Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection

IMPORTANCE

A common hypothesis holds that bats (order Chiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.

Long-term individualized monitoring of sympatric bat species reveals distinct species- and demographic differences in hibernation phenology

Background

Hibernation allows species to conserve energy and thereby bridge unfavorable environmental conditions. At the same time, hibernation imposes substantial ecological and physiological costs. Understanding how hibernation timing differs within and between species can provide insights into the underlying drivers of this trade-off. However, this requires individualized long-term data that are often unavailable. Here, we used automatic monitoring techniques and a reproducible analysis pipeline to assess the individualized hibernation phenology of two sympatric bat species. Our study is based on data of more than 1100 RFID-tagged Daubenton’s bats (Myotis daubentonii) and Natterer’s bats (Myotis nattereri) collected over seven years at a hibernaculum in Germany. We used linear mixed models to analyze species-, sex- and age-specific differences in entrance, emergence and duration of the longest continuous period spent in the hibernaculum.

Results

Overall, Daubenton’s bats entered the hibernaculum earlier and emerged later than Natterer’s bats, resulting in a nearly twice as long hibernation duration. In both species, adult females entered earlier and emerged from hibernation later than adult males. Hibernation duration was shorter for juveniles than adults with the exception of adult male Natterer’s bats whose hibernation duration was shortest of all classes. Finally, hibernation timing differed among years, but yearly variations in entrance and emergence timing were not equally shifted in both species.

Conclusions

Our results suggest that even in sympatric species, and across sex and age classes, hibernation timing may be differentially affected by environmental conditions. This highlights the necessity of using individualized information when studying the impact of changing environments on hibernation phenology.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01962-6.

Differences in seasonal survival suggest species-specific reactions to climate change in two sympatric bat species

Long-lived animals with a low annual reproductive output need a long time to recover from population crashes and are, thus, likely to face high extinction risk, if the current global environmental change will increase mortality rates. To aid conservation of those species, knowledge on the variability of mortality rates is essential. Unfortunately, however, individual-based multiyear data sets that are required for that have only rarely been collected for free-ranging long-lived mammals. Here, we used a five-year data set comprising activity data of 1,445 RFID-tagged individuals of two long-lived temperate zone bat species, Natterer's bats (Myotis nattereri) and Daubenton's bats (Myotis daubentonii), at their joint hibernaculum. Both species are listed as being of high conservation interest by the European Habitats Directive. Applying mixed-effects logistic regression, we explored seasonal survival differences in these two species which differ in foraging strategy and phenology. In both species, survival over the first winter of an individual's life was much lower than survival over subsequent winters. Focussing on adults only, seasonal survival patterns were largely consistent with higher winter and lower summer survival but varied in its level across years in both species. Our analyses, furthermore, highlight the importance of species-specific time periods for survival. Daubenton's bats showed a much stronger difference in survival between the two seasons than Natterer's bats. In one exceptional winter, the population of Natterer's bats crashed, while the survival of Daubenton's bats declined only moderately. While our results confirm the general seasonal survival pattern typical for hibernating mammals with higher winter than summer survival, they also show that this pattern can be reversed under particular conditions. Overall, our study points toward a high importance of specific time periods for population dynamics and suggests species-, population-, and age class-specific responses to global climate change.

Habitat usage of Daubenton's bat (Myotis daubentonii), common pipistrelle (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) in a North Wales upland river catchment

