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

Coprinopsis laanii fruiting on mammal carcasses in an underground mine

Fungi are important decomposers of organic material, including animal waste. Ammonia and postputrefaction fungi grow in soil enriched in ammonium and nitrogen from carcasses. In 2014, we observed mushrooms fruiting on the flesh of a dead muskrat (Ondatra zibethicus) in an abandoned underground copper mine in southeastern New Brunswick, Canada. We placed an adult beaver (Castor canadensis) carcass near the muskrat to facilitate fungal colonization and fruiting. The beaver carcass was colonized by a variety of molds, especially Acaulium caviariforme. We observed mushrooms of an unidentified copriniid on the flesh 6 years and 9 months after carcass placement. Using morphological and molecular (nuclear internal transcribed spacer [nrITS]) data, we identified the mushrooms as Coprinopsis laanii, a rarely encountered species generally considered lignicolous. We discuss the role of C. laanii, and other postputrefaction fungi, in cave environments.

A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats

The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd-positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd-positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.

The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior

Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.

Species-specific responses to white-nose syndrome in the Great Lakes region

White-nose syndrome is a fungal disease that is threatening bat populations across North America. The disease primarily affects cave-hibernating bats by depleting fat reserves during hibernation and causing a range of other physiological consequences when immune responses are suppressed. Since it was first detected in 2006, the disease has killed millions of bats and is responsible for extensive local extinctions. To better understand the effects of white-nose syndrome on various bat species, we analyzed summer acoustic survey data collected from 2016 to 2020 at nine US National Parks within the Great Lakes region. We examined the effect that white-nose syndrome, time of the year relative to pup volancy, habitat type, and regional variation (i.e., park) have on the acoustic abundance (i.e., mean call abundance) of six bat species. As expected, little brown bat (Myotis lucifugus) and northern long-eared bat (Myotis septentrionalis), both hibernating species, experienced a significant decline in acoustic abundance following white-nose syndrome detection. We observed a significant increase in acoustic abundance as white-nose syndrome progressed for hoary bats (Lasiurus cinereus) and silver-haired bats (Lasionycteris noctivagans), both migratory species that are not impacted by the disease. Contrary to our predictions, we observed an increase in big brown bat (Eptesicus fuscus; hibernating) acoustic abundance and a decrease in eastern red bat (Lasiurus borealis; migratory) acoustic abundance following the detection of white-nose syndrome. We did not observe any significant changes after the onset of white-nose syndrome in the seasonal patterns of acoustic activity related to pup volancy, suggesting that production or recruitment of young may not be affected by the disease. Our results suggest that white-nose syndrome is affecting the acoustic abundance of certain species; however, these changes may not be a result of reduced reproductive success caused by the disease. In addition, species population dynamics may be indirectly affected by white-nose syndrome as a result of reduced competition or a foraging niche release. We also found that for parks located at higher latitudes, little brown bat and northern long-eared bat were more likely to experience greater declines in acoustic abundance as a result of white-nose syndrome. Our work provides insight into species-specific responses to white-nose syndrome at a regional scale and examines factors that may facilitate resistance or resiliency to the disease.

Temperature shifts associated with bat arousals during hibernation inhibit the growth of Pseudogymnoascus destructans

Temperature is a critically important factor in many infectious disease systems, because it can regulate responses in both the host and the pathogen. White-nose syndrome (WNS) in bats is a severe infectious disease caused by the temperature-sensitive fungus, Pseudogymnoascus destructans (Pd). One feature of WNS is an increase in the frequency of arousal bouts (i.e. when bat body temperatures are elevated) in Pd-infected bats during hibernation. While several studies have proposed that increased frequency of arousals may play a role in the pathophysiology of WNS, it is unknown if the temperature fluctuations might mediate Pd growth. We hypothesized that exposure to a high frequency of elevated temperatures would reduce Pd growth due to thermal constraints on the pathogen. We simulated the thermal conditions for arousal bouts of uninfected and infected bats during hibernation (fluctuating from 8 to 25°C at two different rates) and quantified Pd growth in vitro. We found that increased exposure to high temperatures significantly reduced Pd growth. Because temperature is one of the most critical abiotic factors mediating host-pathogen interactions, resolving how Pd responds to fluctuating temperatures will provide insights for understanding WNS in bats and other fungal diseases.

