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 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.

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

“…In environments where eDNA diffuses poorly, as in soil, terrestrial ecologists should know that sampling effort will always be more intense. However, using composite soil samples can increase the spatial representativeness of soil sampling, hence limiting experimental costs [ 50 ]. However, such a design should be chosen if it does not compromise the study’ s success.…”

“…Investigations have revealed that eDNA has the potential to measure microbial communities and forest biodiversity. Therefore leveraging these methods will enhance our ability to detect extant species, describe new species and improve our understanding of ecological and community dynamics in forest ecosystems [ 50 ]. In another study, it has been demonstrated that eDNA underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success [ 90 ].…”

Plant–animal interactions in the era of environmental DNA (eDNA)—A review

“…Mutualistic relationships between plants and animals (e.g., insects and nematodes) assist plant growth and development, and these relationships can also be studied effectively through eDNA analysis (Ladin et al, 2021). For example, Rasmussen et al (2021) used eDNA metabarcoding to explore how the diversity of fungi and arthropods was affected by different agricultural management practices.…”

Editorial: Understanding patterns and mechanisms of forest canopy diversity and ecosystem functions in a changing world

“…The recent development of canopy cranes across the globe (Nakamura et al, 2017), for example, makes it possible to carry out spatially replicated intensive surveys and manipulative experiments that were not hitherto possible using conventional techniques such as single rope climbing and scaffolding. The development of mobile aerial platforms combined with advanced robotics (Cannon et al) and next-generation sequencing, such as barcoding mass samples and environmental DNA (Ji et al, 2013;Ladin et al, 2021), provide additional research power that extends the capabilities of conventional surveys. Last, the establishment of multidisciplinary communication platforms (e.g., the Canopy Science Community Forum https://groups.google.com/g/ canopy-science) and canopy-oriented conferences (e.g., the 8th International Canopy Conference in Xishuangbanna, China, October 2023) provide opportunities to share information and to collaborate with multidisciplinary communities for studying arboreality and vertical dynamics of forest ecosystems (Cannon et al).…”