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Das Wissen über fledermausassoziierte Lyssaviren in Hinblick auf die Diversität, Abundanz, geographische Verbreitung, Wirtsspezifität, Pathogenität und mögliche Übertragungswege ist lückenhaft. In Europa wird zur Überwachung der Fledermaustollwut die Untersuchung von moribunden oder toten Tieren (passive Surveillance) und/oder die Beprobung von freilebenden Fledermauspopulationen (aktive Surveillance) empfohlen. Ziel der vorliegenden Arbeit war es, den derzeitigen Kenntnisstand zum Vorkommen von fledermausassoziierten Lyssaviren in Deutschland zu erweitern und mit Daten anderer europäischer Länder zu vergleichen. Die Untersuchungen stützten sich dabei auf drei Teilprojekte: 1) Die initiale Statuserhebung und Analyse der Fledermaustollwut-Surveillance in Europa hat gezeigt, dass trotz internationaler Empfehlungen die Tollwut-Überwachung bei Fledermäusen uneinheitlich durchgeführt wird. Diese Unterschiede sind unter anderem die Folge (i) fehlender Zusammenarbeit zwischen Fledermausbiologen und Veterinär- sowie Gesundheitsbehörden, (ii) fehlender Netzwerke von Fledermaussachverständigen, (iii) länderspezifischer Regelungen, aber auch (iv) fehlenden Bewusstseins sowie Kenntnisstandes für die Fledermaustollwut in der Bevölkerung. 2) In Deutschland wurde zusätzlich zur Tollwut-Routinediagnostik eine intensivierte passive Tollwut-Surveillance (retrospektive Studie, 1998 – 2013) durchgeführt, bei der 5478 Tiere aus insgesamt 21 einheimischen Arten akquiriert und auf das Vorliegen einer Lyssavirusinfektion untersucht wurden. Insgesamt konnten 52 EBLV-1 Infektionen (E. serotinus (n=49), P. pipistrellus, P. nathusii, Pl. auritus) sowie drei EBLV-2 Infektionen (M. daubentonii) diagnostiziert werden. Die Untersuchungen verdeutlichen, dass diese retrospektive Studie im Vergleich zur Routinediagnostik entscheidende Vorteile in Bezug auf den Stichprobenumfang, das Artenspektrum sowie die Fehlerfreiheit von artbezogenen biologischen und epidemiologischen Daten und somit entscheidende Voraussetzungen für eine gezielte Risikobewertung einer potentiellen Gesundheitsgefährdung des Menschen durch fledermausassoziierte Lyssaviren bietet. 3) Im Rahmen der aktiven Tollwut-Surveillance (1998 – 2012) erfolgte an 42 Standorten in Deutschland die Beprobung von Fledermauspopulationen. Es wurden 4546 Maultupfer- und 1226 Serumproben von 18 Fledermausspezies untersucht. EBLV-1-spezifische RNA wurde in Maultupfern von fünf Breitflügelfledermäusen, einer Fransen- und einer Mopsfledermaus detektiert. In dieser Arbeit konnte erstmalig EBLV-1 aus einer RT-PCR-positiven Maultupferprobe von einer scheinbar gesunden Breitflügelfledermaus isoliert werden. Bei der serologischen Testung von Serumproben gegen EBLV-1 wurden virus-neutralisierende Antikörper in acht verschiedenen Spezies festgestellt, wobei hauptsächlich Seren von Breitflügelfledermäusen höhere Titer aufwiesen. Ein Vergleich von Ergebnissen verschiedener Sero-Surveillance-Studien ist durch das Fehlen standardisierter Testverfahren und durch kreuzneutralisierende Antikörper gegenüber Lyssaviren gleicher Phylogruppen kaum möglich. Die Daten der aktiven Surveillance liefern im Gegensatz zur passiven Surveillance nur begrenzte Erkenntnisse zum Vorkommen, der Prävalenz und Dynamik von Fledermaustollwut in einheimischen Fledermauspopulationen. Die Form der intensivierten passiven Surveillance sollte daher als Standard für eine zukünftige Surveillance der Fledermaustollwut in Deutschland und anderen europäischen Ländern betrachtet werden. Darüber hinaus wurde bei natürlich infizierten Fledermäusen (E. serotinus, M. daubentonii, P. nathusii) die Virusverteilung und -last in Geweben verschiedener Organe unter dem Aspekt möglicher Ausscheidungswege untersucht. Virus-spezifische RNA wurde in allen untersuchten Organen nachgewiesen; bedingt durch die neurotropen Eigenschaften der Lyssaviren wurde die höchste Viruslast im Gehirn festgestellt. Signifikant hohe Viruslasten waren zudem in der Speichel¬drüse nachweisbar. Zusätzlich zur Speicheldrüse scheint die Zunge ein Organ zu sein, in dem Virusreplikation und -ausscheidung stattfindet, da in verschiedenen zellulären Strukturen des Zungengewebes Lyssavirusantigen bzw. virale RNA histologisch nachgewiesen wurden. Die Ausscheidung und Übertragung von fledermausassoziierten Lyssaviren über den Harntrakt oder die Atemwege ist wissenschaftlich umstritten und konnte in dieser Studie immunhistochemisch nicht bestätigt werden.
