Pathogen dynamics during invasion and establishment of white-nose syndrome explain mechanisms of host persistence

Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats

The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. The establishment of new wildlife reservoirs for SARS-CoV-2 would further complicate public health control measures and could lead to wildlife health and conservation impacts. Given the likely bat origin of SARS-CoV-2 and related beta-coronaviruses (β-CoVs), free-ranging bats are a key group of concern for spillover from humans back to wildlife. Here, we review the diversity and natural host range of β-CoVs in bats and examine the risk of humans inadvertently infecting free-ranging bats with SARS-CoV-2. Our review of the global distribution and host range of β-CoV evolutionary lineages suggests that 40+ species of temperate-zone North American bats could be immunologically naïve and susceptible to infection by SARS-CoV-2. We highlight an urgent need to proactively connect the wellbeing of human and wildlife health during the current pandemic and to implement new tools to continue wildlife research while avoiding potentially severe health and conservation impacts of SARS-CoV-2 "spilling back" into free-ranging bat populations.

The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen

Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between the fungal pathogen and cutaneous microbial assemblage.

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome

Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.

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.

Genome-Wide Changes in Genetic Diversity in a Population of Myotis lucifugus Affected by White-Nose Syndrome

Novel pathogens can cause massive declines in populations, and even extirpation of hosts. But disease can also act as a selective pressure on survivors, driving the evolution of resistance or tolerance. Bat white-nose syndrome (WNS) is a rapidly spreading wildlife disease in North America. The fungus causing the disease invades skin tissues of hibernating bats, resulting in disruption of hibernation behavior, premature energy depletion, and subsequent death. We used whole-genome sequencing to investigate changes in allele frequencies within a population of Myotis lucifugus in eastern North America to search for genetic resistance to WNS. Our results show low F_ST values within the population across time, i.e., prior to WNS (Pre-WNS) compared to the population that has survived WNS (Post-WNS). However, when dividing the population with a geographical cut-off between the states of Pennsylvania and New York, a sharp increase in values on scaffold GL429776 is evident in the Post-WNS samples. Genes present in the diverged area are associated with thermoregulation and promotion of brown fat production. Thus, although WNS may not have subjected the entire M. lucifugus population to selective pressure, it may have selected for specific alleles in Pennsylvania through decreased gene flow within the population. However, the persistence of remnant sub-populations in the aftermath of WNS is likely due to multiple factors in bat life history.

Seasonal Expression of Avian and Mammalian Daily Torpor and Hibernation: Not a Simple Summer-Winter Affair†

Daily torpor and hibernation (multiday torpor) are the most efficient means for energy conservation in endothermic birds and mammals and are used by many small species to deal with a number of challenges. These include seasonal adverse environmental conditions and low food/water availability, periods of high energetic demands, but also reduced foraging options because of high predation pressure. Because such challenges differ among regions, habitats and food consumed by animals, the seasonal expression of torpor also varies, but the seasonality of torpor is often not as clear-cut as is commonly assumed and differs between hibernators and daily heterotherms expressing daily torpor exclusively. Hibernation is found in mammals from all three subclasses from the arctic to the tropics, but is known for only one bird. Several hibernators can hibernate for an entire year or express torpor throughout the year (8% of species) and more hibernate from late summer to spring (14%). The most typical hibernation season is the cold season from fall to spring (48%), whereas hibernation is rarely restricted to winter (6%). In hibernators, torpor expression changes significantly with season, with strong seasonality mainly found in the sciurid and cricetid rodents, but seasonality is less pronounced in the marsupials, bats and dormice. Daily torpor is diverse in both mammals and birds, typically is not as seasonal as hibernation and torpor expression does not change significantly with season. Torpor in spring/summer has several selective advantages including: energy and water conservation, facilitation of reproduction or growth during development with limited resources, or minimisation of foraging and thus exposure to predators. When torpor is expressed in spring/summer it is usually not as deep and long as in winter, because of higher ambient temperatures, but also due to seasonal functional plasticity. Unlike many other species, subtropical nectarivorous blossom-bats and desert spiny mice use more frequent and pronounced torpor in summer than in winter, which is related to seasonal availability of nectar or water. Thus, seasonal use of torpor is complex and differs among species and habitats.

