Abstract
AbstractAqueous environmental DNA (eDNA) analysis has been applied to the monitoring of various ecosystems and taxa, and the characteristics of aqueous eDNA have been previously studied. In contrast, although sedimentary eDNA has been used to restore past information, the characteristics of sedimentary eDNA are not well understood. In this study, we compared the properties of sedimentary and aqueous eDNA of macro‐organisms. First, to clarify the preservation ability of sediments, we compared the difference in decay rates between aqueous and sedimentary eDNA using samples collected from a biotope (an artificial pond prepared with concrete). Next, to clarify the biological information retained in sedimentary eDNA both qualitatively and quantitatively, we compared eDNA concentrations between sediment and water samples collected simultaneously from a lake, and the fish species detected by eDNA metabarcoding were also compared. The results demonstrated the following: (a) the decay rate (decreased eDNA copy number divided by the initial eDNA copy number per unit time) of sedimentary eDNA (0.00033 ± 0.000049 [mean ± SE]/hr) was lower than that of aqueous eDNA (0.01863 ± 0.0011/hr); (b) sedimentary eDNA concentration of the mitochondrial marker of three fish species was higher than aqueous eDNA concentration for the same sample weight (12.5–1,456.9 times); and (c) the species composition obtained by metabarcoding was not significantly different between sediment and water; however, considering the lower decay rate of sedimentary eDNA, using both sample types may provide more comprehensive information of species distribution. Thus, sedimentary eDNA analysis will expand future biomonitoring and ecological studies by providing a difference in timescale.
Highlights
The results demonstrated the following: (a) the decay rate of sedimentary environmental DNA (eDNA) (0.00033 ± 0.000049 [mean ± SE]/hr) was lower than that of aqueous eDNA (0.01863 ± 0.0011/hr); (b) sedimentary eDNA concentration of the mitochondrial marker of three fish species was higher than aqueous eDNA
Species reads that were detected in both sample and and 0.019 ± 0.0011/hr for sedimentary and aqueous eDNA, repositive control were regarded as possible contamination if the numspectively
The present study revealed the decay rate of sedimentary eDNA in surface sediments compared with aqueous eDNA
Summary
Development Fund, Grant/Award Number: 4RF-1302 and 4RF-1602; Japan Society for the Promotion of Science, Grant/Award. Studies have been developed to and mixed well, and 250 ml of the sample was transferred detect macro-organisms using extracellular DNA remaining in sediinto each of nine 250-ml bottles per one bulk sample (81 water ments (i.e., sedimentary eDNA), for example, for fish (Nelson-Chorney samples in total; Figure 1). To monitor only the water temit is known that DNA molecules remain for a long time in low-oxygen perature fluctuation, a 250-ml bottle with 250 ml of water conenvironments, such as deeper sediments as mentioned above, there taining a temperature logger (HOBO pendant logger, HOBO) was is little information on the decay rate of fish sedimentary eDNA on placed in each box. 2.1.1 | eDNA sampling (Qiagen,) methods and stored at −25°C according to the methods described by Minamoto, Hayami, Sakata, and Imamura (2019)
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