Presumably every organism on earth is involved in at least one mutualistic interaction with one or several other species. To interact with each other, the species need traits that provide benefits to the partner species. Surprisingly, the function of traits for the stabilization of mutualisms has rarely been investigated, despite of a general lack of knowledge how mutualisms are maintained. The aim of this work was to find functional traits, which stabilize the mutualism between a bat species and a carnivorous pitcher plant in Northern Borneo. Kerivoula hardwickii is the only bat species known to roost in pitcher-shaped trapping organs of Palaeotropical pitcher plants (Nepenthes). These bats fertilize the pitcher plant Nepenthes hemsleyana with their nutritious nitrogen-rich faeces while roosting inside the pitchers. The plants have outsourced capture and digestion of arthropod prey to the bats on which they strongly rely for nutrient acquisition. The bats in contrast are less dependent on their mutualism partner as they also roost in pitchers of two further Nepenthes species as well as in developing furled leaves of various plant species in the order Zingiberales. In earlier studies, we found that N. hemsleyana outcompetes alternative roosts by providing high-quality roosts for the bats. However, which traits exactly stabilize the mutualism between K. hardwickii and N. hemsleyana was still unclear. I found that both the bats and the pitcher plants show traits, which have the potential to stabilize their interaction. On the level of morphological traits, I found that the pitchers have a low fluid level and a particular shape that provide just enough roosting space for one individual of the solitary K. hardwickii, a mother with juvenile or a mating couple. The bats have enlarged thumb and foot pads that enable them to cling to the smooth surfaces of their roosts without using their claws. This avoids damage to the sensitive N. hemsleyana pitchers. On the level of communicational traits, again N. hemsleyana acquired morphological structures that act as effective ultrasound-reflectors, which guide the echo-orientating bats to the opening of the pitchers and help the bats to identify their mutualism partner. The bats’ calls on the other hand are characterized by extraordinary high starting frequencies and broad bandwidths, which enable K. hardwickii to easily locate pitchers of N. hemsleyana and other Nepenthes species in their dense habitats. Finally, on the level of behavioural traits the bats often but not always prefer their mutualism partner to other roosts when they can select roosts in their natural environment or in behavioural experiments. The reason for this behaviour seems to be a combination of 1) N. hemsleyana’s superior quality compared to alternative roosts and 2) different roosting traditions of the bats. In conclusion, the mutualism between bats and pitcher plants is asymmetric as N. hemsleyana is more dependent on K. hardwickii than vice versa. For the plants bat faeces present their most important nutrient source. In contrast, K. hardwickii can select between alternative roosting plants. This asymmetric dependency is reflected in the specifity and function of the traits that stabilize the mutualism in each of the two involved species. Especially on the morphological level, N. hemsleyana seems to have evolved several traits that perfectly fit to K. hardwickii. In contrast, the bats’ traits more generally facilitate their roosting in funnel-shaped plant structures and their occurrence in cluttered habitats. Thus, they are probably exaptations (i.e. traits that evolved for another reason) that are nevertheless functional and stabilize the mutualism with N. hemsleyana. This plant‘s superior roost quality is likely a consequence of the competition with alternative roosting plants and is a pre-requisite for the bats to prefer N. hemsleyana. Moreover, my study confirms earlier findings that asymmetric dependencies support the stabilization of mutualistic interactions. Finally, my work indicates that the specifity of functional traits can be used as a measure to determine mutual dependencies of mutualistic partners.
Bats belong to the most gregarious and diverse mammals with highly complex social behaviors. Despite extensive research on their ecology and social behavior in some bat species, gained insights are restricted to only few of the more than 1300 species. In the recent past, bats have also become a central topic of a different branch of research: Since the 1990s bats came to the fore of virologists and immunologists due to the bats’ apparent importance as reservoir hosts and vectors of several (mostly tropical) diseases. While this research is focused mainly on emerging infectious diseases linked to bats, and their zoonotic potential, little has been invested regarding the link between disease transmission and bat social systems.
