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Metabarcoding of soil environmental DNA to estimate plant diversity globally

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 compositio...

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Autores principales: Vasar, Martti, Davison, John, Moora, Mari, Sepp, Siim-Kaarel, Anslan, Sten, Al-Quraishy, Saleh, Bahram, Mohammad, Bueno, C. Guillermo, Cantero, Juan José, Fabiano, Ezequiel Chimbioputo, Decocq, Guillaume, Drenkhan, Rein, Fraser, Lauchlan, Oja, Jane, Garibay-Orijel, Roberto, Hiiesalu, Inga, Koorem, Kadri, Mucina, Ladislav, Öpik, Maarja, Põlme, Sergei, Pärtel, Meelis, Phosri, Cherdchai, Semchenko, Marina, Vahter, Tanel, Doležal, Jiři, Palacios, Aida M. Vasco, Tedersoo, Leho, Zobel, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151745/
https://www.ncbi.nlm.nih.gov/pubmed/37143888
http://dx.doi.org/10.3389/fpls.2023.1106617
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author Vasar, Martti
Davison, John
Moora, Mari
Sepp, Siim-Kaarel
Anslan, Sten
Al-Quraishy, Saleh
Bahram, Mohammad
Bueno, C. Guillermo
Cantero, Juan José
Fabiano, Ezequiel Chimbioputo
Decocq, Guillaume
Drenkhan, Rein
Fraser, Lauchlan
Oja, Jane
Garibay-Orijel, Roberto
Hiiesalu, Inga
Koorem, Kadri
Mucina, Ladislav
Öpik, Maarja
Põlme, Sergei
Pärtel, Meelis
Phosri, Cherdchai
Semchenko, Marina
Vahter, Tanel
Doležal, Jiři
Palacios, Aida M. Vasco
Tedersoo, Leho
Zobel, Martin
author_facet Vasar, Martti
Davison, John
Moora, Mari
Sepp, Siim-Kaarel
Anslan, Sten
Al-Quraishy, Saleh
Bahram, Mohammad
Bueno, C. Guillermo
Cantero, Juan José
Fabiano, Ezequiel Chimbioputo
Decocq, Guillaume
Drenkhan, Rein
Fraser, Lauchlan
Oja, Jane
Garibay-Orijel, Roberto
Hiiesalu, Inga
Koorem, Kadri
Mucina, Ladislav
Öpik, Maarja
Põlme, Sergei
Pärtel, Meelis
Phosri, Cherdchai
Semchenko, Marina
Vahter, Tanel
Doležal, Jiři
Palacios, Aida M. Vasco
Tedersoo, Leho
Zobel, Martin
author_sort Vasar, Martti
collection PubMed
description 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.
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spelling pubmed-101517452023-05-03 Metabarcoding of soil environmental DNA to estimate plant diversity globally Vasar, Martti Davison, John Moora, Mari Sepp, Siim-Kaarel Anslan, Sten Al-Quraishy, Saleh Bahram, Mohammad Bueno, C. Guillermo Cantero, Juan José Fabiano, Ezequiel Chimbioputo Decocq, Guillaume Drenkhan, Rein Fraser, Lauchlan Oja, Jane Garibay-Orijel, Roberto Hiiesalu, Inga Koorem, Kadri Mucina, Ladislav Öpik, Maarja Põlme, Sergei Pärtel, Meelis Phosri, Cherdchai Semchenko, Marina Vahter, Tanel Doležal, Jiři Palacios, Aida M. Vasco Tedersoo, Leho Zobel, Martin Front Plant Sci Plant Science 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. Frontiers Media S.A. 2023-04-18 /pmc/articles/PMC10151745/ /pubmed/37143888 http://dx.doi.org/10.3389/fpls.2023.1106617 Text en Copyright © 2023 Vasar, Davison, Moora, Sepp, Anslan, Al-Quraishy, Bahram, Bueno, Cantero, Fabiano, Decocq, Drenkhan, Fraser, Oja, Garibay-Orijel, Hiiesalu, Koorem, Mucina, Öpik, Põlme, Pärtel, Phosri, Semchenko, Vahter, Doležal, Palacios, Tedersoo and Zobel https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Vasar, Martti
Davison, John
Moora, Mari
Sepp, Siim-Kaarel
Anslan, Sten
Al-Quraishy, Saleh
Bahram, Mohammad
Bueno, C. Guillermo
Cantero, Juan José
Fabiano, Ezequiel Chimbioputo
Decocq, Guillaume
Drenkhan, Rein
Fraser, Lauchlan
Oja, Jane
Garibay-Orijel, Roberto
Hiiesalu, Inga
Koorem, Kadri
Mucina, Ladislav
Öpik, Maarja
Põlme, Sergei
Pärtel, Meelis
Phosri, Cherdchai
Semchenko, Marina
Vahter, Tanel
Doležal, Jiři
Palacios, Aida M. Vasco
Tedersoo, Leho
Zobel, Martin
Metabarcoding of soil environmental DNA to estimate plant diversity globally
title Metabarcoding of soil environmental DNA to estimate plant diversity globally
title_full Metabarcoding of soil environmental DNA to estimate plant diversity globally
title_fullStr Metabarcoding of soil environmental DNA to estimate plant diversity globally
title_full_unstemmed Metabarcoding of soil environmental DNA to estimate plant diversity globally
title_short Metabarcoding of soil environmental DNA to estimate plant diversity globally
title_sort metabarcoding of soil environmental dna to estimate plant diversity globally
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151745/
https://www.ncbi.nlm.nih.gov/pubmed/37143888
http://dx.doi.org/10.3389/fpls.2023.1106617
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