Aquatic suspended particulate matter as source of eDNA for fish metabarcoding

Abstract

The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communities through time. We used archived SPM samples of the German Environmental Specimen Bank (ESB), which were collected using sedimentation traps from different riverine points in Germany. Environmental DNA was extracted from nine SPM samples differing in location, organic content, and porosity (among other factors) using four different methods for the isolation of high-quality DNA. Application of the PowerSoil DNA Isolation Kit with an overnight incubation in lysis buffer, resulted in DNA extraction with the highest purity and eDNA metabarcoding of these eDNA fragments was used to detect a total of 29 fish taxa among the analyzed samples. Here we demonstrated for the first time that SPM is a promising source of eDNA for metabarcoding analysis, which could provide valuable retrospective information (when using archived SPM) for fish monitoring, complementing the currently used approaches. Suspended particulate matter (SPM) is one of the fundamental elements in aquatic ecosystems (in addition to the water phase and the sediment) and, because it can act as a source and transport mechanism for aquatic particles, is useful for assessing the contamination of surface water 1. As such, SPM monitoring is an important consideration under the Water Framework Directive 2000/60/EC (WFD) 2 and is used in European regulatory chemical monitoring programs (e.g. in Germany 3 and Netherlands 4). Among the other quality elements monitored under the WFD is the state of the aquatic macrofauna (e.g. fish communities), which provide a good measure for the biological and chemical status of the water bodies. SPM monitoring for this context is yet to be explored. Traditionally, the response of biotic communities to human-induced stressors are assessed using taxonomic approaches (e.g. electrofishing), but these are typically limited by their scalability, restricted temporal and spatial resolution, invasiveness, and the high level of expertise required to identify the species 5. Moreover, rare taxa (e.g. invasive species-Neogobius melanostomus, or migratory species-Salmo salar, Anguilla anguilla, Alosa alosa) are especially difficult to monitor because they require an intensive survey effort. DNA-based tools can overcome many of the above-mentioned problems and could complement traditional approaches and biomonitoring strategies 6. Recently, the use of environmental DNA (eDNA), which is the trace amounts of DNA discharged by organisms via excretion of urine, feces, body cells, eggs, etc., enables the non-invasive detection of species and their approxima...

One size does not fit all: Tuning eDNA protocols for high‐ and low‐turbidity water sampling

“…Protocol efficacy can vary significantly in response to local environmental conditions (Piggott, 2016). For example, eDNA in water that has high concentrations of suspended particulates is often bound to particles and more resistant to degradation (Alvarez et al, 1998), resulting in higher eDNA yields (Diaz et al, 2020). However, these same environments often contain high levels of compounds such as humic acid and tannins that inhibit PCR (Albers et al, 2013;McKee et al, 2015).…”

Experimental evaluation of environmental DNA detection of a rare fish in turbid water

“…Turbidity in river-dominated estuaries like the SFE is mainly caused by river inputs of suspended particulate matter and resuspension of bottom sediments that reduce phytoplankton biomass (Cloern 1987). While eDNA can be detected in samples of suspended particulate matter collected in sedimentation boxes in rivers (Díaz et al 2020), it is not clear if eDNA co-occurs with other particulates or is stuck to them. In our experiment, turbidity reduced detection rates and we did not see evidence of eDNA sticking to particulates.…”

“…While eDNA can be detected in samples of suspended particulate matter collected in sedimentation boxes in rivers (Díaz et al 2020), it is not clear if eDNA co-occurs with other particulates or is stuck to them. In our experiment, turbidity reduced detection rates and we did not see evidence of eDNA sticking to particulates.…”

Positive effect of filtration additives for increasing environmental DNA detections in summer and winter oceanic waters

“…One observation is that previous studies using eDNA techniques found higher species richness in sediment samples than in paired water column samples (Holman et al, 2019). It has also been reported that suspended particulate materials in aquatic environments were a source of eDNA, which was attached to the particles (Díaz et al, 2020). The higher eDNA levels associated with sediment samples may be caused by particulate matter from organisms settling to the bottom or possibly sticking to sediment particles.…”