Frontiers in Plant Science (Apr 2023)

Metabarcoding of soil environmental DNA to estimate plant diversity globally

  • Martti Vasar,
  • John Davison,
  • Mari Moora,
  • Siim-Kaarel Sepp,
  • Sten Anslan,
  • Saleh Al-Quraishy,
  • Mohammad Bahram,
  • Mohammad Bahram,
  • C. Guillermo Bueno,
  • Juan José Cantero,
  • Juan José Cantero,
  • Ezequiel Chimbioputo Fabiano,
  • Guillaume Decocq,
  • Rein Drenkhan,
  • Lauchlan Fraser,
  • Jane Oja,
  • Roberto Garibay-Orijel,
  • Inga Hiiesalu,
  • Kadri Koorem,
  • Ladislav Mucina,
  • Ladislav Mucina,
  • Maarja Öpik,
  • Sergei Põlme,
  • Meelis Pärtel,
  • Cherdchai Phosri,
  • Marina Semchenko,
  • Tanel Vahter,
  • Jiři Doležal,
  • Jiři Doležal,
  • Aida M. Vasco Palacios,
  • Leho Tedersoo,
  • Leho Tedersoo,
  • Martin Zobel,
  • Martin Zobel

DOI
https://doi.org/10.3389/fpls.2023.1106617
Journal volume & issue
Vol. 14

Abstract

Read online

IntroductionTraditional 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.MethodsWe 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.ResultsLarge-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.DiscussioneDNA 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.

Keywords