DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

Abstract

Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity. Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure. DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data. The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management. OPEN PRACTICES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.

Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

“…Our results are in accordance with several other studies that also identified more species with eDNA compared with other conventional methods in different ecosystems (e.g., Andruszkiewicz et al., 2017; Civade et al., 2016; Handley et al., 2019; Valentini et al., 2016). In addition, eDNA metabarcoding detected 72% of species captured by trawling, which is also congruent with previous comparative studies showing that eDNA detects between 60% and 100% of the species that were detected by other conventional methods (e.g., Fujii et al., 2019; Shaw et al., 2016; Sun et al., 2019; Thomsen et al., 2016; Valentini et al., 2016; Yamamoto et al., 2017). Here, it should be noted that eDNA lower detection of species that were observed by conventional methods could be explained by different sampling efforts.…”

“…Sun et al. (2019) demonstrated that DNA metabarcoding may identify more than twice the number of taxa compared with net‐based morphological identification methods. Altogether, these findings strongly suggest that eDNA at the very least offers similar but often higher performance of detection than those traditional methods.…”

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Coverage and quality of DNA barcode references for Central and Northern European Odonata

“…Yet, the finding that all 39 records with partial DNA barcodes (29 <400 bp; 10 <500 bp) have been assigned successfully to a conspecific BIN cluster ( Supplemental File S3 ) demonstrates that ‘minibarcodes’—more suitable for metabarcoding-based community assessments—have the potential to correctly identify Odonata DNA traces. This finding is in line with several recent studies employing partial COI-based DNA metabarcoding for freshwater community assessments (e.g., Sun et al, 2019 ; Zizka, Geiger & Leese, 2020 ).…”

Airborne eDNA Reflects Human Activity and Seasonal Changes on a Landscape Scale

“…Work has also been done in ocean systems with studies ranging from examining shark diversity response to anthropogenic disturbance to understanding how anthropogenic activities such as oil spills and development impact micro and macro coastal communities (Bakker et al, 2017;Xie et al, 2018;DiBattista et al, 2020). Sun et al (2019) used eDNA metabarcoding to understand Dipteria and other organism populations in human caused roadside stormwater ponds. Additionally, Klymus et al (2017) examined how anthropogenic uranium containment ponds impacted the biodiversity of vertebrate species.…”