In my work, I aim at filling this gap by merging automated daily roosting observations, social network analysis, and a virological screening in Natterer’s bats (Myotis nattereri). In a collaborative approach, my co-workers and I analyzed the social structure of individually marked Natterer’s bats, their astrovirus detection rate and transmission pathways within their colony, as well as roosting interactions between different co-occurring con- and heterospecific bat colonies.
We discovered Natterer’s bats to display a very divergent social network structure that contradicts the findings of previous studies on large fission-fusion groups. Contrary to the modular social network structure found in e.g. primates or other bats species, the social network of Natterer’s bats consists of only one highly interconnected community. Moreover, although the close proximity between bat hosts in the colony should strongly promote direct transmission, we found indications that astrovirus infections follow at least partly an indirect transmission pathway via contaminated roost use. Lastly, our results prove that co-occurring con- and heterospecific bat colonies, e.g. as in this study Natterer’s bats, brown long-eared bats and Bechstein’s bats, can influence each other in their roost use by avoiding conspecific roosts and by being attracted towards those of heterospecifics. This holds implication for the transmission of parasites and pathogens within and between different colonies with opportunities for spillovers. To conclude, this multidisciplinary study led to valuable insights in the hitherto hidden mechanisms within and among bat colonies.
In times of recent climate change, mechanisms to deal with different environments (e.g. via dispersal to other habitats, or via in-situ responses such as genetic adaptation or phenotypic plasticity) are essential. In regions showing seasonality, organisms are already adapted to regular and, thus, often predictable environmental changes. One well-known strategy to survive periods of food shortage, especially during the winter, is hibernation. Although hibernation is already an adaptation to overcome unfavourable conditions, the optimal timing of hibernation to match for example food abundance peaks is likely to be influenced by changing climatic conditions, as expected during human-induced global change. Thus, the ability to respond to changes in optimal timing of hibernation can be crucial for organisms. All hibernators are positioned at the slow end of the slow-fast life history continuum. Longevity combined with a low annual reproductive output can result in slow recovery from population crashes and is expected to be associated with slow genetic adaptation. Therefore, it is assumed that phenotypic plasticity, a rather rapid and sometimes reversible process, is a crucial mechanism in long-lived organisms to adapt to changing environments. However, how differences in individual hibernation behaviour influence mortality and whether individuals are plastic with respect to their hibernation behaviour are largely unknown.
Recent studies suggest that climatic change can influence hibernation behaviour in various species differently, in a positive or negative way. Female Columbian ground squirrels (Urocitellus columbianus) delayed their emergence from hibernation with later snow melt and lower spring temperatures. Next to the environmental impact, emergence date showed a moderate heritability in female Columbian ground squirrels. Yellow-bellied marmots (Marmota flaviventris) emerged earlier from hibernation with warmer spring temperatures which resulted in a longer growing period for their offspring and, therefore, higher survival rates. In contrast, in alpine marmots (Marmota marmota) lower snow cover due to higher temperatures and, thus, less isolation led to lower juvenile survival. Negative effects, such as reduced juvenile survival, would be of high concern, especially for long-lived species with a low reproductive output.
Bats are exceptionally long-lived compared to other mammals of the same size and often show a low reproductive output with one offspring per year. This is especially true in the temperate zone where bats, furthermore, are characterized by seasonality and depend on hibernation during winter period to survive food and water shortage. Because bats are of high conservation concern it is of prime importance to understand their ability to respond to different climatic conditions and associated mortality costs.
The basis of this study was a five-year data set of 1047 RFID-tagged individuals from two bat species, Natterer’s bats (Myotis nattereri) and Daubenton’s bats (Myotis daubentonii), that were automatically tracked when entering or leaving the joint hibernaculum, “Brunnen Meyer”, located in north-western Germany. The two species are similar sized, share demographical traits and often occupy the same areas. Nevertheless, they differ in their foraging strategy and activity pattern during hibernation period. Natterer’s bats are able to glean insects from surfaces, even at low temperatures. Daubenton’s bats depend on flying arthropods and, thus, warmer temperatures. And indeed there is evidence that Natterer’s bats are able to hunt during hibernation period, while in Daubenton’s bats a lack of feeding during the hibernation period is suggested. Furthermore, Natterer’s bats are characterized by a higher activity at the hibernaculum throughout the hibernation period, while Daubenton’s bats on average arrive earlier, stay inactive through the winter and leave later in spring.
In both species, the aim was to investigate the impact of their individual hibernation behaviour, precisely the timing of departure in late winter and early spring, on mortality, their adjustment of departure timing to the North Atlantic Oscillation Index (NAO), as well as differences within and between the two species from 2011 until 2015.
