Ecology and impacts of white-nose syndrome on bats

The importance of peripheral populations in the face of novel environmental change

Anthropogenically driven environmental change has imposed substantial threats on biodiversity, including the emergence of infectious diseases that have resulted in declines of wildlife globally. In response to pathogen invasion, maintaining diversity within host populations across heterogenous environments is essential to facilitating species persistence. White-nose syndrome is an emerging fungal pathogen that has caused mass mortalities of hibernating bats across North America. However, in the northeast, peripheral island populations of the endangered northern myotis (Myotis septentrionalis) appear to be persisting despite infection while mainland populations in the core of the species range have experienced sharp declines. Thus, this study investigated host and environmental factors that may contribute to divergent population responses. We compared patterns of pathogen exposure and infection intensity between populations and documented the environmental conditions and host activity patterns that may promote survival despite disease invasion. For island populations, we found lower prevalence and less severe infections, possibly due to a shorter hibernation duration compared to the mainland, which may reduce the time for disease progression. The coastal region of the northern myotis range may serve as habitat refugia that enables this species to persist despite pathogen exposure; however, conservation efforts could be critical to supporting species survival in the long term.

Coevolution promotes the coexistence of Tasmanian devils and a fatal, transmissible cancer

Emerging infectious diseases threaten natural populations, and data-driven modeling is critical for predicting population dynamics. Despite the importance of integrating ecology and evolution in models of host-pathogen dynamics, there are few wild populations for which long-term ecological datasets have been coupled with genome-scale data. Tasmanian devil (Sarcophilus harrisii) populations have declined range wide due to devil facial tumor disease (DFTD), a fatal transmissible cancer. Although early ecological models predicted imminent devil extinction, diseased devil populations persist at low densities, and recent ecological models predict long-term devil persistence. Substantial evidence supports the evolution of both devils and DFTD, suggesting coevolution may also influence continued devil persistence. Thus, we developed an individual-based, eco-evolutionary model of devil-DFTD coevolution parameterized with nearly 2 decades of devil demography, DFTD epidemiology, and genome-wide association studies. We characterized potential devil-DFTD coevolutionary outcomes and predicted the effects of coevolution on devil persistence and devil-DFTD coexistence. We found a high probability of devil persistence over 50 devil generations (100 years) and a higher likelihood of devil-DFTD coexistence, with greater devil recovery than predicted by previous ecological models. These novel results add to growing evidence for long-term devil persistence and highlight the importance of eco-evolutionary modeling for emerging infectious diseases.

Disparities in Perimyotis subflavus Body Mass Between Cave and Culvert Hibernacula in Georgia, USA

The tricolored bat (Perimyotis subflavus), once common in the eastern United States, has experienced significant mortality due to white-nose syndrome (WNS), a fungal disease that primarily affects bats hibernating in caves and mines. In coastal regions of the southeastern United States, where caves and mines are scarce, tricolored bats often use roadway culverts as hibernacula. However, WNS infection dynamics in culverts are poorly understood. Previous research indicated that bats with higher body mass at the onset of hibernation have a higher probability of surviving repeated arousal events from WNS. Therefore, we compared tricolored bat winter body mass between cave and culvert hibernacula and identified culvert characteristics influencing body mass during hibernation in Georgia, USA. From 2018 to 2022, we measured body mass of 754 individuals in early and late hibernation across 32 culverts (n = 497) and four caves (n = 257). Our study revealed a southward spread of the fungus over multiple years, with the first confirmed case of WNS in a Georgia culvert in 2022. Overall, tricolored bats in caves weighed more in early hibernation than those in culverts, but bats in culverts weighed more in late hibernation. Across all sites, female tricolored bats entering and leaving hibernation had greater mass than males but lost more mass during hibernation, possibly due to differences in torpor-arousal patterns and WNS infection rates. Additionally, all bats lost more mass in longer culverts. Understanding culvert characteristics affecting bat body mass will inform management strategies to mitigate WNS effects. Identifying risk factors for specific tricolored bat hibernacula can guide managers on where to focus winter WNS monitoring efforts and potential treatments.

Early Detection of Wildlife Disease Pathogens Using CRISPR-Cas System Methods

Wildlife diseases are a considerable threat to human health, conservation, and the economy. Surveillance is a critical component to mitigate the impact of animal diseases in these sectors. To monitor human diseases, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein) biosensors have proven instrumental as diagnostic tools capable of detecting unique DNA and RNA sequences related to their associated pathogens. However, despite the significant advances in the general development of CRISPR-Cas biosensors, their use to support wildlife disease management is lagging. In some cases, wildlife diseases of concern could be rapidly surveyed using these tools with minimal technical, operational, or cost requirements to end users. This review explores the potential to further leverage this technology to advance wildlife disease monitoring and highlights how concerted standardization of protocols can help to ensure data reliability.

Effects of snake fungal disease (ophidiomycosis) on the skin microbiome across two major experimental scales

Emerging infectious diseases are increasingly recognized as a significant threat to global biodiversity conservation. Elucidating the relationship between pathogens and the host microbiome could lead to novel approaches for mitigating disease impacts. Pathogens can alter the host microbiome by inducing dysbiosis, an ecological state characterized by a reduction in bacterial alpha diversity, an increase in pathobionts, or a shift in beta diversity. We used the snake fungal disease (SFD; ophidiomycosis), system to examine how an emerging pathogen may induce dysbiosis across two experimental scales. We used quantitative polymerase chain reaction, bacterial amplicon sequencing, and a deep learning neural network to characterize the skin microbiome of free-ranging snakes across a broad phylogenetic and spatial extent. Habitat suitability models were used to find variables associated with fungal presence on the landscape. We also conducted a laboratory study of northern watersnakes to examine temporal changes in the skin microbiome following inoculation with Ophidiomyces ophidiicola. Patterns characteristic of dysbiosis were found at both scales, as were nonlinear changes in alpha and alterations in beta diversity, although structural-level and dispersion changes differed between field and laboratory contexts. The neural network was far more accurate (99.8% positive predictive value [PPV]) in predicting disease state than other analytic techniques (36.4% PPV). The genus Pseudomonas was characteristic of disease-negative microbiomes, whereas, positive snakes were characterized by the pathobionts Chryseobacterium, Paracoccus, and Sphingobacterium. Geographic regions suitable for O. ophidiicola had high pathogen loads (>0.66 maximum sensitivity + specificity). We found that pathogen-induced dysbiosis of the microbiome followed predictable trends, that disease state could be classified with neural network analyses, and that habitat suitability models predicted habitat for the SFD pathogen.