Changes in hibernating tricolored bat (Perimyotis subflavus) roosting behavior in response to white-nose syndrome

Understanding animals' behavioral and physiological responses to pathogenic diseases is critical for management and conservation. One such disease, white‐nose syndrome (WNS), has greatly affected bat populations throughout eastern North America leading to significant population declines in several species. Although tricolored bat (Perimyotis subflavus) populations have experienced significant declines, little research has been conducted on their responses to the disease, particularly in the southeastern United States. Our objective was to document changes in tricolored bat roost site use after the appearance of WNS in a hibernaculum in the southeastern U.S. and relate these to microsite temperatures, ambient conditions, and population trends. We censused a tricolored bat hibernaculum in northwestern South Carolina, USA, once each year between February 26 and March 2, 2014–2021, and recorded species, section of the tunnel, distance from the entrance, and wall temperature next to each bat. The number of tricolored bats in the hibernaculum dropped by 90.3% during the first 3 years after the arrival of WNS. However, numbers stabilized and slightly increased from 2018 to 2021. Prior to the arrival of WNS, 95.6% of tricolored bats roosted in the back portion of the tunnel that was the warmest. After the arrival of WNS, we observed a significant increase in the proportion of bats using the front, colder portions of the tunnel, particularly during the period of population stabilization and increase. Roost temperatures of bats were also positively associated with February external temperatures. Our results suggest that greater use of the colder sections of the tunnel by tricolored bats could have led to increased survival due to slower growth rates of the fungus that causes WNS in colder temperatures or decreased energetic costs associated with colder hibernation temperatures. Thus, management actions that provide cold hibernacula may be an option for long‐term management of hibernacula, particularly in southern regions.

Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings

Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.

Cooling of bat hibernacula to mitigate white-nose syndrome

White-nose syndrome (WNS) is a fungal disease that has caused precipitous declines in several North American bat species, creating an urgent need for conservation. We examined how microclimates and other characteristics of hibernacula have affected bat populations following WNS-associated declines and evaluated whether cooling of warm, little-used hibernacula could benefit bats. During the period following mass mortality (2013-2020), we conducted 191 winter surveys of 25 unmanipulated hibernacula and 6 manipulated hibernacula across Pennsylvania (USA). We joined these data with additional datasets on historical (pre-WNS) bat counts and on the spatial distribution of underground sites. We used generalized linear mixed models and model selection to identify factors affecting bat populations. Winter counts of Myotis lucifugus were higher and increased over time in colder hibernacula (those with midwinter temperatures of 3-6 °C) compared with warmer (7-11 °C) hibernacula. Counts of Eptesicus fuscus, Myotis leibii, and Myotis septentrionalis were likewise higher in colder hibernacula (temperature effects = -0.73 [SE 0.15], -0.51 [0.18], and -0.97 [0.28], respectively). Populations of M. lucifugus and M. septentrionalis increased most over time in hibernacula surrounded by more nearby sites, whereas Eptesicus fuscus counts remained high where they had been high before WNS onset (pre-WNS high count effect = 0.59 [0.22]). Winter counts of M. leibii were higher in hibernacula with high vapor pressure deficits (VPDs) (particularly over 0.1 kPa) compared with sites with lower VPDs (VPD effect = 15.3 [4.6]). Counts of M. lucifugus and E. fuscus also appeared higher where VPD was higher. In contrast, Perimyotis subflavus counts increased over time in relatively warm hibernacula and were unaffected by VPD. Where we manipulated hibernacula, we achieved cooling of on average 2.1 °C. At manipulated hibernacula, counts of M. lucifugus and P. subflavus increased over time (years since manipulation effect = 0.70 [0.28] and 0.51 [0.15], respectively). Further, there were more E. fuscus where cooling was greatest (temperature difference effect = -0.46 [SE 0.11]), and there was some evidence there were more P. subflavus in hibernacula sections that remained warm after manipulation. These data show bats are responding effectively to WNS through habitat selection. In M. lucifugus, M. septentrionalis, and possibly P. subflavus, this response is ongoing, with bats increasingly aggregating at suitable hibernacula, whereas E. fuscus remain in previously favored sites. Our results suggest that cooling warm sites receiving little use by bats is a viable strategy for combating WNS.

