The diet ofMyotis lucifugusacross Canada: assessing foraging quality and diet variability

Molecular Diet Analysis of Leaf-Grazing Katydids Based on DNA Barcoding

The diversity of herbivorous insects is associated with host plant diversity. The determination of dietary profile is a central topic in insect ecology. DNA barcoding, that is, taxon identification using a standardized DNA region, have been important to the recent advances in food web understandings. In this study, three commonly plant barcoding loci (i.e., rbcL, matK, and trnH-psbA) were chosen for screening of ingested plant DNA in 207 specimens of 18 leaf-grazing katydid species representing 4 subfamilies in China. The obtained sequences were queried against the Barcode of Life Database (BOLD) and GenBank for taxa identification. The results of identification were as follow: 3 Conocephalinae species consumed 10 plant families, with preference for Poaceae; 1 Mecopodinae species consumed 18 plant families, with preference for Fabaceae and Vitaceae; 11 Phaneropterinae species consumed 43 plant families, with preference for Juglandaceae; 3 species Pseudophyllinae species consumed 9 plant families, with preference for Balsaminaceae. Among these, only 81 out of 207 samples were identified at the species level when compares with NCBI and BOLD database. Our study added a significant amount of dietary information for leaf-grazing katydids in China. It is crucial to fully understand coevolution of katydids and plant, katydids diet resource requirements, and best practices for habitat conservation.

Learning to Hunt on the Go: Dietary Changes During Development of Rhinolophid Bats

Mammals may experience physical changes from birth, and their diet varies at different stages of life. This study investigates the impact of development on the diet composition of three horseshoe bats: Rhinolophus euryale, R. hipposideros, and R. ferrumequinum in the Basque Country, north of the Iberian Peninsula. The diets of juvenile and adult individuals of each species were obtained by analysing their droppings using metabarcoding and then compared at (1) the taxonomic and (2) prey trait levels (size, flying speed, hardness). The diets of juvenile and adult individuals of R. euryale and R. hipposideros showed significant differences at the taxonomic level and regarding prey traits. In contrast, in the case of R. ferrumequinum, we could only observe discernible diet patterns through the trait analysis. Additionally, we discovered a shared pattern: younger individuals tend to feed on easier-to-hunt and/or handle smaller and smoother prey. The varying degrees of dissimilarity between juvenile and adult diets observed in this study suggest that the relative importance of psychomotor development, foraging strategies, prey discrimination, and/or spatial learning may differ among species. These findings contribute to conservation efforts, especially by recognising the dietary needs of juveniles for their survival and successful development.

Ecological Niche Characteristics of the Diets of Three Sympatric Rodents in the Meili Snow Mountain, Yunnan

Understanding the dietary preferences and ecological niche characteristics of mammals not only reveals their adaptive strategies under environmental changes but also reveals the interspecific relationships and coexistence mechanisms among sympatric species. Nevertheless, such data are scarce for rodents inhabiting areas spanning a wide altitude range. This study employed DNA metabarcoding technology to analyze the stomach contents of Apodemus ilex, Apodemus chevrieri, and Niviventer confucianus, aiming to investigate their dietary compositions and diversity in the Meili Snow Mountain in Yunnan Province, China. Levins's and Pianka's indices were used to compare the interspecific niche breadth and niche overlaps. The results revealed the following: (1) Insecta (relative abundance: 59.4-78.4%) and Clitellata (relative abundance: 5.2-25.5%) were the primary animal food sources for the three species, while Magnoliopsida (relative abundance: 90.3-99.9%) constitutes their main plant food source. Considerable interspecific differences were detected in the relative abundance of primary animal and plant foods among the three species; (2) There was partial overlap in the genus-level animal food between A. ilex and N. confucianus (Ojk = 0.4648), and partial overlap in plant food between A. ilex and A. chevrieri (Ojk = 0.3418). However, no overlap exists between A. chevrieri and N. confucianus, either in animal or plant food; (3) There were no significant interspecific differences in the α-diversity of animal and plant foods among the three species. The feeding strategies and ecological niche variations of these rodents support the niche differentiation hypothesis, indicating that they have diversified in their primary food sources. This diversification may be a strategy to reduce competition and achieve long-term coexistence by adjusting the types and proportions of primary foods consumed.