Survival and persistence of tricolored bats hibernating in Arkansas mines

White-nose syndrome (WNS) has caused large declines in bat populations across eastern North America, making information on demographics of affected species critical to determining their risk for extinction. We used Cormack–Jolly–Seber models to estimate apparent survival rates of hibernating tricolored bats (Perimyotis subflavus) for 5 years in four small abandoned mines in the Ouachita Mountains of Arkansas, located within the WNS endemic area of the United States. Populations in individual mines varied greatly in survival rates, with one mine displaying annual survival rates as high as 0.706 and another as low as 0.101. Differences in survival among bats in different mines could not definitively be attributed to WNS, but may have varied based on a combination of WNS, disturbance, mine climate, and other unknown factors. Further, some hibernacula may have served as temporary winter shelter for young transient males. Sites housing small colonies of hibernating bats may result in high survival rates despite WNS, and protecting these smaller sites may be important for overall species perseverance.

Systematic Review of the Roost-Site Characteristics of North American Forest Bats: Implications for Conservation

Continued declines in North American bat populations can be largely attributed to habitat loss, disease, and wind turbines. These declines can be partially mitigated through actions that boost reproductive success; therefore, management aimed at promoting availability of high-quality roosting habitat is an important conservation goal. Following the principles of the umbrella species concept, if co-occurring species share similar roost-tree preferences, then management practices targeting one species may confer conservation benefits to another. We conducted a systematic review of roost-site characteristics of thirteen species inhabiting eastern temperate forests to: (1) synthesize existing knowledge across species; (2) assess niche overlap among co-occurring species; and (3) evaluate the potential for currently protected species to serve as conservation umbrellas. We performed multivariate ordination techniques to group species based on the seven most-reported roost-site characteristics, including tree species, diameter at breast height, tree health, roost type, tree height, canopy closure, and roost height. Species sorted into three roosting guilds: (1) southern wetland inhabitants; (2) foliage specialists; and (3) dead tree generalists. Myotis septentrionalis and Perimyotis subflavus had significant roost-niche overlap with five and four other species respectively, and their existing protections make them suitable umbrellas for other bats in the North American eastern temperate forests.

Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano

Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer roosts as well as movement from maternity colonies fall swarms. We detected Pd DNA in guano 56 and 70 days after inoculation with 1 million and 100,000 fg respectively, while the lowest quantity (1,000 fg) was detected until 42 days. Detection probability was variable among sites and lower where samples were left exposed without overhead cover. If Pd is shed as extracellular DNA in guano at quantities above 1,000 fg, then guano collection is likely to provide an effective tool for environmental screening of Pd that can be employed in an early detection and rapid response framework throughout Washington and other regions where this disease is rapidly emerging.

External temperature and distance from nearest entrance influence microclimates of cave and culvert-roosting tri-colored bats (Perimyotis subflavus)

Many North American bat species hibernate in both natural and artificial roosts. Although hibernacula can have high internal climate stability, they still retain spatial variability in their thermal regimes, resulting in various "microclimates" throughout the roost that differ in their characteristics (e.g., temperature and air moisture). These microclimate components can be influenced by factors such as the number of entrances, the depth of the roost, and distance to the nearest entrance of the roost. Tri-colored bats are commonly found roosting in caves in winter, but they can also be found roosting in large numbers in culverts, providing the unique opportunity to investigate factors influencing microclimates of bats in both natural and artificial roost sites. As tri-colored bats are currently under consideration for federal listing, information of this type could be useful in aiding in the conservation and management of this species through a better understanding of what factors affect the microclimate near roosting bats. We collected data on microclimate temperature and microclimate actual water vapor pressure (AWVP) from a total of 760 overwintering tri-colored bats at 18 caves and 44 culverts. Using linear mixed models analysis, we found that variation in bat microclimate temperatures was best explained by external temperature and distance from nearest entrance in both caves and culverts. External temperature had a greater influence on microclimate temperatures in culverts than caves. We found that variation in microclimate AWVP was best explained by external temperature, distance from nearest entrance, and proportion from entrance (proportion of the total length of the roost from the nearest entrance) in culvert-roosting bats. Variation in microclimate AWVP was best explained by external temperature and proportion from entrance in cave-roosting bats. Our results suggest that bat microclimate temperature and AWVP are influenced by similar factors in both artificial and natural roosts, although the relative contribution of these factors differs between roost types.