To later on estimate the potential mortality costs of departure timing, gaining knowledge about the seasonal survival pattern (winter vs. summer) in the two species was a first necessity. In birds, particularly small species were described as winter-regulated populations with a higher mortality during winter. In contrast, in hibernating mammal species, such as bats, a relatively lower or similar winter survival compared to summer survival was shown. In this study, the analysed data demonstrated that the winter 2010/2011 was exceptionally catastrophic in Natterer’s bats and did not impact Daubenton’s bats. When excluding this catastrophic winter in Natterer’ bats, our results revealed a stable winter-summer-survival difference (higher winter and lower summer survival) in adult Natterer’s and Daubenton’s bats, with inter-annual variation in the level of survival which indicates a potential environmental impact on survival. This winter-summer survival pattern is in line with the survival pattern shown for other hibernators. Juveniles always had a lower survival rate than adult bats in both species. Nevertheless, the extent to which the species differ between seasons and age classes was stronger in Daubenton’s bats. They always showed a slightly higher winter survival and a lower summer survival than Natterer’s bats. Together with the catastrophic winter 2010/2011 in Natterer’s bats, this indicates a species-specific sensitivity to the timing of specific weather events which is in line with their foraging strategies and activity pattern during hibernation period.
With respect to emergence behaviour from the hibernaculum, the results of this study suggest considerable differences among individuals within as well as between bat species. In comparison to Daubenton’s bats, Natterer’s bats tuned their emergence more closely to weather conditions, specifically the NAO, a large scale weather index related to winter severity, and showed individual variation in behavioural plasticity. In Daubenton’s bats only the females responded to changing conditions and left earlier in individually-experienced warmer and milder winters, comparable to Natterer’s bats females. A potential reason might be reproductive advantages for the females resulting in a longer growing period for their offspring. The shown higher winter survival in adult bats of both species indicated already higher energy expenditure outside the hibernaculum. Thus, leaving early, being active and staying outside longer by itself bore a risk (exposure risk effect). Under consideration of longer exposure times, early departing individuals had on top of that an increased risk to die. This was not given in each year, but a species- and year-specific pattern was revealed. Natterer’s bats were only significantly affected by early departure in 2011, while the remaining years show no significant additional risk of leaving early. In Daubenton’s bats, the years 2014 and 2015 were associated with a significantly higher mortality of leaving early. This is in line with the hypothesis that Daubenton’s bats might not be able to hunt for insects leaving too early and do so as a best out of a bad job. Nevertheless, the year-specific pattern suggests that early bats might profit from advantageous weather conditions during early spring.
An additional hint for an environmental impact on early bat survival in at least Daubenton’s bats is that the median proportion of night hours above 3 °C within five days after departure was included in the model with the lowest AIC. However, the effect was not strong enough to be selected as the best model and, therefore, further analyses are needed to investigate this first hint.
In conclusion, the reduced winter survival of juveniles compared to adults highlights the importance of considering age class effects in studies that investigate seasonal survival patterns. The stable species-specific winter-summer-survival difference with a higher winter survival compared to summer survival, as well as the one catastrophic winter in Natterer’s bats underline the importance of including seasonal survival patterns in assessing potential fitness costs of changed behaviour. Furthermore, our results suggest that long-lived hibernating bat species have the potential to plastically adjust to changing climatic conditions, but this potential differs between species. Among-individual differences in emergence together with species-specific mortality costs of early emergence suggest the potential for natural selection to shape hibernation phenology. In summary, our findings suggest species-, population- and group-specific differences in the ability to respond to changing environments and, therefore, underline the necessity to further investigate local responses in various organisms to estimate consequences of recent climate change on a wider range.
Bats are special: although they have a small body size, bats are extremely long-lived and have a low annual reproductive output, which puts them at the ‘slow’ end of the slow-fast continuum of mammalian life-histories. Species typically respond to climate change by genetic adaptation, range shifts or phenotypic plasticity. However, limited dispersal behavior in many bat species and long generation times make it very likely, that adaptive responses in bats are rather driven by phenotypic plasticity than by genetic adaptation or range shifts. Changing weather patterns, a higher frequency of extreme weather events and overall rising temperatures, caused by climate change, will impact phenology, energy supply and energy expenditure. In species where adult survival largely shapes population dynamics, it is thus of crucial importance to understand how climate change affects individual fitness and fitness relevant traits by altering behavior and development.