The state of the bats in North America

The world's rich diversity of bats supports healthy ecosystems and important ecosystem services. Maintaining healthy biological systems requires prompt identification of threats to biodiversity and immediate action to protect species, which for wide-ranging bat species that span geopolitical boundaries warrants international coordination. Anthropogenic forces drive the threats to bats throughout North America and the world. We conducted an international expert elicitation to assess the status of 153 bat species in Canada, the United States, and Mexico. We used expert assessment to determine the conservation status, highest impact threats, and recent population trends for these species. We found that 53% of North American bat species have moderate to very high risk of extinction in the next 15 years. The highest impact threats varied with species and country, and four IUCN threat categories had the greatest overall impacts: Climate Change, Problematic Species (including disease), Agriculture, and Energy Production. Experts estimated that 90% of species assessed had decreasing population trends over the past 15 years, demonstrating the need for conservation action. Although the state of North American bats is concerning, we identify threats that can be addressed through internationally collaborative, proactive, and protective actions to support the recovery and resilience of North American bat species.

Bat Ecology and Microbiome of the Gut: A Narrative Review of Associated Potentials in Emerging and Zoonotic Diseases

In this review, we tentatively tried to connect the most recent findings on the bat microbiome and to investigate on their microbial communities, that may vary even in conspecific hosts and are influenced by host physiology, feeding behavior and diet, social interactions, but also by habitat diversity and climate change. From a conservation perspective, understanding the potentially negative and indirect effects of habitat destruction on animal microbiota can also play a crucial role in the conservation and management of the host itself. According to the One Health concept, which recognizes an interdependence between humans, animals, and the environment, bat microbiota represents an indicator of host and environmental health, besides allowing for evaluation of the risk of emerging infectious diseases. We noticed that a growing number of studies suggest that animal microbiota may respond in various ways to changes in land use, particularly when such changes lead to altered or deficient food resources. We have highlighted that the current literature is strongly focused on the initial phase of investigating the microbial communities found in Chiroptera from various habitats. However, there are gaps in effectively assessing the impacts of pathogens and microbial communities in general in animal conservation, veterinary, and public health. A deeper understanding of bat microbiomes is paramount to the implementation of correct habitat and host management and to the development of effective surveillance protocols worldwide.

Inter- and intraspecific variability of total mercury concentrations in bats of Texas (USA)

Exposure to mercury (Hg) may cause deleterious health effects in wildlife, including bats. Texas produces more Hg pollution than any other state in the United States, yet only one study has examined Hg accumulation in bats. This study measured the concentration of total Hg (THg) in fur (n = 411) collected from ten bat species across 32 sites in eastern and central Texas, USA. Fur THg concentrations were compared among species, and when samples sizes were large enough, between sex and life stage within a species, and the proximity to coal-fired power plants. For all sites combined and species with a sample size ≥8, mean THg concentrations (μg/g dry weight) were greatest in tri-colored bats (Perimyotis subflavus; 6.04), followed by evening bats (Nycticeius humeralis; 5.89), cave myotis (Myotis velifer; 2.11), northern yellow bats (Lasiurus intermedius; 1.85), Brazilian free-tailed bats (Tadarida brasiliensis; 1.03), and red bats (Lasiurus borealis/blossevillii; 0.974), and lowest in hoary bats (Lasiurus cinereus; 0.809). Within a species, fur THg concentrations did not significantly vary between sex for the five examined species (red bat, northern yellow bat, cave myotis, evening bat, Brazilian free-tailed bat) and only between life stage in evening bats. Site variations in fur THg concentrations were observed for evening bats, tri-colored bats, and Brazilian free-tailed bats. Evening bats sampled closer to point sources of Hg pollution had greater fur THg concentrations than individuals sampled further away. Sixteen percent of evening bats and 8.7% of tri-colored bats had a fur THg concentration exceeding the 10 μg/g toxicity threshold level, suggesting that THg exposure may pose a risk to the health of bats in Texas, particularly those residing in east Texas and on the upper Gulf coast. The results of this study can be incorporated into future management and recovery plans for bats in Texas.

Fungal and bat diversities along a landscape gradient in central Mexico

Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern.

Structure and assembly process of skin fungal communities among bat species in northern China

Background

The skin fungal communities of animals play a crucial role in maintaining host health and defending against pathogens. Because fungal infections can affect the skin microbiota of bats, gaining a comprehensive understanding of the characteristics of healthy bat skin fungal communities and the ecological processes driving them provides valuable insights into the interactions between pathogens and fungi.

Methods

We used Kruskal-Wallis tests and Permutational Multivariate Analysis of Variance (PERMANOVA) to clarify differences in skin fungal community structure among bat species. A Generalized Linear Model (GLM) based on a quasi-Poisson distribution and partial distance-based redundancy analysis (db-RDA) was performed to assess the influence of variables on skin fungal communities. Using community construction models to explore the ecological processes driving fungal community changes, t-tests and Wilcoxon tests were used to compare the alpha diversity and species abundance differences between the fungal structure on bat species' skin and the environmental fungal pool.

Results

We found significant differences in the composition and diversity of skin fungal communities among bat species influenced by temperature, sampling site, and body mass index. Trophic modes and skin fungal community complexity also varied among bat species. Null model and neutral model analysis demonstrated that deterministic processes dominated the assembly of skin fungal communities, with homogeneous selection as the predominant process. Skin fungal communities on bat species were impacted by the environmental fungal reservoir, and actively selected certain amplicon sequence variants (ASVs) from the environmental reservoir to adhere to the skin.

