have been isolated from different environments in the Northern Hemisphere. In contrast, species of Pseudogymnoascus from the Southern Hemisphere have not yet been described. In this work, we characterized four fungal strains obtained from Antarctic marine sponges. Based on multilocus phylogenetic analyses and morphological characterizations we determined that these strains are new species, for which the names Pseudogymnoascus antarcticus sp. nov., Pseudogymnoascus australis sp. nov., Pseudogymnoascus griseus sp. nov., and Pseudogymnoascus lanuginosus sp. nov. are proposed. Phylogenetic analyses indicate that the new species form distinct lineages separated from other species of Pseudogymnoascus with strong support. The new species do not form sexual structures and differ from the currently known species mainly in the shape and size of their conidia, the presence of chains of arthroconidia, and the appearance of their colonies. This is the first report of new species of Pseudogymnoascus not only from Antarctica but also from the Southern Hemisphere.

Inopinatum lactosum gen. & comb. nov., the first yeast-like fungus in Leotiomycetes

Sporobolomyces lactosus is a pink yeast-like fungus that is not congeneric with other members of Sporobolomyces (Basidiomycota, Microbotryomycetes, Sporidiobolales). During our ongoing studies of pink yeasts we determined that S. lactosus was most closely related to Pseudeurotium zonatum (Ascomycota, Leotiomycetes, Thelebolales). A molecular phylogenetic analysis using sequences of the ITS region and the small and large subunit (SSU, LSU) rRNA genes, indicated that four isolates of S. lactosus, including three ex-type isolates, were placed in Thelebolales with maximum support. A new genus is proposed to accommodate S. lactosus, Inopinatum. This is the first pink yeast reported in Leotiomycetes.

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding

We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.

DNA Metabarcoding to Assess the Diversity of Airborne Fungi Present over Keller Peninsula, King George Island, Antarctica

We assessed fungal diversity present in air samples obtained from King George Island, Antarctica, using DNA metabarcoding through high-throughput sequencing. We detected 186 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, and Chytridiomycota. Fungi sp. 1, Agaricomycetes sp. 1, Mortierella parvispora, Mortierella sp. 2, Penicillium sp., Pseudogymnoascus roseus, Microdochium lycopodinum, Mortierella gamsii, Arrhenia sp., Cladosporium sp., Mortierella fimbricystis, Moniliella pollinis, Omphalina sp., Mortierella antarctica, and Pseudogymnoascus appendiculatus were the most dominant ASVs. In addition, several ASVs could only be identified at higher taxonomic levels and may represent previously unknown fungi and/or new records for Antarctica. The fungi detected in the air displayed high indices of diversity, richness, and dominance. The airborne fungal diversity included saprophytic, mutualistic, and plant and animal opportunistic pathogenic taxa. The diversity of taxa detected reinforces the hypothesis that the Antarctic airspora includes fungal propagules of both intra- and inter-continental origin. If regional Antarctic environmental conditions ameliorate further in concert with climate warming, these fungi might be able to reactivate and colonize different Antarctic ecosystems, with as yet unknown consequences for ecosystem function in Antarctica. Further aeromycological studies are necessary to understand how and from where these fungi arrive and move within Antarctica and if environmental changes will encourage the development of non-native fungal species in Antarctica.

Laboratory Maintenance and Culture of Pseudogymnoascus destructans, the Fungus That Causes Bat White-Nose Syndrome

Pseudogymnoascus destructans is a fungal pathogen that causes white-nose syndrome, an emerging and fatal disease of North American bats that has led to unprecedented population declines. As a psychrophile, P. destructans is adapted to infect bats during winter hibernation, when host metabolic activity and core body temperature are greatly reduced. The ability to maintain and cultivate isolates of P. destructans in the laboratory is necessary for conducting research with this fungus. This article describes protocols for culturing P. destructans from bat wing skin and soil, for cryopreserving the fungus, and for preparing liquid suspensions for laboratory experimentation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Isolating Pseudogymnoascus destructans from bat wing skin Basic Protocol 2: Isolating Pseudogymnoascus destructans from soil Basic Protocol 3: Cryopreservation of Pseudogymnoascus destructans Basic Protocol 4: Preparing liquid conidial suspension of Pseudogymnoascus destructans.

Ten-year projection of white-nose syndrome disease dynamics at the southern leading-edge of infection in North America

Predicting the emergence and spread of infectious diseases is critical for the effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary by geography. Environmental conditions in the southern part of the continent are different than the northeast, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modelled WNS pathogen spread in Texas based on cave densities and average dispersal distances of hosts, projecting these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on bat populations with observed cave environmental data. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation and highlight the importance of understanding host, pathogen and environmental conditions across a breadth of environments.