Mercury bioaccumulation in bats in Madre de Dios, Peru: implications for Hg bioindicators for tropical ecosystems impacted by artisanal and small-scale gold mining

Mercury (Hg) endangers human and wildlife health globally, primarily due to its release from artisanal small-scale gold mining (ASGM). During gold extraction, Hg is emitted into the environment and converted to highly toxic methylmercury by microorganisms. In Madre de Dios (MDD), Peru, ASGM dominates the economy and has transformed rainforests into expansive deforested areas punctuated by abandoned mining ponds. The aim of this study was to evaluate the use of bats as bioindicators for mercury pollution intensity in tropical terrestrial ecosystems impacted by ASGM. We collected 290 bat fur samples from three post-ASGM sites and one control site in Madre de Dios. Our results showed a wide Hg distribution in bats (0.001 to 117.71 mg/kg) strongly influenced by feeding habits. Insectivorous and piscivorous bats from ASGM sites presented elevated levels of Hg surpassing the mercury small mammal threshold for small mammals (10 mg/kg). We observed the highest reported fur mercury concentrations for insectivorous Neotropical bats reported to date (Rhynchonycteris naso, 117 mg/kg). Our findings further confirm that Hg emissions from ASGM are entering local food webs and exposing wildlife species at several trophic levels to higher levels of Hg than in areas not impacted by mining. We also found that three bat genera consistently showed increased Hg levels in ASGM sites relative to controls indicating potential usefulness as bioindicators of mercury loading in terrestrial ecosystems impacted by artisanal and small-scale gold mining.

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.

Variation in habitat use and its consequences for mercury exposure in two Eastern Ontario bat species, Myotis lucifugus and Eptesicus fuscus

The St. Lawrence River in Eastern Ontario, Canada, has been a designated an area of concern due to past industrial contamination of sediment in some areas and transport of mercury from tributaries. Previous research using bats as sentinel species identified elevated concentrations of total mercury (THg) in fur of local bats and species-specific variation between little brown bats (Myotis lucifugus) and big brown bats (Eptesicus fuscus). Here, we investigated the mercury exposure pathways for these two species by testing the hypothesis that diet variation, particularly the reliance on aquatic over terrestrial insects, is a determinant of local bat mercury concentrations. We analyzed THg concentration and stable isotope ratios of δ15N and δ13C in fur of little and big brown bats, and in aquatic and terrestrial insects. Big brown bats, especially males, accumulated significantly higher THg concentrations in their fur compared to little brown bats. However, this difference was not related to diet because big brown bats consumed terrestrial insects, which were lower in mercury than aquatic insects, the primary prey for little brown bats. We also evaluated whether fur THg concentrations translate into molecular changes in tissues linked to (methyl)mercury toxicity by quantifying tissue changes in global DNA methylation and mitochondrial DNA abundance. No significant changes in DNA molecular markers were observed in relation to fur THg concentration, suggesting mercury exposure to local bats did not impact molecular level changes at the DNA level. Higher mercury in bats was not associated with local aquatic contamination or genotoxicity in this study area.

