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 collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). 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%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, 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.

Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico

“…Likewise, the identification of additional species of mammals, birds and amphibians using the cenotes may facilitate a more complete picture of their role in local ecosystems. Our study adds to a growing number of metabarcoding studies that have documented the detection of vertebrate "bycatch", offering insights into non-fish vertebrate communities associated with aquatic habitats, and highlighting the potential of aquatic eDNA samples to characterize non-aquatic communities (Macher et al 2021;Mariani et al 2021;Duarte Ritter et al 2022).…”

Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities

“…However, this reproducibility might not be achieved for environmental samples. Here, a generally lower reproducibility is expected and it is recommended to consider sufficient field and laboratory replicates to maximise species detection and minimize stochastic sampling effects (Sato et al 2017, Bylemans et al 2018b, Macher et al 2021b, Rojahn et al 2021. Particularly the SeaDNA-mid primer pair might suffer from lower reproducibility for environmental samples due to the strong co-amplification.…”

BeeDNA: Microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

“…Similarly, more biological replication may be necessary to enhance pollinator eDNA detection rates, as has been observed for eDNA detection of terrestrial vertebrates from water (Broadhurst et al, 2021;Macher et al, 2021). Here, only one flower per plant was sampled with each sampling method, but plant-associated arthropods may not have interacted with this particular flower.…”