Diversity of fungal DNA in lake sediments on Vega Island, north-east Antarctic Peninsula assessed using DNA metabarcoding

We assessed the diversity of fungal DNA present in sediments of three lakes on Vega Island, north-east Antarctic Peninsula using metabarcoding through high-throughput sequencing (HTS). A total of 640,902 fungal DNA reads were detected, which were assigned to 224 taxa of the phyla Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota and Mortierellomycota, in rank order of abundance. The most abundant genera were Pseudogymnoascus, Penicillium and Mortierella. However, a majority (423,508, 66%) of the reads, representing by 43 ASVs, could only be assigned at higher taxonomic levels and may represent taxa not currently included in the sequence databases used or be new or previously unreported taxa present in Antarctic lakes. The three lakes were characterized by high sequence diversity, richness, and moderate dominance indices. The ASVs were dominated by psychrotolerant and cosmopolitan cold-adapted Ascomycota, Basidiomycota and Mortierellomycota commonly reported in Antarctic environments. However, other taxa detected included unidentified members of Rozellomycota and Chytridiomycota species not previously reported in Antarctic lakes. The assigned diversity was composed mainly of taxa recognized as decomposers and pathogens of plants and invertebrates.

Skin fungal assemblages of bats vary based on susceptibility to white-nose syndrome

Microbial skin assemblages, including fungal communities, can influence host resistance to infectious diseases. The diversity-invasibility hypothesis predicts that high-diversity communities are less easily invaded than species-poor communities, and thus diverse microbial communities may prevent pathogens from colonizing a host. To explore the hypothesis that host fungal communities mediate resistance to infection by fungal pathogens, we investigated characteristics of bat skin fungal communities as they relate to susceptibility to the emerging disease white-nose syndrome (WNS). Using a culture-based approach, we compared skin fungal assemblage characteristics of 10 bat species that differ in susceptibility to WNS across 10 eastern U.S. states. The fungal assemblages on WNS-susceptible bat species had significantly lower alpha diversity and abundance compared to WNS-resistant species. Overall fungal assemblage structure did not vary based on WNS-susceptibility, but several yeast species were differentially abundant on WNS-resistant bat species. One yeast species inhibited Pseudogymnoascus destructans (Pd), the causative agent on WNS, in vitro under certain conditions, suggesting a possible role in host protection. Further exploration of interactions between Pd and constituents of skin fungal assemblages may prove useful for predicting susceptibility of bat populations to WNS and for developing effective mitigation strategies.

Hibernacula microclimate and declines in overwintering bats during an outbreak of white-nose syndrome near the northern range limit of infection in North America

We document white-nose syndrome (WNS), a lethal disease of bats caused by the fungus Pseudogymnoascus destructans (Pd), and hibernacula microclimate in New Brunswick, Canada. Our study area represents a more northern region than is common for hibernacula microclimate investigations, providing insight as to how WNS may impact bats at higher latitudes. To determine the impact of the March 2011 arrival of Pd in New Brunswick and the role of hibernacula microclimate on overwintering bat mortality, we surveyed bat numbers at hibernacula twice a year from 2009 to 2015. We also collected data from iButton temperature loggers deployed at all sites and data from HOBO temperature and humidity loggers at three sites. Bat species found in New Brunswick hibernacula include Myotis lucifugus (Little Brown Bat) and M. septentrionalis (Northern Long-eared Bat), with small numbers of Perimyotis subflavus (Tricolored Bat). All known hibernacula in the province were Pd-positive with WNS-positive bats by winter 2013. A 99% decrease in the overwintering bat population in New Brunswick was observed between 2011 and 2015. We did not observe P. subflavus during surveys 2013-2015 and the species appears to be extirpated from these sites. Bats did not appear to choose hibernacula based on winter temperatures, but dark zone (zone where no light penetrates) winter temperatures did not differ among our study sites. Winter dark zone temperatures were warmer and less variable than entrance or above ground temperatures. We observed visible Pd growth on hibernating bats in New Brunswick during early winter surveys (November), even though hibernacula temperatures were colder than optimum for in vitro Pd growth. This suggests that cold hibernacula temperatures encountered near the apparent northern range limit for Pd do not sufficiently slow fungal growth to prevent the onset of WNS and associated bat mortality over the winter.

Pseudogymnoascus destructans growth in wood, soil and guano substrates

Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.

Fungal Planet description sheets: 1112-1181

Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum.China, Colletotrichum cycadis on leaves of Cycas revoluta.Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens.Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora.Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis.Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis.Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber.Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.

DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica

We assessed soil fungal diversity at two sites on Deception Island, South Shetland Islands, Antarctica using DNA metabarcoding analysis. The first site was a relatively undisturbed area, and the second was much more heavily impacted by research and tourism. We detected 346 fungal amplicon sequence variants dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota. We also detected taxa belonging to the rare phyla Mucoromycota and Rozellomycota, which have been difficult to detect in Antarctica by traditional isolation methods. Cladosporium sp., Pseudogymnoascus roseus, Leotiomycetes sp. 2, Penicillium sp., Mortierella sp. 1, Mortierella sp. 2, Pseudogymnoascus appendiculatus and Pseudogymnoascus sp. were the most dominant fungi. In addition, 440,153 of the total of 1,214,875 reads detected could be classified only at the level of Fungi. In both sampling areas the DNA of opportunistic, phytopathogenic and symbiotic fungi were detected, which might have been introduced by human activities, transported by birds or wind, and/or represent resident fungi not previously reported from Antarctica. Further long-term studies are required to elucidate how biological colonization in the island may be affected by climatic changes and/or other anthropogenic influences.

DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

We assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

Living in the dark: Bat caves as hotspots of fungal diversity

Bat caves are very special roosts that harbour thousands of bats of one or more species. Such sites may hold an incredible “dark fungal diversity” which is still underestimated. We explored the culturable fungal richness in the air, on bats, and in the guano in a bat cave in Brazil’s Caatinga dry forest. Fungal abundance was 683 colony-forming units (CFU) in the guano, 673 CFU in the air, and 105 CFU on the bats. Based on morphological and phylogenetic analysis of ITS, LSU, and TUB2 sequences, fungal isolates of 59 taxa belonging to 37 genera in the phyla Ascomycota (28 genera, including Aspergillus, Penicillium, Cladosporium, and Talaromyces), Basidiomycota (eight genera, including Rhodotorula and Schizophyllum), and Mucoromycota (only Rhizopus) were identified. The fungal richness in the air was 23 taxa (especially Aspergillus taxa), mainly found at 15 m and 45 m from the cave entrance; on the bodies of bats it was 36 taxa (mainly Aspergillus taxa), especially on their wing membranes (21 taxa, nine of which were exclusively found in this microhabitat); and in guano 10 fungal taxa (especially Aspergillus and Penicillium) were found. The fungal richness associated with guano (fresh and non-fresh) was similar from bats with different eating habits (insectivorous, frugivorous, and haematophagous). Sampling effort was not sufficient to reveal the total fungal taxa richness estimated. Eight (21.6%) of the 37 genera and 17 (53.1%) of the 32 identified fungal species are reported for the first time in caves. Our results highlight bat caves in Brazil as hotspots of fungal diversity, emphasizing the need to protect such special roosts.

Comparative eco-physiology revealed extensive enzymatic curtailment, lipases production and strong conidial resilience of the bat pathogenic fungus Pseudogymnoascus destructans

The genus Pseudogymnoascus encompasses soil psychrophilic fungi living also in caves. Some are opportunistic pathogens; nevertheless, they do not cause outbreaks. Pseudogymnoascus destructans is the causative agent of the white-nose syndrome, which is decimating cave-hibernating bats. We used comparative eco-physiology to contrast the enzymatic potential and conidial resilience of P. destructans with that of phylogenetically diverse cave fungi, including Pseudogymnoascus spp., dermatophytes and outdoor saprotrophs. Enzymatic potential was assessed by Biolog MicroArray and by growth on labelled substrates and conidial viability was detected by flow cytometry. Pseudogymnoascus destructans was specific by extensive losses of metabolic variability and by ability of lipid degradation. We suppose that lipases are important enzymes allowing fungal hyphae to digest and invade the skin. Pseudogymnoascus destructans prefers nitrogenous substrates occurring in bat skin and lipids. Additionally, P. destructans alkalizes growth medium, which points to another possible virulence mechanism. Temperature above 30 °C substantially decreases conidial viability of cave fungi including P. destructans. Nevertheless, survival of P. destructans conidia prolongs by the temperature regime simulating beginning of the flight season, what suggests that conidia could persist on the body surface of bats and contribute to disease spreading during bats active season.

A common partitivirus infection in United States and Czech Republic isolates of bat white-nose syndrome fungal pathogen Pseudogymnoascus destructans

The psychrophilic (cold-loving) fungus Pseudogymnoascus destructans was discovered more than a decade ago to be the pathogen responsible for white-nose syndrome, an emerging disease of North American bats causing unprecedented population declines. The same species of fungus is found in Europe but without associated mortality in bats. We found P. destructans was infected with a mycovirus [named Pseudogymnoascus destructans partitivirus 1 (PdPV-1)]. The virus is bipartite, containing two double-stranded RNA (dsRNA) segments designated as dsRNA1 and dsRNA2. The cDNA sequences revealed that dsRNA1 dsRNA is 1,683 bp in length with an open reading frame (ORF) that encodes 539 amino acids (molecular mass of 62.7 kDa); dsRNA2 dsRNA is 1,524 bp in length with an ORF that encodes 434 amino acids (molecular mass of 46.9 kDa). The dsRNA1 ORF contains motifs representative of RNA-dependent RNA polymerase (RdRp), whereas the dsRNA2 ORF sequence showed homology with the putative capsid proteins (CPs) of mycoviruses. Phylogenetic analyses with PdPV-1 RdRp and CP sequences indicated that both segments constitute the genome of a novel virus in the family Partitiviridae. The purified virions were isometric with an estimated diameter of 33 nm. Reverse transcription PCR (RT-PCR) and sequencing revealed that all US isolates and a subset of Czech Republic isolates of P. destructans were infected with PdPV-1. However, PdPV-1 appears to be not widely dispersed in the fungal genus Pseudogymnoascus, as non-pathogenic fungi P. appendiculatus (1 isolate) and P. roseus (6 isolates) tested negative. P. destructans PdPV-1 could be a valuable tool to investigate fungal biogeography and the host-pathogen interactions in bat WNS.