Conclusion

In this study, we revealed the structure and the ecological process driving the skin fungal community across bat species in northern China. Overall, these results broaden our knowledge of skin fungal communities among bat species, which may be beneficial to potential strategies for the protection of bats in China.

Impact of putatively beneficial genomic loci on gene expression in little brown bats (Myotis lucifugus, Le Conte, 1831) affected by white-nose syndrome

Genome-wide scans for selection have become a popular tool for investigating evolutionary responses in wildlife to emerging diseases. However, genome scans are susceptible to false positives and do little to demonstrate specific mechanisms by which loci impact survival. Linking putatively resistant genotypes to observable phenotypes increases confidence in genome scan results and provides evidence of survival mechanisms that can guide conservation and management efforts. Here we used an expression quantitative trait loci (eQTL) analysis to uncover relationships between gene expression and alleles associated with the survival of little brown bats (Myotis lucifugus) despite infection with the causative agent of white-nose syndrome. We found that 25 of the 63 single-nucleotide polymorphisms (SNPs) associated with survival were related to gene expression in wing tissue. The differentially expressed genes have functional annotations associated with the innate immune system, metabolism, circadian rhythms, and the cellular response to stress. In addition, we observed differential expression of multiple genes with survival implications related to loci in linkage disequilibrium with focal SNPs. Together, these findings support the selective function of these loci and suggest that part of the mechanism driving survival may be the alteration of immune and other responses in epithelial tissue.

White adipose tissue remodeling in Little Brown Myotis (Myotis lucifugus) with white-nose syndrome

White-nose syndrome (WNS) is a fungal wildlife disease of bats that has caused precipitous declines in certain Nearctic bat species. A key driver of mortality is premature exhaustion of fat reserves, primarily white adipose tissue (WAT), that bats rely on to meet their metabolic needs during winter. However, the pathophysiological and metabolic effects of WNS have remained ill-defined. To elucidate metabolic mechanisms associated with WNS mortality, we infected a WNS susceptible species, the Little Brown Myotis (Myotis lucifugus), with Pseudogymnoascus destructans (Pd) and collected WAT biopsies for histology and targeted lipidomics. These results were compared to the WNS-resistant Big Brown Bat (Eptesicus fuscus). A similar distribution in broad lipid class was observed in both species, with total WAT primarily consisting of triacylglycerides. Baseline differences in WAT chemical composition between species showed that higher glycerophospholipids (GPs) levels in E. fuscus were dominated by unsaturated or monounsaturated moieties and n-6 (18:2, 20:2, 20:3, 20:4) fatty acids. Conversely, higher GP levels in M. lucifugus WAT were primarily compounds containing n-3 (20:5 and 22:5) fatty acids. Following Pd-infection, we found that perturbation to WAT reserves occurs in M. lucifugus, but not in the resistant E. fuscus. A total of 66 GPs (primarily glycerophosphocholines and glycerophosphoethanolamines) were higher in Pd-infected M. lucifugus, indicating perturbation to the WAT structural component. In addition to changes in lipid chemistry, smaller adipocyte sizes and increased extracellular matrix deposition was observed in Pd-infected M. lucifugus. This is the first study to describe WAT GP composition of bats with different susceptibilities to WNS and highlights that recovery from WNS may require repair from adipose remodeling in addition to replenishing depot fat during spring emergence.

The skin I live in: Pathogenesis of white-nose syndrome of bats

The emergence of white-nose syndrome (WNS) in North America has resulted in mass mortalities of hibernating bats and total extirpation of local populations. The need to mitigate this disease has stirred a significant body of research to understand its pathogenesis. Pseudogymnoascus destructans, the causative agent of WNS, is a psychrophilic (cold-loving) fungus that resides within the class Leotiomycetes, which contains mainly plant pathogens and is unrelated to other consequential pathogens of animals. In this review, we revisit the unique biology of hibernating bats and P. destructans and provide an updated analysis of the stages and mechanisms of WNS progression. The extreme life history of hibernating bats, the psychrophilic nature of P. destructans, and its evolutionary distance from other well-characterized animal-infecting fungi translate into unique host-pathogen interactions, many of them yet to be discovered.

Pathogenic strategies of Pseudogymnoascus destructans during torpor and arousal of hibernating bats

Millions of hibernating bats across North America have died from white-nose syndrome (WNS), an emerging disease caused by a psychrophilic (cold-loving) fungus, Pseudogymnoascus destructans, that invades their skin. Mechanisms of P. destructans invasion of bat epidermis remain obscure. Guided by our in vivo observations, we modeled hibernation with a newly generated little brown bat (Myotis lucifugus) keratinocyte cell line. We uncovered the stealth intracellular lifestyle of P. destructans, which inhibits apoptosis of keratinocytes and spreads through the cells by two epidermal growth factor receptor (EGFR)-dependent mechanisms: active penetration during torpor and induced endocytosis during arousal. Melanin of endocytosed P. destructans blocks endolysosomal maturation, facilitating P. destructans survival and germination after return to torpor. Blockade of EGFR aborts P. destructans entry into keratinocytes.

Heart rate monitoring reveals differential seasonal energetic trade-offs in male noctule bats

Understanding how animals meet their daily energy requirements is critical in our rapidly changing world. Small organisms with high metabolic rates can conserve stored energy when food availability is low or increase energy intake when energetic requirements are high, but how they balance this in the wild remains largely unknown. Using miniaturized heart rate transmitters, we continuously quantified energy expenditure, torpor use and foraging behaviour of free-ranging male bats (Nyctalus noctula) in spring and summer. In spring, bats used torpor extensively, characterized by lowered heart rates and consequently low energy expenditures. In contrast, in summer, bats consistently avoided torpor, even though they could have used this low-energy mode. As a consequence, daytime heart rates in summer were three times as high compared with the heart rates in spring. Daily energy use increased by 42% during summer, despite lower thermogenesis costs at higher ambient temperatures. Likely, as a consequence, bats nearly doubled their foraging duration. Overall, our results indicate that summer torpor avoidance, beneficial for sperm production and self-maintenance, comes with a high energetic cost. The ability to identify and monitor such vulnerable energetic life-history stages is particularly important to predict how species will deal with increasing temperatures and changes in their resource landscapes.

