Global biodiversity loss is currently one of the most critical ecological challenges, particularly in the ocean, but it is generally difficult to obtain accurate information about species distribution and population size. For example, traditional survey methods such as visual surveys, capturing, and tracking with biotelemetry, require substantial efforts and costs. The analysis of environmental DNA (eDNA), which is the DNA shed by organisms into the environment, 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 test this hypothesis, we compared temporal change in the copy number of a long eDNA fragment (719 bp) with that of a short eDNA fragment (127 bp), using Japanese Jack Mackerel (Trachurus japonicus) as a model species. We isolated rearing water from the target fish and monitored the copy number of the long and short eDNA fragments in water samples for 48 h. Next, we quantified longer eDNA fragments in field samples obtained in a previous survey, and compared the result with the distribution of biomass estimated from echo sounder data.
As expected, slopes of the two regression lines based on all eDNA concentrations at each time point significantly differed (P < 0.05) depending on the length of the DNA fragments. The decay curves of primers short and long were estimated as Cshort (t) = 507.3e-0.044t and Clong (t) = 158.74e-0.09t, respectively, where Ci(t) is eDNA concentration at time t as measured by the primer i (short or long). We compared the echo intensity and eDNA concentrations measured with two primer sets to clarify whether the eDNA decay rate varies depending on the length of DNA fragments also in the field. Although a previous study suggested that short eDNA fragments could be overestimated because of non-target 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.