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island)

Glacial retreat is one of the most conspicuous signs of warming in Antarctic regions. Glacier soils harbor an active microbial community of decomposers, and under the continuous retraction of glaciers, the soil starts to present a gradient of physical, chemical, and biological factors reflecting regional changes over time. Little is known about the biological nature of fungi in Antarctic glacier soils. In this sense, this work aimed at studying the behavior of fungal community structure from samples of glacier soil collected after glacial retreat (Collins Glacier). A total of 309 fungi distributed in 19 genera were obtained from eleven soil samples. Representatives of the genera Pseudogymnoascus (Ascomycota) and Mortierella (Mortierellomycota) were the most abundant isolates in all samples. The data revealed the presence of filamentous fungi belonging to the phylum Basidiomycota, rarely found in Antarctica. Analysis of the generalized linear models revealed that the distance from the glacier as well as phosphorus and clay were able to modify the distribution of fungal species. Environmental variations proved to have influenced the genera Pseudogymnoascus and Pseudeutorium.

Diverse subterranean fungi of an underground iron ore mine

Mines and caves are unusual ecosystems containing unique fungi and are greatly understudied compared to other environments. The Soudan Mine in Tower, MN, an iron ore mine that closed in 1963 after operating for 80 years, was sampled to explore fungal diversity and to investigate taxa that tolerate heavy metals for potential bioprocessing technologies or as sources of bioactive molecules for drug discovery and possible biocontrol for white-nose syndrome (WNS) of bats. The mine is 714 m deep, has 18 levels and contains large quantities of wooden timbers, in contrast to many other oligotrophic subterranean environments. Fungi were cultured from samples and the ITS region was sequenced for identification and phylogenetic analysis. Results show Ascomycota are the dominant fungi followed by Basidiomycota and Mucoromycota. Out of 164 identified taxa, 108 belong to the Ascomycota and 26 and 31 to Basidiomycota and Mucoromycota, respectively. There are also 46 taxa that do not match (<97% BLAST GenBank identity) sequenced fungal species. Examples of the most commonly isolated Ascomycota include Scytalidium sp., Mariannaea comptospora, Hypocrea pachybasidioides, Oidiodendron griseum and Pochonia bulbillosa; Basidiomycota include Postia sp., Sistotrema brinkmannii, Calocera sp., Amylocorticiellum sp.; Mucoromycota include Mortierella parvispora, M. gamsii, M. hyaline, M. basiparvispora and Mortierella sp. Unusual growth forms were also found including large quantities of black rhizomorphs of Armillaria sinapina and white mycelial cords of Postia sp. mycelium, as well as Pseudogymnoascus species growing over large areas of mine walls and ceiling. The mine environment is a relatively extreme environment for fungi, with the presence of high levels of heavy metals, complete darkness and poor nutrient availability. Several genera are similar to those isolated in other extreme environments but phylogenetic analyses show differences in species between these environments. Results indicate this subterranean environment hosts a wide diversity of fungi, many of them not found in above ground environments.

Volatile organic compounds kill the white-nose syndrome fungus, Pseudogymnoascus destructans, in hibernaculum sediment

Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome, has killed millions of bats across eastern North America and continues to threaten new bat populations. The spread and persistence of P. destructans has likely been worsened by the ability of this fungus to grow as a saprotroph in the hibernaculum environment. Reducing the environmental growth of P. destructans may improve bat survival. Volatile organic compounds (VOCs) are attractive candidates to target environmental P. destructans, as they can permeate through textured environments that may be difficult to thoroughly contact with other control mechanisms. We tested in hibernaculum sediment the performance of VOCs that were previously shown to inhibit P. destructans growth in agar cultures and examined the inhibition kinetics and specificity of these compounds. Three VOCs, 2-methyl-1-butanol, 2-methyl-1-propanol, and 1-pentanol, were fungicidal towards P. destructans in hibernaculum sediment, fast-acting, and had greater effects against P. destructans than other Pseudogymnoascus species. Our results suggest that use of these VOCs may be considered further as an effective management strategy to reduce the environmental exposure of bats to P. destructans in hibernacula.

