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

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.

Particle size influences decay rates of environmental DNA in aquatic systems

“…Detecting macro‐organisms using environmental DNA (eDNA), especially in aquatic ecosystems, is quickly becoming one of the most prevalent environmental monitoring methods for the detection of single target‐species (e.g., Baudry et al, 2021; Dougherty et al, 2016; Gantz et al, 2018; Jerde et al, 2013) and monitoring of entire communities (Deiner et al, 2017; Drummond et al, 2021; Ruppert et al, 2019). Despite the rising popularity of eDNA for species detection and monitoring, the interpretation of eDNA concentrations beyond binary presence/absence of target organisms remains technically challenging and has yet to become commonplace in real‐world applications (Beng & Corlett, 2020).…”

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

“…Tsukamoto et al, 2021), a list of species detected at the spring (Palacios Mejia et al, 2021), or in a given area (e.g. Drummond et al, 2021), or a more complete version providing abundance and biomass estimates (e.g. Ji et al, 2021).…”

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

“…Letters correspond to the following studies: a. Matsuhashi et al (2016); b. Fujiwara et al (2016); c. Cannon et al (2016); d. Gantz et al (2018); e. Kuzmina et al (2018); f. Alsos et al (2018); g. Anglès d'Auriac et al (2019); h. Shackleton et al (2019); i. Matsuhashi et al (2019); j. Chase et al (2020); k. Coghlan et al (2021); l. Kuehne et al (2020); m. Miyazono et al (2021); n. Doi et al (2021); o. Adame and Reef (2020); p. Schabacker et al (2020); q. Drummond et al (2021); r. Ji et al (2021); s. Kodama et al (2021); t. Tsukamoto et al (2021).…”

“…Six studies use water eDNA to monitor macrophyte communities (Figure 1, Cannon et al, 2016; Coghlan et al, 2021; Drummond et al, 2021; Foster et al, 2021; Ji et al, 2021; Kuzmina et al, 2018). Cannon et al (2016) seminal research assessing the biodiversity of macroorganisms (fauna and flora) from the Cuyahoga River (USA) (137 km long river) was an unprecedented effort.…”

“…What is more, Alsos et al (2018) also showed that rare aquatic taxa were highly detected with eDNA, a result that contrasts with the detection of terrestrial plants which correlates to the species abundance in the vegetation. Not only can terrestrial plant eDNA be found in river and lake sediments but also within the water column, although it appears to be sporadic and does not seem to represent the entire surrounding terrestrial vegetation (Drummond et al, 2021).…”