Metabarcoding a Metacommunity: detecting change in a wetland wilderness

Abstract

The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large-scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed, and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification, and DNA metabarcoding. Using multi-species occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification, and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera, and for the first time, quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were near random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales, but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.

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

“…Expanding metacommunity research to understudied geographical areas, and/or poorly known taxonomic groups, is complicated by the "taxonomic impediment" (Cicconardi et al, 2013;Young et al, 2019). The development of metabarcoding provides new opportunities to accelerate studies on metacommunity structure across underexplored fractions of biodiversity and greatly increases their taxonomic resolution (Arribas, Andújar, Salces-Castellano, et al, 2021;Bush et al, 2020;Martin et al, 2021;Zinger et al, 2019). Recent advances in field, laboratory and bioinformatic protocols for community metabarcoding have led to improvements in both the efficiency for the generation of such high-resolution taxonomic inventories (Arribas et al, 2016;Elbrecht et al, 2018), and the reliability of α and β diversity estimates (Andújar et al, 2018;Creedy et al, 2019).…”

Spatio-temporal determinants of arthropod biodiversity across an agro-ecosystem landscape

“…Metabarcoding has many advantages over morphological identification. It provides a standardized method for species assignment even when a species has not been formally described, allows finer taxonomic resolution, speeds sample processing time, and is very costeffective (Cristescu 2014;Bush et al 2020). Using barcoding rather than morphological identification can also increase estimates of species richness and beta diversity by revealing cryptic species (Brehm et al 2016;D'Souza & Hebert 2018), which allows for a more robust 19 assessment to be made about the factors that drive variation in community composition (Bush et al 2020).…”

Unraveling the plant diversity of the Amazonian canga through DNA barcoding

“…As mentioned above, inventorying species through DNA-based tools has consistently gained ground along the years, achieving further importance with the development of multispecies identification approaches based on high-throughput sequencing technologies (Deiner et al, 2017;Kress et al, 2015). Several authors have pointed out the many advantages of using DNA metabarcoding for monitoring biodiversity, especially considering robustness and efficiency of this analytical system (Bush et al, 2020;Deiner et al, 2017;Zinger et al, 2019). Certainly, the effectiveness of metabarcoding can be greatly affected depending on the completeness level of the reference DNA barcode library (Alsos et al, 2018); thus, care must be taken for its use for identification of specimens at species level until a complete barcode library is available, especially in areas with several narrowly distributed endemics.…”