Validation of laboratory tests for infectious diseases in wild mammals: review and recommendations

Evaluation of the diagnostic sensitivity (DSe) and specificity (DSp) of tests for infectious diseases in wild animals is challenging, and some of the limitations may affect compliance with the OIE-recommended test validation pathway. We conducted a methodologic review of test validation studies for OIE-listed diseases in wild mammals published between 2008 and 2017 and focused on study design, statistical analysis, and reporting of results. Most published papers addressed Mycobacterium bovis infection in one or more wildlife species. Our review revealed limitations or missing information about sampled animals, identification criteria for positive and negative samples (case definition), representativeness of source and target populations, and species in the study, as well as information identifying animals sampled for calculations of DSe and DSp as naturally infected captive, free-ranging, or experimentally challenged animals. The deficiencies may have reflected omissions in reporting rather than design flaws, although lack of random sampling might have induced bias in estimates of DSe and DSp. We used case studies of validation of tests for hemorrhagic diseases in deer and white-nose syndrome in hibernating bats to demonstrate approaches for validation when new pathogen serotypes or genotypes are detected and diagnostic algorithms are changed, and how purposes of tests evolve together with the evolution of the pathogen after identification. We describe potential benefits of experimental challenge studies for obtaining DSe and DSp estimates, methods to maintain sample integrity, and Bayesian latent class models for statistical analysis. We make recommendations for improvements in future studies of detection test accuracy in wild mammals.

Diversity, distribution, and ecology of viable fungi in permafrost and active layer of Maritime Antarctica

We evaluated the diversity and distribution of viable fungi present in permafrost and active layers obtained from three islands of Maritime Antarctica. A total of 213 fungal isolates were recovered from the permafrost, and 351 from the active layer, which were identified in 58 taxa; 27 from permafrost and 31 from the active layer. Oidiodendron, Penicillium, and Pseudogymnoascus taxa were the most abundant in permafrost. Bionectriaceae, Helotiales, Mortierellaceae, and Pseudeurotium were the most abundant in the active layer. Only five shared both substrates. The yeast Mrakia blollopis represented is the first reported on Antarctic permafrost. The fungal diversity detected was moderate to high, and composed of cosmopolitan, cold-adapted, and endemic taxa, reported as saprobic, mutualistic, and parasitic species. Our results demonstrate that permafrost shelters viable fungi across the Maritime Antarctica, and that they are contrasting to the overlying active layer. We detected important fungal taxa represented by potential new species, particularly, those genetically close to Pseudogymnoascus destructans, which can cause extinction of bats in North America and Eurasia. The detection of viable fungi trapped in permafrost deserves further studies on the extension of its fungal diversity and its capability to expand from permafrost to other habitats in Antarctica, and elsewhere.

Antifungal Norditerpene Oidiolactones from the Fungus Oidiodendron truncatum, a Potential Biocontrol Agent for White-Nose Syndrome in Bats

White-nose syndrome (WNS) is a devastating disease of hibernating bats caused by the fungus Pseudogymnoascus destructans. We obtained 383 fungal and bacterial isolates from the Soudan Iron Mine, an important bat hibernaculum in Minnesota, then screened this library for antifungal activity to develop biological control treatments for WNS. An extract from the fungus Oidiodendron truncatum was subjected to bioassay-guided fractionation, which led to the isolation of 14 norditerpene and three anthraquinone metabolites. Ten of these compounds were previously described in the literature, and here we present the structures of seven new norditerpene analogues. Additionally, this is the first report of 4-chlorophyscion from a natural source, previously identified as a semisynthetic product. The compounds PR 1388 and LL-Z1271α were the only inhibitors of P. destructans (MIC = 7.5 and 15 μg/mL, respectively). Compounds were tested for cytotoxicity against fibroblast cell cultures obtained from Myotis septentrionalis (northern long eared bat) and M. grisescens (gray bat) using a standard MTT viability assay. The most active antifungal compound, PR 1388, was nontoxic toward cells from both bat species (IC₅₀ > 100 μM). We discuss the implications of these results in the context of the challenges and logistics of developing a substrate treatment or prophylactic for WNS.

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: Marthamycetales ord. nov., and Drepanopezizaceae and Mniaeciaceae fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.

Diversity and distribution of hidden cultivable fungi associated with marine animals of Antarctica

In the present study, we surveyed the distribution and diversity of fungal assemblages associated with 10 species of marine animals from Antarctica. The collections yielded 83 taxa from 27 distinct genera, which were identified using molecular biology methods. The most abundant taxa were Cladosporium sp. 1, Debaryomyces hansenii, Glaciozyma martinii, Metschnikowia australis, Pseudogymnoascus destructans, Thelebolus cf. globosus, Pseudogymnoascus pannorum, Tolypocladium tundrense, Metschnikowia australis, and different Penicillium species. The diversity, richness, and dominance of fungal assemblages ranged among the host; however, in general, the fungal community, which was composed of endemic and cold-adapted cosmopolitan taxa distributed across the different sites of Antarctic Peninsula, displayed high diversity, richness, and dominance indices. Our results contribute to knowledge about fungal diversity in the marine environment across the Antarctic Peninsula and their phylogenetic relationships with species that occur in other cold, temperate, and tropical regions of the World. Additionally, despite their extreme habitats, marine Antarctic animals shelter cryptic and complex fungal assemblages represented by endemic and cosmopolitan cold-adapted taxa, which may represent interesting models to study different symbiotic associations between fungi and their animal hosts in the extreme conditions of Antarctica.