Biomarker Metabolites Discriminate between Physiological States of Field, Cave and White-nose Syndrome Diseased Bats

Analysis of volatile organic compound (VOC) emissions using electronic-nose (e-nose) devices has shown promise for early detection of white-nose syndrome (WNS) in bats. Tricolored bats, Perimyotis subflavus, from three separate sampling groups defined by environmental conditions, levels of physical activity, and WNS-disease status were captured temporarily for collection of VOC emissions to determine relationships between these combinations of factors and physiological states, Pseudogymnoascus destructans (Pd)-infection status, and metabolic conditions. Physiologically active (non-torpid) healthy individuals were captured outside of caves in Arkansas and Louisiana. In addition, healthy and WNS-diseased torpid bats were sampled within caves in Arkansas. Whole-body VOC emissions from bats were collected using portable air-collection and sampling-chamber devices in tandem. Electronic aroma-detection data using three-dimensional Principal Component Analysis provided strong evidence that the three groups of bats had significantly different e-nose aroma signatures, indicative of different VOC profiles. This was confirmed by differences in peak numbers, peak areas, and tentative chemical identities indicated by chromatograms from dual-column GC-analyses. The numbers and quantities of VOCs present in whole-body emissions from physiologically active healthy field bats were significantly greater than those of torpid healthy and diseased cave bats. Specific VOCs were identified as chemical biomarkers of healthy and diseased states, environmental conditions (outside and inside of caves), and levels of physiological activity. These results suggest that GC/E-nose dual-technologies based on VOC-detection and analyses of physiological states, provide noninvasive alternative means for early assessments of Pd-infection, WNS-disease status, and other physiological states.

Experimental inoculation trial to determine the effects of temperature and humidity on White-nose Syndrome in hibernating bats

Disease results from interactions among the host, pathogen, and environment. Inoculation trials can quantify interactions among these players and explain aspects of disease ecology to inform management in variable and dynamic natural environments. White-nose Syndrome, a disease caused by the fungal pathogen, Pseudogymnoascus destructans (Pd), has caused severe population declines of several bat species in North America. We conducted the first experimental infection trial on the tri-colored bat, Perimyotis subflavus, to test the effect of temperature and humidity on disease severity. We also tested the effects of temperature and humidity on fungal growth and persistence on substrates. Unexpectedly, only 37% (35/95) of bats experimentally inoculated with Pd at the start of the experiment showed any infection response or disease symptoms after 83 days of captive hibernation. There was no evidence that temperature or humidity influenced infection response. Temperature had a strong effect on fungal growth on media plates, but the influence of humidity was more variable and uncertain. Designing laboratory studies to maximize research outcomes would be beneficial given the high costs of such efforts and potential for unexpected outcomes. Understanding the influence of microclimates on host-pathogen interactions remains an important consideration for managing wildlife diseases, particularly in variable environments.