In my study, I investigated how weather impacts behavior, fitness and fitness relevant traits in free ranging Natterer’s bats from two geographical regions (south vs. north) in Germany. In the Nature Park Nossentiner/Schwinzer Heide (northern region, NSH), long-term data for investigations on population dynamics are partially collected by hibernation counts. Although counting hibernating bats is a regularly applied method, it is still unclear to which degree human visits in the hibernaculum trigger energy consuming arousals and thus increase energy expenditure. Thus, I first investigated if hibernation counts potentially threaten winter survival by assessing the number of energy consuming arousals of hibernating Natterer’s bats (Myotis nattereri) and two other bat species (Pipistrellus spp., Plecotus auritus) using thermal imaging. Additionally, I used light barriers in the hibernacula to investigate the relative impact of winter temperatures and human visits on flight activity of hibernating bats. Secondly, I investigated effects on survival and reproduction during summer by analyzing capture-mark-recapture data from summer roosts. Data from summer roosts have been collected since 2011 in Würzburg (WB, south) and 1990 in the Nature Park (NSH, north). Based on these data, I analyzed the effect of intrinsic (e.g. age) and extrinsic(e.g. different weather parameters) factors on individual survival probability and reproductive success. I further focused on the question if individual body size is a fitness relevant trait in Natterer’s bats and how body size of young bats is affected by summer temperatures.
During hibernation, ambient temperatures were the most important driver for bat activity and were positively correlated with the number of flight passes in the light barrier, suggesting that bats can exploit foraging opportunities more frequently during warm weather bouts. Monitoring caused only a small number of arousals and only a slight increase in activity, which was less severe on warmer days, when activity was generally higher. Thus, I propose that benefits of hibernation counts outweigh the costs of human presence in the hibernaculum and unlikely threaten winter survival in hibernating bats.
In spring, increased precipitation during a short time window strongly reduced the probability of successful reproduction in first-year females (females that returned from first hibernation, FY). In terms of timing, this sensitive period comprises the implantation or early pregnancy, a time before substantial investment into embryo development. Moreover, I identified a positive correlation between a large body size and reproductive success in FY females. Given the evidence that suitable weather conditions during early life support juvenile growth and thus a large body size, my findings suggest that reproduction may be condition dependent in young females. Reproductive success of older females was not affected by either weather or individual parameters. This suggests that older and experienced females can better deal with adverse conditions.
To examine if beneficial weather conditions are linked to a large body size, I investigated the effect of ambient temperatures during the growing season on body size. I found that higher ambient temperatures during summer led to larger individuals, however, only in the northern population. In the on average colder North, warmer summers may benefit juvenile growth by reducing thermoregulatory costs and increasing prey abundance, whereas in the general warmer South, this effect might not be visible or relevant. When I analyzed the link between body size and survival, I revealed that larger adult females have higher survival rates. Given the fact, that a large body size is a response to beneficial early life conditions, this demonstrates the impact of early life conditions on long lasting fitness effects.
The results of my research lead to the assumption that warmer ambient temperatures have positive effects on Natterer’s bats, both during winter and summer. However, increased activity in response to rising winter temperatures, as expected under climate change scenarios, could be a serious thread for hibernating bats, if food availability does not increase in the same amount as bat activity. During summer, warmer temperatures may have positive effects on juvenile development in northern regions, but this effect could be negative in more southern regions by exceeding heat tolerance and resulting in water stress. This research highlights, that investigating periods of weather sensitivity on a finer time scale and also in a spatial context is of crucial importance to gain a better understanding for mechanisms leading to the impacts of weather on fitness.
As the animal-to-human interface becomes increasingly narrow, transmission events of zoonotic pathogens between animals and humans become more and more probable. While SARS-CoV-2 already accomplished a spillover infection to humans and is responsible for the current pandemic, the bat H9N2 IAV with so far unknown zoonotic potential was only recently discovered. In order to identify I) the role and potential of a newly discovered, potentially pre-pandemic virus, such as the bat H9N2, or II) possible future prevailing virus mutant variants of an already known pandemic virus, such as SARS-CoV-2, it is important to characterize these emerging viruses in vivo as soon and as good as possible.
The first objective in this dissertation (Publications I and II) therefore deals with the characterization of bat H9N2 and the estimation of its zoonotic or even pandemic potential.
In Publication I, a general susceptibility of directly inoculated Egyptian fruit bats to bat H9N2 was confirmed by successful seroconversion, although exhibiting only moderate viral shedding. All three contact animals remained seronegative, though one contact bat showed slight lesions in the histopathological analysis.
Publication II further addressed the question of the zoonotic potential of this virus. Inoculation of day-old turkey hatchlings demonstrated moderate susceptibility to bat H9N2 infection with a measurable seroconversion, while day-old chicken hatchlings were not susceptible to bat H9N2. Ferrets proved to be highly susceptible to bat H9N2 with high viral shedding, a transmission efficiency rate of 100% to direct contact animals at 2 days post contact, but with only minimal clinical signs. Importantly, the virus demonstrated the ability to evade the MxA-restriction factor and to replicate efficiently in human lung tissue explants. Furthermore, seasonal IAV- and standard IAV-vaccines showed no cross reactivity against the bat-N2 protein in humans. Therefore, further research on such viruses is urgently needed in order to prevent a renewed pandemic situation in the future as caused by SARS-CoV-2.