Testing the "Fasting While Foraging" Hypothesis: Effects of Recent Feeding on Plasma Metabolite Concentrations in Little Brown Bats (Myotis lucifugus)

Plasma metabolite concentrations can be used to understand nutritional status and foraging behavior across ecological contexts including prehibernation fattening, migration refueling, and variation in foraging habitat quality. Generally, high plasma concentrations of the ketone β-hydroxybutyrate, a product of fat catabolism, indicate fasting, while triglycerides indicate recent feeding and fat accumulation. In recent studies of insectivorous bats, triglyceride concentration increased after feeding as expected, but β-hydroxybutyrate also unexpectedly increased rather than decreased. An aerial-hawking foraging strategy is energetically demanding, and thus it has been hypothesized that foraging by insectivorous bats requires catabolism of stored fat. We tested this hypothesis by quantifying plasma β-hydroxybutyrate and triglyceride concentration following feeding in little brown bats (Myotis lucifugus) that were temporarily housed in individual cages to prevent flight. We provided a fixed amount of food and collected blood samples at different intervals after feeding to produce variation in plasma metabolite concentrations. Plasma triglyceride concentration responded as predicted, but similar to previous studies and contrary to our prediction, when flight was eliminated plasma β-hydroxybutyrate concentration responded similarly to triglyceride. Thus, it is unlikely that the unexpected plasma β-hydroxybutyrate patterns observed in previous studies were related to flight. The mechanism underlying this unexpected pattern remains unknown, but the response has been consistent in all studies to date. Thus, plasma metabolite analysis provides an effective tool for studies of nutritional status, although more work is needed to understand why insectivorous bats respond differently than other taxa.

Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis

Abstract

Resistance and tolerance allow organisms to cope with potentially life-threatening pathogens. Recently introduced pathogens initially induce resistance responses, but natural selection favors the development of tolerance, allowing for a commensal relationship to evolve. Mycosis by Pseudogymnoascus destructans, causing white-nose syndrome (WNS) in Nearctic hibernating bats, has resulted in population declines since 2006. The pathogen, which spread from Europe, has infected species of Palearctic Myotis for a longer period. We compared ecologically relevant responses to the fungal infection in the susceptible Nearctic M. lucifugus and less susceptible Palearctic M. myotis, to uncover factors contributing to survival differences in the two species. Samples were collected from euthermic bats during arousal from hibernation, a naturally occurring phenomenon, during which transcriptional responses are activated. We compared the whole-transcriptome responses in wild bats infected with P. destructans hibernating in their natural habitat. Our results show dramatically different local transcriptional responses to the pathogen between uninfected and infected samples from the two species. Whereas we found 1526 significantly upregulated or downregulated transcripts in infected M. lucifugus, only one transcript was downregulated in M. myotis. The upregulated response pathways in M. lucifugus include immune cell activation and migration, and inflammatory pathways, indicative of an unsuccessful attempt to resist the infection. In contrast, M. myotis appears to tolerate P. destructans infection by not activating a transcriptional response. These host-microbe interactions determine pathology, contributing to WNS susceptibility, or commensalism, promoting tolerance to fungal colonization during hibernation that favors survival.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00442-019-04499-6) contains supplementary material, which is available to authorized users.

Multiscale model of regional population decline in little brown bats due to white-nose syndrome

The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white-nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, but linking these scales is necessary to quantify the mechanisms of transmission and assess population-scale declines.We built a model connecting within-hibernaculum disease dynamics of little brown bats to regional-scale dispersal, reproduction, and disease spread, including multiple plausible mechanisms of transmission.We parameterized the model using the approach of plausible parameter sets, by comparing stochastic simulation results to statistical probes from empirical data on within-hibernaculum prevalence and survival, as well as among-hibernacula spread across a region.Our results are consistent with frequency-dependent transmission between bats, support an important role of environmental transmission, and show very little effect of dispersal among colonies on metapopulation survival.The results help identify the influential parameters and largest sources of uncertainty. The model also offers a generalizable method to assess hypotheses about hibernaculum-to-hibernaculum transmission and to identify gaps in knowledge about key processes, and could be expanded to include additional mechanisms or bat species.

Field trial of a probiotic bacteria to protect bats from white-nose syndrome

Tools for reducing wildlife disease impacts are needed to conserve biodiversity. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in North American bat populations and threatens several species with extinction. Few tools exist for managers to reduce WNS impacts. We tested the efficacy of a probiotic bacterium, Pseudomonas fluorescens, to reduce impacts of WNS in two simultaneous experiments with caged and free-flying Myotis lucifugus bats at a mine in Wisconsin, USA. In the cage experiment there was no difference in survival between control and P. fluorescens-treated bats. However, body mass, not infection intensity, predicted mortality, suggesting that within-cage disturbance influenced the cage experiment. In the free-flying experiment, where bats were able to avoid conspecific disturbance, infection intensity predicted the date of emergence from the mine. In this experiment treatment with P. fluorescens increased apparent overwinter survival five-fold compared to the control group (from 8.4% to 46.2%) by delaying emergence of bats from the site by approximately 32 days. These results suggest that treatment of bats with P. fluorescens may substantially reduce WNS mortality, and, if used in combination with other interventions, could stop population declines.

