Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

Lopes, Carla Martins; Baêta, Délio; Sasso, Thais; Vanzetti, Agustín; Zamudio, Kelly R.; Taberlet, Pierre; Haddad, Célio F. B.

doi:10.1002/edn3.142

Cited by 5 publications

(2 citation statements)

References 49 publications

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“…We recovered that total and extracellular extractions were ecologically congruent for estimating overall beta diversity and showed good potential for monitoring the biodiversity of eukaryotes, especially for active and dominant taxa in terrestrial communities, such as Fungi and invertebrates. However, our results do not support the eDNA from leaf litter as a reliable tool for monitoring vertebrate species in general (Lopes et al 2021c).…”

Section: The Use Of Environmental Dna To Monitor Biodiversity and Its...contrasting

confidence: 96%

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

et al. 2022

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Here, we summarize examples of significant advances in amphibian research supported by the São Paulo Research Foundation (FAPESP), focusing on recent discoveries in the fields of community ecology, habitat change, infection diseases, and multipurpose DNA sequencing. We demonstrated that FAPESP has been fundamental not only by directly funding research projects and scholarships, but also through its science training policy, fostering international collaborations with world-class research institutions, improving and consolidating new lines of research that often depended on a synergetic combination of different knowledge and complex tools. We emphasized that future studies will continue to focus on basic questions, such as description of new species, as well as taxonomic and systematic corrections. Furthermore, we also expect that there will be a strong integration among different disciplines using novel bioinformatics tools and modeling approaches, such as machine learning. These new approaches will be critical to further develop our understanding of foundational questions of amphibian life-history trait variation, disease transmission, community assembly, biogeography, and population forecasts under different global change scenarios such as agricultural expansion, agrochemical use, habitat loss, and climate change.

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Section: The Use Of Environmental Dna To Monitor Biodiversity and Its...contrasting

confidence: 96%

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

et al. 2022

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“…Although eDNA research has increased dramatically over the last decade (Lear et al 2018), the effects of protocol choice on assessments of diversity using eDNA from soil samples are not well characterized in the published literature. Usually, studies have focused on interpreting eDNA sequencing results, and less attention has been given to investigating the effects of eDNA method selection (Table S1; Drummond et al 2015, Horton et al 2017, Lanzén et al 2017, Walker et al 2017, Sikder et al 2020, Calderón-Sanou et al 2021, Kirse et al 2021, Lopes et al 2021, Pansu et al 2021. Currently, there are a few typical methods for analysing eDNA (Table S1; Lear et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica

et al. 2023

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Environmental DNA is a powerful tool for monitoring biodiversity. Although environmental DNA surveys have successfully been implemented in various environments, protocol choice has been shown to affect results and inferences. Thus far, few method comparison studies for soil have been undertaken. Here, we optimized the workflow for soil metabarcoding through a comparative study encompassing variation in sampling strategy (individual and combined samples), DNA extraction (PowerSoil®, NucleoSpin® Soil, PowerSoil® + phosphate buffer and NucleoSpin® Soil + phosphate buffer) and library preparation (one-step and two-step quantitative polymerase chain reaction methods). Using a partial 18S rRNA marker, a total of 309 eukaryotic taxa across 21 phyla were identified from Antarctic soil from one site in the Larsemann Hills. Our optimized workflow was effective with no notable reduction in data quality for a considerable increase in time and cost efficiency. The NucleoSpin® Soil + phosphate buffer was the best-performing extraction method. Compared to similar studies in other regions, we obtained low taxonomic coverage, perhaps because of the paucity of Antarctic terrestrial organisms in genetic reference databases. Our findings provide useful methodological insights for maximizing efficiency in soil metabarcoding studies in Antarctica and other low-biomass environments.

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Environmental and Invertebrate-Derived DNA: A Powerful Approach for Surveying and Monitoring Biodiversity

Rodríguez-Castro,

Saranholi,

de Oliveira

et al. 2023

Conservation Genetics in the Neotropics

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Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

Cited by 5 publications

References 49 publications

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica

Environmental and Invertebrate-Derived DNA: A Powerful Approach for Surveying and Monitoring Biodiversity

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