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Journal article
Metabarcoding of soil environmental DNA to estimate plant diversity globally
Frontiers in plant science, Vol.14, Art. 1106617
2023
PMID: 37143888
Abstract
Introduction: Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods.
Methods: We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data.
Results: Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region.
Discussion: eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
Details
- Title
- Metabarcoding of soil environmental DNA to estimate plant diversity globally
- Authors/Creators
- Martti Vasar - University of TartuJohn Davison - University of TartuMari Moora - University of TartuSiim-Kaarel Sepp - University of TartuSten Anslan - University of TartuSaleh Al-Quraishy - Zoology Department, College of Science, King Saud University, Riyadh, Saudi ArabiaMohammad Bahram - Swedish University of Agricultural SciencesC Guillermo Bueno - University of TartuJuan José Cantero - National University of Río CuartoEzequiel Chimbioputo Fabiano - University of NamibiaGuillaume Decocq - Thompson Rivers UniversityRein Drenkhan - Estonian University of Life SciencesLauchlan Fraser - Thompson Rivers UniversityJane Oja - University of TartuRoberto Garibay-Orijel - CIUDADInga Hiiesalu - University of TartuKadri Koorem - University of TartuLadislav Mucina - Stellenbosch UniversityMaarja Öpik - University of TartuSergei Põlme - University of TartuMeelis Pärtel - Institute of Ecology and Earth Sciences, University of Tartu, Tartu, EstoniaCherdchai Phosri - Department of Biology, Nakhon Phanom University, Nakhon Phanom, ThailandMarina Semchenko - University of TartuTanel Vahter - University of TartuJiři Doležal - Faculty (United Kingdom)Aida M Vasco Palacios - Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, ColombiaLeho Tedersoo - University of TartuMartin Zobel - University of Tartu
- Publication Details
- Frontiers in plant science, Vol.14, Art. 1106617
- Publisher
- Frontiers Media SA
- Identifiers
- 991005572569307891
- Copyright
- © 2023 Vasar et al.
- Murdoch Affiliation
- Harry Butler Institute; Centre for Terrestrial Ecosystem Science and Sustainability
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.64 Phylogenetics & Genomics
- 3.64.2564 Environmental DNA
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science