Persistence of sedimentary DNA in burrowing marine benthos: evidence from the decapod Upogebia major

Abstract

Environmental DNA (eDNA) analysis is an increasingly important tool for surveying marine organisms. Requiring only small environmental samples, eDNA analysis enables efficient assessment of the occurrence and distribution of target taxa based on eDNA detection and concentration. This approach is particularly effective for organisms difficult to observe and collect conventionally. However, knowledge of eDNA persistence in the environment remains limited. A better understanding of taxon-specific eDNA persistence is essential for accurate interpretation of eDNA data. Burrowing benthic organisms are suitable targets for eDNA-based surveys because they are difficult to collect and observe directly, making field surveys time-consuming and labor-intensive. However, little is known about the persistence of their eDNA. Because burrowing benthos remain in close contact with sediments, their eDNA is expected to occur predominantly in sediments as sedimentary DNA (sedDNA). Therefore, we evaluated the persistence of sedDNA in a tank experiment with burrowing decapod Upogebia major , a species widely distributed in tidal flats throughout East Asia. The results suggest that, at least under tank conditions, the sedDNA of this species can persist in sediments for at least 30 days and up to 50 days without substantial changes in concentration. Three explanations are possible: (1) the amount of sedDNA produced by U. major may have greatly exceeded its rate of degradation, resulting in very slow degradation; (2) bacterial activity, one of the drivers of sedDNA degradation, may have been lower under tank conditions than under natural field conditions; and (3) the burrows may have functioned as a continuous source of sedDNA, allowing sedDNA to be intermittently released from the burrows even in the absence of animals. Collectively, these factors may have contributed to the long-term persistence of sedDNA without substantial changes in its concentration. However, the detection frequency and concentration of sedDNA varied among sampling locations and days. Both differences in the behavior of U. major and the low mobility of the sediment, which limited sediment mixing and redistribution of sedDNA, likely influenced this variability. This study provides new insights into the dynamics of sedDNA in burrowing benthos and highlights the importance of considering its persistence when interpreting sedDNA data.