Hyporheic exchange (HE) contributes to the biogeochemical turnover of macro- and micro-pollutants in rivers. However, the spatiotemporal complexity and variability of HE hinder understanding of its role in the overall functioning of riverine ecosystems. The present study focuses on investigating the role of bacterial diversity and sediment morphology on HE using a multi-flume experiment. A fully coupled surface–subsurface numerical model was used to highlight complex exchange patterns between surface water and the underlying flow field in the sediments. Under the experimental conditions, the surface water flow induced by bedforms has a prominent effect on both local trajectories and residence time distributions of hyporheic flow paths, whereas mean hyporheic retention times are mainly modulated by average surface flowrates. In case of complex bedform morphologies, the numerical model successfully reproduces the HE estimated by means of salt dilution tests. However, the 2D numerical representation of the system falls short in predicting HE in absence of bedforms, highlighting the intrinsic complexity of water circulation patterns in real scenarios. Finally, results show that higher bacterial diversities in the stream sediments can significantly reduce hyporheic fluxes. This work provides a framework to interpret micropollutants turnover in light of the underlying physical transport processes in the hyporheic zone. The study emphasizes the importance of better understanding the tradeoff between physically driven transport processes and bacterial dynamics in the hyporheic zone to quantify the fate of pollutants in streams and rivers.

Urban streams receive increasing loads of organic micropollutants from treated wastewaters. A comprehensive understanding of the in-stream fate of micropollutants is thus of high interest for water quality management. Bedforms induce pumping effects considerably contributing to whole stream hyporheic exchange and are hotspots of biogeochemical turnover processes. However, little is known about the transformation of micropollutants in such structures. In the present study, we set up recirculating flumes to examine the transformation of a set of micropollutants along single flowpaths in two triangular bedforms. We sampled porewater from four locations in the bedforms over 78 days and analysed the resulting concentration curves using the results of a hydrodynamic model in combination with a reactive transport model accounting for advection, dispersion, first-order removal and retardation. The four porewater sampling locations were positioned on individual flowpaths with median solute travel times ranging from 11.5 to 43.3 h as shown in a hydrodynamic model previously. Highest stability was estimated for hydrochlorothiazide on all flowpaths. Lowest detectable half-lives were estimated for sotalol (0.7 h) and sitagliptin (0.2 h) along the shortest flowpath. Also, venlafaxine, acesulfame, bezafibrate, irbesartan, valsartan, ibuprofen and naproxen displayed lower half-lives at shorter flowpaths in the first bedform. However, the behavior of many compounds in the second bedform deviated from expectations, where particularly transformation products, e.g. valsartan acid, showed high concentrations. Flowpath-specific behavior as observed for metformin or flume-specific behavior as observed for metoprolol acid, for instance, was attributed to potential small-scale or flume-scale heterogeneity of microbial community compositions, respectively. The results of the study indicate that the shallow hyporheic flow field and the small-scale heterogeneity of the microbial community are major controlling factors for the transformation of relevant micropollutants in river sediments.

Assessment of micropollutant biodegradation is essential to determine the persistence of potentially hazardous chemicals in aquatic ecosystems. We studied the dissipation half-lives of 10 micropollutants in sediment–water incubations (based on the OECD 308 standard) with sediment from two European rivers sampled upstream and downstream of wastewater treatment plant (WWTP) discharge. Dissipation half-lives (DT50s) were highly variable between the tested compounds, ranging from 1.5 to 772 days. Sediment from one river sampled downstream from the WWTP showed the fastest dissipation of all micropollutants after sediment RNA normalization. By characterizing sediment bacteria using 16S rRNA sequences, bacterial community composition of a sediment was associated with its capacity for dissipating micropollutants. Bacterial amplicon sequence variants of the genera Ralstonia, Pseudomonas, Hyphomicrobium, and Novosphingobium, which are known degraders of contaminants, were significantly more abundant in the sediment incubations where fast dissipation was observed. Our study illuminates the limitations of the OECD 308 standard to account for variation of dissipation rates of micropollutants due to differences in bacterial community composition. This limitation is problematic particularly for those compounds with DT50s close to regulatory persistence criteria. Thus, it is essential to consider bacterial community composition as a source of variability in regulatory biodegradation and persistence assessments.

