Dataset Information

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal 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. By using multispecies 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 quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly 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.

SUBMITTER: Bush A

PROVIDER: S-EPMC7165428 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness.

Bush Alex A Monk Wendy A WA Compson Zacchaeus G ZG Peters Daniel L DL Porter Teresita M TM Shokralla Shadi S Wright Michael T G MTG Hajibabaei Mehrdad M Baird Donald J DJ

Proceedings of the National Academy of Sciences of the United States of America 20200326 15

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 hydroe ...[more]

PMID: 32217735

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Project description:Abstract Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their ecology and conservation requirements. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (Sistrurus catenatus), a Federally Threatened snake found throughout the Great Lakes region. Eighty‐three fecal samples collected across 10 different massasauga populations located in Michigan, USA, were sequenced, with 70 samples containing prey DNA. We used universal metazoan primers and developed a host‐specific oligonucleotide blocker to characterize their diet. We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. Meadow voles (Microtus pennsylvanicus) were the most common prey item (70% of diet) followed by the northern short‐tailed shrew (Blarina brevicauda) and masked shrew (Sorex cinereus; 15.7% of diet each), along with occasional bird and snake prey. Adult individuals exhibited a more generalized diet, consuming a larger number of prey taxa on average. Younger snakes consumed a smaller variety of prey items and tended to consume smaller‐sized mammals such as masked shrews (Sorex cinereus) and northern short‐tailed shrews (Blarina brevicauda). We conclude that small mammals are a crucial part of eastern massasauga rattlesnake diet and recommend this be taken into consideration when conservation strategies are developed. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at‐risk reptile species. We applied a DNA metabarcoding approach to study the diet of the threatened eastern massasauga rattlesnake (Sistrurus catenatus). We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at‐risk species.

Project description:BackgroundFreshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use and recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally. Aquatic insects and other macroinvertebrates are often used as indicators of ecological condition in freshwater biomonitoring programs; however, these diverse groups can present challenges to morphological identification and coarse-level taxonomic resolution can mask patterns in community composition. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. While individual stream reaches can be very heterogenous, most community ecology studies focus on larger, landscape-level patterns of community composition. A high degree of community variability at the local scale has important implications for both biomonitoring and ecological research, and the incorporation of DNA metabarcoding into local biodiversity assessments will inform future sampling protocols.ResultsWe sampled twenty streams in southern Ontario, Canada, for aquatic macroinvertebrates across multiple time points and assessed local community variability by comparing field replicates taken ten meters apart within the same stream. Using bulk-tissue DNA metabarcoding, we revealed that aquatic macroinvertebrate communities are highly diverse at small spatial scales with unprecedented levels of local taxonomic turnover. We detected over 1600 Operational Taxonomic Units (OTUs) from 149 families, and a single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Benthic communities were largely comprised of rare taxa detected only once per stream despite multiple biological replicates (24-94% rare taxa per site). In addition to numerous rare taxa, our species pool estimates indicated that there was a large proportion of taxa that remained undetected by our sampling regime (14-94% per site). Our sites were located across a gradient of agricultural activity, and while we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use. Within-stream dissimilarity estimates were consistently high for all levels of taxonomic resolution (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales.

Dataset Information

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness.

Publications

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness.

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