Dietary niche partitioning of three Sky Island Sceloporus lizards as revealed through DNA metabarcoding

Lizard diets are highly diverse and have contributed to the diversification, biogeographical distributions, and evolution of novel traits across this global radiation. Many parts of a lizard's ecology-including habitat preferences, foraging modes, predation risks, interspecific competition, and thermal constraints, among others-interact to shape diets, and dietary niche partitioning simultaneously contributes to co-occurrence within communities. We used DNA metabarcoding of fecal samples to identify prey items in the diets of three sympatric Sceloporus lizards in the Madrean Sky Islands of Arizona, USA. We found evidence for dietary niche partitioning between interacting species concomitant with their respective ecologies. We also compared diet composition between populations to understand how conserved or plastic species' diets are between different environments. Our findings suggest that habitat generalists are also diet generalists in this system, while the same may be true for specialists. The identification of prey items to much lower taxonomic levels than previously documented further reveals hidden diversity in the diets of these species and underscores the utility of metabarcoding for understanding the full complexity of lizard diets.

Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats

The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host-pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.

Multi-marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird

Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker fecal metabarcoding to provide in-depth dietary analysis of a declining passerine in the UK, the Hawfinch (Coccothraustes coccothraustes). We collected fecal samples from (n = 262) UK Hawfinches prior to, and during, the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilize multiple resources within their foraging environments.

Adults of Alderflies, Fishflies, and Dobsonflies (Megaloptera) Expel Meconial Fluid When Disturbed

Chemical secretions are an effective means by which insects may deter potential enemies, already being studied extensively with regard to their chemicals, synthesis, toxicity, and functions. However, these defensive secretions have been little studied in Megaloptera. Herein, the fluid expelling behavior of adult alderflies (Sialidae), fishflies (Corydalidae: Chauliodinae), and dobsonflies (Corydalidae: Corydalinae), all of the order Megaloptera, is described in detail regarding the timing and possible function of this behavior. When disturbed artificially, both males and females could expel fluid from the anus. However, the frequency of expelling was much lower in alderflies than in fishflies and dobsonflies. The amount of expelled fluid relative to body weight was also smaller in alderflies. In fishflies and dobsonflies, the amount of expelled fluid decreased with adult age, probably because the fluid is little replenished once expelled. The cream-colored fluid seems to be meconial fluid produced via the Malpighian tubules at the pupal stage, which is usually discharged at adult emergence in most other holometabolous insects. However, adult fishflies and dobsonflies often expel it vigorously by bending their abdomen when disturbed after emergence. Thus, the fluid expelling may be an anti-predatory behavior, particularly in younger adults that can expel a relatively large amount of fluid.

Molecular identification of individual and seasonal variation in incidental ingestion of arthropods by free-ranging goats

The extent of direct interactions between large mammalian herbivores (LMH) and plant-dwelling arthropods (PDA), i.e., the ingestion of PDA by LMH, remains largely unexplored. Grazing LMH may ingest a variety of PDA, yet, it is unknown how different foraging strategies (i.e., browsing, grazing, etc.) influence the ingestion of PDA or whether individual variation within herds affects it. Here we examine how individual variation within a herd of browsing LMH impacts PDA ingestion. This was done using a DNA metabarcoding analysis on feces collected monthly from marked individuals within a herd of free-ranging goats. We found that goats frequently ingest PDA while feeding (all samples contains PDA), including a complex food-chain of herbivores, predators and parasites, which differed over the season and among individual goats. In total, 63 families of insects and 9 families of arachnids from 15 orders were ingested by the goats. Most ingested PDA were herbivores with reduced mobility, such as immature or sessile species. Highly mobile and noxious PDA were rarely detected. We show for the first time that ingestion of PDA by LMH is influenced by seasonal and individual variation within the herd and that it is common among LMH, regardless of feeding strategy or habitat.

