Detection of vertebrates from natural and artificial inland water bodies in a semi‐arid habitat using eDNA from filtered, swept, and sediment samples

Abstract

Biomonitoring is vital for establishing baseline data that is needed to identify and quantify ecological change and to inform management and conservation activities. However, biomonitoring and biodiversity assessment in arid environments, which are predicted to cover 56% of the Earth's land surface by 2100, can be prohibitively time consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high‐throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human‐constructed and natural water sources in a semi‐arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S‐V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term–granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling that simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.

Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA

“…Even when traps were located in enclosures close to reptile and bird species, detection success was poor. These results are comparable to those of other studies using different eDNA substrates to detect vertebrates, such as air [13], water [8,62] and soil [7], where mammals were most commonly represented in detections, and reptile species were poorly represented or completely absent. The difficulties associated with detecting reptiles through metabarcoding could possibly be explained by the relatively lower deposition rate of reptile DNA compared to other classes of vertebrates [36,63]; however, tortoise faeces, which would theoretically provide a food source for carrion flies, was observed in the enclosures of both species.…”

“…Several methods, such as camera traps and passive acoustic loggers, have been developed to reduce the direct human costs associated with monitoring ecosystems. Recently, DNA metabarcoding of environmental substrates, such as soil [6,7], water [8][9][10], flowers [11] and air [12,13], has been used to monitor vertebrate biodiversity. An extension of this is the use of invertebrate-derived DNA (iDNA), whereby vertebrate diversity is monitored using invertebrates that feed on the blood, flesh or scat of vertebrates and therefore carry their DNA signal [14][15][16][17].…”

Spider webs capture environmental DNA from terrestrial vertebrates

“…For these reasons, new eDNA substrates are continually being explored, and eDNA based biomonitoring using water, 22 soil, 23 ingested or invertebrate-derived DNA (iDNA), 24 , 25 flowers, 26 , 27 and swabbed surfaces, 6 , 15 are now common. Recently, the detection of species through airborne DNA has also been trialled to detect vertebrate taxa.…”

Spider Webs Capture Environmental DNA from Terrestrial Vertebrates

“…At the extreme ends of the spectrum eDNA, in many aquatic environments seems to disappear within 24-48 h, 19,20 whereas in permafrozen soil it has been shown to preserve for up to 2 million years. 21 For these reasons, new eDNA substrates are continually being explored, and eDNA based biomonitoring using water, 22 soil, 23 ingested or invertebrate-derived DNA (iDNA), 24,25 flowers, 26,27 and swabbed surfaces, 6,15 are now common. Recently, the detection of species through airborne DNA has also been trialled to detect vertebrate taxa.…”