eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection

Abstract

Fauna monitoring often relies on visual monitoring techniques such as camera trapping, which have biases leading to underestimates of vertebrate species diversity. Environmental DNA (eDNA) metabarcoding has emerged as a new source of biodiversity data that may improve biomonitoring; however, eDNA‐based assessments of species richness remain relatively untested in terrestrial environments. We investigated the suitability of fallen log hollow sediment as a source of vertebrate eDNA, across two sites in southwestern Australia—one with a Mediterranean climate and the other semi‐arid. We compared two different approaches (camera trapping and eDNA metabarcoding) for monitoring of vertebrate species, and investigated the effect of other factors (frequency of species, timing of visits, frequency of sampling, and body size) on vertebrate species detectability. Metabarcoding of hollow sediments resulted in the detection of higher species richness in comparison (29 taxa: six birds, three reptiles, and 20 mammals) to metabarcoding of soil at the entrance of the hollow (13 taxa: three birds, two reptiles, and eight mammals). We detected 31 taxa in total with eDNA metabarcoding and 47 with camera traps, with 14 taxa detected by both (12 mammals and two birds). By comparing camera trap data with eDNA read abundance, we were able to detect vertebrates through eDNA metabarcoding that had visited the area up to two months prior to sample collection. Larger animals were more likely to be detected, and so were vertebrates that were identified multiple times in the camera traps. These findings demonstrate the importance of substrate selection, frequency of sampling, and animal size, on eDNA‐based monitoring. Future eDNA experimental design should consider all these factors as they affect detection of target taxa.

Home is where the hollow is: Revealing vertebrate tree hollow user biodiversity with eDNA metabarcoding

“…While the use of eDNA metabarcoding for vertebrate hollow user surveys shows great promise, with vertebrate taxa detected in only 56% of 138 samples, our study suggests that there is a need to increase sampling effort to detect the full range of vertebrate hollow users. Further studies are required, in our system and others, to determine the number of trees and hollows that need to be sampled, ideally in conjunction with camera trapping (e.g., Leempoel et al, 2020; Ryan et al, 2022), to determine the accuracy of this new survey method.…”

“…In silico studies were conducted using DNA sequences from the 12S and 16S rRNA marker regions (Othman et al, 2021) to identify the assay able to amplify the widest range of vertebrate taxa in the study region. The primer set 12S-V5 F2/R2 (Riaz et al, 2011), previously used to successfully amplify vertebrate taxa within the study region (Ryan et al, 2022;Van Der Heyde et al, 2020, 2021, was broad enough to amplify avian, mammalian and reptilian DNA, and short enough to pick up degraded DNA. As such, we amplified DNA with the general vertebrate primer 12S-V5 (Riaz et al, 2011), designed to amplify a 98 bp fragment which includes the V5 variable region of the 12S rRNA gene with the primers F2 (5′-TAGAACAGGCTCCTCTAG-3′) and R2 (5′-TTAGATACCCCACTATGC-3′).…”

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

“…Mammals and potentially endangered species can also be detected using samples from natural saltlicks utilizing eDNA metabarcoding [ 104 ]. Using eDNA from the soil to trace mammals [ 105 ] is not only environment dependent but also dependent on mammal abundance and size [ 106 ]. Hence, knowledge of the ecological behavior of the mammal is essential for the sampling design [ 99 ].…”

Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals

“…Fully terrestrial eDNA-based techniques to sample vertebrates (i.e., those not tied to water bodies) have included sampling eDNA found in soil or air 17,22,31 , and testing residues left on arti cial attractants such as coverboards 21,23 . Such methods circumvent the geographic limitations of those tied to water by allowing researchers to decide precisely where in the landscape to take samples.…”

“…For fully terrestrial species, eDNA detection techniques represent a rapidly expanding area of research [21][22][23] . Building off of early efforts at recovering DNA from physical traces such as tracks, hair, and scat 24,25 , mammal researchers have recently branched out into sampling eDNA from entire communities that has been deposited or transported into ponds and rivers 16,26−29 or left on attractants such as natural saltlicks or hollow logs 30,31 , including for some cryptic arboreal species. While such approaches are appealing for their ability to produce community-level inventories at large spatial scales, sampling is limited to wherever such natural features occur and is therefore inadequate for ner-scale monitoring.…”