Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass

Abstract

AbstractBackground Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA).Materials & MethodsTank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers.Results & DiscussionModel fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.