Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

Abstract

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24%, and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 69% and 84%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called 'bycatch'. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

“…The copyright holder for this preprint (which this version posted April 28, 2021. ; https://doi.org/10.1101/2021.04.27.441610 doi: bioRxiv preprint replicates taken within a small geographic area for eDNA-based monitoring of mammals (Figs 1 and 2; Macher et al, 2021). A total of eight species were detected in only one or two locations (Fig.…”

“…McDevitt et al, 2019;Valentini et al, 2016). However, recent studies have demonstrated that eDNA retrieved from water from both lotic (Sales, McKenzie et al, 2020;Sales, Kaizer et al, 2020;Lozano & Caballero, 2021;Macher et al, 2021;Mariani et al, 2021) and lentic (Ushio et al, 2017;Harper et al, 2019) systems can detect components of the overall terrestrial and semi-aquatic mammalian community.…”

Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

“…Altogether, the information included in the non-target part of the dataset obtained might provide valuable information about the surrounding ecosystem. More and more studies indicate the significance and validity of information contained in so-called bycatch derived from aquatic eDNA data (Macher et al 2021b; Mariani et al 2021). Thus, including and sharing the entire eDNA sequence dataset could be of paramount importance for further studies from the region and effort should be made towards their storage and public availability (Berry et al 2020; Makiola et al 2020).…”

Fresh insights into Mediterranean biodiversity: environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

“…Altogether, the information included in the non-target part of the dataset might provide valuable information about the surrounding ecosystem. More and more studies indicate the significance and validity of information contained in so-called bycatch derived from aquatic eDNA data (Macher et al, 2021b;Mariani et al, 2021). Thus, including and sharing the entire eDNA sequence dataset could be of paramount importance for further studies from the region and effort should be made towards their storage and public availability (Berry et al, 2020;Makiola et al, 2020).…”