General Advantages and Disadvantages of eDNA
Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds
Advantages:
eDNA approaches are often more affordable and logistically feasible than conventional counterparts, and have enormous potential to enable ecological study at greater temporal and spatial scales.
Prospects of eDNA monitoring in ponds:
- The most obvious potential is enhanced biological recording and assessment of pond biodiversity. The complementarity of eDNA analysis and conventional methods for monitoring pond biodiversity has been repeatedly demonstrated, and the work of Thomsen et al. (2012) on ponds and other freshwater habitats was pivotal to the development of eDNA surveillance for many rare and endangered species across the globe.
- eDNA analysis has since shown potential for estimation of relative abundance and biomass (Takahara et al., 2012; Thomsen et al., 2012; Buxton et al., 2017b), and has begun to outperform conventional counterparts, for example, large-scale sampling and distribution modelling of the threatened great crested newt Triturus cristatus (Laurenti, 1768) (Biggs et al., 2015), and may deepen our understanding of species distribution patterns and activity.
- eDNA analysis in ponds offers endless experimental opportunities to heighten understanding of eDNA dynamics due to the vast physical and chemical heterogeneity of these ecosystems. Pond water is comparatively stagnant, and the lack of flow and relatively small water volumes in ponds allows eDNA to accumulate over time to concentrations not attainable in most other water bodies. This has benefits for the amount of target DNA present and subsequent detection probability
Disadvantages (unique to the ponds):
Examinations of eDNA in relation to specific environments are distinctly lacking. These challenges are largely related to the physical and chemical properties of ponds that influence eDNA capture and detection, which are not taken into account by current methodologies.
Challenges of eDNA monitoring in ponds:
- eDNA accumulation can reduce ability to distinguish contemporary from recent or historic presence (Rees et al., 2014b). Under stagnant conditions, eDNA can settle out of suspension, but become incorporated into the water column again following sediment disturbance (Turner et al., 2015; Buxton et al., 2018). Therefore, eDNA may remain detectable in ponds for several weeks under ‘optimal’ conditions (Buxton et al., 2017a), but can also degrade rapidly with complete disappearance of target eDNA within 1 week (Brys, R. & Halfmaerten, D., unpublished results).
- Ponds are further influenced by the activity of domestic and wild animals which can increase suspended solids within the water column and change the properties of an eDNA sample. These external influences may also transfer eDNA between water bodies and potentially cause false positive detections (Klymus et al., 2017b).
- Due to their nature larger fluctuations in temperature range and potentially greater exposure to ultraviolet (UV) light are common in ponds. Temperature, UV light, and pH all influence eDNA shedding and degradation rates, and can affect the amount of eDNA present within a waterbody (Strickler et al., 2015; Robson et al., 2016; Buxton et al., 2017b; Goldberg et al., 2018)
- As water volume decreases over time, ponds become increasingly ephemeral or seasonal (Wood et al., 2003). Accessing these waters via wet, vegetated margins may make cross-contamination (see Online Resource 2 for potential sources and their mitigation) between sites hard to avoid, while high levels of organic debris in late succession ponds and duckweed-dominated (Lemna spp.) ponds can exacerbate difficulties in collecting clean, debrisfree samples
- Anoxic conditions in ponds were shown to slow marine eDNA decay (Weltz et al., 2017) but impacts of anoxia on pond eDNA have not been investigated. Slow decay may affect inferences made from eDNA regarding contemporary species presence.
Other Disadvantages:
- the rate of shedding of target species is highly variable, including seasonally and throughout their lifespans
- the rate of DNA degradation is dependent on environmental variables such as temperature and microbial activity
References