Fine-tuning the performance of abundance estimation based on
environmental DNA (eDNA) focusing on eDNA particle size and marker
length
Abstract
Reliable abundance estimation is a primary challenge in environmental
DNA (eDNA) analysis, which has been addressed by considering the effects
of eDNA transport and degradation. However, these eDNA spatial dynamics
depend on the cellular and molecular structure of eDNA, with its
persistence state (particle size and DNA fragment length) being
essential for improved abundance estimation. This existing knowledge gap
is bridged by utilizing datasets obtained from two types of aquarium
experiments (targeting zebrafish [Danio rerio] and Japanese
jack mackerel [Trachurus japonicus]) and comparing the
relationships between eDNA concentration and species abundance among
different eDNA size fractions and target marker lengths. We reared the
fish in experimental tanks with different individual numbers or biomass
densities, filtered rearing water using different pore size filters, and
quantified eDNA concentrations targeting different fragment lengths or
genetic regions. Consequently, both experiments showed that the accuracy
and sensitivity in abundance estimation were improved (i.e.,
R2 values and slopes of linear regressions increased)
when targeting eDNA at the 3–10-µm size fraction. On the other hand,
targeting eDNA at the >10 µm size fraction yielded a lower
R2 value. This result indicates that an
“appropriately” larger eDNA particle is vital for improving abundance
estimation accuracy and sensitivity. Conversely, the target marker
length negatively affected the R2 value. This study
proposes that the relationship between eDNA concentration and species
abundance relies on the complex interactions between the particle size,
persistence, and spatial heterogeneity of eDNA in water.