Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples

Abstract

Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods failed in the past, thereby hampering reliable assessments, a prerequisite for conservation. Here, we describe the development and application of an environmental DNA (eDNA) metabarcoding approach for detecting rare sturgeons in large rivers. Exemplarily, we developed a reference database for five native Danube sturgeons (Acipenser stellatus, Acipenser gueldenstaedtii, Acipenser ruthenus, Acipenser nudiventris, and Huso huso) and two non-native species (Acipenser baerii and Acipenser transmontanus), assessed these ex situ, and used eDNA as a detection tool along the entire length of the Danube (Europe, ~ 2850 km) and major tributaries. In ex situ analyses, all assays yielded positive amplifications for the assessed sturgeon species. In the Danube, the presence of A. ruthenus was confirmed at 14 of 29 sites (48.3%), and in 2 of 18 tributary sites (11.1%), providing the first comprehensive large-scale biogeographical snapshot of this species. Relative number of reads assigned to A. ruthenus varied between 0 and 2.5%, with sites registering positive detections being clustered in 3 sections of the Danube. Our findings enabled us to confirm the advantages of eDNA monitoring over traditional sampling methods for comprehensive whole-river snapshot studies of sturgeons conducted on a large geographical scale, and therefore we consider it to be a promising approach for application in conservation measures, fisheries management, scientific studies, and adaptive management plans for sturgeons on a global scale.

Environmental DNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River

“…Moreover, the presence of sturgeons in all spring and autumn samples may indicate their sufficient abundance, although species affiliation remains questionable. As identification of sturgeon species by classical species‐specific detection is currently challenging, total eDNA analysis with high‐throughput sequencing may be a solution (Meulenbroek et al., 2022; Yang et al., 2023). Thus, our experimental studies contribute to the methodology of free eDNA analysis and expand the potential for monitoring sturgeon fishes of the Ural River basin creating prerequisites for location mapping and quantitative assessment of population status using eDNA.…”

“…It is known that under mesocosm conditions, eDNA can be detected for up to 2 or 3 weeks (Dejean et al., 2012; Thomsen, Kielgast, Iversen, Wiuf, et al., 2012), or even 58 days according to one study (Strickler et al., 2015). Target sturgeon eDNA was detected in low numbers (two replicates among 25 eDNA samples) for a single individual from the reservoir within a week after the individual was removed (Meulenbroek et al., 2022; Strickler et al., 2015). For marine systems, a period of up to 48 h has been suggested for optimal processing before eDNA starts to degrade (Collins et al., 2018).…”

“…As an alternative to species-specific detection, metabarcoding using universal "teleo" primers amplifying the 12S mtDNA fragment successfully detected Danube sturgeons (Meulenbroek et al, 2022;Pont et al, 2023). This study proposes an efficient eDNA isolation technique and demonstrates the effective use of eDNA as a tool for detecting and obtaining a snapshot of the seasonal distribution of rare and endangered Ural-Caspian sturgeons in the Lower Ural River (~1084 km).…”

“…Despite the ongoing development of species-specific primers for sturgeons, their reliable species identification remains questionable. The difficulty in their genetic determination lies in the high degree of similarity between different species of Eurasian sturgeon (for example, only one base differentiates Acipenser stellatus from A. ruthenus) and consequently their frequent interspecific hybridization (Ludwig et al, 2002;Meulenbroek et al, 2022) Specific primers are being developed for the unique mitochondrial haplotypes of the target species within this family. Thus, the existing test systems for distinguishing native (A. sturio and A. oxyrinchus) and non-native (A. baerii, A. gueldenstaedtii, A. ruthenus, and A. stellatus) sturgeon species in Danish marine waters have proven to be efficient in both in silico and in vivo sampling.…”

Designing, implementing and monitoring the translocation of a highly threatened freshwater fish

“…abundance and age structure) and dispersal of the translocated fish that must combine various monitoring methods (such as those implemented in the present study) depending on the cost‐effectiveness in both economic and human resources. Species‐specific eDNA monitoring is increasingly used for assessing the distribution of rare or scarce species and has been shown to be more sensitive than conventional electrofishing and optical methods (Beng & Corlett, 2020; Brys et al, 2020; Dimond et al, 2022; Goldberg, Strickler & Fremier, 2018; Meulenbroek et al, 2022; Rojahn et al, 2021; Sepulveda et al, 2019). It should be noted that the presence of the Corfu killifish was confirmed with underwater footage and electrofishing only in the spring area, which was the release site, but these two methods did not detect the species in the mid‐section or lower section of the stream, indicating poor dispersal.…”