Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

Abstract

Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live‐trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live‐trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap‐nights); in addition to 16 pitfall traps (1,408 trap‐nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera‐days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3‐km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample‐based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large‐ and medium‐sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community.

Airborne environmental DNA for terrestrial vertebrate community monitoring

“…In freshwater, terrestrial vertebrates can be detected through the DNA they leave when e.g. drinking or defecating [24][25][26][27][28] , and DNA from vertebrates can be detected in the gut contents of parasitic, scavenging or coprophagous invertebrates 13,[29][30][31][32] .…”

Measuring biodiversity from DNA in the air

“…As the field matures, considerable research effort now focuses on the "ecology of eDNA" (Barnes & Turner, 2016) quantifying and understanding factors influencing eDNA detections beyond inventories alone. Comparative studies have shown that metabarcoding of aquatic eDNA matches or even outperforms conventional methods of community sampling (Bessey et al, 2021;Mena et al, 2021;Ruppert et al, 2019). Additionally, an indication of terrestrial biodiversity can also be obtained from eDNA analysis of water and sediments sampled from aquatic systems (Sales et al, 2020;Ushio et al, 2017), though detections may be biased towards semi-aquatic species.…”

“…Additionally, an indication of terrestrial biodiversity can also be obtained from eDNA analysis of water and sediments sampled from aquatic systems (Sales et al, 2020;Ushio et al, 2017), though detections may be biased towards semi-aquatic species. A comparison of tropical mammal detection methods (Mena et al, 2021) including eDNA from lentic and lotic systems, live-trapping, pitfall traps, camera traps, and mistnets found integrated methods provide best estimates of community composition.…”

“…Although aquatic eDNA alone recovered much of the diversity of mammals (Mena et al, 2021) this would be limited when aquatic systems are not in the vicinity.…”

Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology

“…There is a large range of possible TAS applications including variant detection and tumour profiling in cancer research, the detection of somatic mutations or those associated with susceptibility to disease, new findings in the field of phylogeny and taxonomy studies or the discovery of useful genes for applications in molecular breeding 2 , 3 , 9 , 10 . In the field of environmental sciences, TAS is becoming increasingly important, as it facilitates the assessment of the taxonomic composition of environmental samples with the help of metabarcoding approaches such as environmental DNA (eDNA) based biomonitoring or food web studies 11 – 13 .…”