Spatial and temporal variation in New Hampshire bat diets

Insectivorous bats consume a diverse array of arthropod prey, with diets varying by bat species, sampling location, and season. North American bat diets remain incompletely described, which is concerning at a time when many bat and insect populations appear to be declining. Understanding the variability in foraging is thus an essential component for effective bat conservation. To comprehensively evaluate local foraging, we assessed the spatial and temporal variability in prey consumed by the little brown bat, Myotis lucifugus, in New Hampshire, USA. We collected bat guano samples from 20 sites over 2 years and analyzed sequence data for 899 of these samples using a molecular metabarcoding approach targeting the cytochrome oxidase I subunit (COI) gene. Some prey items were broadly shared across locations and sampling dates, with the most frequently detected arthropod orders broadly similar to previous morphological and molecular analyses; at least one representative sequence variant was assigned to Coleoptera in 92% of samples, with other frequently detected orders including Diptera (73%), Lepidoptera (65%), Trichoptera (38%), and Ephemeroptera (32%). More specifically, two turf and forest pests were routinely detected: white grubs in the genus Phyllophaga (50%), and the Asiatic Garden beetle, Maladera castanea (36%). Despite the prevalence of a few taxa shared among many samples and distinct seasonal peaks in consumption of specific arthropods, diet composition varied both temporally and spatially. However, species richness did not strongly vary indicating consumption of a broad diversity of taxa throughout the summer. These data characterize little brown bats as flexible foragers adept at consuming a broad array of locally available prey resources.

Disease-related population declines in bats demonstrate non-exchangeability in generalist predators

The extent to which persisting species may fill the functional role of extirpated or declining species has profound implications for the structure of biological communities and ecosystem functioning. In North America, arthropodivorous bats are threatened on a continent-wide scale by the spread of white-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans. We tested whether bat species that display lower mortality from this disease can partially fill the functional role of other bat species experiencing population declines. Specifically, we performed high-throughput amplicon sequencing of guano from two generalist predators: the little brown bat (Myotis lucifugus) and big brown bat (Eptesicus fuscus). We then compared changes in prey consumption before versus after population declines related to WNS. Dietary niches contracted for both species after large and abrupt declines in little brown bats and smaller declines in big brown bats, but interspecific dietary overlap did not change. Furthermore, the incidence and taxonomic richness of agricultural pest taxa detected in diet samples decreased following bat population declines. Our results suggest that persisting generalist predators do not necessarily expand their dietary niches following population declines in other predators, providing further evidence that the functional roles of different generalist predators are ecologically distinct.

Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.

The structure of tropical bat-plant interaction networks during an extreme El Niño-Southern Oscillation event

Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal–plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat–plant network structure during an extreme El Niño‐Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole‐year bat–plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non‐El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability.

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.

Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

Selective Logging Shows No Impact on the Dietary Breadth of a Generalist Bat Species: The Fawn Leaf-Nosed Bat (Hipposideros cervinus)

Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Diptera, Blattodea, and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed per-bat in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites. Multiple bioinformatic parameters were used, to assess how they altered our perception of sampling completeness. While parameter choice altered estimates of completeness, a very high sampling effort was always required to detect the entire prey community.

Feasting, not fasting: winter diets of cave hibernating bats in the United States

Temperate bat species use extended torpor to conserve energy when ambient temperatures are low and food resources are scarce. Previous research suggests that migratory bat species and species known to roost in thermally unstable locations, such as those that roost in trees, are more likely to remain active during winter. However, hibernating colonies of cave roosting bats in the southeastern United States may also be active and emerge from caves throughout the hibernation period. We report what bats are eating during these bouts of winter activity. We captured 2,044 bats of 10 species that emerged from six hibernacula over the course of 5 winters (October–April 2012/2013, 2013/2014, 2015/2016, 2016/2017, and 2017/2018). Using Next Generation sequencing of DNA from 284 fecal samples, we determined bats consumed at least 14 Orders of insect prey while active. Dietary composition did not vary among bat species; however, we did record variation in the dominant prey items represented in species’ diets. We recorded Lepidoptera in the diet of 72.2% of individual Corynorhinus rafinesquii and 67.4% of individual Lasiurus borealis. Diptera were recorded in 32.4% of Myotis leibii, 37.4% of M. lucifugus, 35.5% of M. sodalis and 68.8% of Perimyotis subflavus. Our study is the first to use molecular genetic techniques to identify the winter diet of North American hibernating bats. The information from this study is integral to managing the landscape around bat hibernacula for insect prey, particularly in areas where hibernating bat populations are threatened by white-nose syndrome.

