Ladin, Zachary S.;
Ferrell, Barbra;
Dums, Jacob T.;
Moore, Ryan M.;
Levia, Delphis F.;
Shriver, W. Gregory;
D’Amico, Vincent;
Trammell, Tara L. E.;
Setubal, João Carlos;
Wommack, K. Eric
Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
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Media type:
E-Article
Title:
Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
Contributor:
Ladin, Zachary S.;
Ferrell, Barbra;
Dums, Jacob T.;
Moore, Ryan M.;
Levia, Delphis F.;
Shriver, W. Gregory;
D’Amico, Vincent;
Trammell, Tara L. E.;
Setubal, João Carlos;
Wommack, K. Eric
imprint:
Springer Science and Business Media LLC, 2021
Published in:Scientific Reports
Language:
English
DOI:
10.1038/s41598-020-80602-9
ISSN:
2045-2322
Origination:
Footnote:
Description:
<jats:title>Abstract</jats:title><jats:p>We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including <jats:italic>Mycoplasma</jats:italic> sp., <jats:italic>Spirosoma</jats:italic> sp., <jats:italic>Roseomonas</jats:italic> sp., and <jats:italic>Lactococcus</jats:italic> sp. were present only in throughfall samples. <jats:italic>Spiroplasma</jats:italic> sp., <jats:italic>Methylobacterium</jats:italic> sp., <jats:italic>Massilia</jats:italic> sp., <jats:italic>Pantoea</jats:italic> sp., and <jats:italic>Sphingomonas</jats:italic> sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.</jats:p>