Disturbance of hibernating bats due to researchers entering caves to conduct hibernacula surveys

Estimating population changes of bats is important for their conservation. Population estimates of hibernating bats are often calculated by researchers entering hibernacula to count bats; however, the disturbance caused by these surveys can cause bats to arouse unnaturally, fly, and lose body mass. We conducted 17 hibernacula surveys in 9 caves from 2013 to 2018 and used acoustic detectors to document cave-exiting bats the night following our surveys. We predicted that cave-exiting flights (i.e., bats flying out and then back into caves) of Townsend's big-eared bats (Corynorhinus townsendii) and western small-footed myotis (Myotis ciliolabrum) would be higher the night following hibernacula surveys than on nights following no surveys. Those two species, however, did not fly out of caves more than predicted the night following 82% of surveys. Nonetheless, the activity of bats flying out of caves following surveys was related to a disturbance factor (i.e., number of researchers × total time in a cave). We produced a parsimonious model for predicting the probability of Townsend's big-eared bats flying out of caves as a function of disturbance factor and ambient temperature. That model can be used to help biologists plan for the number of researchers, and the length of time those individuals are in a cave to minimize disturbing bats.

Automated echolocation classifiers vary in accuracy for northeastern U.S. bat species

Acoustic surveys of bat echolocation calls are an important management tool for determining presence and probable absence of threatened and endangered bat species. In the northeastern United States, software programs such as Bat Call Identification (BCID), Kaleidoscope Pro (KPro), and Sonobat can automatically classify ultrasonic detector sound files, yet the programs' accuracy in correctly classifying calls to species has not been independently assessed. We used 1,500 full-spectrum reference calls with known identities for nine northeastern United States bat species to test the accuracy of these programs using calculations of Positive Predictive Value (PPV), Negative Predictive Value (NPV), Sensitivity (SN), Specificity (SP), Overall Accuracy, and No Information Rate. We found that BCID performed less accurately than other programs, likely because it only operates on zero-crossing data and may be less accurate for recordings converted from full-spectrum to zero-crossing. NPV and SP values were high across all species categories for SonoBat and KPro, indicating these programs' success at avoiding false positives. However, PPV and SN values were relatively low, particularly for individual Myotis species, indicating these programs are prone to false negatives. SonoBat and KPro performed better when distinguishing Myotis species from non-Myotis species. We expect less accuracy from these programs for acoustic recordings collected under normal working conditions, and caution that a bat acoustic expert should verify automatically classified files when making species-specific regulatory or conservation decisions.

Rapid Evolution of Resistance and Tolerance Leads to Variable Host Recoveries following Disease-Induced Declines

AbstractRecoveries of populations that have suffered severe disease-induced declines are being observed across disparate taxa. Yet we lack theoretical understanding of the drivers and dynamics of recovery in host populations and communities impacted by infectious disease. Motivated by disease-induced declines and nascent recoveries in amphibians, we developed a model to ask the following question: How does the rapid evolution of different host defense strategies affect the transient recovery trajectories of hosts following pathogen invasion and disease-induced declines? We found that while host life history is predictably a major driver of variability in population recovery trajectories (including declines and recoveries), populations that use different host defense strategies (i.e., tolerance, avoidance resistance, and intensity-reduction resistance) experience notably different recoveries. In single-species host populations, populations evolving tolerance recovered on average four times slower than populations evolving resistance. Moreover, while populations using avoidance resistance strategies had the fastest potential recovery rates, these populations could get trapped in long transient states at low abundance prior to recovery. In contrast, the recovery of populations evolving intensity-reduction resistance strategies were more consistent across ecological contexts. Overall, host defense strategies strongly affect the transient dynamics of population recovery and may affect the ultimate fate of real populations recovering from disease-induced declines.

Multiresidue analysis of bat guano using GC-MS/MS

Bats are the second largest mammalian order and are an endangered species group with a strong need for contamination monitoring. To facilitate non-invasive monitoring of the ecological burden in bat populations, a multiresidue method for the simultaneous quantification of 119 analytes including pesticides, persistent organic pollutants (POPs), active pharmaceutical ingredients (APIs), polycyclic aromatic hydrocarbons (PAHs), UV blockers, plasticizers, and other emerging pollutants in bat guano with gas chromatography tandem mass spectrometry (GC-MS/MS) was developed. Sample preparation and clean-up were performed with a modified QuEChERS approach based on DIN EN 15662. The method uses 1.00 g bat guano as sample with acetonitrile and water for liquid-liquid extraction. Phase separation is assisted by citrate-buffered salting out agent. For clean-up of the extract, primary secondary amine (PSA) was combined with graphitized carbon black (GCB). The lower limits of quantification (LLOQ) ranged between 2.5 and 250 µg kg-1. Linearity was shown in a concentration range from the respective LLOQs to 1250 µg kg-1. The median of the mean recovery was 102.4%. Precision was tested at three concentrations. Method and injection precision were adequate with a relative standard deviation (RSD) below 20%. Furthermore, the comparative analysis with LC-MS/MS demonstrated the reliability of the results and provided a valuable extension of the analytical scope. As proof of concept, three guano samples from a German nursery roost of Myotis myotis were analysed. The results show a time-dependent change in contaminant concentration, highlighting the strong need for non-invasive contamination monitoring of whole bat populations.