Modeling R₀ for Pathogens with Environmental Transmission: Animal Movements, Pathogen Populations, and Local Infectious Zones

How a disease is transmitted affects our ability to determine R₀, the average number of new cases caused by an infectious host at the onset of an epidemic. R₀ becomes progressively more difficult to compute as transmission varies from directly transmitted diseases to diseases that are vector-borne to environmentally transmitted diseases. Pathogens responsible for diseases with environmental transmission are typically maintained in environmental reservoirs that exhibit a complex spatial distribution of local infectious zones (LIZs). Understanding host encounters with LIZs and pathogen persistence within LIZs is required for an accurate R₀ and modeling these contacts requires an integrated geospatial and dynamical systems approach. Here we review how interactions between host and pathogen populations and environmental reservoirs are driven by landscape-level variables, and synthesize the quantitative framework needed to formulate outbreak response and disease control.

Two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in southern Australia have diverse fungal skin flora but not Pseudogymnoascus destructans

Fungi are increasingly being documented as causing disease in a wide range of faunal species, including Pseudogymnoascus destructans, the fungus responsible for white nose syndrome which is having a devastating impact on bats in North America. The population size of the Australian southern bent-winged bat (Miniopterus orianae bassanii), a critically endangered subspecies, has declined over the past 50 years. As part of a larger study to determine whether disease could be a contributing factor to this decline, southern bent-winged bats were tested for the presence of a range of potentially pathogenic fungi: P. destructans, dermatophytes and Histoplasma capsulatum (a potential human pathogen commonly associated with caves inhabited by bats). Results were compared with those obtained for the more common eastern bent-winged bat (M. orianae oceanensis). All bats and their environment were negative for P. destructans. A large number of fungi were found on the skin and fur of bats, most of which were environmental or plant associated, and none of which were likely to be of significant pathogenicity for bats. A 0–19% prevalence of H. capsulatum was detected in the bat populations sampled, but not in the environment, indicative of a low zoonotic risk. Based on the results of this study, fungi are unlikely to be contributing significantly to the population decline of the southern bent-winged bat.

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites

Molecular biology techniques were used to identify 218 fungi from soil samples collected from four islands of Antarctica. These consisted of 22 taxa of 15 different genera belonging to the Zygomycota, Ascomycota, and Basidiomycota. Mortierella, Antarctomyces, Pseudogymnoascus, and Penicillium were the most frequently isolated genera and Penicillium tardochrysogenum, Penicillium verrucosus, Goffeauzyma gilvescens, and Mortierella sp. 2 the most abundant taxa. All fungal isolates were cultivated using solid-state fermentation to obtain their crude extracts. Pseudogymnoascus destructans, Mortierella parvispora, and Penicillium chrysogenum displayed antiparasitic activities, whilst extracts of P. destructans, Mortierella amoeboidea, Mortierella sp. 3, and P. tardochrysogenum showed herbicidal activities. Reported as pathogenic for bats, different isolates of P. destructans exhibited trypanocidal activities and herbicidal activity, and may be a source of bioactive molecules to be considered for chemotherapy against neglected tropical diseases. The abundant presence of P. destructans in soils of the four islands gives evidence supporting that soils in the Antarctic Peninsula constitute a natural source of strains of this genus, including some P. destructans strains that are phylogenetically close to those that infect bats in North America and Europe/Palearctic Asia.

Determinants of Pseudogymnoascus destructans within bat hibernacula: implications for surveillance and management of white-nose syndrome

1. Fungal diseases are an emerging global problem affecting human health, food security and biodiversity. Ability of many fungal pathogens to persist within environmental reservoirs can increase extinction risks for host species and presents challenges for disease control. Understanding factors that regulate pathogen spread and persistence in these reservoirs is critical for effective disease management. 2. White-nose syndrome (WNS) is a disease of hibernating bats caused by Pseudogymnoascus destructans (Pd), a fungus that establishes persistent environmental reservoirs within bat hibernacula, which contribute to seasonal disease transmission dynamics in bats. However, host and environmental factors influencing distribution of Pd within these reservoirs are unknown. 3. We used model selection on longitudinally collected field data to test multiple hypotheses describing presence-absence and abundance of Pd in environmental substrates and on bats within hibernacula at different stages of WNS. 4. First detection of Pd in the environment lagged up to one year after first detection on bats within that hibernaculum. Once detected, the probability of detecting Pd within environmental samples from a hibernaculum increased over time and was higher in sediment compared to wall surfaces. Temperature had marginal effects on the distribution of Pd. For bats, prevalence and abundance of Pd were highest on Myotis lucifugus and on bats with visible signs of WNS. 5. Synthesis and applications. Our results indicate that distribution of Pseudogymnoascus destructans (Pd) within a hibernaculum is driven primarily by bats with delayed establishment of environmental reservoirs. Thus, collection of samples from Myotis lucifugus, or from sediment if bats cannot be sampled, should be prioritized to improve detection probabilities for Pd surveillance. Long-term persistence of Pd in sediment suggests that disease management for white-nose syndrome should address risks of sustained transmission from environmental reservoirs.