Distributions of Daubenton's bat (Myotis daubentonii), common pipistrelle, (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) were investigated along and altitudinal gradient of the Lledr River, Conwy, North Wales, and presence assessed in relation to the water surface condition, presence/absence of bank-side trees, and elevation. Ultrasound recordings of bats made on timed transects in summer 1999 were used to quantify habitat usage. All species significantly preferred smooth water sections of the river with trees on either one or both banks; P. pygmaeus also preferred smooth water with no trees. Bats avoided rough and cluttered water areas, as rapids may generate high-frequency echolocation-interfering noise and cluttered areas present obstacles to flight. In lower river regions, detections of bats reflected the proportion of suitable habitat available. At higher elevations, sufficient habitat was available; however, bats were likely restricted due to other factors such as a less predictable food source. This study emphasizes the importance of riparian habitat, bank-side trees, and smooth water as foraging habitat for bats in marginal upland areas until a certain elevation, beyond which bats in these areas likely cease to forage. These small-scale altitudinal differences in habitat selection should be factored in when designing future bat distribution studies and taken into consideration by conservation planners when reviewing habitat requirements of these species in Welsh river valleys, and elsewhere within the United Kingdom.

No effect of artificial light of different colors on commuting Daubenton's bats (Myotis daubentonii) in a choice experiment

Progressive illumination at night poses an increasing threat to species worldwide. Light at night is particularly problematic for bats as most species are nocturnal and often cross relatively large distances when commuting between roosts and foraging grounds. Earlier studies have shown that illumination of linear structures in the landscape disturbs commuting bats, and that the response of bats to light may strongly depend on the light spectrum. Here, we studied the impact of white, green, and red light on commuting Daubenton's bats (Myotis daubentonii). We used a unique location where commuting bats cross a road by flying through two identical, parallel culverts underneath. We illuminated the culverts with white, red, and green light, with an intensity of 5 lux at the water surface. Bats had to choose between the two culverts, each with a different lighting condition every night. We presented all paired combinations of white, green, and red light and dark control in a factorial design. Contrary to our expectations, the number of bat passes through a culvert was unaffected by the presence of light. Furthermore, bats did not show any preference for light color. These results show that the response of commuting Daubenton's bats to different colors of light at night with a realistic intensity may be limited when passing through culverts.

Second case of European bat lyssavirus type 2 detected in a Daubenton's bat in Finland

European bat lyssavirus type 2 (EBLV-2) was detected in Finland in a Daubenton’s bat (Myotis daubentonii) found in the municipality of Inkoo (60°02′45″N, 024°00′20″E). The bat showed neurological signs and was later found dead. The laboratory analysis revealed the presence of lyssavirus, and the virus was characterized as EBLV-2. This isolation of EBLV-2 was the second time that the virus has been detected in a Daubenton’s bat in Finland. This provides additional proof that EBLV-2 is endemic in the Finnish Daubenton’s bat population.

Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

Chlamydia-like organisms (CLOs) are recently identified members of the Chlamydiales order. CLOs share intracellular lifestyles and biphasic developmental cycles, and they have been detected in environmental samples as well as in various hosts such as amoebae and arthropods. In this study, we screened bat feces for the presence of CLOs by molecular analysis. Using pan-Chlamydiales PCR targeting the 16S rRNA gene, Chlamydiales DNA was detected in 54% of the specimens. PCR amplification, sequencing, and phylogenetic analysis of the 16S rRNA and 23S rRNA genes were used to classify positive specimens and infer their phylogenetic relationships. Most sequences matched best with Rhabdochlamydia species or uncultured Chlamydia sequences identified in ticks. Another set of sequences matched best with sequences of the Chlamydia genus or uncultured Chlamydiales from snakes. To gain evidence of whether CLOs in bat feces are merely diet borne, we analyzed insects trapped from the same location where the bats foraged. Interestingly, the CLO sequences resembling Rhabdochlamydia spp. were detected in insect material as well, but the other set of CLO sequences was not, suggesting that this set might not originate from prey. Thus, bats represent another potential host for Chlamydiales and could harbor novel, previously unidentified members of this order.

IMPORTANCE

Several pathogenic viruses are known to colonize bats, and recent analyses indicate that bats are also reservoir hosts for bacterial genera. Chlamydia-like organisms (CLOs) have been detected in several animal species. CLOs have high 16S rRNA sequence similarity to Chlamydiaceae and exhibit similar intracellular lifestyles and biphasic developmental cycles. Our study describes the frequent occurrence of CLO DNA in bat feces, suggesting an expanding host species spectrum for the Chlamydiales As bats can acquire various infectious agents through their diet, prey insects were also studied. We identified CLO sequences in bats that matched best with sequences in prey insects but also CLO sequences not detected in prey insects. This suggests that a portion of CLO DNA present in bat feces is not prey borne. Furthermore, some sequences from bat droppings not originating from their diet might well represent novel, previously unidentified members of the Chlamydiales order.

Lyssavirus-reactive antibodies in Swedish bats

Introduction

To study the presence of European bat lyssavirus (EBLV) infections in bat reservoirs in Sweden, active surveillance was performed during the summers from 2008 to 2013.

Material and methods

Bat specimens were collected at >20 bat colonies in the central, southeastern, and southern parts of Sweden. In total, blood and saliva of 452 bats were examined by a virus neutralization test and by reverse transcription polymerase chain reactions (RT-PCRs).

Results and discussion

EBLV neutralizing antibodies were detected in 14 Daubenton's bats (Myotis daubentonii), all trapped in Skåne or Småland (south and southeast of Sweden). The result was not unexpected since EBLV has been shown to be present in many neighboring countries, for example, Denmark, Finland, Germany, and Norway. However, Sweden has been regarded free of rabies in terrestrial mammals since 1896. Although very rare, spillover of EBLV into other animals and humans have occurred, and the risk of EBLV infection to other species including humans should not be ignored. This is the first report of lyssavirus infection in Swedish bats.

How anthropogenic noise affects foraging

The influence of human activity on the biosphere is increasing. While direct damage (e.g. habitat destruction) is relatively well understood, many activities affect wildlife in less apparent ways. Here, we investigate how anthropogenic noise impairs foraging, which has direct consequences for animal survival and reproductive success. Noise can disturb foraging via several mechanisms that may operate simultaneously, and thus, their effects could not be disentangled hitherto. We developed a diagnostic framework that can be applied to identify the potential mechanisms of disturbance in any species capable of detecting the noise. We tested this framework using Daubenton's bats, which find prey by echolocation. We found that traffic noise reduced foraging efficiency in most bats. Unexpectedly, this effect was present even if the playback noise did not overlap in frequency with the prey echoes. Neither overlapping noise nor nonoverlapping noise influenced the search effort required for a successful prey capture. Hence, noise did not mask prey echoes or reduce the attention of bats. Instead, noise acted as an aversive stimulus that caused avoidance response, thereby reducing foraging efficiency. We conclude that conservation policies may seriously underestimate numbers of species affected and the multilevel effects on animal fitness, if the mechanisms of disturbance are not considered.

Trawling bats exploit an echo-acoustic ground effect

A water surface acts not only as an optic mirror but also as an acoustic mirror. Echolocation calls emitted by bats at low heights above water are reflected away from the bat, and hence the background clutter is reduced. Moreover, targets on the surface create an enhanced echo. Here, we formally quantified the effect of the surface and target height on both target detection and -discrimination in a combined laboratory and field approach with Myotis daubentonii. In a two-alternative, forced-choice paradigm, the bats had to detect a mealworm and discriminate it from an inedible dummy (20 mm PVC disc). Psychophysical performance was measured as a function of height above either smooth surfaces (water or PVC) or above a clutter surface (artificial grass). At low heights above the clutter surface (10, 20, or 35 cm), the bats' detection performance was worse than above a smooth surface. At a height of 50 cm, the surface structure had no influence on target detection. Above the clutter surface, also target discrimination was significantly impaired with decreasing target height. A detailed analysis of the bats' echolocation calls during target approach shows that above the clutter surface, the bats produce calls with significantly higher peak frequency. Flight-path reconstruction revealed that the bats attacked an target from below over water but from above over a clutter surface. These results are consistent with the hypothesis that trawling bats exploit an echo-acoustic ground effect, in terms of a spatio-temporal integration of direct reflections with indirect reflections from the water surface, to optimize prey detection and -discrimination not only for prey on the water but also for some range above.