A Palearctic view of a bat fungal disease

The fungal infection causing white-nose disease in hibernating bats in North America has resulted in dramatic population declines of affected species, since the introduction of the causative agent Pseudogymnoascus destructans. The fungus is native to the Palearctic, where it also infects several bat species, yet rarely causes severe pathology or the death of the host. Pseudogymnoascus destructans infects bats during hibernation by invading and digesting the skin tissue, resulting in the disruption of torpor patterns and consequent emaciation. Relations among pathogen, host, and environment are complex, and individuals, populations, and species respond to the fungal pathogen in different ways. For example, the Nearctic Myotis lucifugus responds to infection by mounting a robust immune response, leading to immunopathology often contributing to mortality. In contrast, the Palearctic M. myotis shows no significant immunological response to infection. This lack of a strong response, resulting from the long coevolution between the hosts and the pathogen in the pathogen's native range, likely contributes to survival in tolerant species. After more than 15 years since the initial introduction of the fungus to North America, some of the affected populations are showing signs of recovery, suggesting that the fungus, hosts, or both are undergoing processes that may eventually lead to coexistence. The suggested or implemented management methods of the disease in North America have encompassed, for example, the use of probiotics and fungicides, vaccinations, and modifying the environmental conditions of the hibernation sites to limit the growth of the pathogen, intensity of infection, or the hosts' responses to it. Based on current knowledge from Eurasia, policy makers and conservation managers should refrain from disrupting the ongoing evolutionary processes and adopt a holistic approach to managing the epizootic.

The effects of spatially-constrained treatment regions upon a model of wombat mange

The use of therapeutic agents is a critical option to manage wildlife disease, but their implementation is usually spatially constrained. We seek to expand knowledge around the effectiveness of management of environmentally-transmitted Sarcoptes scabiei on a host population, by studying the effect of a spatially constrained treatment regime on disease dynamics in the bare-nosed wombat Vombatus ursinus. A host population of wombats is modelled using a system of non-linear partial differential equations, a spatially-varying treatment regime is applied to this population and the dynamics are studied over a period of several years. Treatment could result in mite decrease within the treatment region, extending to a lesser degree outside, with significant increases in wombat population. However, the benefits of targeted treatment regions within an environment are shown to be dependent on conditions at the start (endemic vs. disease free), as well as on the locations of these special regions (centre of the wombat population or against a geographical boundary). This research demonstrates the importance of understanding the state of the environment and populations before treatment commences, the effects of re-treatment schedules within the treatment region, and the transient large-scale changes in mite numbers that can be brought about by sudden changes to the environment. It also demonstrates that, with good knowledge of the host-pathogen dynamics and the spatial terrain, it is possible to achieve substantial reduction in mite numbers within the target region, with increases in wombat numbers throughout the environment.

Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats

Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.

Validation of a Field-Portable, Handheld Real-Time PCR System for Detecting Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome in Bats

White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has decimated bat populations across North America. Despite ongoing management programs, WNS continues to expand into new populations, including in US states previously thought to be free from the pathogen and disease. This expansion highlights a growing need for surveillance tools that can be used to enhance existing monitoring programs and support the early detection of P. destructans in new areas. We evaluated the feasibility of using a handheld, field-portable, real-time (quantitative) PCR (qPCR) thermocycler known as the Biomeme two3 and the associated field-based nucleic acid extraction kit and assay reagents for the detection of P. destructans in little brown bats (Myotis lucifugus). Results from the field-based protocol using the Biomeme platform were compared with those from a commonly used laboratory-based qPCR protocol. When using dilutions of known conidia concentrations, the lowest detectable concentration with the laboratory-based approach was 108.8 conidia/mL, compared with 1,087.5 conidia/mL (10 times higher, i.e., one fewer 10× dilution) using the field-based approach. Further comparisons using field samples suggest a high level of concordance between the two protocols, with positive and negative agreements of 98.2% and 100% respectively. The cycle threshold values were marginally higher for most samples using the field-based protocol. These results are an important step in establishing and validating a rapid, field-assessable detection platform for P. destructans, which is urgently needed to improve the surveillance and monitoring capacity for WNS and support on-the-ground management and response efforts.

Advances in understanding bat infection dynamics across biological scales

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

Hibernating female big brown bats (Eptesicus fuscus) adjust huddling and drinking behaviour, but not arousal frequency, in response to low humidity

Many mammals hibernate during winter, reducing energy expenditure via bouts of torpor. The majority of a hibernator's energy reserves are used to fuel brief, but costly, arousals from torpor. Although arousals likely serve multiple functions, an important one is to restore water stores depleted during torpor. Many hibernating bat species require high humidity, presumably to reduce torpid water loss, but big brown bats (Eptesicus fuscus) appear tolerant of a wide humidity range. We tested the hypothesis that hibernating female E. fuscus use behavioural flexibility during torpor and arousals to maintain water balance and reduce energy expenditure. We predicted: (1) E. fuscus hibernating in dry conditions would exhibit more compact huddles during torpor and drink more frequently than bats in high humidity conditions; and (2) the frequency and duration of torpor bouts and arousals, and thus total loss of body mass would not differ between bats in the two environments. We housed hibernating E. fuscus in temperature- and humidity-controlled incubators at 50% or 98% relative humidity (8°C, 110 days). Bats in the dry environment maintained a more compact huddle during torpor and drank more frequently during arousals. Bats in the two environments had a similar number of arousals, but arousal duration was shorter in the dry environment. However, total loss of body mass over hibernation did not differ between treatments, indicating that the two groups used similar amounts of energy. Our results suggest that behavioural flexibility allows hibernating E. fuscus to maintain water balance and reduce energy costs across a wide range of hibernation humidities.

