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

Tytuł:: Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems.
Autorzy:: Ladin ZS; Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA. .
Ferrell B; Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA.
Dums JT; Biotechnology Program, North Carolina State University, Raleigh, NC, 27695, USA.
Moore RM; Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA.
Levia DF; Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, Newark, DE, 19716, USA.
Shriver WG; Departments of Geography and Spatial Sciences and Plant and Soil Sciences, University of Delaware, 216C Pearson Hall, Newark, DE, 19716, USA.
D'Amico V; US Forest Service, Northern Research Station, Newark, DE, USA.
Trammell TLE; Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
Setubal JC; Instituto de Química, University of Sao Paulo, São Paulo, SP, 05508-000, Brazil.
Wommack KE; Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
Źródło:: Scientific reports [Sci Rep] 2021 Jan 15; Vol. 11 (1), pp. 1629. Date of Electronic Publication: 2021 Jan 15.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: London : Nature Publishing Group, copyright 2011-
MeSH Terms:: Forests*
DNA Barcoding, Taxonomic/*methods
DNA, Environmental/*analysis
Biodiversity ; Cluster Analysis ; Cytophagaceae/genetics ; Cytophagaceae/isolation & purification ; Fresh Water/microbiology ; Lactococcus/genetics ; Lactococcus/isolation & purification ; Mycoplasma/genetics ; Mycoplasma/isolation & purification ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 16S/metabolism
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Substance Nomenclature:: 0 (DNA, Environmental)
0 (RNA, Ribosomal, 16S)
Entry Date(s):: Date Created: 20210116 Date Completed: 20210913 Latest Revision: 20231110
Update Code:: 20240105
PubMed Central ID:: PMC7811025
DOI:: 10.1038/s41598-020-80602-9
PMID:: 33452291
: Czasopismo naukowe

Pełny tekst

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.

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