Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination

Aerospace-foraging bats eat seasonably across varying habitats

Recent research has confirmed the efficiency of insectivorous bats as pest suppressors, underlining the ecological services they offer in agroecosystems. Therefore, some efforts try to enhance bat foraging in agricultural landscapes by acting upon environmental factors favouring them. In this study, we monitored a Miniopterus schreibersii colony, in the southern Iberian Peninsula. We intensively sampled their faeces and analysed them by metabarcoding to describe how the bent-winged bat diet would change with time, and to test whether their most-consumed prey would seasonally depend on different landscapes or habitats. Our results confirm that M. schreibersii are selective opportunist predators of moths, dipterans, mayflies, and other fluttering insects, shifting their diet to temporary peaks of prey availability in their foraging range, including both pest and non-pest insects. Supporting our hypothesis, throughout the year, M. schreibersii consume insects linked to diverse open habitats, including wetlands, grassland, diverse croplands, and woodland. The importance of each prey habitat varies seasonally, depending on their insect phenology, making bats indirectly dependent on a diverse landscape as their primary prey source. Bats' predation upon pest insects is quantitatively high, consuming around 1610 kg in 5 months, of which 1467 kg correspond to ten species. So, their suppression effect may be relevant, mainly in patchy heterogeneous landscapes, where bats' foraging may concentrate in successive outbursts of pests, affecting different crops or woodlands. Our results stress that to take advantage of the ecosystem services of bats or other generalist insectivores, keeping the environmental conditions they require to thrive, particularly a heterogeneous landscape within the colony's foraging area, is crucial.

Pest suppression by bats and management strategies to favour it: a global review

Fighting insect pests is a major challenge for agriculture worldwide, and biological control and integrated pest management constitute well-recognised, cost-effective ways to prevent and overcome this problem. Bats are important arthropod predators globally and, in recent decades, an increasing number of studies have focused on the role of bats as natural enemies of agricultural pests. This review assesses the state of knowledge of the ecosystem services provided by bats as pest consumers at a global level and provides recommendations that may favour the efficiency of pest predation by bats. Through a systematic review, we assess evidence for predation, the top-down effect of bats on crops and the economic value of ecosystem services these mammals provide, describing the different methodological approaches used in a total of 66 reviewed articles and 18 agroecosystem types. We also provide a list of detailed conservation measures and management recommendations found in the scientific literature that may favour the delivery of this important ecosystem service, including actions aimed at restoring bat populations in agroecosystems. The most frequent recommendations include increasing habitat heterogeneity, providing additional roosts, and implementing laws to protect bats and reduce agrochemical use. However, very little evidence is available on the direct consequences of these practices on bat insectivory in farmland. Additionally, through a second in-depth systematic review of scientific articles focused on bat diet and, as part of the ongoing European Cost Action project CA18107, we provide a complete list of 2308 documented interactions between bat species and their respective insect pest prey. These pertain to 81 bat species belonging to 36 different genera preying upon 760 insect pests from 14 orders in agroecosystems and other habitats such as forest or urban areas. The data set is publicly available and updatable.

DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish

Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.

Dietary preferences and feeding strategies of Colombian highland woolly monkeys

Primates are very selective in the foods they include in their diets with foraging strategies that respond to spatial and temporal changes in resource availability, distribution and quality. Colombian woolly monkeys (Lagothrix lagotricha lugens), one of the largest primate species in the Americas, feed mainly on fruits, but they also eat a high percentage of arthropods. This differs from closely related Atelid species that supplement their diet with leaves. In an 11 month study, we investigated the foraging strategies of this endemic monkey and assessed how resource availability affects dietary selection. Using behavioural, phenological, arthropod sampling and metabarcoding methods, we recorded respectively foraging time, forest productivity, arthropod availability in the forest and arthropod consumption. Scat samples and capturing canopy substrates (i.e. moss, bromeliads, aerial insects) were used for assigning arthropod taxonomy. The most important resource in the diet was fruits (54%), followed by arthropods (28%). Resource availability predicted feeding time for arthropods but not for fruits. Further, there was a positive relationship between feeding time on fruits and arthropods, suggesting that eating both resources during the same periods might work as an optimal strategy to maximize nutrient intake. Woolly monkeys preferred and avoided some fruit and arthropod items available in their home range, choosing a wide variety of arthropods. Geometrid moths (Lepidoptera) were the most important and consistent insects eaten over time. We found no differences in the type of arthropods adults and juveniles ate, but adults invested more time foraging for this resource, especially in moss. Although woolly monkeys are generalist foragers, they do not select their food items randomly or opportunistically.

Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas)

The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.

DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.

Molecular assays to reliably detect and quantify predation on a forest pest in bats faeces

Targeted molecular methods such as conventional PCR (cPCR) and quantitative PCR (qPCR), combined with species-specific primers and probes, are widely applied for pest species detection. Besides, the potential of qPCR to quantify DNA in samples makes it an invaluable molecular tool to infer the predation levels on specific prey by analysing predators’ stools. Nevertheless, studies on the diet of bats failed to find any empirical relationship, and it remains to be evaluated. Thus, we developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, the pine processionary, Thaumetopoea pityocampa, in bats’ faeces. Further, we empirically compared a range of different known DNA concentrations (input) of the target species mixed with mocks and bat faecal samples against DNA abundances yielded by qPCR (output) for a quantitative assessment. Overall, cPCR showed a lower detection rate than qPCR, but augmenting the replicate effort from one to three replicates led to a greater increase in the detection rate of the cPCR (from 57 to 80%) than the qPCR (from 90 to 99%). The quantitative experiment results showed a highly significant correlation between the input and output DNA concentrations (t = 10.84, p < 0.001) with a mean slope value of 1.05, indicating the accuracy of our qPCR assay to estimate DNA abundance of T. pityocampa in bat faeces. The framework of this study can be taken as a model to design similar assays applicable to other species of interest, such as agricultural pests or insects of public health concern.

Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding

Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture. Thus, for quality control purposes, an accurate and effective method should be provided for taxonomic identification of Faeces Vespertilionis. In this study, 26 samples of Faeces Vespertilionis from ten provinces in China were tested using DNA metabarcoding. Seven operational taxonomic units (OTUs) were detected as belonging to bats. Among them, Hipposideros armiger (Hodgson, 1835) and Rhinolophus ferrumequinum (Schober and Grimmberger, 1997) were the main host sources of Faeces Vespertilionis samples, with average relative abundances of 59.3% and 24.1%, respectively. Biodiversity analysis showed that Diptera and Lepidoptera were the most frequently consumed insects. At the species level, 19 taxa were clearly identified. Overall, our study used DNA metabarcoding to analyze the biological composition of Faeces Vespertilionis, which provides a new idea for the quality control of this special traditional Chinese medicine.

Do the evolutionary interactions between moths and bats promote niche partitioning between bats and birds?

Ecological theory suggests that the coexistence of species is promoted by the partitioning of available resources, as in dietary niche partitioning where predators partition prey. Yet, the mechanisms underlying dietary niche partitioning are not always clear. We used fecal DNA metabarcoding to investigate the diets of seven nocturnal insectivorous bird and bat species. Low diet overlap (2%-22%) supported resource partitioning among all species. Differences in diet corresponded with species identity, prey detection method, and foraging behavior of predators. Insects with ultrasonic hearing capabilities were consumed significantly more often by birds than bats, consistent with an evolved avoidance of echolocating strategies. In turn, bats consumed a greater proportion of noneared insects such as spruce budworms. Overall, our results suggest that evolutionary interactions among bats and moths translate to dietary niche partitioning and coexistence among bats and nocturnal birds.

Nontuberculous Mycobacteria Prevalence in Bats' Guano from Caves and Attics of Buildings Studied by Culture and qPCR Examinations

A total of 281 guano samples were collected from caves (N = 181) in eight European countries (Bulgaria, Czech Republic, France, Hungary, Italy, Romania, Slovakia and Slovenia) and attics in the Czech R. (N = 100). The correlation of detection of mycobacteria between Ziehl–Neelsen (ZN) microscopy and culture examination and qPCR was strong. ZN microscopy was positive in guano from caves (58.6%) more than double than positivity in guano from attics (21.0%; p < 0.01). From 89 mycobacterial isolates (73 isolates from cave guano and 16 isolates from attics’ guano), 68 (76.4%) isolates of 19 sp., ssp. and complex were identified as members of three Groups (M. fortuitum, M.chelonae, and M. mucogenicum) and four complexes (M. avium, M. terrae, M.vaccae, and M.smegmatis). A total of 20 isolates (22.5%) belonged to risk group 1 (environmental saprophytes), 48 isolates (53.9%) belonged to risk group 2 (potential pathogens), and none of the isolates belonged to risk group 3 (obligatory pathogens). When comparing bat guano collected from caves and attics, differences (p < 0.01; Mann–Whitney test) were observed for the electrical conductivity, total carbon, total organic, and total inorganic carbon. No difference (p > 0.05; Mann–Whitney test) was found for pH and oxidation-reduction potential parameters.

Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding

Ecological theory postulates that niches of co‐occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely‐related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra‐ and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat‐driven. The two most‐closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly‐related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.

Perch time allocation and feeding efficiency of flycatching Rhinolophus formosae: an optimal foraging behavior?

Background

Flycatching bats are species-rare and comprise predominantly horseshoe bats (Rhinolophidae). Their hang-and-wait foraging mode and long constant-frequency echolocation calls offer advantages in energetics and prey detection, and may enable them apt to foraging optimally, yet not much is known about the foraging behavior of flycatching bats. Thus we assessed the perch use and foraging performance in the field by one of the largest horseshoe bats, Rhinolophus formosae, and offered insights on their perch time allocation.

Results

The perching-foraging behaviors of the bats did not differ significantly between forest settings, but the residence and giving-up time, mean attack, and attack rate were higher in the late spring-early summer, whereas the mean capture, capture rate, and attack efficiency were lower in the late summer when volant juveniles joined the nocturnal activity. The bats maintained flycatching and exhibited largely similar attack rates through the night with peak residence time around the midnight, but the capture rate and attack efficiency both reduced toward midnight and then increased toward the hours right before dawn. The attack rate was negatively correlated to the number of perches used and perch switch; by contrast, the capture rate was positively correlated with both factors. The total residence time at a site increased but mean residence time per perch decreased as the number of perches used and perch-switch increased. The giving-up time was inversely correlated to the attack rate and attack efficiency, and decreased with an increasing capture rate.

Conclusions

The bats increased perch switch at lower attack rates in early spring, but switched less frequently in late spring and prime summer months when insect abundance is higher. By scanning through a broad angular range for prey detection, and switching more frequently among perches, R. formosae foraged with an increased capture rate, and were able to remain at the site longer by slightly reducing their mean residence time per perch. Our results concur with the predictions of optimal foraging theory for patch selection and offer implications for further exploration of the foraging behavior of flycatching horseshoe bats.

Body Size Variation in Italian Lesser Horseshoe Bats Rhinolophus hipposideros over 147 Years: Exploring the Effects of Climate Change, Urbanization and Geography

Body size in animals commonly shows geographic and temporal variations that may depend upon several environmental drivers, including climatic conditions, productivity, geography and species interactions. The topic of body size trends across time has gained momentum in recent years since this has been proposed as a third universal response to climate change along with changes in distribution and phenology. However, disentangling the genuine effects of climate change from those of other environmental factors is often far from trivial. In this study, we tested a set of hypotheses concerning body size variation across time and space in Italian populations of a rhinolophid bat, the lesser horseshoe bat Rhinolophus hipposideros. We examined forearm length (FAL) and cranial linear traits in a unique historical collection of this species covering years from 1869 to 2016, representing, to the best of our knowledge, the longest time series ever considered in a morphological assessment of a bat species. No temporal changes occurred, rejecting the hypotheses that body size varied in response to climate change or urbanization (light pollution). We found that FAL increased with latitude following a Bergmann's rule trend, whereas the width of upper incisors, likely a diet-related trait, showed an opposite pattern which awaits explanation. We also confirmed that FAL is sexually dimorphic in this species and ruled out that insularity has any detectable effect on the linear traits we considered. This suggests that positive responses of body size to latitude do not mean per se that concurring temporal responses to climate change are also expected. Further investigations should explore the occurrence of these patterns over larger spatial scales and more species in order to detect the existence of general patterns across time and space.

Trophic resource partitioning drives fine-scale coexistence in cryptic bat species

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and high-throughput sequencing to characterize for the first time the trophic ecology of two recently described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected fecal samples from allopatric and sympatric regions and from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly similar diets characterized by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey item level was lower in syntopic populations, supporting trophic shift under fine-scale co-occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.

DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats

Inferences of the interactions between species' ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats' hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.