Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks

Seymour, Mathew; Edwards, François; Cosby, B. J.; Kelly, Martyn; Bruyn, Mark de; Carvalho, Gary R.; Creer, Simon

doi:10.1016/j.scitotenv.2020.138801

Cited by 60 publications

(48 citation statements)

References 45 publications

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“…Although our study focused on a limited part of community diversity, sample diversity within each station was successfully recovered, as confirmed by previous studies on meiofauna in Lima estuary (Fais et al, 2020a;2020b). The present study not only re-captured the high turnover within and between the sampling stations in Lima estuary (Fais et al, 2020a;2020b), but highlighted a similar situation in two other distinct estuarine systems in (which was not certified by peer review) is the author/funder. All rights reserved.…”

Section: Discussionsupporting

confidence: 81%

The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

Bellisario

Fais

Duarte

et al. 2021

Preprint

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The identification of the patterns and mechanisms behind species distribution is one of the major challenges in ecology, having also important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their real taxonomic diversity due to their high degree of cryptic diversity and inherent diagnosis difficulties, such as meiofaunal communities. Environmental DNA (eDNA) metabarcoding may provide a fast and reliable way to refine and scale-up the characterization of biological diversity in complex environmental samples, allowing to bypass such drawbacks and increase the resolution of biodiversity estimates. Moreover, the possibility of integrating eDNA metabarcoding-derived data with tools and methods rooted in network theory would deepen the knowledge of the structuring processes of ecological communities in ways that cannot be predicted from studying individual species/communities in isolation. Here, a sediment eDNA metabarcoding of mitochondrial cytochrome c oxidase I (COI) and the nuclear hypervariable V4 region of the 18S rDNA (18S) was used to reconstruct the spatial networks of intertidal meiofaunal OTUs from three estuaries of North-Western Iberian Peninsula. Null models were used to identify the role of environmental and spatial constraints on the structure of COI- and 18S-derived spatial networks and to characterize the macroecological features of surveyed phyla. Our results show the feasibility of eDNA metabarcoding, not only to capture a fair amount of diversity hard to detect with standard surveys procedures, but also to identify hierarchical spatial structures in intertidal meiofaunal assemblages. This suggests that exclusivity of occurrence rather than pervasiveness appears to be the norm in meiofaunal organisms and that niche-based processes predominantly drive the spatial aggregation and contemporary distribution of meiofaunal phyla within the system.

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Section: Discussionsupporting

confidence: 81%

The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

Bellisario

Fais

Duarte

et al. 2021

Preprint

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“…COI is not a well-established barcode marker for many of these groups. A more suitable universal target locus for these taxa is found in the nuclear ribosomal RNA genes (Cabra et al 2016, Giebner et al 2020, Seymour et al 2020). Here we focused on the 18SrDNA as a potential marker to exclude Dreissena from amplification, while retaining a broad specificity for various planktonic taxa.…”

Section: Methodsmentioning

confidence: 99%

Molecular diet analysis in zebra and quagga mussels (Dreissenaspp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

Weber

Brink

Wörner

et al. 2021

Preprint

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Molecular gut content analysis is a popular tool to study food web interactions and was recently also suggested as an alternative source for DNA based biomonitoring. However, the overabundant consumer’s DNA often outcompetes that of its diet during PCR. Blocking approaches are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. We here designed an assay to monitor the eukaryotic diet of mussels and test their utility as biological eDNA filters to monitor planktonic communities. We designed several rDNA primer sets with a broad taxonomic suitability for eukaryotes, which suppress the amplification of mussels. The primers were tested using mussel DNA extracts and the results were compared to eDNA water samples collected next to the mussel colonies. Taxonomic recovery, as well as patterns of alpha and beta diversity, were compared between mussels and water samples. In addition, we analyzed time series samples of mussel samples from different German rivers. Our primer sets efficiently block the amplification of various mussel genera. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also recover various taxa of possible commensals and parasites, associated with the mussels. Our protocol will enable large scale dietary analysis in mussels, facilitate aquatic food web analysis, elucidate the ecological impact of invasive bivalves and the rapid survey of mussel aquacultures for pathogens. Moreover, we show that mussels could serve as an interesting complementary DNA source for biomonitoring.

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“…Combined with high throughput sequencing (HTS) applications, such as metabarcoding, eDNA based sampling is rapidly being integrated into standard ecological monitoring practices. Previous eDNA biomonitoring studies in natural environments have assessed population and communities across spatial and temporal scales for rivers [24][25][26] , lakes [27][28][29] and marine environments [30][31][32] . What is currently lacking is the link between functional and community diversity dynamics using eDNA across appropriate spatial and temporal scales.…”

Section: Introductionmentioning

confidence: 99%

Nestedness and turnover of riverine species and functional diverity using eDNA and traditional approaches.

Seymour

Edwards²,

Cosby

et al. 2020

Preprint

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Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and their responses to environmental factors. Recently, eDNA metabarcoding based sampling and identification has been shown to increase the accuracy of biodiversity assessments, while reducing cost and time, compared to traditional methods. Here, we present results from a field comparison of eDNA versus traditional riverine biodiversity techniques to assess freshwater macroinvertebrates. In addition, we investigated the effects of landuse and seasonality on community and functional diversity, to infer the underlying regional ecological temporal and spatial dynamics. Comparison of biodiversity dynamics based on traditional and eDNA survey methods showed significant differences in taxonomic groups identified between methods, landuse type, and method x season interactions. Our findings are the first example of eDNA derived functional spatio-temporal and dynamics, indicating that the regional shifts in diversity and function are linked to regional seasonal fluctuations in fine particle matter versus localized landuse type. Beta diversity components (nestedness and turnover) differed significantly along the environmental gradient, but in different directions, for each methodology. Overall, our findings show that eDNA based ecological assessment is effective in assessing temporal and spatial diversity and functional dynamics of macroinvertebrates, while demonstrating that these data can be used to infer effective biodiversity assessment and management strategies.

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Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks

Cited by 60 publications

References 45 publications

The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

Molecular diet analysis in zebra and quagga mussels (Dreissenaspp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

Nestedness and turnover of riverine species and functional diverity using eDNA and traditional approaches.

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