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

Zachary S Ladin,Barbra Ferrell,Vincent D’Amico,Delphis F Levia,Tara L E Trammell,Jacob T Dums,W Gregory Shriver,João Carlos Setubal,Ryan M Moore,K Eric Wommack

doi:10.1038/s41598-020-80602-9

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.

Highlights

Approaching the nature of interrelations that can influence community d ynamics[16,17]
Despite the impressive use of environmental DNA (eDNA) metabarcoding as a tool to increase our ability to measure biodiversity, eDNA metabarcoding has been limited to applications which use aquatic samples containing DNA, given the inherently fragile nature of organismal tissue containing DNA and its rapid degradation when exposed to typical environmental forces[48]
The number of unique amplicon sequence variants (ASVs) differed among groups (Kruskal–Wallis chi-sq. = 6.82, df = 2, P < 0.05), and the count of ASVs found solely within throughfall samples (1170.4 ± 266) was greater than those found in rainwater-only samples (81 ± 58; Z = − 2.51, P < 0.05, Fig. 2)

Summary

Introduction

Approaching the nature of interrelations that can influence community d ynamics[16,17]. Another study exploring persistence and factors influencing eDNA within soils found that eDNA became undetectable after roughly one week, this may vary as a function of soil moisture, temperature, and habitat characteristics[51] Despite these methodological challenges, innovative use of eDNA metabarcoding is increasingly being used to detect species within terrestrial ecosystems[52,53,54,55]. We wanted to test the hypothesis that there would be additive effects of bioprecipitation and collection of forest canopy phytobiome communities compared to rainwater alone This is important given the demonstrated linkages of and need for plant-associated bacteria and key functional roles these interactions can have

Methods

Results

Discussion

Conclusion