Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos

Abstract

38Genetic diversity is the most basal level of biodiversity and determines the evolutionary capacity of 39 species to adapt to changing environments, yet it is typically neglected in routine biomonitoring and 40 stressor impact assessment. For a comprehensive analysis of stressor impacts on genetic diversity, it is 41 necessary to assess genetic variants simultaneously in many individuals and species. Such an assessment 42 is not as straight-forward and usually limited to one or few individual species. However, nowadays 43 species diversity can be assessed by analysing thousands of individuals of a community simultaneously 44 with DNA metabarcoding. Recent bioinformatic advances also allow for the extraction of exact 45 sequence variants (ESVs or haplotypes) in addition to Operational Taxonomic Units (OTUs). By using 46 this new capability, we here evaluated if the analysis of mitochondrial genetic diversity in addition to 47 species diversity can provide insights into responses of stream macrozoobenthic communities to 48 environmental stressors. For this purpose, we analysed macroinvertebrate bulk samples of three German 49 river systems with different stressor levels using DNA metabarcoding. While OTU and haplotype 50 number were negatively correlated with stressor impact, this association was not as clear when looking 51 at haplotype diversity. Here, stressor responses were only found for sensitive EPT (Ephemeroptera, 52Plecoptera, Trichoptera) taxa, and those exceedingly resistant to organic stress. An increase in haplotype 53 number per OTU and haplotype diversity of sensitive taxa was observed with an increase in ecosystem 54 quality and stability, while the opposite pattern was detected for pollution resistant taxa. However, this 55 pattern was less prominent than expected based on the strong differences in stressor intensity between 56 sites. To compare genetic diversity among river systems, only OTUs could be used, which were present 57 in all systems. As OTU composition differed strongly between the rivers, this led to the exclusion of a 58 high number of OTUs, especially in diverse river systems of good quality, which potentially diminished 59 the genetic diversity patterns. To better understand responses of genetic diversity to environmental 60 stressors for example in river ecosystems, it would be important to increase OTU overlap between sites 61 of comparisons, e.g. by sampling a narrower stressor gradient, and to perform calibrated studies 62 controlling for the number and individual genotypes. However, this pioneer study shows that the 63 extraction of haplotypes from DNA metabarcoding datasets is a promising tool to simultaneously assess 64 mitochondrial genetic diversity changes in response to environmental impacts for a metacommunity. 66 67Degradation, pollution, and exploitation of freshwater ecosystems has resulted in a drastic decline of 68 biodiversity (Vörösmarty et al., 2010; WWF, 2018). The magnitude of biodiversity loss depends on 69 stressor intensities as well as on resistance and re...

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

“…Based on our results, we advocate stringent ASV filtering, as it can provide informative data sets without compromising the required reliability for haplotype-level metabarcoding. Even if we cannot be fully confident that all erroneous haplotypes were filtered out, as the performance of the approach depends on the completeness of the reference sequence catalogue (Andújar et al, 2021), the future incorporation of intraspecific genetic data in local reference databases will provide further confidence and the opportunities for intra-OTU analyses of ASV variation (Elbrecht et al, 2018;Zizka et al, 2020).…”

Debar: A sequence‐by‐sequence denoiser for COI‐5P DNA barcode data

“…Understanding within-species patterns of genetic diversity is an essential metric for characterizing community health. High intra-species genetic diversity is assumed to indicate healthy ecosystems, comprised of large and stable populations with the standing genetic variation needed to survive environmental stressors (Zizka et al, 2020). The characterization of ESVs within OTUs can provide intra-species diversity measures for member species of a community (Frøslev et al, 2017) Note: Sequencing and processing results in two sets of data, groups of sequences assigned to BINs and groups of sequences clustered into operational taxonomic units (OTUs).…”

“…Additionally, rare sequences or important intraspecies variants need not be discarded based solely on their abundance and can be retained with higher confidence if they conform to the expected gene structure. This latter benefit will be particularly valuable for work on hyperdiverse communities, (e.g., tropical insects) and for analyses of metabarcode data, where uneven sampling is often the norm and the resolution of intraspecies variation is challenging (Braukmann et al, 2019;Elbrecht et al, 2018;Nearing et al, 2018;Zizka et al, 2020).…”

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

“…Metabarcoding has been successfully used to detect the responses of macroinvertebrate communities to environmental gradients (Emilson et al 2017) and pesticide spills (Andújar et al 2018). Novel bioinformatic approaches also allow inferences of haplotypes from macroinvertebrate metabarcoding data (Elbrecht et al 2018, Zizka et al 2020. Although metabarcoding represents a cost-and time-efficient alternative to morphological identification , its usefulness in studying macroinvertebrate dynamics in IRES needs to be tested (Stubbington et al 2018).…”