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Effects of ophidiomycosis on movement, survival, and reproduction of eastern foxsnakes (Pantherophis vulpinus)

Ophidiomycosis (snake fungal disease) is caused by the fungal pathogen Ophidiomyces ophidiicola, which causes dermal lesions, occasional systemic infections, and in some cases, mortality. To better understand potential conservation implications of ophidiomycosis (i.e., population-level effects), we investigated its impacts on individual fitness in a population of endangered eastern foxsnakes (Pantherophis vulpinus). We tracked 38 foxsnakes over 6 years and quantified body condition, movement patterns, oviposition rates, and survival. Body condition, distance travelled, and oviposition rates were similar between snakes with and without ophidiomycosis. Interestingly, snakes that tested positive for the pathogen travelled farther, suggesting that movement through a greater diversity of habitats increases risk of exposure. Ophidiomycosis did not negatively affect survival, and most apparently infected snakes persisted in a manner comparable to snakes without ophidiomycosis. Only one mortality was directly attributed to ophidiomycosis, although infected snakes were overrepresented in a sample of snakes killed by predators. Overall, our results suggest that ophidiomycosis may have sublethal effects on eastern foxsnakes, but do not suggest direct effects on survival, ovipositioning, or viability of the study population.

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.

Effective conservation of subterranean-roosting bats

Bats frequently inhabit caves and other subterranean habitats and play a critical role in subterranean food webs. With escalating threats to subterranean ecosystems, identifying the most effective measures to protect subterranean-roosting bats is critical. We conducted a meta-analysis to evaluate the effectiveness of conservation and management interventions for subterranean-roosting bats. We used network analyses to determine to what extent interventions for bats overlap those used for other subterranean taxa. We conducted our analyses with data extracted from 345 papers recommending a total of 910 conservation interventions. Gating of roost entrances was applied to preserve bat populations in 21 studies, but its effectiveness was unclear. Habitat restoration and disturbance reduction positively affected bat populations and bat behavior, respectively, in ≤4 studies. Decontamination was assessed in 2 studies and positively affected bat populations, particularly in studies focused on reducing fungal spores associated with white-nose syndrome in North America. Monitoring of bat populations as an effective conservation strategy was unclear and infrequently tested. Only 4% of bat studies simultaneously considered other subterranean organisms. However, effective interventions for bat conservation had similarities with all other organisms. If other subterranean organisms are considered when applying interventions to conserve bats, they might also benefit.

Shifts in population density centers of a hibernating mammal driven by conflicting effects of climate change and disease

Populations wax and wane over time in response to an organism's interactions with abiotic and biotic forces. Numerous studies demonstrate that fluctuations in local populations can lead to shifts in relative population densities across the geographic range of a species over time. Fewer studies attempt to disentangle the causes of such shifts. Over four decades (1983-2022), we monitored populations of hibernating Indiana bats (Myotis sodalis) in two areas separated by ~110 km. The number of bats hibernating in the northern area increased from 1983 to 2011, while populations in the southern area remained relatively constant. We used simulation models and long-term weather data to demonstrate the duration of time bats must rely on stored fat during hibernation has decreased in both areas over that period, but at a faster rate in the northern area. Likewise, increasing autumn and spring temperatures shortened the periods of sporadic prey (flying insect) availability at the beginning and end of hibernation. Climate change thus increased the viability of northern hibernacula for an increasing number of bats by decreasing energetic costs of hibernation. Then in 2011, white-nose syndrome (WNS), a disease of hibernating bats that increases energetic costs of hibernation, was detected in the area. From 2011 to 2022, the population rapidly decreased in the northern area and increased in the southern area, completely reversing the northerly shift in population densities associated with climate change. Energy balance during hibernation is the singular link explaining the northerly shift under a changing climate and the southerly shift in response to a novel disease. Continued population persistence suggests that bats may mitigate many impacts of WNS by hibernating farther south, where insects are available longer each year.

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

Factors Predicting Apparent Ophidiomycosis in Wild Brown Watersnakes (Nerodia taxispilota)

Ophidiomycosis, also known as snake fungal disease, is caused by Ophidiomyces ophidiicola and is a threat to snake conservation worldwide. Ophidiomycosis has been reported throughout much of the eastern US, and outbreaks have been associated with local population declines of already strained populations. Previous studies report significant variability in ophidiomycosis among species sampled, with higher prevalence typically observed in Nerodia spp. Although ophidiomycosis can lead to morbidity and mortality in affected individuals, little is known about disease dynamics in free-ranging populations. Herein, we examine how individual-specific factors (e.g., life stage [immature, mature], contaminant status, sex, hemograms) may be associated with ophidiomycosis status in the brown watersnake (Nerodia taxispilota). During 2018-19, we sampled 97 N. taxispilota from five locations along the Savannah River in South Carolina and Georgia, US. Ophidiomyces ophidiicola DNA was detected in 66 snakes for a prevalence of 68% (95% confidence interval, 59-77). Mature snakes had a significantly higher risk of apparent ophidiomycosis (skin lesions present and quantitative PCR [qPCR], positive) relative to immature snakes. Snakes classified as having possible (skin lesions present, but qPCR negative) or apparent ophidiomycosis exhibited a relative azurophilia and heterophilia compared with individuals classified as negative (P≤0.037). Nerodia taxispilota in this region appear to have a high prevalence of apparent ophidiomycosis (22%; 95% CI, 14-31), similar to previous reports from the southeastern US. Additional epidemiologic investigations are warranted to further elucidate other individual-specific and environmental factors that may dictate disease risk and outcomes in affected populations.

When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation

The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.

White-nose syndrome restructures bat skin microbiomes

IMPORTANCE

Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative. The results of this study potentially suggest that microbiome-host interactions may determine the likelihood of infection. However, the contrasting relationship between Pd and the bacterial microbiomes of Myotis lucifugus and Perimyotis subflavus indicate that we are just beginning to understand how the bat microbiome interacts with a fungal invader such as Pd.

The rapid emergence of antifungal-resistant human-pathogenic fungi

During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.