High-throughput sequencing reveals dietary segregation in Malaysian babblers

The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection, and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the 4 genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris, and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran, and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and ˂35% were shared simultaneously by ≥3 babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.

Bats partition activity in space and time in a large, heterogeneous landscape

Diverse species assemblages theoretically partition along multiple resource axes to maintain niche separation between all species. Temporal partitioning has received less attention than spatial or dietary partitioning but may facilitate niche separation when species overlap along other resource axes. We conducted a broad-scale acoustic study of the diverse and heterogeneous Great Smoky Mountains National Park in the Appalachian Mountains. Between 2015 and 2016, we deployed acoustic bat detectors at 50 sites (for a total of 322 survey nights). We examined spatiotemporal patterns of bat activity (by phonic group: Low, Mid, and Myotis) to test the hypothesis that bats partition both space and time. Myotis and Low bats were the most spatially and temporally dissimilar, while Mid bats were more general in their resource use. Low bats were active in early successional openings or low-elevation forests, near water, and early in the evening. Mid bats were similarly active in all land cover classes, regardless of distance from water, throughout the night. Myotis avoided early successional openings and were active in forested land cover classes, near water, and throughout the night. Myotis and Mid bats did not alter their spatial activity patterns from 2015 to 2016, while Low bats did. We observed disparate temporal activity peaks between phonic groups that varied between years and by land cover class. The temporal separation between phonic groups relaxed from 2015 to 2016, possibly related to changes in the relative abundance of bats or changes in insect abundance or diversity. Temporal separation was more pronounced in the land cover classes that saw greater overall bat activity. These findings support the hypothesis that niche separation in diverse assemblages may occur along multiple resource axes and adds to the growing body of evidence that bats partition their temporal activity.

Consumption of spiders by the little brown bat (Myotis lucifugus) and the long-eared myotis (Myotis evotis) in the Rocky Mountains of Alberta, Canada

Intraspecific variation in diet and (or) foraging behaviour is one way in which species are able to occupy wide geographical areas with variable environments. The little brown bat (Myotis lucifugus (Le Conte, 1831)), a primarily aerial insectivorous bat, consumes spiders in low temperatures at the start and end of summer in Northwest Territories, Canada, but it consumes spiders all summer, even during high aerial insect abundance, in Alaska, USA. There are no competitors of M. lucifugus in Alaska, but there are in Northwest Territories, suggesting that aerial insect abundance and competition from gleaning bats influences when M. lucifugus consumes spiders. In the Kananaskis area of the Rocky Mountains of Alberta, Canada, we investigated spider consumption by M. lucifugus and the long-eared myotis (Myotis evotis (H. Allen, 1864)), a species more adept at gleaning, to better understand when bats consume spiders. Fecal sample analysis indicated that M. evotis consumed spiders all season long, with greater consumption when the bats were caught near water. Myotis lucifugus did not consume spiders at all. This suggests that M. lucifugus opportunistically consumes spiders when encountered, but does not encounter them in Kananaskis where it forages primarily over open water, unlike in Northwest Territories where it forages in the interior of forests and may encounter spiders more frequently.

Ecology and impacts of white-nose syndrome on bats

The recent introduction of Pseudogymnoascus destructans (the fungal pathogen that causes white-nose syndrome in bats) from Eurasia to North America has resulted in the collapse of North American bat populations and restructured species communities. The long evolutionary history between P. destructans and bats in Eurasia makes understanding host life history essential to uncovering the ecology of P. destructans. In this Review, we combine information on pathogen and host biology to understand the patterns of P. destructans spread, seasonal transmission ecology, the pathogenesis of white-nose syndrome and the cross-scale impact from individual hosts to ecosystems. Collectively, this research highlights how early pathogen detection and quantification of host impacts has accelerated the understanding of this newly emerging infectious disease.