The second objective in this dissertation dealt with the identification and characterization of emerging SARS-CoV-2 Variants of Concern (VOCs).
Therefore, in Publication III, competitive infection experiments were performed using the Syrian golden hamster, the ferret, and transgenic mouse models (K18-hACE2 and hACE2-KI). These studies revealed replicative and transmissive predominance of Alpha VOC over Beta VOC, but not over SARS-CoV-2 WT in the hamster model, although Beta VOC substantially replicated in the lungs of donor animals. In contrast, the Alpha VOC had an unambiguous replication and transmission advantage over WT SARS-CoV-2 in the ferret and both mouse models. A recombinant SARS-CoV-2 WT-SAlpha virus helped to assign the fitness advantage of this variant particularly to the spike protein-associated mutations.
In Publication IV, in vitro results inferred an early replicative fitness advantage of Omicron BA.1 over Delta VOC, although the opposite was observed in competitively inoculated hamsters, ferrets and naive hACE2-KI mice. In addition, Publication IV demonstrated a disadvantage in transmission for the VOC Omicron BA.1 over the Delta VOC and a lack of susceptibility of ferrets after a single infection with the VOC Omicron BA.1. An mRNA vaccination of K18-hACE2 mice caused a drastic reduction of infectious virus particles in organ material following an infection with a recombinant SARS-CoV-2 WT-SDelta, but not when challenged with the SARS-CoV-2 SOmicron BA.1 clone.
This dissertation includes numerous, comprehensive experimental studies that are generally important for the characterization of emerging, potentially pre-pandemic viruses and may provide crucial information about the future dominance of certain virus variants in an ongoing pandemic. Here, the need for the use of a variety of animal models becomes apparent. By characterizing and classifying potentially zoonotic strains, these methods will help to better prepare for potentially upcoming pandemics and, in the case of a zoonotic or even pandemic event, to better detect and understand the circulating strains and their evolution.
Amid the current global biodiversity crisis, being able to accurately monitor the changing state of biodiversity is essential for successful conservation actions and policy. Despite the pressing need for reliable and cost-effective monitoring methods, collecting such data remains extremely difficult for elusive species, such as temperate zone bats. Although bats are important indicators of environmental changes, monitoring bat populations is challenging because they are nocturnal, volant, small, and highly sensitive to human activities and disturbance. Thus far, population trends of temperate zone bats have been mainly based on visual surveys, including winter hibernation counts at underground sites. However, as bats may not always be roosting in visible locations within the hibernacula, it is currently unknown how these estimates relate to actual population sizes.
Infrared light barriers combined with camera traps are a novel method to monitor bats at underground sites. When installed at the entrance of hibernacula, infrared light barriers have the potential to estimate site-level population sizes more accurately than visual surveys, by counting all bats flying in and out of the site. Moreover, camera traps, consisting of a digital camera and white flash, can be used for species-level identification. However, for this new method to be applicable as a large-scale bat monitoring technique, it is important to characterize it with regard to three main criteria: is the method minimally invasive, is it accurate, and is it scalable in terms of spatial and temporal resolution? Therefore, the purpose of this thesis was to investigate the invasiveness and accuracy of this novel bat monitoring method, and to develop standardized and automated data analysis pipelines, both for the light barrier and camera trap data, to support the deployment of this method at scale.
In Publication I, we used light barrier data, infrared video recordings and acoustic data from an experimental field study to investigate whether the white flash of the camera trap has any measurable short- or long-term effect on bat activity and behavior. The flash of the camera trap was turned on and off every week at each site, which allowed us to compare the activity and behavior of bats between flash-on and flash-off nights. We found that despite the high sensitivity of bats to disturbance, they did not change their nightly activity patterns, flight direction, echolocation behavior, or long-term site use in response to the white flash of the camera trap. Based on these results, we concluded that camera traps using a white flash are a minimally invasive method for monitoring bat populations at hibernacula, providing high quality images that allows species-level identification.
In Publication II, we used infrared video surveillance to quantify the accuracy of infrared light barriers, and we described a standardized methodology to estimate population sizes and trends of hibernating bat assemblages using light barrier data. We showed that light barrier accuracy varies based on the model and location of the installation relative to the entrance, with the best combination achieving nearly perfect accuracy over the spring emergence phase. When compared to light barrier-based estimates, we found that visual counts markedly underestimated population sizes, recovering less than 10% of the bats at the most complex hibernacula. Moreover, light barrier-based population trends showed regional patterns of growth and decline that were not detectable using the visual count data. Overall, we established that the light barrier data can be used to estimate the population size and trends of hibernating bat assemblages with unprecedented accuracy and in a standardized way.
