Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

Abstract

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Rivers are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. Traditional monitoring methods for ecological assessments are costly and time-intensive. Here, we compared monitoring of macroinvertebrates based on environmental DNA (eDNA) sampling with monitoring based on traditional kick-net sampling to assess biodiversity patterns at 92 river sites covering all major Swiss river catchments. From the kick-net community data, a biotic index (IBCH) based on 145 indicator taxa had been established. The index was matched by the taxonomically annotated eDNA data by using a machine learning approach. Our comparison of diversity patterns only uses the zero-radius Operational Taxonomic Units assigned to the indicator taxa. Overall, we found a strong congruence between both methods for the assessment of the total indicator community composition (gamma diversity). However, when assessing biodiversity at the site level (alpha diversity), the methods were less consistent and gave complementary data on composition. Specifically, environmental DNA retrieved significantly fewer indicator taxa per site than the kick-net approach. Importantly, however, the subsequent ecological classification of rivers based on the detected indicators resulted in similar biotic index scores for the kick-net and the eDNA data that was classified using a random forest approach. The majority of the predictions (72%) from the random forest classification resulted in the same river status categories as the kick-net approach. Thus, environmental DNA validly detected indicator communities and, combined with machine learning, provided reliable classifications of the ecological state of rivers. Overall, while environmental DNA gives complementary data on the macroinvertebrate community composition compared to the kick-net approach, the subsequently calculated indices for the ecological classification of river sites are nevertheless directly comparable and consistent.

Consideration of Multitrophic Biodiversity and Ecosystem Functions Improves Indices on River Ecological Status

“…For example, we identified that the relative abundance of 81 OTU-based indicators was strongly associated with different human disturbance groups (range from 1 to 100 times), although only 37 of them have clear classification at the genus or species level. This result indicates that OTU-based indicators can make up for the deficiency of the traditional species annotation strategy to a great extent because the traditional strategy is limited to the part of biodiversity with obvious morphological characteristics, which often has high coverage of public reference sequences, such as fish and birds. , Recent studies have indeed found that for well-studied groups, eDNA-based assessments give comparable results with respect to ecological indices. , Although eDNA metabarcoding may reduce cost and is a less invasive sampling process, ,, the deficiency of reference databases and the deviation of OTU species annotation are still one of the biggest shortcomings of this method. An OTU-based indicator strategy obviously reduces or bypasses the dependence of species annotation on reference databases .…”

“…58,59 Recent studies have indeed found that for well-studied groups, eDNA-based assessments give comparable results with respect to ecological indices. 60,61 Although eDNA metabarcoding may reduce cost and is a less invasive sampling process, 23,62,63 the deficiency of reference databases and the deviation of OTU species annotation are still one of the biggest shortcomings of this method. An OTU-based indicator strategy obviously reduces or bypasses the dependence of species annotation on reference databases.…”

Monitoring invasive alien macroinvertebrate species with environmental DNA

“…Successful detection using an eDNA metabarcoding approach is underpinned by the primers used to amplify target species. However, due to the traditional methods, which previously established the ‘freshwater macroinvertebrate’ group, this refers to detecting a polyphyletic group (Brantschen et al, 2021; Carew, Miller, & Hoffmann, 2011; Leese et al, 2021), which makes finding a conserved primer region for multiple groups difficult. Here, we used one general metazoan primer pair for the CO1 marker (Leray et al, 2013; Geller et al, 2013), which may not be ideal for the successful detection of some of the target IAS.…”

“…After bioinformatic quality assurance, each dataset was subject to further quality assurance steps for tag‐jumping or minor contamination in library preparation. For the national samples, only ZOTUs, which appeared in at least two out of the four replicates, were kept (See Brantschen, Blackman, Walser, & Altermatt, 2021 for full details). For the catchment sampling campaign, 0.1% of reads in each sample were removed from each taxon found in that sample, in line with other studies (Hänfling et al, 2016, see Blackman et al, 2021 for full details).…”

“…In 2008, Ficetola and colleagues used DNA extracted from pond water to detect the American bull frog, a prominent IAS in Europe. Since this study, research application of eDNA has ballooned to include different taxonomic groups by either a species‐specific method (conventional PCR, qPCR and ddPCR), or whole communities such as fish (Hänfling et al, 2016; Pont et al, 2018), macroinvertebrates (Fernández, Rodríguez‐Martínez, Martínez, Garcia‐Vazquez, & Ardura, 2019; Brantschen et al, 2021), and zooplankton (Brown, Chain, Zhan, MacIsaac, & Cristescu, 2016; Djurhuus et al, 2018) using a metabarcoding approach. A key advantage of eDNA sampling, which makes it particularly well suited for IAS monitoring, is its scalability.…”