Environmental DNA (eDNA) analysis has successfully detected organisms in various aquatic environments. However, there is little basic information on eDNA, including the eDNA shedding and degradation processes. This study focused on water temperature and fish biomass and showed that eDNA shedding, degradation, and size distribution varied depending on water temperature and fish biomass. The tank experiments consisted of four temperature levels and three fish biomass levels. The total eDNA and size‐fractioned eDNA from Japanese Jack Mackerels (Trachurus japonicus) were quantified before and after removing the fish. The results showed that the eDNA shedding rate increased at higher water temperature and larger fish biomass, and the eDNA decay rate also increased at higher temperature and fish biomass. In addition, the small‐sized eDNA fractions were proportionally larger at higher temperatures, and these proportions varied among fish biomass. After removing the fish from the tanks, the percentage of eDNA temporally decreased when the eDNA size fraction was >10 µm, while the smaller size fractions increased. These results have the potential to make the use of eDNA analysis more widespread in the future.

The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide-range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel (Trachurus japonicus), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish. Long DNA fragments showed a higher decay rate than short fragments. Next, we measured the eDNA copy numbers of long and short DNA fragments using field samples, and compared them with fish biomass as measured by echo intensity. Although a previous study suggested that short eDNA fragments could be overestimated because of nontarget eDNA from a nearby fish market and carcasses, the eDNA concentrations of long fragments were correlated with echo intensity. This suggests that the concentration of longer eDNA fragments reflects fish biomass more accurately than the previous study by removing the effects of the fish market and carcasses. The length-related differences in eDNA have a substantial potential to improve estimation of species biomass.

Environmental DNA (eDNA) analyses have enabled more efficient surveillance of species distribution and composition than conventional methods. However, the characteristics and 3 dynamics of eDNA (e.g., origin, state, transport, and fate) remain unknown. This is especially limited for the eDNA derived from nuclei (nu-eDNA), which has recently been used in eDNA analyses. Here, we compared the particle size distribution (PSD) of nu-eDNA from Japanese Jack Mackerel (Trachurus japonicus) with that of mt-eDNA (eDNA derived from mitochondria) reported in previous studies. We repeatedly sampled rearing water from the tanks with multiple temperature and fish biomass levels, and quantified the copy numbers of size-fractioned nu-eDNA. We found that the concentration of nu-eDNA was higher than that of mt-eDNA at 3-10 µm size fraction. Moreover, at the 0.8-3 µm and 0.4-0.8 µm size fractions, eDNA concentrations of both types increased with higher temperature and their degradation tended to be suppressed. These results imply that the production of eDNA from large to small size fractions could buffer the degradation of small-sized eDNA, which could improve its persistence in water. Our findings will contribute to refine the difference between nu-and mt-eDNA properties, and assist eDNA analyses as an efficient tool for the conservation of aquatic species.

Background  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 & Methods Tank 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 & Discussion Model 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.