In Publication III, we described a deep learning-based tool, BatNet, that can accurately and efficiently identify bat species from camera trap images. The baseline model was trained to identify 13 European bat species or species complexes using camera trap images collected at 32 hibernation sites (i.e., trained sites). We showed that the baseline model performance was very high across all 13 bat species on trained sites, as well as on untrained sites when the camera angle and distance from the entrance were comparable to the training images. At untrained sites with more atypical camera placements, we demonstrated the ability to retrain the baseline model and achieve an accuracy comparable to the trained sites. Additionally, we showed that the model can learn to identify a new species, while maintaining high classification accuracy for all original species. Finally, we established that BatNet can be used to accurately describe ecological metrics from camera trap images (i.e., species diversity, relative abundance, and species-specific phenology) that are relevant for bat conservation.
We conclude that infrared light barriers and camera traps offer a minimally invasive and accurate method to monitor site-level bat population trends and species-specific phenological estimates at underground sites. Such remote data collection approaches are particularly relevant for monitoring large, complex hibernation sites, where traditional visual surveys are not feasible or account only for a small fraction of the actual population. Combining this automated monitoring method with a deep learning-based species identification tool, BatNet, allows us quickly and accurately analyze millions of camera trap images resulting from large-scale, long-term camera trap studies. As a result, we can gain unprecedented insights into the behavior and population dynamics of these enigmatic species, drastically improving our ability to support data-driven bat conservation.
Emerging infectious diseases are among the greatest threats to human, animal and plant health as well as to global biodiversity. They often arise following the human-mediated transport of a pathogen beyond its natural geographic range, where host species are typically not well adapted due to a lack of co-evolutionary host-pathogen dynamics. One such pathogen is the fungus Pseudogymnoascus destructans (Pd), which causes White-Nose disease in hibernating bats. While Pd was first observed in North America where it has led to mass-mortalities in some bat species, the pathogen originates from Eurasia where infection is not associated with mortality. Most of the Pd research has focused on the invasive North American range, which likely underestimated the genetic structure of the pathogen and the role it might play in the disease dynamics.
In my work, I therefore evaluated the genetic structure of Pd in its native range with the aim of uncovering cryptic diversity and further use population genetic data to address some key ecological aspects of the disease dynamics. With an extensive reference collection of more than 5,000 isolates from 27 countries I first demonstrated strong differentiation between two monophyletic clades across several genetic measures (multi-locus genotypes, full genome long-read sequencing and Illumina NovaSeq on isolate pools). These findings are consistent with the presence of two cryptic species which are both causative agents of bat White-Nose disease (‘Pd-1’, which corresponds to P. destructans sensu stricto, and ‘Pd-2’). Both species exist in the same geographic range and co-occur in the same hibernacula (i.e., in sympatry), though with specialised host preferences. I further described the fine-scale population structure in Eurasia which revealed that most genotypes are unique to single hibernacula (more than 95% of genotypes). The associated differences in microsatellite allele frequencies among hibernacula allowed the use of assignment methods to assign the North American isolates (exclusively Pd-1) to regions in Eurasia. Hence, a region in Ukraine (Podilia) is the most likely origin of the North American introduction.
To gain further insights into the spatial and temporal dynamics of White-Nose disease on a localised scale, several hibernacula were sampled with high intensity (artificial hibernaculum in Germany and natural karst caves in Bulgaria). Low rates of Pd gene flow were observed even among closely situated hibernacula. This indicates that Pd does not remain viable on bats over summer or it would be frequently exchanged among bats (and hence hibernacula) resulting in a homogenous distribution of genotypes. Instead, bats need to become re-infected each hibernation season to explain the yearly re-occurrence of White-Nose disease. Given the distribution and richness of Pd genotypes on hibrnacula walls and infected bats of the same hibernacula, bats become infected from the hibernacula walls when they return after summer. This means that environmental reservoirs exist within hibernacula (i.e., the walls) on which Pd spores persist during bat absence and which drive the yearly re-occurrence of White-Nose disease. In an experimental setup, I confirmed the long-term viability of Pd spores on abiotic substrate for at least two years and furthermore discovered temporal variations in Pd spores’ ability to germinate. In fact, these variations followed a seasonal pattern consistent with the timing of bats absence (reduced germination) and presence (increased germination) and could indicate adaptations of Pd to the bats’ life-cycle. The infection of bats from environmental reservoirs hence seems to be a central aspect of White-Nose disease dynamics and Pd biology.
