Fish diversity assessment in the headwaters of the Volga River using environmental DNA metabarcoding

Abstract

The headwaters of the Volga River exhibit large reaches with near‐pristine conditions, and therefore long‐term biodiversity monitoring of this catchment can provide rare and valuable information on a European lowland river. More specifically, freshwater fish species assemblages are a good indicator of ecosystem status, as they are particularly sensitive to environmental changes and hydromorphological alterations. Historical records show that the fish fauna of the Upper Volga has changed over time, both in species composition and in abundance. The construction of the Volga–Kama cascade (a series of large dams) has specifically affected the migration of diadromous species. Environmental DNA metabarcoding offers a non‐invasive approach to determine the number of species in an aquatic ecosystem, as well as their identity and distribution. This approach is especially useful for fish fauna surveys along large rivers and long‐term biomonitoring, with the advantage of having no impact on the species and their habitats. To infer the current fish species diversity and the spatial distribution of each species in the free‐flowing section of the Upper Volga River, as well as in selected tributaries, an environmental DNA metabarcoding approach was applied, using three mitochondrial DNA markers. This method allowed the positive identification of 23 fish species and their respective distributions in the headwaters of the Volga. This assessment provides a valuable example of the application of environmental DNA metabarcoding in a large river system, and constitutes a starting point for future investigations and long‐term biomonitoring in the Upper Volga system. In addition, the results can also serve as a reference for fish diversity assessments of other large European lowland rivers, and can guide future conservation and management measures in the headwaters of the Volga.

Development of a TaqMan qPCR protocol for detecting Acipenser ruthenus in the Volga headwaters from eDNA samples

“…No amplification was observed from any eDNA samples corroborating the results of Lecaudey et al (2019). The non-detection could be caused by seasonal migrations during summer months (Kubala et al 2019, Sorokin et al 2002, orvery low abundances ("rarely caught andin single instances"- Sorokin et al 2002), that may have led to eDNAconcentrations below the detection threshold of the assay.…”

“…Main threats involve habitat fragmentation and loss and overexploitation (IUCN 2019). Using an eDNA-metabarcoding approach, Lecaudey et al (2019) identified 23 fish species in the Upper Volga catchment. However, the sterlet, a species of conservation interest in this area (Schletterer 2006;Schletterer et al 2018), was not detected.…”

“…We designed TaqMan primers (AruF: 5′-TCT ACC GTC ACC CAG GTC AT-3′; AruR: 5′-CGC CTG TTA AGG TTG TGT TCT TTT -3′) and probe (AruPr: 5′-FAM-GAG AGG TAC AGC TCT CTT G-MGB-Q500-3′) in the 16S rRNA gene using the DECIPHER package (Wright et al 2014;Wright 2015). We utilized the reference database of Lecaudey et al (2019) containing 150 sequences of 45 native and invasive fishes, covering 19 Palearctic fish families, including sterlet and Russian sturgeon A. gueldenstaedtii (Supplemental 1). Primers and probe were quality-checked with MultiplePri-merAnalyzer (Thermo Fisher Scientific).…”

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

“…We tested for the influence of three potential problems – an incomplete reference database, PCR inhibition and primer bias – on the results of our own, recently carried out, metabarcoding study in the headwaters of the Volga River (Lecaudey, Schletterer, Kuzovlev, Hahn, & Weiss, ). Lecaudey et al (), detected 23 fish species across the sampled stretches, but the number of detected species varied considerably between the three barcode markers used, namely 12S rRNA, 16S rRNA, and cytochrome B (CytB).…”

“…We tested for the influence of three potential problems – an incomplete reference database, PCR inhibition and primer bias – on the results of our own, recently carried out, metabarcoding study in the headwaters of the Volga River (Lecaudey, Schletterer, Kuzovlev, Hahn, & Weiss, ). Lecaudey et al (), detected 23 fish species across the sampled stretches, but the number of detected species varied considerably between the three barcode markers used, namely 12S rRNA, 16S rRNA, and cytochrome B (CytB). The Ukrainian brook lamprey ( Eudontomyzon mariae ), blue bream ( Ballerus ballerus ), white‐eye bream ( Ballerus sapa ), asp ( Leuciscus aspius ), Siberian spiny loach ( Cobitis sibirica ), wels catfish ( Silurus glanis ), and European eel ( Anguilla anguilla ) were not detected by any of the three markers used.…”