An experimental test of energy and electrolyte supplementation as a mitigation strategy for white-nose syndrome

Fungi are increasingly recognised as harmful pathogens of wildlife. White-nose syndrome (WNS) is a fungal disease that has killed millions of hibernating bats in North America. High mortality has driven research to identify management strategies for the disease. Increased energy expenditure and fat depletion, as well as fluid loss, hypotonic dehydration and electrolyte depletion appear to be key aspects of WNS pathophysiology. Bats with WNS spend energy too quickly and also lose fluids containing water and electrolytes from lesions on exposed skin surfaces. During periodic arousals, bats often drink water but, in most of the WNS-affected area, food is not available during winter and, therefore, they cannot maintain energy balance or replace lost electrolytes. Therefore, providing a liquid caloric/electrolyte/nutrient supplement could be useful for treating WNS. We studied captive, hibernating little brown bats (Myotis lucifugus) to test whether providing supplemental energy and electrolytes (a 1:1 dilution of unflavoured Pedialyte) to hibernating bats could reduce severity of WNS symptoms and increase survival. Infected bats in the Pedialyte-supplemented group generally avoided the Pedialyte and preferentially drank plain water. We did not observe any differences in survival, arousal frequency or blood chemistry, but bats in the Pedialyte-supplemented group had higher fungal load and more UV fluorescence than the control group that was only provided with water. Supplemental electrolytes would be an attractive management strategy because of their low cost and logistic feasibility but our results suggest this approach would be ineffective. However, it could be useful to conduct preference experiments with multiple dilutions and/or flavours of electrolyte solution. Although they did not prefer Pedialyte in our experiment, bats in the hand readily drink it and electrolyte supplementation remains an important tool for rehabilitation of captive bats recovering from WNS and other causes of dehydration.

Higher fat stores contribute to persistence of little brown bat populations with white-nose syndrome

The persistence of populations declining from novel stressors depends, in part, on their ability to respond by trait change via evolution or plasticity. White-nose syndrome (WNS) has caused rapid declines in several North America bat species by disrupting hibernation behaviour, leading to body fat depletion and starvation. However, some populations of Myotis lucifugus now persist with WNS by unknown mechanisms. We examined whether persistence of M. lucifigus with WNS could be explained by increased body fat in early winter, which would allow bats to tolerate the increased energetic costs associated with WNS. We also investigated whether bats were escaping infection or resistant to infection as an alternative mechanism explaining persistence. We measured body fat in early and late winter during initial WNS invasion and 8 years later at six sites where bats are now persisting. We also measured infection prevalence and intensity in persisting populations. Infection prevalence was not significantly lower than observed in declining populations. However, at two sites, infection loads were lower than observed in declining populations. Body fat in early winter was significantly higher in four of the six persisting populations than during WNS invasion. Physiological models of energy use indicated that these higher fat stores could reduce WNS mortality by 58%-70%. These results suggest that differences in fat storage and infection dynamics have reduced the impacts of WNS in many populations. Increases in body fat provide a potential mechanism for management intervention to help conserve bat populations.

Does the fungus causing white-nose syndrome pose a significant risk to Australian bats?

Abstract ContextPseudogymnoascus destructans is the fungus responsible for white-nose syndrome (WNS), which has killed millions of hibernating bats in North America, but also occurs in bats in Europe and China without causing large-scale population effects. This is likely to be due to differences in species susceptibility and behaviour, and environmental factors, such as temperature and humidity. Pseudogymnoascus destructans is currently believed to be absent from Australia. AimsTo ascertain the level of risk that white-nose syndrome poses for Australian bats. Methods This risk analysis examines the likelihood that P. destructans enters Australia, the likelihood of the fungus coming in contact with native bats on successful entry, and the potential consequences should this occur. Key results This risk assessment concluded that it is very likely to almost certain that P. destructans will enter Australia, and it is likely that bats will be exposed to the fungus over the next 10 years. Eight cave-dwelling bat species from southern Australia are the ones most likely to be affected. ConclusionsThe risk was assessed as medium for the critically endangered southern bent-winged bat (Miniopterus orianae bassanii), because any increase in mortality could affect its long-term survival. The risk to other species was deemed to range from low to very low, owing to their wider distribution, which extends beyond the P. destructans risk zone. Implications Although Australia’s milder climate may preclude the large mortality events seen in North America, the fungus could still significantly affect Australian bat populations, particularly bent-winged bats. Active surveillance is required to confirm Australia’s continuing WNS-free status, and to detect the presence of P. destructans should it enter the country. Although White-nose Syndrome Response Guidelines have been developed by Wildlife Health Australia to assist response agencies in the event of an incursion of WNS into bats in Australia, these guidelines would be strengthened by further research to characterise Australian cave temperatures and hibernating bat biology, such as length of torpor bouts and movement over winter. Risk-mitigation strategies should focus on education programs that target cavers, show-cave managers and tourists, particularly those who have visited regions where WNS is known to occur.

