Diversity Metrics Are Robust to Differences in Sampling Location and Depth for Environmental DNA of Plants in Small Temperate Lakes

Jennifer A Drummond,Scott P Egan,Yiyuan Li,Michael E Pfrender,David M Lodge,Eric R Larson,Crysta A Gantz,Mark A Renshaw,Adrienne M S Correa

doi:10.3389/fenvs.2021.617924

Abstract

Environmental DNA (eDNA) analysis methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort. However, considerable uncertainty remains regarding the spatial resolution necessary for effective sampling, especially in aquatic environments. Also, contemporary plant communities are under-investigated with eDNA methods relative to animals and microbes. We analyzed eDNA samples from six small temperate lakes to elucidate spatial patterns in the distributions of algae and aquatic and terrestrial plants, using metabarcoding of the Internal Transcribed Spacer-1 (ITS1) genomic region. Sampling locations were varied across horizontal and vertical space: sites in each lake included a mixture of nearshore and offshore positions, each of which was stratified into surface (shallow) and benthic (deep) samples. We detected the expected community variation (beta diversity) from lake to lake, but only small effects of offshore distance and sampling depth. Taxon richness (alpha diversity) was slightly higher in nearshore samples, but displayed no other significant spatial effects. These diversity metrics imply that plant eDNA is more evenly distributed than its generating organisms in these small lake environments. Read abundances were heavily weighted toward aquatic macrophytes, though taxon richness was greatest in the algae and other non-vascular plants. We also identified representatives of many phylogenetically and ecologically varied plant taxa, including terrestrial species from surrounding areas. We conclude that freshwater plant eDNA surveys successfully capture differences among lake communities, and that easily accessible, shore-based sampling may be a reliable technique for informing research and management in similar ecosystems.

Highlights

Questions and experiments in ecology rely on knowledge of what organisms are present in a system, and how their patterns change over space and time
We investigate the contribution of terrestrial plants to the reservoir of Environmental DNA (eDNA) in these lakes, in part because recent studies have revealed the potential for widespread terrestrial biodiversity sampling based on the collection of eDNA in river and lake water and sediment (Giguet-Covex et al, 2014; Cannon et al, 2015; Deiner et al, 2016; Harper et al, 2019)
We report here on the six-lake subset of samples that was amplified with our novel Internal Transcribed Spacer1 (ITS1) primer set described below

Summary

Introduction

Questions and experiments in ecology rely on knowledge of what organisms are present in a system, and how their patterns change over space and time. To support and complement traditional approaches to ecosystem monitoring, new tools have been developed over the last decade, including field detection technologies and lab-based high-throughput molecular techniques (Egan et al, 2013, 2015; Larson et al, 2020). One such technique is the analysis of DNA extsracted from bulk environmental samples of air, water, or soil, which is known as environmental DNA or eDNA. This spatial uncertainty is one of the most significant remaining challenges for eDNA methods when they aim to characterize aquatic communities in detail (Barnes et al, 2014; Deiner et al, 2017a)

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