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats

Bat white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, has decimated North American hibernating bats since its emergence in 2006. Here, we utilize comparative genomics to examine the evolutionary history of this pathogen in comparison to six closely related nonpathogenic species. P. destructans displays a large reduction in carbohydrate-utilizing enzymes (CAZymes) and in the predicted secretome (~50%), and an increase in lineage-specific genes. The pathogen has lost a key enzyme, UVE1, in the alternate excision repair (AER) pathway, which is known to contribute to repair of DNA lesions induced by ultraviolet (UV) light. Consistent with a nonfunctional AER pathway, P. destructans is extremely sensitive to UV light, as well as the DNA alkylating agent methyl methanesulfonate (MMS). The differential susceptibility of P. destructans to UV light in comparison to other hibernacula-inhabiting fungi represents a potential “Achilles’ heel” of P. destructans that might be exploited for treatment of bats with WNS.

White-nose syndrome, caused by the fungus Pseudogymnoascus destructans, is decimating North American bats. Here, Palmer et al. use comparative genomics to examine the evolutionary history of this pathogen, and show that it has lost a crucial DNA repair enzyme and is extremely sensitive to UV light.

Resistance in persisting bat populations after white-nose syndrome invasion

Increases in anthropogenic movement have led to a rise in pathogen introductions and the emergence of infectious diseases in naive host communities worldwide. We combined empirical data and mathematical models to examine changes in disease dynamics in little brown bat (Myotis lucifugus) populations following the introduction of the emerging fungal pathogen Pseudogymnoascus destructans, which causes the disease white-nose syndrome. We found that infection intensity was much lower in persisting populations than in declining populations where the fungus has recently invaded. Fitted models indicate that this is most consistent with a reduction in the growth rate of the pathogen when fungal loads become high. The data are inconsistent with the evolution of tolerance or an overall reduced pathogen growth rate that might be caused by environmental factors. The existence of resistance in some persisting populations of little brown bats offers a glimmer of hope that a precipitously declining species will persist in the face of this deadly pathogen.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Resource capture and competitive ability of non-pathogenic Pseudogymnoascus spp. and P. destructans, the cause of white-nose syndrome in bats

White-nose syndrome (WNS) is a devastating fungal disease that has been causing the mass mortality of hibernating bats in North America since 2006 and is caused by the psychrophilic dermatophyte Pseudogymnoascus destructans. Infected bats shed conidia into hibernaculum sediments and surfaces, but it is unknown if P. destructans can form stable, reproductive populations outside its bat hosts. Previous studies have found non-pathogenic Pseudogymnoascus in bat hibernacula, and these fungi may provide insight into the natural history of P. destructans. We compared the relatedness, resource capture, and competitive ability of non-pathogenic Pseudogymnoascus isolates with P. destructans to determine if they have similar adaptations for survival in hibernacula sediment. All non-pathogenic Pseudogymnoascus isolates grew faster, utilized a broader range of substrates with higher efficiency, and were generally more resistant to antifungals compared to P. destructans. All isolates also showed the ability to displace P. destructans in co-culture assays, but only some produced extractible antifungal metabolites. These results suggest that P. destructans would perform poorly in the same environmental niche as non-pathogenic Pseudogymnoascus, and must have an alternative saprophytic survival strategy if it establishes active populations in hibernaculum sediment and non-host surfaces.

DIVERSITY OF THE TYPE 1 INTRON-ITS REGION OF THE 18S rRNA GENE IN PSEUDOGYMNOASCUS SPECIES FROM THE RED HILLS OF KANSAS

Gypsum caves found throughout the Red Hills of Kansas have the state's most diverse and largest population of cave-roosting bats. White-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans, which threatens all temperate bat species, has not been previously detected in the gypsum caves as this disease moves westward from the eastern United States. Cave soil was obtained from the gypsum caves, and using the polymerase chain reaction, a 624-nucleotide DNA fragment specific to the Type 1 intron-internal transcribed spacer region of the 18S rRNA gene from Pseudogymnoascus species was amplified. Subsequent cloning and DNA sequencing indicated P. destructans DNA was present, along with 26 uncharacterized Pseudogymnoascus DNA variants. However, no evidence of WNS was observed in bat populations residing in these caves.

White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America

A striking feature of white-nose syndrome, a fungal infection of hibernating bats, is the difference in infection outcome between North America and Europe. Here we show high WNS prevalence both in Europe and on the West Siberian Plain in Asia. Palearctic bat communities tolerate similar fungal loads of Pseudogymnoascus destructans infection as their Nearctic counterparts and histopathology indicates equal focal skin tissue invasiveness pathognomonic for WNS lesions. Fungal load positively correlates with disease intensity and it reaches highest values at intermediate latitudes. Prevalence and fungal load dynamics in Palearctic bats remained persistent and high between 2012 and 2014. Dominant haplotypes of five genes are widespread in North America, Europe and Asia, expanding the source region of white-nose syndrome to non-European hibernacula. Our data provides evidence for both endemicity and tolerance to this persistent virulent fungus in the Palearctic, suggesting that host-pathogen interaction equilibrium has been established.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems.

Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds

This study assessed the diversity of cultivable rock-associated fungi from Atacama Desert. A total of 81 fungal isolates obtained were identified as 29 Ascomycota taxa by sequencing different regions of DNA. Cladosporium halotolerans, Penicillium chrysogenum and Penicillium cf. citrinum were the most frequent species, which occur at least in four different altitudes. The diversity and similarity indices ranged in the fungal communities across the latitudinal gradient. The Fisher-α index displayed the higher values for the fungal communities obtained from the siltstone and fine matrix of pyroclastic rocks with finer grain size, which are more degraded. A total of 23 fungal extracts displayed activity against the different targets screened. The extract of P. chrysogenum afforded the compounds α-linolenic acid and ergosterol endoperoxide, which were active against Cryptococcus neoformans and methicillin-resistance Staphylococcus aureus respectively. Our study represents the first report of a new habitat of fungi associated with rocks of the Atacama Desert and indicated the presence of interesting fungal community, including species related with saprobes, parasite/pathogen and mycotoxigenic taxa. The geological characteristics of the rocks, associated with the presence of rich resident/resilient fungal communities suggests that the rocks may provide a favourable microenvironment fungal colonization, survival and dispersal in extreme conditions.

Lichensphere: a protected natural microhabitat of the non-lichenised fungal communities living in extreme environments of Antarctica

We surveyed the diversity, distribution and ecology of non-lichenised fungal communities associated with the Antarctic lichens Usnea antarctica and Usnea aurantiaco-atra across Antarctica. The phylogenetic study of the 438 fungi isolates identified 74 taxa from 21 genera of Ascomycota, Basidiomycota and Zygomycota. The most abundant taxa were Pseudogymnoascus sp., Thelebolus sp., Antarctomyces psychrotrophicus and Cryptococcus victoriae, which are considered endemic and/or highly adapted to Antarctica. Thirty-five fungi may represent new and/or endemic species. The fungal communities displayed high diversity, richness and dominance indices; however, the similarity among the communities was variable. After discovering rich and diverse fungal communities composed of symbionts, decomposers, parasites and endemic and cold-adapted cosmopolitan taxa, we introduced the term "lichensphere". We hypothesised that the lichensphere may represent a protected natural microhabitat with favourable conditions able to help non-lichenised fungi and other Antarctic life forms survive and disperse in the extreme environments of Antarctica.

The fungus Trichophyton redellii sp. Nov. Causes skin infections that resemble white-nose syndrome of hibernating bats

Before the discovery of white-nose syndrome (WNS), a fungal disease caused by Pseudogymnoascus destructans, there were no reports of fungal skin infections in bats during hibernation. In 2011, bats with grossly visible fungal skin infections similar in appearance to WNS were reported from multiple sites in Wisconsin, US, a state outside the known range of P. destructans and WNS at that time. Tape impressions or swab samples were collected from affected areas of skin from bats with these fungal infections in 2012 and analyzed by microscopy, culture, or direct DNA amplification and sequencing of the fungal internal transcribed spacer region (ITS). A psychrophilic species of Trichophyton was isolated in culture, detected by direct DNA amplification and sequencing, and observed on tape impressions. Deoxyribonucleic acid indicative of the same fungus was also detected on three of five bat carcasses collected in 2011 and 2012 from Wisconsin, Indiana, and Texas, US. Superficial fungal skin infections caused by Trichophyton sp. were observed in histopathology for all three bats. Sequencing of the ITS of Trichophyton sp., along with its inability to grow at 25 C, indicated that it represented a previously unknown species, described herein as Trichophyton redellii sp. nov. Genetic diversity present within T. redellii suggests it is native to North America but that it had been overlooked before enhanced efforts to study fungi associated with bats in response to the emergence of WNS.

Effect of Trans, Trans-Farnesol on Pseudogymnoascus destructans and Several Closely Related Species

Bat white-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, has dramatically reduced the populations of many hibernating North American bat species. The search for effective biological control agents targeting P. destructans is of great importance. We report that the sesquiterpene trans, trans-farnesol, which is also a Candida albicans quorum sensing compound, prevented in vitro conidial germination for at least 14 days and inhibited growth of preexisting hyphae of five P. destructans isolates in filtered potato dextrose broth at 10 °C. Depending on the inoculation concentrations, both spore and hyphal inhibition occurred upon exposure to concentrations as low as 15-20 µM trans, trans-farnesol. In contrast, most North American Pseudogymnoascus isolates were more tolerant to the exposure of trans, trans-farnesol. Our results suggest that some Candida isolates may have the potential to inhibit the growth of P. destructans and that the sesquiterpene trans, trans-farnesol has the potential to be utilized as a biological control agent.