Temperature Controls eDNA Persistence across Physicochemical Conditions in Seawater

Abstract

Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.

Using eDNA and SCUBA surveys for detection and monitoring of a threatened marine cryptic fish

“…effects of water currents, dispersion of DNA in the area and its stability/persistence through time. For example, the impacts of temperature on the longevity of eDNA in sea water appears to be quite variable, with durations ranging from as low as two days (Collins et al, 2018) to over two weeks (McCartin et al, 2022), and appearing to be influenced by other factors such as pH and salinity. Additionally, it is uncertain if any PCR inhibitors are present in the water, such as tannins, which can block detection (Hunter et al, 2019).…”

“…This is possibly due to the small size of red handfish, the low density of fish in this population and the low likelihood of shedding (see below), which presumably result in extremely low amounts of red handfish DNA making their way into the water column, coupled with unknown effects of water currents, dispersion of DNA in the area and its stability/persistence through time. For example, the impacts of temperature on the longevity of eDNA in sea water appears to be quite variable, with durations ranging from as low as two days (Collins et al, 2018) to over two weeks (McCartin et al, 2022), and appearing to be influenced by other factors such as pH and salinity. Additionally, it is uncertain if any PCR inhibitors are present in the water, such as tannins, which can block detection (Hunter et al, 2019).…”

Elasmobranchs’ metabarcoding requires a pragmatic approach to reach its promises

“…For example, it is known that eDNA degrades relatively quickly in marine systems (Collins et al, 2018). Particularly, high temperatures and ultraviolet (UV) radiation can decrease the eDNA signal (Barnes et al, 2014; Andruszkiewicz et al, 2017; McCartin et al, 2022). It is possible that this occurred due to the implementation of a realistic sampling strategy – similar to what MPA’s managers in tropical areas would use (i.e., lack of refrigeration, logistical constraints, and prolonged periods of time before the filtering procedure).…”

Insights from the management of offshore energy resources: Toward an ecosystem-services based management approach for deep-ocean industries

“…A major limitation of this technique in the deep sea is the general lack of taxonomic knowledge resulting in incomplete reference databases for identifying the barcode sequences (Hestetun et al, 2020). Interpretation of the results of eDNA sequencing is also hampered by an incomplete knowledge of degradation rates under different environmental conditions in the deep sea (McCartin et al, 2022). Accurate voucher specimen provision/ validation will likely remain a limitation in deep-sea metabarcoding strategies, although ecological status can be assessed from metabarcode data using taxonomy-free approaches to construct de novo biotic indices via the identification of indicator taxa (Lanzeń et al, 2021a, Lanzeń et al, 2021b, Mauffrey et al, 2021 or through supervised machine learning (Cordier et al, 2018, Lanzeń et al, 2021b.…”