Fine‐tuning the performance of abundance estimation based on environmental <scp>DNA</scp> (<scp>eDNA</scp>) focusing on <scp>eDNA</scp> particle size and marker length

The concentration of eDNA in an environment can provide important ecological information of relevance for management and conservation, but little research has explored optimizing sampling strategies to estimate mean eDNA concentrations in natural environments. Inter‐replicate eDNA concentrations often exhibit right‐skewed “clustered” or “clumped” distributions, likely due to the stochastic capture of large “aggregate” particles with high eDNA copy numbers. This has important potential implications for modeling the resulting sampling effort necessary to accurately quantify eDNA concentrations. In a previous study, 17–20 Brook Charr eDNA samples were collected from 28 lakes in Québec, Canada. We explored how variation in eDNA concentrations within a lake was affected by several habitat characteristics. We then conducted a power analysis to determine the sampling effort (“minimum n”) necessary to accurately quantify mean lake eDNA concentrations and, using simulations, explored how a bimodal distribution of eDNA particle copy count could affect inter‐replicate variability. The median sample size such that 90% of sample mean estimates were within 20% of the “true” mean was 12.5; a sample size of 20 was sufficient to quantify mean concentrations in 21/28 lakes. We found no evidence that temperature or lake size impacted sample variability. We also found that variance among replicates was non‐linearly related to mean lake eDNA concentration across years: variability was lowest at low and high concentrations and highest at intermediate concentrations. We hypothesize that this resulted from the stochastic capture of large “aggregate” particles at intermediate concentrations; at low concentrations, aggregates were likely rarely captured and at high concentrations may represent a consistent component of total eDNA. Simulations demonstrated that these patterns can emerge from some bimodal eDNA particle “size” distributions. Overall, we conclude that sampling efforts in many previous studies (notably including the authors' own) were potentially low, emphasizing the need to increase spatial replication in lentic surveys.

Section: Discussionsupporting

confidence: 89%

How much is enough? Examining the sampling effort necessary to estimate mean eDNA concentrations in lentic systems

Yates,

Gaudet‐Boulay,

Garcia Machado

et al. 2023

“…All water samples were previously collected in Jo and Yamanaka (2022); the study was originally conducted to examine how the relationships between eDNA concentration and fish abundance varied depending on eDNA size fractions and target marker lengths. In brief, five replicates of 25 L tanks filled with 20 L of aged tap water aerated by a pump were used.…”

Section: Aquarium Set-up and Water Samplingmentioning

confidence: 99%

“…Total eDNA on the filter was extracted using a DNeasy Blood and Tissue Kit (Qiagen, Germany) according to the method described by Jo and Yamanaka (2022). The zebrafish eDNA concentration in the water sample was estimated by quantifying the copy number of mitochondrial genes using the StepOnePlus Real-Time PCR system (Thermo Fisher Scientific, USA).…”

Section: Dna Extraction and Quantitative Real-time Pcr (Qpcr)mentioning

confidence: 99%

A higher DNA damage rate in aqueous eDNA particles suggests intra‐cellular eDNA degradation in cellular environments

2022

Self Cite

“…Demonstrated by the above examples, the inference of presence/absence of species using eDNA approaches has been well documented across multiple taxonomic groups. Moving beyond this, several laboratory studies have found positive correlations between species abundance/biomass and eDNA particle concentration or relative read abundance (Hilário et al, 2023;Jo & Yamanaka, 2022). However, in the natural environment, these relationships have been found to be weaker, most likely due to more dilute DNA concentrations and stochasticity in environmental parameters and organism behavior that are known to impact the release, transport, and degradation of eDNA (Rourke et al, 2021;Yates et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA captures diurnal fluctuations of surface eukaryotes on a tropical coral reef

Dowell,

Dunn,

Head

et al. 2024

Environmental DNA (eDNA) metabarcoding has been widely employed to describe biological communities in the marine environment and to compare the richness and diversity of sites across large spatial scales. However, fine‐scale temporal eDNA dynamics are poorly understood and the time of eDNA sample collection is rarely reported in publications. Here, we collected surface eDNA samples every 6 h, for 3 days, at two coral reef sites to assess fine‐scale changes in the eukaryotic communities detected. Distinct eukaryotic communities were detected at two sites within the same lagoon. Sampling time was found to have a significant effect on ESV and class richness, both peaking during the 1 p.m. sampling time at both sites. Sampling time also had a significant effect on the detection of eukaryotic taxa, with relative read frequency showing clear diurnal patterns in line with the migratory behavior of planktonic groups. Other groups of organisms showed considerable variation in read frequency, highlighting the dynamic nature of marine eukaryotic communities and potential stochasticity of eDNA detections. For eukaryotic communities, eDNA samples can provide a “snapshot” of contemporary biodiversity and provide information on short‐term community dynamics on hyperdiverse coral reefs. However, our findings add to growing evidence that sampling time should be clearly considered and reported in marine eDNA studies and that multiple samples from the same site are needed to facilitate more robust comparisons across sites.