Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

Abstract 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...

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Autores principales:	Zachary S. Ladin, Barbra Ferrell, Jacob T. Dums, Ryan M. Moore, Delphis F. Levia, W. Gregory Shriver, Vincent D’Amico, Tara L. E. Trammell, João Carlos Setubal, K. Eric Wommack
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4a4d781637ce45f3914fbe87610d9859
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spelling	oai:doaj.org-article:4a4d781637ce45f3914fbe87610d98592021-12-02T15:23:05ZAssessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems10.1038/s41598-020-80602-92045-2322https://doaj.org/article/4a4d781637ce45f3914fbe87610d98592021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80602-9https://doaj.org/toc/2045-2322Abstract 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 Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas 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.Zachary S. LadinBarbra FerrellJacob T. DumsRyan M. MooreDelphis F. LeviaW. Gregory ShriverVincent D’AmicoTara L. E. TrammellJoão Carlos SetubalK. Eric WommackNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zachary S. Ladin Barbra Ferrell Jacob T. Dums Ryan M. Moore Delphis F. Levia W. Gregory Shriver Vincent D’Amico Tara L. E. Trammell João Carlos Setubal K. Eric Wommack Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
description	Abstract 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 Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas 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.
format	article
author	Zachary S. Ladin Barbra Ferrell Jacob T. Dums Ryan M. Moore Delphis F. Levia W. Gregory Shriver Vincent D’Amico Tara L. E. Trammell João Carlos Setubal K. Eric Wommack
author_facet	Zachary S. Ladin Barbra Ferrell Jacob T. Dums Ryan M. Moore Delphis F. Levia W. Gregory Shriver Vincent D’Amico Tara L. E. Trammell João Carlos Setubal K. Eric Wommack
author_sort	Zachary S. Ladin
title	Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
title_short	Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
title_full	Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
title_fullStr	Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
title_full_unstemmed	Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
title_sort	assessing the efficacy of edna metabarcoding for measuring microbial biodiversity within forest ecosystems
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4a4d781637ce45f3914fbe87610d9859
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Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

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