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      Can eDNA metabarcoding offer a catchment-based approach for biodiversity monitoring?

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      ARPHA Conference Abstracts

      Pensoft Publishers

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          Abstract

          In previous studies eDNA metabarcoding has been demonstrated as a viable tool for catchment-level biodiversity sampling in rivers (Deiner et al. 2016). However, questions still remain over the appropriate sampling protocol for large spatial scale sampling. River reaches are composed of multiple habitats with species composition varying from one to the next (Costa and Melo 2007). Therefore, how many spatial replicates are needed to reliably represent the river network? Is the previously used approach to sample at every river confluence (Deiner et al. 2016) sufficient or is more needed? These questions were addressed using a case study in the headwaters of the Cound Brook, a tributary to the River Severn in Shropshire, UK.Two sub-catchments of the Cound Brook were used. One sub-catchment had a sample taken at the most downstream point before the confluence. Additionally, a sample at the upstream extent of the same sub-catchment was taken to estimate any correlation between the species found at the beginning of the river reach and at the end. Another sub-catchment also had the same up- and downstream sample design. However, in between was a systemic sampling regime every 500 m. This is to test if increasing the spatial resolution gave significantly different results to the sparser sampling regime.At each sample location, a 1 L water sample was sequentially filtered through membranes of three different mesh sizes: 5µm, 0.45µm and 0.2µm. Sequential filtering was performed because DNA resides in two forms in the environment (Civade et al. 2017), within whole cells (cellular DNA) and outside of cells (extracellular). The theory is that the coarser filters predominantly collect cellular DNA and the finer filters collect predominantly extracellular DNA of increasingly smaller fragment lengths. Consequently, sequential filtering could represent DNA degradation in the environment (Fig. 1). Also, Turner et al. 2014 suggested that the larger particles could determine very recent or local organisms. Therefore, we hypothesised that the DNA collected by the coarser filters would represent local diversity and the DNA collected by the finer filters would reflect biodiversity further upstream.Initial results suggest sequential filtering through the 5µm and 0.45µm filters caught detectable levels of eDNA where the 0.2µm did not catch enough to show up through gel electrophoresis. The relevance of the initial finding suggests that if we only used a 5µm filter the data collected at 0.45µm could have been discarded. Further investigations of any differences in species compositions between filters and the relationships to other sampling locations is still to be determined. This ongoing research is intended to determine the appropriate sampling protocol for a large-scale biodiversity assessment regime combining eDNA metabarcoding and species distribution modelling.

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          Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

          In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.
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            Beta diversity in stream macroinvertebrate assemblages: among-site and among-microhabitat components

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              Particle size distribution and optimal capture of aqueous macrobial eDNA

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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                ARPHA Conference Abstracts
                ACA
                Pensoft Publishers
                2603-3925
                March 08 2021
                March 08 2021
                : 4
                Article
                10.3897/aca.4.e65651
                © 2021

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