Hyporheic zones are the water-saturated flow-through subsurfaces of rivers which are characterized by the simultaneous occurrence of multiple physical, biological, and chemical processes. Two factors playing a role in the hyporheic attenuation of organic contaminants are sediment bedforms (a major driver of hyporheic exchange) and the composition of the sediment microbial community. How these factors act on the diverse range of organic contaminants encountered downstream from wastewater treatment plants is not well understood. To address this knowledge gap, we investigated dissipation half-lives (DT50s) of 31 substances (mainly pharmaceuticals) under different combinations of bacterial diversity and bedform-induced hyporheic flow using 20 recirculating flumes in a central composite face factorial design. By combining small-volume pore water sampling, targeted analysis, and suspect screening, along with quantitative real-time PCR and time-resolved amplicon Illumina MiSeq sequencing, we determined a comprehensive set of DT50s, associated bacterial communities, and microbial transformation products. The resulting DT50s of parent compounds ranged from 0.5 (fluoxetine) to 306 days (carbamazepine), with 20 substances responding significantly to bacterial diversity and four to both diversity and hyporheic flow. Bacterial taxa that were associated with biodegradation included Acidobacteria (groups 6, 17, and 22), Actinobacteria (Nocardioides and Illumatobacter), Bacteroidetes (Terrimonas and Flavobacterium) and diverse Proteobacteria (Pseudomonadaceae, Sphingomonadaceae, and Xanthomonadaceae). Notable were the formation of valsartan acid from irbesartan and valsartan, the persistence of N-desmethylvenlafaxine across all treatments, and the identification of biuret as a novel transformation product of metformin. Twelve additional target transformation products were identified, which were persistent in either pore or surface water of at least one treatment, indicating their environmental relevance.

Organic micropollutants such as food additives, pharmaceuticals and personal care products are found in rivers worldwide. Persistence is a key criteria in chemical risk assessment as micropollutants that are persistent pose an exposure hazard to humans and the environment. As biodegradation is the most relevant removal process for many micropollutants in rivers, persistence assessment relies on the estimation of the biodegradation half-life.  This thesis presents new approaches to understand the biodegradation of organic pollutants in rivers.

The application of Junge relationships (previously established for atmospheric pollutants), to river systems, was investigated in paper I to assess if biodegradation half-lives in the Danube river are correlated with variability in measured concentrations. Model scenarios show Junge relationships could potentially be found in measurements performed near the mouth of the river, but Junge relationships were not found in currently available monitoring data. In paper II an experimental design and response surface model were developed to study the effect of hyporheic exchange (induced by flowing water) and bacterial diversity in sediment on dissipation half-lives of two micropollutants in flumes. Faster dissipation was observed in flumes with high bacterial diversity and higher hyporheic exchange, and thus both variables are relevant to study dissipation processes in rivers. The influence of biological factors beyond bacteria diversity is explored in papers III and IV, by characterizing the bacteria community composition of sediment in OECD 308 bottle incubations (a standard test that is often recommended in risk assessment guidelines). In paper III, higher variation in half-lives (e.g. relative standard deviations > 50%) were found for micropollutants with longer half-lives (e.g. from 40 to more than 120 days). Higher variation in half-lives also corresponded to differences in bacteria community composition and specifically to increased or decreased abundance of certain bacteria genera. Although the exact bacteria genera involved in the biodegradation of the micropollutants cannot be determined in papers II or III, our results suggest bacteria community composition and diversity should be considered in the interpretation of biodegradation half-lives since they are related to variability in biodegradation and to understand extrapolation from laboratory to the field. Finally in paper IV, it is investigated if the bacteria communities are affected by the OECD 308 test conditions. Changes in the bacteria communities in the sediment between the initial river community, the beginning and the end of the incubation, at high and a low concentrations are reported. Overall, 8% of bacteria genera increased or decreased in relative abundance in all comparisons, and it is unclear if these small changes in bacteria communities could have had an effect on the observed half-lives in paper III.

This thesis contributes to the understanding of physical and biological factors influencing biodegradation and potential implications for risk assessment of organic micropollutants in rivers.

Rivers are important ecosystems under continuous anthropogenic stresses. The hyporheic zone is a ubiquitous, reactive interface between the main channel and its surrounding sediments along the river network. We elaborate on the main physical, biological, and biogeochemical drivers and processes within the hyporheic zone that have been studied by multiple scientific disciplines for almost half a century. These previous efforts have shown that the hyporheic zone is a modulator for most metabolic stream processes and serves as a refuge and habitat for a diverse range of aquatic organisms. It also exerts a major control on river water quality by increasing the contact time with reactive environments, which in turn results in retention and transformation of nutrients, trace organic compounds, fine suspended particles, and microplastics, among others. The paper showcases the critical importance of hyporheic zones, both from a scientific and an applied perspective, and their role in ecosystem services to answer the question of the manuscript title. It identifies major research gaps in our understanding of hyporheic processes. In conclusion, we highlight the potential of hyporheic restoration to efficiently manage and reactivate ecosystem functions and services in river corridors.