Temporal dynamics of the bat wing transcriptome: Insight into gene-expression changes that enable protection against pathogen

Skin acts as a mechanical barrier between the body and its surrounding environment and plays an important role in resistance to pathogens. However, we still know little regarding skin responses to physiological changes, particularly with regard to responses against potential pathogens. We herein executed RNA-seq on the wing of the Rhinolophus ferrumequinum to assess gene-expression variations at four physiological stages: pre-hibernation, hibernation (early-hibernation and late-hibernation), and post-hibernation, as well as the gene-expression patterns of infected and uninfected bats with the Pseudogymnoascus destructans (Pd). Our results showed that a greater number of differentially expressed genes between the more disparate physiological stages. Functional enrichment analysis showed that the down-regulated response pathways in hibernating bats included phosphorus metabolism and immune response, indicating metabolic suppression and decreased whole immune function. We also found up-regulated genes in post-hibernating bats that included C-type lectin receptor signalling, Toll-like receptor signalling pathway, and cell adhesion, suggesting that the immune response and skin integrity of the wing were improved after bats emerged from their hibernation and that this facilitated clearing Pd from the integument. Additionally, we found that the genes involved in cytokine or chemokine activity were up-regulated in late-hibernation compared to early-hibernation and that FOSB regulation of immune cell activation was differentially expressed in bats infected with Pd during late-hibernation, implying that the host's innate immune function was enhanced during late-hibernation so as to resist pathogenic infection. Our findings highlight the concept that maintenance of intrinsic immunity provides protection against pathogenic infections in highly resistant bats.

Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation

The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.

Habitat suitability mapping using logistic regression analysis of long-term bioacoustic bat survey dataset in the Cassadaga Creek watershed (USA)

Bat species show global ecological importance, yet their numbers are declining worldwide. Understanding bat-habitat interactions is crucial in terms of developing effective conservation plans. In an effort to model bat habitat suitability in the Cassadaga Creek watershed, long-term bioacoustic bat data (spanning 2009-2020) was compiled, georeferenced and statistically analyzed using logistic regression techniques. In total, 1600 bat occurrence records from five species of bat (559 Eptesicus fuscus, 560 Lasionycteris noctivagans, 143 Lasiurus borealis, 260 Lasiurus cinereus, and 78 Myotis lucifugus) were paired with pseudo-absence points to study the relationship between bat calling behavior and land cover. All bats but Myotis lucifugus had a statistically significant relationship with forested land cover, and all bats had negative interactions with agricultural habitats. Geospatial data was coupled with the statistical output to create maps of habitat suitability and echolocation calling density. This work provides a model that can be employed worldwide to evaluate bat habitat needs or patterns in echolocation behavior. Future research will incorporate a more recently collected dataset that is of greater geographic diversity with a larger number of environmental variables in the species distribution model.

KEEPING THE HEAT ON: WEIGHTED SURVEILLANCE FOR CHYTRID FUNGUS (BATRACHOCHYTRIUM DENDROBATIDIS) IN DIXIE VALLEY TOADS (ANAXYRUS [= BUFO] WILLIAMSI)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecurity measures to prevent the spread of pathogens, surveillance programs may enable early detection of pathogens, when management actions to limit the effects of pathogens on naïve hosts might be most beneficial. We analyzed surveillance data for the endangered and narrowly endemic Dixie Valley toad (Anaxyrus [= Bufo] williamsi) from two time periods (2011-2014 and 2019-2021) to estimate the minimum detectable prevalence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). We assessed if detection efficiency could be improved by using samples from both Dixie Valley toads and co-occurring introduced American bullfrogs (Lithobates catesbeianus) and literature-derived surveillance weights. We further evaluated a weighted surveillance design to increase the efficiency of surveillance efforts for Bd within the toad's small (<6 km2) range. We found that monitoring adult and larval American bullfrogs would probably detect Bd more efficiently than monitoring Dixie Valley toads alone. Given that no Bd was detected, minimum detectable prevalence of Bd was <3% in 2011-2014, and <5% (Dixie Valley toads only) and <10% (American bullfrogs only) in 2019-2021. Optimal management for Bd depends on the mechanisms underlying its apparent absence from the range of Dixie Valley toads, but a balanced surveillance scheme that includes sampling American bullfrogs to increase the likelihood of detecting Bd, and adult Dixie Valley toads to ensure broad spatial coverage where American bullfrogs do not occur, would probably result in efficient surveillance, which might permit timely management of Bd if it is detected.

Host infection and disease-induced mortality modify species contributions to the environmental reservoir

Environmental pathogen reservoirs exist for many globally important diseases and can fuel epidemics, influence pathogen evolution, and increase the threat of host extinction. Species composition can be an important factor that shapes reservoir dynamics and ultimately determines the outcome of a disease outbreak. However, disease-induced mortality can change species communities, indicating that species responsible for environmental reservoir maintenance may change over time. Here we examine the reservoir dynamics of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We quantified changes in pathogen shedding, infection prevalence and intensity, host abundance, and the subsequent propagule pressure imposed by each species over time. We find that highly shedding species are important during pathogen invasion, but contribute less over time to environmental contamination as they also suffer the greatest declines. Less infected species remain more abundant, resulting in equivalent or higher propagule pressure. More broadly, we demonstrate that high infection intensity and subsequent mortality during disease progression can reduce the contributions of high-shedding species to long-term pathogen maintenance.

Fungi's Swiss Army Knife: Pleiotropic Effect of Melanin in Fungal Pathogenesis during Cattle Mycosis

Fungal threats to public health, food security, and biodiversity have escalated, with a significant rise in mycosis cases globally. Around 300 million people suffer from severe fungal diseases annually, while one-third of food crops are decimated by fungi. Vertebrate, including livestock, are also affected. Our limited understanding of fungal virulence mechanisms hampers our ability to prevent and treat cattle mycoses. Here we aim to bridge knowledge gaps in fungal virulence factors and the role of melanin in evading bovine immune responses. We investigate mycosis in bovines employing a PRISMA-based methodology, bioinformatics, and data mining techniques. Our analysis identified 107 fungal species causing mycoses, primarily within the Ascomycota division. Candida, Aspergillus, Malassezia, and Trichophyton were the most prevalent genera. Of these pathogens, 25% produce melanin. Further research is required to explore the involvement of melanin and develop intervention strategies. While the literature on melanin-mediated fungal evasion mechanisms in cattle is lacking, we successfully evaluated the transferability of immunological mechanisms from other model mammals through homology. Bioinformatics enables knowledge transfer and enhances our understanding of mycosis in cattle. This synthesis fills critical information gaps and paves the way for proposing biotechnological strategies to mitigate the impact of mycoses in cattle.

Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions

More than 70 bat species are found in mainland Australia. While most studies of bat viromes focus on sampling seemingly healthy individuals, little is known about the viruses and bacteria associated with diseased bats. We performed traditional diagnostic techniques and metatranscriptomic sequencing on tissue samples from 43 Australian bats, comprising three flying fox (Pteropodidae) and two microbat species experiencing a range of disease syndromes, including mass mortality, neurological signs, pneumonia and skin lesions. Of note, we identified the recently discovered Hervey pteropid gammaretrovirus in a bat with lymphoid leukemia, with evidence of replication consistent with an exogenous virus. The possible association of Hervey pteropid gammaretrovirus with lymphoid leukemia clearly merits additional investigation. One novel picornavirus and at least three new astroviruses and bat pegiviruses were also identified in a variety of tissue types, as well as a number of likely bacterial pathogens or opportunistic infections, most notably Pseudomonas aeruginosa.

Antigenic and molecular evidence of Brucella sp.-associated epididymo-orchitis in frugivorous (Artibeus lituratus) and nectarivorous (Glossophaga soricina) bats in Brazil

This study included 47 free-ranging bats from the State of Minas Gerais, Brazil. Six bats (12.8%) had genital inflammatory lesions, and two of them (one Artibeus lituratus and one Glossophaga soricina, a frugivorous and a nectarivorous, respectively) were diagnosed with Brucella sp. infection through PCR, and antigens in intralesional macrophages were detected using immunohistochemistry.

Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA

Fungal pathogens threaten ecosystems and human health. Understanding the molecular basis of their virulence is key to develop new treatment strategies. Here, we characterize NCS2*, a point mutation identified in a clinical baker's yeast isolate. Ncs2 is essential for 2-thiolation of tRNA and the NCS2* mutation leads to increased thiolation at body temperature. NCS2* yeast exhibits enhanced fitness when grown at elevated temperatures or when exposed to oxidative stress, inhibition of nutrient signalling, and cell-wall stress. Importantly, Ncs2* alters the interaction and stability of the thiolase complex likely mediated by nucleotide binding. The absence of 2-thiolation abrogates the in vivo virulence of pathogenic baker's yeast in infected mice. Finally, hypomodification triggers changes in colony morphology and hyphae formation in the common commensal pathogen Candida albicans resulting in decreased virulence in a human cell culture model. These findings demonstrate that 2-thiolation of tRNA acts as a key mediator of fungal virulence and reveal new mechanistic insights into the function of the highly conserved tRNA-thiolase complex.

Infection of bats with Histoplasma species

Histoplasma species infect humans and animals, notably bats. Histoplasma species are thermally dimorphic fungi existing in mycelial form in the natural environment and in yeast form in infected tissues. In this narrative literature review, we summarize the occurrence of Histoplasma spp. in different species of bat tissues (n = 49) and in soil admixed with bat guano where the species of bat dwelling nearby has been identified (an additional 18 species likely infected) to provide an up-to-date summary of data. Most positive isolations are from the Americas and Caribbean, with some studies from Thailand, Malaysia, Nigeria, Slovenia, France, and Australia. We also summarize some of the early experimental work to elucidate pathogenicity, latency, immune response, and faecal excretion in bats. Given the recent recognition of the global extent of histoplasmosis, thermal dimorphism in Histoplasma spp., and global heating, additional work on understanding the complex relationship between Histoplasma and bats is desirable.

COULD WHITE-NOSE SYNDROME MANIFEST DIFFERENTLY IN MYOTIS LUCIFUGUS IN WESTERN VERSUS EASTERN REGIONS OF NORTH AMERICA? A REVIEW OF FACTORS

White-nose syndrome (WNS) has notably affected the abundance of Myotis lucifugus (little brown myotis) in North America. Thus far, substantial mortality has been restricted to the eastern part of the continent where the cause of WNS, the invasive fungus Pseudogymnoascus destructans, has infected bats since 2006. To date, the state of Washington is the only area in the Western US or Canada (the Rocky Mountains and further west in North America) with confirmed cases of WNS in bats, and there the disease has spread more slowly than it did in Eastern North America. Here, we review differences between M. lucifugus in western and eastern parts of the continent that may affect transmission, spread, and severity of WNS in the West and highlight important gaps in knowledge. We explore the hypothesis that western M. lucifugus may respond differently to WNS on the basis of different hibernation strategies, habitat use, and greater genetic structure. To document the effect of WNS on M. lucifugus in the West most effectively, we recommend focusing on maternity roosts for strategic disease surveillance and monitoring abundance. We further recommend continuing the challenging work of identifying hibernation and swarming sites to better understand the microclimates, microbial communities, and role in disease transmission of these sites, as well as the ecology and hibernation physiology of bats in noncavernous hibernacula.

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.

Assessing the threat of bat-associated fungal pathogens

Fungal pathogens have become an increasingly important topic in recent decades. Yet whilst various cankers and blights have gained attention in temperate woodlands and crops, the scope for fungal pathogens of animals and their potential threat has received far less attention. With a shifting climate, the threat from fungal pathogens is predicted to increase in the future, thus understanding the spread of fungi over landscapes as well as taxa that may be at risk is of particular importance. Cave ecosystems provide potential refugia for various fungi, and roosts for bats. With their well vascularized wings and wide-ranging distributions, bats present potential fungal vectors. Furthermore, whilst bat immune systems are generally robust to bacterial and viral pathogens, they can be susceptible to fungal pathogens, particularly during periods of stress such as hibernation. Here we explore why bats are important and interesting vectors for fungi across landscapes and discuss knowledge gaps that require further research.

A big data-model integration approach for predicting epizootics and population recovery in a keystone species

Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.