FOR 5288: Fast and invisible: Conquering Subsurface Stormflow
through an Interdisciplinary Multi-Site Approach

Abstract:

Extreme rainfall events are likely to increase in intensity and frequency due to climatic changes and therefore the forecast of flooding events will become more important in the following decades. The flow properties of rainwater in the subsurface play a critical role in the flood formation process, but the underlying mechanism of this subsurface stormflow (SSF) formation has not been fully understood so far. Here, we explore the viability of environmental DNA (eDNA) as an indicator for small-scale flow pathway reconstruction. eDNA comprises genetic signatures from organisms across the Tree of Life (ToL), from whole microorganisms to molecular traces of higher taxa, such as plants or animals. The degree of similarity of biodiversity patterns indicates biological and therefore, in principle, also hydrological connectivity. As part of the SSF Research Unit we characterised 3 trenched hillslopes in 4 catchment areas in Germany and Austria through eDNA ToL-metabarcoding. With this broad-range approach, we aim to understand whether and how eDNA diversity patterns can inform subsurface flow pathways. We found three-dimensional connectivity patterns of biodiversity indicating systematic barriers as well as pathways of hydrological connectivity within each hillslope. Variation between catchments reflects their geographic differences as well as geological peculiarities. Although our results support the potential of eDNA to identify flow pathways and enhance our understanding of SSF, we are still at the beginning of understanding the viability of eDNA as a tracer in hydrological research. Nonetheless, making use of such natural occurring tracers can extend our understanding of hydrological phenomena and can contribute to a more accurate flood prediction.

Abstract:

Rainfall runoff contributes to a large proportion of the discharge in streams and therefore, heavily influences stream water quality but also flood generation. Rainfall runoff generation is usually a combination of overland and subsurface flow processes, the latter of which being especially difficult to trace. Here, we explored the viability of environmental DNA (eDNA) for subsurface water flow pathway reconstruction and simultaneous biodiversity assessment. The degree of similarity of community patterns indicates biological and therefore, in principle, also hydrological connectivity. We applied eDNA metabarcoding to characterise 10 drilling cores (0.7-3.2 m depth) on 3 hillslopes (10x50 m) in 4 catchment areas in Germany and Austria. In total, more than 2000 species across taxonomic groups could be identified down to species level. Analysis of alpha and beta diversity in the different catchments showed significant differences in spatial clustering patterns between taxonomic groups, but also between geomorphological and geochemical properties, such as the composition of dissolved organic carbon, of the respective catchment. We could assign indicator species sets in all taxonomic groups to various depth layers and identify habitat-specific communities that can be used as hydrological tracers. Although our results support the potential of eDNA to identify flow pathways and enhance our understanding of subsurface flow processes, we are still at the beginning of understanding the viability of eDNA as a tracer in hydrological research. However, our results show that making use of such naturally occurring tracers can expand our understanding of hydrological phenomena, especially those hidden in the subsurface.

Abstract:

Abstract DNA metabarcoding of freshwater communities typically relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase I (COI) gene with degenerate primers. The advantage of COI is its taxonomic resolution and the availability of an extensive reference database. However, when universal primers are used on environmental DNA (eDNA) isolated from water, benthic invertebrate read and OTU numbers are typically “watered down,” that is, under represented, compared to whole specimen “bulk samples” due to greater co-amplification of abundant nontarget taxa (e.g., fungi, algae, and bacteria). Because benthic stream invertebrate taxa are of prime importance for regulatory biomonitoring, more effective ways to capture their diversity via eDNA isolated from water are important. In this study, we aimed to improve benthic invertebrate assessment from eDNA by minimizing nontarget amplification. Therefore, we generated eDNA data using universal primers BF2/BR2 on samples collected throughout 15 months from a German Long-Term Ecological Research site (Rhine-Main-Observatory, Kinzig River) to identify most abundant nontarget taxa. Based on these data, we designed a new reverse primer (EPTDr2n) with 3’-specificity toward benthic invertebrate taxa and validated its specificity in silico together with universal forward primer fwhF2 using available data from GenBank and BOLD. We then performed in situ tests using 20 Kinzig River eDNA samples. We found that the percentage of target reads was much higher for the new primer combination compared to two universal benthic invertebrate primer pairs, BF2/BR2 and fwhF2/fwhR2n (99.6% versus 25.89% and 39.04%, respectively). Likewise, the number of detected benthic invertebrate species was substantially higher (305 versus 113 and 185) and exceeded the number of 153 species identified by expert taxonomists at nearby sites across two decades of sampling. While few taxa, such as flatworms, were not detected, we show that the optimized primer avoids the nontarget amplification bias and thus significantly improves benthic invertebrate detection from eDNA.