Biologie | Umwelt
Romane Bauer, 2005 | Zürich, ZH
As climate change intensifies and trade activities along the Rhine increase, the invasion of Swiss freshwater ecosystems by alien species will become a rising concern. As such, time- and cost-efficient monitoring strategies will be needed to mitigate the drastic environmental and economic impacts of invasive species on the “Wasserschloss Europas,” as well as to maintain good water quality in Switzerland. This project aimed at evaluating whether the detection of environmental DNA (eDNA) by real-time quantitative PCR is a promising method for identifying a correlation between the presence of the invasive mussel Dreissena polymorpha and the invasive amphipod Dikerogammarus villosus in the Lake of Zurich and the Limmat. It is important to study the hazards associated with the collective spread of invasive species. Following the experimental pipeline, eDNA from both invasive species was reliably detected at all sampling sites, confirming their co-occurrence in the freshwater bodies investigated. Although previous observations had suggested that both species could interact for micronutrient supply and habitat preferences, no significant positive correlation was found between their respective eDNA amounts, suggesting no quantitative association between them at present.
Introduction
The research question investigated was: Is there a correlation between the spatial distributions of D. polymorpha and D. villosus, as measured by the presence of eDNA of both species detected by qPCR at four sampling sites distributed along the river Limmat and the Lake of Zurich? In addition, this paper also examined 1) the optimization of extraction methods and qPCR mixes for eDNA and their limitations, 2) the effect of both predator species on local ecosystems, and 3) possible strategies to mitigate their impact.
Methods
The main steps of the design consisted of 1) freshwater sampling at four sites along the Lake of Zurich and the Limmat, 2) eDNA filtering on microporous membranes, 3) eDNA extraction, 4) eDNA yield quantification using a Qubit fluorometer, and 5) species-specific detection by qPCR. eDNA yield and qPCR amplification cycle values (Cq values, indicator of relative eDNA abundance of each species) were acquired from multiple sampling sites and replicates. E. coli was used as a positive control as it was expected to be in all samples. Negative controls were performed at each procedural step using distilled water. Three different eDNA extraction methods were used, aiming at optimizing the yield of eDNA for subsequent analyses. A PowerTrack SYBR Green Master Mix was used for qPCR as it was sensible to low eDNA concentrations.
Results
Overall, D. polymorpha eDNA was detected at small amplification cycles (Cq from 25.36 to 28.05), meaning that it was a well-detected species. D. villosus eDNA was detected at mean Cq values from 33.75 to 39.33, indicating smaller eDNA abundance in the samples. No significant positive correlation was found between the Cq values of D. villosus and D. polymorpha with both extraction methods at the 95% confidence level as tested with linear regression (p-values 0.1390 and 0.1796) and Spearman’s Rank Coefficient (p-values 0.1286 and 0.3961).
Discussion
Some unspecific products were found when analyzing the melting curves, which could be related to polymerase inhibition and stochastic effects when working with low DNA concentrations, as well as primer dimers. The initial hypothesis, predicting a positive correlation between the eDNA levels of both species, was not confirmed. It is to be noted that the Cq value is an indirect indicator of species abundance, especially when comparing organisms that have different physiologies and paraphyletic groups. Stream biology, as well as the reproductive life stage of the species, could also have influenced their eDNA levels in the water. Nevertheless, the presence of both species in the Limmat and the Lake of Zurich was confirmed. D. polymorpha and D. villosus will continue to threaten the extinction of local mussel and macroinvertebrate communities, causing massive biodiversity loss and promoting cyanobacterial growth in the water.
Conclusions
eDNA from both invasive species was detected at all sites, although no significant correlation between their levels was found. Nevertheless, through this project, the possibility to exploit eDNA to detect both species in freshwater was demonstrated. This paper also highlights that everyone can get involved in environmental protection in their own way, which we will need more than ever with the current spread of, inter alia, the quagga mussel in Switzerland.
Würdigung durch die Expertin
Dr. Elvira Mächler
Die vorliegende Arbeit von Romane Bauer beeindruckt durch ihre eigenständige Herangehensweise an ein hochaktuelles Thema. Durch ihre detaillierte Analyse und innovative Methodik hebt sich die Arbeit hervor und leistet einen bedeutenden Beitrag zur aktuellen Forschung im Bereich der Umwelt-DNA. Die präzise Ausführung der Studie, sowie die darauf basierenden fundierten Ergebnisse, reflektieren gründlich erarbeite Fachliteratur und akkurate ausgeführte Forschungsarbeit. Herzliche Gratulation an die Autorin!
Prädikat:
sehr gut
Realgymnasium Rämibühl, Zürich
Lehrerin: Kathy Lieb Guhl