Effects of capture on stress-axis measures in endangered little brown bats (Myotis lucifugus)

Little brown bats (Myotis lucifugus) are a widely distributed species in North America that have been decimated by the fungal disease white-nose syndrome. As such, little brown bats are the focus of monitoring and research initiatives that often include capturing and handling free-ranging individuals. We examined the stress response of 198 adult female little brown bats after being captured from three bat houses, during the summer. Our objective was to inform best practices to researchers capturing and handling bats in the wild. We compared the stress response among bats held for <3 min (baseline), 15–30 min, or >30 min, and then among bats held alone or in a group with conspecifics. We measured the levels of plasma total and free cortisol, maximum corticosteroid binding capacity (MCBC), and blood glucose. Relative to baseline, total and free cortisol levels were significantly higher in bats held for 15–30 min and higher still in those held for > 30 min. Blood glucose levels were elevated after >30 min of holding. MCBC levels showed no differences among holding times. We detected a weak effect of social holding condition, with solitary-held bats having lower total cortisol levels than group-held bats, but MCBC, free cortisol, and blood glucose levels showed no effect of social holding condition. Our findings demonstrate that capture time should be minimized and suggest that little brown bats should be handled and released within 30 min of capture as means of reducing stress. Further, solitary holding did not appear to increase stress measures, which supports holding bats individually after capture, instead of in groups, to reduce risk of pathogen and parasite transmission.

First Speleomycological Study on the Occurrence of Psychrophilic and Psychrotolerant Aeromycota in the Brestovská Cave (Western Tatras Mts., Slovakia) and First Reports for Some Species at Underground Sites

Most underground ecosystems are heterotrophic, fungi in these objects are dispersed in the air in the form of spores, and they may be potentially hazardous to mammals. Research in underground sites has focused on mesophilic airborne fungi and only a few concerned cold-adapted species. Therefore, the goal of our research was the first report of psychrophilic and psychrotolerant aeromycota in the Brestovská Cave using culture-based techniques with genetic and phenotypic identification. Plates with PDA medium containing sampled biological material were incubated at 8 ± 0.5 °C. The density of mycobiota inside the cave ranged from 37.4 to 71 CFU 1 m-3 of air and 63.3 CFU 1 m-3 of air outside the cave. Thus, the level of fungal spores did not exceed the standards for the mycological quality of the air. A total of 18 species were isolated during the study, and some species may be potentially dangerous to people with weakened immune system. All fungal species were present inside the cave and only seven of them were outside. Cladosporium cladosporioides dominated in the external air samples and Mortierella parvispora was cultured most frequently from internal air samples. To our knowledge, this is the first discovery of the fungal species such as Coniothyrium pyrinum, Cystobasidium laryngis, Filobasidium wieringae, Leucosporidium drummii, M. parvispora, Mrakia blollopis, Nakazawaea holstii, and Vishniacozyma victoriae in the air inside the underground sites. Moreover, C. pyrinum, C. laryngis, L. drummii, M. blollopis, and N. holstii have never been detected in any component of the underground ecosystems. There are possible reasons explaining the detection of those species, but global warming is the most likely.

Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans

White-Nose Syndrome is an ongoing fungal epizootic caused by epidermal infections of the fungus, Pseudogymnoascus destructans (P. destructans), affecting hibernating bat species in North America. Emerging early in 2006 in New York State, infections of P. destructans have spread to 38 US States and seven Canadian Provinces. Since then, clonal isolates of P. destructans have accumulated genotypic and phenotypic variations in North America. Using microsatellite and single nucleotide polymorphism markers, we investigated the population structure and genetic relationships among P. destructans isolates from diverse regions in North America to understand its pattern of spread, and to test hypotheses about factors that contribute to transmission. We found limited support for genetic isolation of P. destructans populations by geographic distance, and instead identified evidence for gene flow among geographic regions. Interestingly, allelic association tests revealed evidence for recombination in the North American P. destructans population. Our landscape genetic analyses revealed that the population structure of P. destructans in North America was significantly influenced by anthropogenic impacts on the landscape. Our results have important implications for understanding the mechanism(s) of P. destructans spread.