Persistence of chemical pollutants is difficult to measure in the field. Junge variability-lifetime relationships, correlating the relative standard deviation of measured concentrations with residence time, have been used to estimate persistence of air pollutants. Junge relationships for micropollutants in rivers could provide evidence that half-lives of compounds estimated from laboratory and field data are representative of half-lives in a specific system, location and time. Here, we explore the hypothesis that Junge relationships could exist for micropollutants in the Danube river using: (1) concentrations of six hypothetical chemicals modeled using the STREAM-EU fate and transport model, and (2) concentrations of nine micropollutants measured in the third Joint Danube Survey (JDS3) combined with biodegradation half-lives reported in the literature. Using STREAM-EU, we found that spatial and temporal variability in modeled concentrations was inversely correlated with half-life for the four micropollutants with half-lives <= 90 days. For these four modeled micropollutants, we found Junge relationships with slopes significantly different from zero in the temporal variability of concentrations at 88% of the 67 JDS3 measurement sites, and in the spatial variability of concentrations on 36% out of 365 modeled days. A Junge relationship significant at the 95% confidence level was not found in the spatial variability of nine micropollutants measured in the JDS3, nor in STREAM-EU-modeled concentrations extracted for the dates and locations of the JDS3. Nevertheless, our model scenarios suggest that Junge relationships might be found in future measurements of spatial and temporal variability of micropollutants, especially in temporal variability of pollutants measured downstream in the Danube river.

Contamination of rivers by trace organic compounds (TrOCs) poses a risk for aquatic ecosystems and drinking water quality. Spatially- and temporally varying environmental conditions are expected to play a major role in controlling in-stream attenuation of TrOCs. This variability is rarely captured by in situ studies of TrOC attenuation. Instead, snap-shots or time-weighted average conditions and corresponding attenuation rates are reported. The present work sought to investigate this variability and factors controlling it by analysis of 24 TrOCs over a 4.7 km reach of the River Erpe (Berlin, Germany). The factors investigated included sunlight and water temperature as well as the presence of macrophytes. Attenuation rate constants in 48 consecutive hourly water parcels were tracked along two contiguous river sections of different characteristics. Section 1 was less shaded and more densely covered with submerged macrophytes compared to section 2. The sampling campaign was repeated after macrophyte removal from section 1. The findings show, that section 1 generally provided more favorable conditions for both photo- and biodegradation. Macrophyte removal enhanced photolysis of some compounds (e.g., hydrochlorothiazide and diclofenac) while reducing the biodegradation of metoprolol. The transformation products metoprolol acid and valsartan acid were formed along the reach under all conditions.

Enhancing the understanding of the fate of wastewater-derived organic micropollutants in rivers is crucial to improve risk assessment, regulatory decision making and river management. Hyporheic exchange and sediment bacterial diversity are two factors gaining increasing importance as drivers for micropollutant degradation, but are complex to study in field experiments and usually ignored in laboratory tests aimed to estimate environmental half-lives. Flume mesocosms are useful to investigate micropollutant degradation processes, bridging the gap between the field and batch experiments. However, few studies have used flumes in this context. We present a novel experimental setup using 20 recirculating flumes and a response surface model to study the influence of hyporheic exchange and sediment bacterial diversity on half-lives of the anti-epileptic drug carbamazepine (CBZ) and the artificial sweetener acesulfame (ACS). The effect of bedform-induced hyporheic exchange was tested by three treatment levels differing in number of bedforms (0, 3 and 6). Three levels of sediment bacterial diversity were obtained by diluting sediment from the River Erpe in Berlin, Germany, with sand (1 : 10, 1 : 1000 and 1 : 100 000). Our results show that ACS half-lives were significantly influenced by sediment dilution and number of bedforms. Half-lives of CBZ were higher than ACS, and were significantly affected only by the sediment dilution variable, and thus by bacterial diversity. Our results show that (1) the flume-setup is a useful tool to study the fate of micropollutants in rivers, and that (2) higher hyporheic exchange and bacterial diversity in the sediment can increase the degradation of micropollutants in rivers.