A New Non-invasive Method for Collecting DNA From Small Mammals in the Field, and Its Application in Simultaneous Vector and Disease Monitoring in Brushtail Possums

Abstract

Large-scale monitoring of wild populations in remote areas using traditional live-capturing methods is logistically and financially challenging. Devices that can be used to obtain biological material remotely and store it for an extended period have considerable potential to monitor population densities and health status, but their applicability remains largely unexplored. The present study describes a device that collects trace amounts of DNA from the saliva of small mammals that is deposited on the surface of a collection medium (WaxTags®). The device’s performance was evaluated on Australian brushtail possums (Trichosurus vulpecula), an invasive pest species and the most significant vector of bovine tuberculosis infective agent (Mycobacterium bovis), under field conditions in Canterbury, New Zealand. The retrieved DNA was used to amplify eight possum-specific microsatellite markers and bacterial 16S rRNA. The design is mechanically robust, and the quality of the recovered DNA was adequate for microsatellite-based identification of individual possums, estimation of population density, and partial reconstruction of their oral microbiomes as a potential indicator of health. Several medically important bacteria, including strains of environmental Mycobacterium sp., were detected. The design can be refined to monitor other animals’ populations proactively and provide different levels of information necessary to manage wild populations.

Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta)

“…Some cells collected from feces may not represent living gut cells, and can as such, be less informative about biological processes. Even so, they may be of sufficient quality to investigate some genetic questions 68,69 . Gut epithelium collected from feces can contain beside hyena DNA, DNA from gut bacteria, fungi, parasites, and of prey species recently consumed 70 .…”

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New?

“…Stress monitoring is possible both by cortisol measurement [127,128] and by detecting a suppression in secretory Immunoglobulin A, an indicator of chronic stress [129], given that baseline values are established for the species and population under investigation. Both bacterial pathogens excreted orally such as Mycobacterium bovis in Australian brushtail possums and oral microbiomes can be assessed by extracting bacterial DNA and RNA from saliva [130,131]. A wide range of viruses can be isolated from saliva including economically relevant viruses such as foot-and-mouth disease virus [132,133], and classical and African swine fever [134,135] as well as viruses of conservation concern such as the elephant endotheliotropic herpesvirus [136].…”

“…An artificial object that can be attractive to a range of inquisitive mammalian species including, for example, suids and primates, are ropes covered in bait [133][134][135]137,140]. Baited salt licks [132], interactive enrichment toys [139], and WaxTags ® [130] are other objects that encourage animals to lick them and leave saliva behind for collection. Natural objects include all items that a specific species tends to chew and discharge, for example, leaves in some primates [138].…”

“…To optimise sampling, pre-trials with different objects are often necessary. The risk of interactions of non-target species with the object, objects becoming unretrievable or being swallowed also need to be managed [130,135,137]. Some objects such as cotton ropes may contain natural PCR inhibitors that need to be considered when samples are processed [135,137].…”

An evaluation of DNA extraction methods on historical and roadkill mammalian specimen

“…While the field of museomics is expanding due to the potential of museum samples as a vast source of DNA 1 , 2 , samples from live animals—mainly blood and soft tissues—are more challenging to collect, especially for endangered species. Recently, non-lethal and non-invasive sampling strategies have become increasingly popular as they alleviate needs over trapping and sedation of living animals 3 , therefore minimizing additional stress on individuals and natural populations. Among them, roadkill represents an underutilized source of molecular data for DNA-based studies.…”