Hibernation temperature-dependent Pseudogymnoascus destructans infection intensity in Palearctic bats

White-nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans that is devastating to Nearctic bat populations but tolerated by Palearctic bats. Temperature is a factor known to be important for fungal growth and bat choice of hibernation. Here we investigated the effect of temperature on the pathogenic fungal growth in the wild across the Palearctic. We modelled body surface temperature of bats with respect to fungal infection intensity and disease severity and were able to relate this to the mean annual surface temperature at the site. Bats that hibernated at lower temperatures had less fungal growth and fewer skin lesions on their wings. Contrary to expectation derived from laboratory P. destructans culture experiments, natural infection intensity peaked between 5 and 6°C and decreased at warmer hibernating temperature. We made predictive maps based on bat species distributions, temperature and infection intensity and disease severity data to determine not only where P. destructans will be found but also where the infection will be invasive to bats across the Palearctic. Together these data highlight the mechanistic model of the interplay between environmental and biological factors, which determine progression in a wildlife disease.

Eco-evolutionary rescue promotes host-pathogen coexistence

Emerging infectious pathogens are responsible for some of the most severe host mass mortality events in wild populations. Yet, effective pathogen control strategies are notoriously difficult to identify, in part because quantifying and forecasting pathogen spread and disease dynamics is challenging. Following an outbreak, hosts must cope with the presence of the pathogen, leading to host-pathogen coexistence or extirpation. Despite decades of research, little is known about host-pathogen coexistence post-outbreak when low host abundances and cryptic species make these interactions difficult to study. Using a novel disease-structured N-mixture model, we evaluate empirical support for three host-pathogen coexistence hypotheses (source-sink, eco-evolutionary rescue, and spatial variation in pathogen transmission) in a Neotropical amphibian community decimated by Batrachochytrium dendrobatidis (Bd) in 2004. During 2010-2014, we surveyed amphibians in Parque Nacional G. D. Omar Torríjos Herrera, Coclé Province, El Copé, Panama. We found that the primary driver of host-pathogen coexistence was eco-evolutionary rescue, as evidenced by similar amphibian survival and recruitment rates between infected and uninfected hosts. Average apparent monthly survival rates of uninfected and infected hosts were both close to 96%, and the expected number of uninfected and infected hosts recruited (via immigration/reproduction) was less than one host per disease state per 20-m site. The secondary driver of host-pathogen coexistence was spatial variation in pathogen transmission as we found that transmission was highest in areas of low abundance but there was no support for the source-sink hypothesis. Our results indicate that changes in the host community (i.e., through genetic or species composition) can reduce the impacts of emerging infectious disease post-outbreak. Our disease-structured N-mixture model represents a valuable advancement for conservation managers trying to understand underlying host-pathogen interactions and provides new opportunities to study disease dynamics in remnant host populations decimated by virulent pathogens.

Using noninvasive metagenomics to characterize viral communities from wildlife

Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.

The impact of the built environment on health behaviours and disease transmission in social systems

The environment plays an important role in disease dynamics and in determining the health of individuals. Specifically, the built environment has a large impact on the prevention and containment of both chronic and infectious disease in humans and in non-human animals. The effects of the built environment on health can be direct, for example, by influencing environmental quality, or indirect by influencing behaviours that impact disease transmission and health. Furthermore, these impacts can happen at many scales, from the individual to the society, and from the design of the plates we eat from to the design of cities. In this paper, we review the ways that the built environment affects both the prevention and the containment of chronic and infectious disease. We bring examples from both human and animal societies and attempt to identify parallels and gaps between the study of humans and animals that can be capitalized on to advance the scope and perspective of research in each respective field. By consolidating this literature, we hope to highlight the importance of built structures in determining the complex dynamics of disease and in impacting the health behaviours of both humans and animals.This article is part of the theme issue 'Interdisciplinary approaches for uncovering the impacts of architecture on collective behaviour'.