Lord of the Diptera (and Moths and a Spider): Molecular Diet Analyses and Foraging Ecology of Indiana Bats in Illinois

Effective management of endangered or threatened wildlife requires an understanding of how foraging habitats are used by those populations. Molecular diet analysis of fecal samples offers a cost-effective and non-invasive method to investigate how diets of wild populations vary with respect to spatial and temporal factors. For the federally endangered Indiana bat (Myotis sodalis), documenting its preferred food sources can provide critical information to promote effective conservation of this federally endangered species. Using cytochrome oxidase I amplicon sequence data from Indiana bat guano samples collected at two roosting areas in Cypress Creek National Wildlife Refuge, we found that dipteran taxa (i.e., flies) associated with riparian habitats were the most frequently detected taxon and represented the majority of the sequence diversity among the arthropods sampled. A select few arthropods from other taxa—especially spiders—are also likely important to Indiana bat diets in this refuge. A supervised learning analysis of diet components suggest only a small fraction of the frequently detected taxa are important contributors to spatial and temporal variation. Overall, these data depict the Indiana bat as a generalist consumer whose diet includes some prey items associated with particular seasonal or spatial components, along with other taxa repeatedly consumed throughout the entire foraging season. These molecular diet analyses suggest that protecting foraging resources specifically associated with the riparian habitat of Cypress Creek National Wildlife Refuge is essential to promote effective Indiana bat conservation.

Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance

Although most predators are generalists, the majority of studies on the association between prey availability and prey consumption have focused on specialist predators. To investigate the role of highly generalist predators in a complex food web, we measured the relationships between prey consumption and prey availability in two common arthropodivorous bats. Specifically, we used high-throughput amplicon sequencing coupled with a known mock community to characterize seasonal changes in little brown and big brown bat diets. We then linked spatiotemporal variation in prey consumption with quantitative prey availability estimated from intensive prey community sampling. We found that although quantitative prey availability fluctuated substantially over space and time, the most commonly consumed prey items were consistently detected in bat diets independently of their respective abundance. Positive relationships between prey abundance and probability of consumption were found only among prey groups that were less frequently detected in bat diets. While the probability of prey consumption was largely unrelated to abundance, the community structure of prey detected in bat diets was influenced by the local or regional abundance of prey. Observed patterns suggest that while little brown and big brown bats maintain preferences for particular prey independently of quantitative prey availability, total dietary composition may reflect some degree of opportunistic foraging. Overall, our findings suggest that generalist predators can display strong prey preferences that persist despite quantitative changes in prey availability.

Assessing the impact of taxon resolution on network structure

Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research vary widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to molecular operational taxonomic units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large data sets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 data sets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied.

Bats actively prey on mosquitoes and other deleterious insects in rice paddies: Potential impact on human health and agriculture

BACKGROUND

The fact that bats suppress agricultural pests has been measured for some particular dyads of predator and prey species in both economic and food security terms. The recent emergence of new molecular techniques allows for more precise screenings of bat's diet than the traditional visual identification systems and provides further evidence that bats consume an ample array of agricultural pest species. The main focus of the regulatory services that bats provide in agroecosystems has been on crop pests that cause yield losses. Rice paddies constitute a particular agronomic system with specific challenges, not only related to crop productivity but also to human health. Dipteran density in such ecosystems poses a serious threat to human wellbeing and hinders crop production. Mosquitoes cause direct harm to human populations, transmitting a number of infectious diseases. Non-biting midges (Chironomidae) can consume and weaken rice seedlings and can cause major yield losses.

RESULTS

Mosquito populations and bat activity were assessed in rice paddies of Montgrí, Medes i Baix Ter Natural Park (NE Iberian Peninsula). Molecular analyses of bats faeces (6-weekly samples of 15 faeces each between mid-August and September) proved the presence of both mosquitoes and nonbiting midges in all diet samples. Furthermore, bat activity at the sampling locations was related to adult mosquito density.

CONCLUSION

Our results suggest that bats actively exploit the emergence of adult mosquitoes and further prove that they prey on mosquitoes, nonbiting midges and other deleterious insects. Promoting the presence of bats next to human settlements in such agroecosystems may constitute a biological control system with direct impact on both human health and crop yield. © 2020 Society of Chemical Industry.

A global class reunion with multiple groups feasting on the declining insect smorgasbord

We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.

Gradients in richness and turnover of a forest passerine's diet prior to breeding: A mixed model approach applied to faecal metabarcoding data

Rather little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding, we provide the most comprehensive analysis of a passerine's diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39 site and 2° latitudinal transect in Scotland. Faecal samples were collected in 2014-2015 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon-rich prey order. Here, we present a statistical approach for estimation of gradients and intersample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model-based estimation of repeatability, taxon richness and Jaccard indices. We found that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.

An appetite for pests: Synanthropic insectivorous bats exploit cotton pest irruptions and consume various deleterious arthropods

Conservation biological control (CBC) seeks to minimize the deleterious effects of agricultural pests by enhancing the efficiency of natural enemies. Despite the documented potential of insectivorous bats to consume pests, many synanthropic bat species are still underappreciated as beneficial species. We investigated the diet of Kuhl's pipistrelle (Pipistrellus kuhlii), a common synanthropic insectivorous bat that forages in urban and agricultural areas, to determine whether it may function as a natural enemy in CBC. Faecal samples of P. kuhlii were collected throughout the cotton-growing season from five roost sites near cotton fields located in a Mediterranean agroecosystem, Israel, and analyzed using DNA metabarcoding. Additionally, data on estimated abundance of major cotton pests were collected. We found that the diet of P. kuhlii significantly varied according to sites and dates and comprised 27 species of agricultural pests that were found in 77.2% of the samples, including pests of key economic concern. The dominant prey was the widespread cotton pest, the pink bollworm, Pectinophora gossypiella, found in 31% of the samples and in all the roosts. Pink bollworm abundance was positively correlated with its occurrence in the bat diet. Furthermore, the bats' dietary breadth narrowed, while temporal dietary overlap increased, in relation to increasing frequencies of pink bollworms in the diet. This suggests that P. kuhlii exploits pink bollworm irruptions by opportunistic feeding. We suggest that synanthropic bats provide important pest suppression services, may function as CBC agents of cotton pests and potentially contribute to suppress additional deleterious arthropods found in their diet in high frequencies.

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

Knowledge on the trophic interactions among predators and their prey is important in order to understand ecology and behaviour of animals. Traditionally studies on the diet composition of insectivorous bats have been based on the morphological identification of prey remains, but the accuracy of the results has been hampered due to methodological limitations. Lately, the DNA metabarcoding and High Throughput Sequencing (HTS) techniques have changed the scene since they allows prey identification to the species level, ultimately giving more precision to the results. Nevertheless, the use of one single primer set to amplify faecal DNA produces biases in the assessed dietary composition. Three horseshoe bats overlap extensively in their distribution range in Europe: Rhinolophus euryale, R. hipposideros and R. ferrumequinum. In order to achieve the deepest insight on their prey list we combined two different primers. Results showed that the used primers were complementary at the order and species levels, only 22 out of 135 prey species being amplified by both. The most frequent prey of R. hipposideros belonged to Diptera and Lepidoptera, to Lepidoptera in R. euryale, and Lepidoptera, Diptera and Coleoptera in R. ferrumequinum. The three bats show significant resource partitioning, since their trophic niche overlap is not higher than 34%. Our results confirm the importance of combining complementary primers to describe the diet of generalist insectivorous bats with amplicon metabarcoding techniques. Overall, each primer set showed a subset of the prey composition, with a small portion of the total prey being identified by both of them. Therefore, each primer presented a different picture of the niche overlap among the three horseshoe bats due to their taxonomic affinity.

Bats from different foraging guilds prey upon the pine processionary moth

Outbreaks of the processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller, 1775), a forest pest from the Palearctic, are thought to induce a behavioral response of bats, but up to now the moth has been seldom identified as bats’ prey. Studies on bat diets suggest moths with cyclical outbreaks attract a wide array of bat species from different foraging guilds. We test whether bats feed upon T. pityocampa in the Iberian Peninsula irrespective of the predator’s ecological and morphological features. We found that seven out of ten bat species belonging to different foraging guilds contained T. pityocampa DNA in their faeces and no difference was found in the foraging frequency among foraging guilds. A different size of the typical prey or the lack of fondness for moths can explain the absence of the pest in some bat species. Moreover, the intraspecific foraging frequency of T. pityocampa also changed with the sampling site likely representing differential availability of the moth. Lack of information on flight and dispersal behavior or the tympanate nature of the adult moth complicates understanding how different foraging guilds of bats prey upon the same prey. Our data suggests that T. pityocampa is a remarkable food source for many thousands of individual bats in the study area and we anticipate that more bats besides the species studied here are consuming this moth.

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals

DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML." To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.

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

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

From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web

Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.

Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus)

Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. In this pilot study we test a range of available primers to optimise diet analysis from metabarcoding of faeces of a generalist aquatic insectivore, the endangered Pyrenean desman (Galemys pyrenaicus, É. Geoffroy Saint-Hilaire, 1811, Talpidae), as a step to improve the knowledge of the conservation biology of this species. Twenty-four faeces were collected in the field, DNA was extracted from them, and fragments of the standard barcode region (COI) were PCR amplified by using five primer sets (Brandon-Mong, Gillet, Leray, Meusnier and Zeale). PCR outputs were sequenced on the Illumina MiSeq platform, sequences were processed, clustered into OTUs (Operational Taxonomic Units) using UPARSE algorithm and BLASTed against the NCBI database. Although all primer sets successfully amplified their target fragments, they differed considerably in the amounts of sequence reads, rough OTUs, and taxonomically assigned OTUs. Primer sets consistently identified a few abundant prey taxa, probably representing the staple food of the Pyrenean desman. However, they differed in the less common prey groups. Overall, the combination of Gillet and Zeale primer sets were most cost-effective to identify the widest taxonomic range of prey as well as the desman itself, which could be further improved stepwise by adding sequentially the outputs of Leray, Brandon-Mong and Meusnier primers. These results are relevant for the conservation biology of this endangered species as they allow a better characterization of its food and habitat requirements.

Table for five, please: Dietary partitioning in boreal bats

Differences in diet can explain resource partitioning in apparently similar, sympatric species. Here, we analyzed 1,252 fecal droppings from five species (Eptesicus nilssonii, Myotis brandtii, M. daubentonii, M. mystacinus, and Plecotus auritus) to reveal their dietary niches using fecal DNA metabarcoding. We identified nearly 550 prey species in 13 arthropod orders. Two main orders (Diptera and Lepidoptera) formed the majority of the diet for all species, constituting roughly 80%-90% of the diet. All five species had different dietary assemblages. We also found significant differences in the size of prey species between the bat species. Our results on diet composition remain mostly unchanged when using either read counts as a proxy for quantitative diet or presence-absence data, indicating a strong biological pattern. We conclude that although bats share major components in their ecology (nocturnal life style, insectivory, and echolocation), species differ in feeding behavior, suggesting bats may have distinctive evolutionary strategies. Diet analysis helps illuminate life history traits of various species, adding to sparse ecological knowledge, which can be utilized in conservation planning.