Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
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Metabarcoding of soil environmental DNA replicates plant community variation but not specificity. / Barnes, Christopher James; Nielsen, Ida Broman; Aagaard, Anne; Ejrnæs, Rasmus; Hansen, Anders Johannes; Frøslev, Tobias Guldberg.
In: Environmental DNA, Vol. 4, No. 4, 2022, p. 732-746.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
AU - Barnes, Christopher James
AU - Nielsen, Ida Broman
AU - Aagaard, Anne
AU - Ejrnæs, Rasmus
AU - Hansen, Anders Johannes
AU - Frøslev, Tobias Guldberg
N1 - Publisher Copyright: © 2022 The Authors. Environmental DNA published by John Wiley & Sons Ltd.
PY - 2022
Y1 - 2022
N2 - While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast trnL region (10–143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the trnL sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the specificity of assignments made by the trnL primers, and improves the accuracy of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.
AB - While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast trnL region (10–143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the trnL sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the specificity of assignments made by the trnL primers, and improves the accuracy of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.
KW - biodiversity
KW - biological monitoring
KW - ecology
KW - environmental DNA
KW - metabarcoding
KW - molecular ecology
KW - morphological survey
U2 - 10.1002/edn3.287
DO - 10.1002/edn3.287
M3 - Journal article
AN - SCOPUS:85125055109
VL - 4
SP - 732
EP - 746
JO - Environmental DNA
JF - Environmental DNA
SN - 2637-4943
IS - 4
ER -
ID: 307289477