Pds ability to remain viable for extended periods outside the host increases its risk of being anthropogenically transported and might have played a role in the emergence of White-Nose disease in North America. The existence of a second species (Pd-2) poses a great additional danger to North American bats considering that its introduction there could lead to deaths and associated population declines in so-far unaffected species given what is known about differing host species preferences in Eurasian bats. Even within the native range of Pd, the movement of Pd between differentiated fungal populations could facilitate genetic exchanges (e.g., through sexual reproduction) between genetically distant genotypes. Such genetic exchanges could lead to phenotypic jumps in pathogenicity or host-species preferences and should hence be prevented.
The native range of a pathogen holds great potential to better understand the genetic and ecological basis of a (wildlife) disease. My work informs about the dangers associated with the accidental transport of Pd (and other pathogens) and highlights the need for ‘prezootic’ biosecurity-oriented strategies to prevent disease outbreaks globally. Once a pathogen has arrived in a new geographic range, and particularly if it has environmentally durable spores (as demonstrated for Pd), it will be difficult/impossible to eradicate. Furthermore, a pathogen’s ability to remain viable outside the host and infect them from environmental reservoirs has been associated with an increased risk of species extinctions and needs to be considered when designing management strategies to mitigate disease impact.
Species persistence in the face of rapidly progressing environmental change requires adaptive responses that allow organisms to either cope with the novel conditions in their habitat or to follow their environmental niche in space. A poleward range shift due to global warming induced habitat loss in the south has been predicted for the lesser horseshoe bat, Rhinolophus hipposideros. Theoretical as well as numerous empirical studies link range expansion success to increased dispersal and reproduction rates due to spatial sorting and r-selection resulting from low population densities at the expansion front. R. hipposideros females however are highly philopatric and the species’ life history reflects a K- rather than an r-strategy, encompassing a long life span and limited individual annual reproductive output. I therefore investigated if adaptations in these traits determining range expansion success (dispersal and reproduction) can be observed in this bat species of high conservation concern. Genetic diversity presents a critical factor for adaptive responses to global change, both for range expansion and for coping with novel environmental conditions. I hence explored the genetic diversity levels of European R. hipposideros leading edge populations and their drivers for an assessment of these populations’ evolutionary potential and the development of conservation recommendations.
Comparing range expansion traits between an expanding R. hipposideros metapopulation in Germany and a non-expanding one in France revealed that range expansion was associated with an increase in juvenile survival and fecundity, and no decrease in adult survival. These results demonstrate than an increase in reproduction and growth rates is generally possible in R. hipposideros, indicating a potential adaptation (sensu lato) to range expansion. A positive correlation between adult and juvenile survival in the expanding metapopulation suggests higher resource acquisition in the expanding metapopulation, giving rise to the question if the observed demographic changes have a genetic basis or if they are rather induced by differences in environmental conditions between the two metapopulations. Long-term range expansion success requires adaptive evolutionary changes. The relative contribution of the former and that of undirected changes resulting e.g. from differences in resource availability therefore will have to be investigated in more detail in the future to allow predictions about range expansion dynamics in R. hipposideros.
The number of individuals within a radius of approximately 60 to 90 km around a population (as a measure of connectivity) was identified as the main positive driver of the studied populations’ genetic diversity. Overall genetic diversity levels in German R. hipposideros populations were found to be reduced compared to populations in France as a legacy of demographic bottlenecks resulting from severe population declines in the mid-20th century. This finding is alarming as future range expansion can be expected to entail a further decrease in genetic diversity. The resulting loss of genetic diversity can be expected to be particularly strong in R. hipposideros due to the detected dependence of genetic diversity on connectivity, because range expansion often results in small and patchy populations.
Protecting and ideally re-installing genetic diversity in R. hipposideros leading edge populations therefore presents a conservation goal of utmost importance. To achieve this endeavour, conservation efforts should target the protection of extensive networks of well-connected populations. Geographical concentration of individuals should be avoided and populations in key locations that connect clusters must be protected particularly well to prevent populations from becoming isolated. Continuous, regular monitoring of population trends is also important for a quick registration of disturbances or threats, and the subsequent rapid development of countermeasures to preclude further demographic declines.
The reduced levels of genetic diversity in the German metapopulation precluded a reliable quantification of dispersal rates due to the reduced power of discrimination between individuals. While ongoing re-colonization and the establishment of new maternity colonies provide evidence for increased dispersal in the expanding metapopulation, evaluating the expected range expansion velocity of R. hipposideros in relation to the estimated velocity of global warming induced habitat loss will require the confirmation of the existing preliminary dispersal data by employing more genetic markers.