Trade-offs Influencing the Physiological Ecology of Hibernation in Temperate-Zone Bats

Seasonality of temperature and food availability can lead to trade-offs between the benefits of immediate reproduction and costs associated with mortality risk from starvation, inclement weather, or predation. Hibernating mammals exhibit an enormous seasonal shift in physiology and behavior and provide a useful system to examine the effect of this trade-off on key events in the annual cycle. Most of what we understand about the ecological energetics and phenology of hibernation comes from studies of rodent hibernators such as ground squirrels, chipmunks, and dormice. Temperate-zone, insectivorous bats, however, provide another useful model system to examine trade-offs influencing seasonal change within individuals. Here, I review recent studies from my laboratory on little brown bats (Myotis lucifugus) from central Canada to understand the interplay between capacity for energy storage, energy expenditure during hibernation, and the timing of key events in the annual cycle of hibernating mammals. These studies have relied on measurements of body condition to assess energetic status, biologging of skin temperature using temperature telemetry, and use of passive transponders (i.e., PIT tags) to quantify emergence timing. In general, these studies suggest that, in part due to constraints associated with flight, bats exhibit unique, or at least unusual, adaptations for extreme energy savings during winter. The results also support the optimization hypothesis that current energetic status and future energy requirements influence energy expenditure during hibernation and the timing of emergence from hibernation in spring. Taken together, this work provides insight into the influence of reproductive timing and energy availability on hibernation behavior and physiology. It also has implications for understanding responses of bat populations to anthropogenic impacts like climate change and white-nose syndrome.

Observed Resiliency of Little Brown Myotis to Long-Term White-Nose Syndrome Exposure

White-nose syndrome (WNS) is a disease that has killed millions of bats in eastern North America and has steadily been spreading across the continent. Little brown myotis Myotis lucifugus populations have experienced extensive declines; however, some localized populations have remained resilient, with bats surviving multiple years past initial WNS exposure. These persistent populations may be critical to species recovery, and understanding mechanisms leading to this long-term survival and persistence may provide insight into overall bat and disease management. We monitored a maternity colony of little brown myotis on Fort Drum Military Installation in northern New York between 2006 and 2017 to determine basic demographic parameters and find evidence of what may be leading to resiliency and persistence at this site. Total colony size declined by approximately 88% from 2008 to 2010 due primarily to impacts of WNS. Counts of all adults returning to the colony stabilized during 2010–2014 (mean = 94, range 84–101) and increased after 2014 (mean = 132, range = 108–166). We captured 727 little brown myotis (575 females, 152 males) and banded 534 individuals (389 females, 145 males) at the colony. The majority of sampled bats showed evidence of recent past WNS infection and exposure to Pseudogymnoascus destructans, and we documented pervasive presence and limited viability of the fungus within the colony's main roosting structure. We recaptured 98 individually marked females in years after initial banding, and some individuals survived at least 6 y. Ninety-one percent of all adult females, 93% of recaptured bats, and 90% of 1-y-old females (i.e., bats recaptured the first year after initial capture as juveniles) showed evidence of reproduction during the monitoring period. Using mark–recapture models, we estimated annual survival rates of juvenile and adult little brown myotis during 2009–2016 and examined whether reproductive condition or evidence of recent infection of WNS had any effect on survival. Annual survival rates were similar between juveniles and adults, but highly variable, ranging from 41.0 to 86.5%. Models indicated that neither evidence of recent past exposure to WNS nor reproductive status were related to survival. No one parameter stood out as being responsible for this colony's continued existence, and it is likely that many interwoven factors were responsible for the observed resilience. Although relatively high reproductive effort from all females (i.e., both1-y-old and >1-y-old ) and intermittently suitable survival rates have led to the continued persistence of, and population increases in, this summer colony, mortality from WNS and inherently low reproductive potential still seemed to be limiting population growth. Until there is a better understanding of this overall potential resiliency in little brown myotis, we recommend considering minimizing disturbance and direct human involvement within these persisting populations to allow whatever natural recovery that may be occurring to evolve uninterrupted.

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.

Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome

The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen’s spread is associated with the genetic population structure of a host ( Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species’ northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size ( Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Ne were unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses.