Multifaceted DNA metabarcoding: Validation of a noninvasive, next‐generation approach to studying bat populations

Abstract

As multiple species of bats are currently experiencing dramatic declines in populations due to white‐nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once‐common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high‐throughput, DNA‐based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next‐generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics.

Bats as potential suppressors of multiple agricultural pests: A case study from Madagascar

“…The DNA metabarcoding of bat faecal pellets can offer valuable insights into the dietary preferences of bats and their potential role as pest suppressors (Bohmann et al, 2014;Swift et al, 2018). Recent diet analyses of multiple bat species have detected a wide range of arthropods in bat populations (Galan et al, 2017) including several economically important pest species (Taylor et al, 2017).…”

Interspecific competition in bats and diet shifts in response to white‐nose syndrome

“…Our study showed that both E. fuscus and M. lucifugus consumed insect pest species, although these data cannot be used to quantify the abundance of these species in the diet or the overall effect on the population of these insect pests (Swift et al. ). Also, of the insect pests consumed by M. lucifugus , there was an increase in the number of these consumed by E. fuscus in response to the decline of M. lucifugus .…”

“…), but DNA processing methods are still not suitable for directly quantifying the abundance of prey items in the bat diet (Swift et al. ). Therefore, future studies should focus on ways to calculate the volume of each prey item in a sample, which can then be extrapolated to determine the impact of bats feeding on insects.…”

Next‐generation conservation genetics and biodiversity monitoring

“…Swift et al. () utilized MIS methods and multifaceted DNA metabarcoding (MDM) to obtain six different data classes of genetic information from bat guano. Next‐generation sequencing was used to collect data on bat species composition, individual genotypes, sex ratios, diet, parasites, and the presence of White‐nose syndrome.…”

“…Carroll et al (2018) target the interface between MIS methods and NGS approaches. Minimally invasive samples are often opportunistically collected from the environment and consequently contain limited amounts of DNA, which can restrict the subsequent molecular analyses of these samples, especially when applying NGS methods.The authors provide guidance on how to transition legacy datasets of microsatellites or mitochondrial DNA to genomic platforms and integrate novel methods such as microbiome and epigenetic studies Swift et al (2018). utilized MIS methods and multifaceted DNA metabarcoding (MDM) to obtain six different data classes of genetic information from bat guano.…”