Variation of Environmental DNA in Sediment at Different Temporal Scales in Nearshore Area of Tokyo Bay

Abstract

Environmental DNA (eDNA) is a non-invasive and less labor-intensive tool for biological survey. The advantages enable more frequent sampling work, but there is a lack of fundamental field data on the variation of eDNA in sediment in different timescales. We conducted a yearlong sampling at two marine parks of Tokyo Bay (Odaiba Marine Park and Kasai Marine Park) to investigate the temporal variation of sediment eDNA at scales of one year, one month and one tidal period. Grandidierella japonica, an indicator benthic species of water quality in Japan and also an invasive species in other countries, was chosen as target species. In yearlong scales, the total eDNA content and the copy number of the amphipod eDNA in both parks showed a seasonal variation pattern as low in cold season (89 ± 14 ng DNA/g sediment, 583 ± 64 copies/g sediment) and high in warm season (884 ± 97 ng DNA/g sediment, 9,501 ± 3,553 copies/g sediment). In scales shorter than one month, eDNA kept stable and did not show clear variation. The results indicated that eDNA in sediment is useful for biological survey by reflecting the well-averaged state of the species abundance in the environment and not showing the erroneous sudden variation in a short timescale.

Sediment Toxicity Testing with the Amphipod <i>Grandidierella Japonica</i> and Effects of Sediment Particle Size Distribution

“…Tokyo Bay has receiving discharges from sewage treatment plants, road runoff, and agricultural runoff [25], and thus sediment in this area reportedly contains high levels of many anthropogenic chemicals such as metals [26] and polycyclic aromatic hydrocarbons [25]. G. japonica has been reported to be present in coastal zones of Tokyo Bay [27]. Second, the effects of sediment particle size distribution on 10-day amphipod survival and body length were examined using formulated sediment comprising quartz sand and kaolin.…”

Development of Quantitative Real-Time PCR for Detecting Environmental DNA Derived from Marine Macrophytes and Its Application to a Field Survey in Hiroshima Bay, Japan

“…and kelps Saccharina spp., to the blue carbon assessment around Japan merits detailed investigation. In addition, the sediments of Hiroshima Bay were surveyed only once in our study, yet Wei et al [74] reported seasonal variations in fish-derived eDNA in the sediments of Tokyo Bay, which is a similar estuary to Hiroshima Bay. If annual surveys were conducted in Hiroshima Bay, it is possible that the results would differ from the present results.…”

Using eDNA to survey amphibians: Methods, applications, and challenges

“…In addition, temperature alterations caused by seasonal changes will also affect the content of eDNA in samples. For example, Wei et al (2019) studied the variation over time of eDNA in sediments over periods of 1 year, 1 month and one tidal period, and found that eDNA content was higher in the warm season and lower in the cold season. Similarly, the concentration and distribution of eDNA can be influenced by spatial factors such as spatial dissipation of eDNA and the flow of the water column.…”