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.

1) We describe the hierarchical interplay of hydrology, hyporheic ecology and transformation of nutrients and pollutants in the hyporheic zone (HZ). The exchange of water between the surface-subsurface generates the hyporheic exchange flow: the engine that drives the ecological functioning of the HZ. The magnitude and direction of hydrological fluxes in the HZ follow complex spatial patterns, strongly influenced by the temporal dynamics of surface flow in rivers. 2) The direction and magnitude of hydrological fluxes also shapes the structure of hyporheic communities (hyporheos). During surface disturbances such as flooding or drought, benthic organisms may also use the HZ as a refuge, although the importance of this role is debated. 3) Streambed organisms differ in their ability to colonise the HZ depending on the biological traits they possess. The reduction in oxygen concentration and pore size with increasing sediment depth imposes a limit on the distribution of macroinvertebrates, which are replaced by a suite of smaller organisms (meiofauna and protists) at deeper sediment layers. Therefore, a concomitant reduction in net biomass and productivity might be expected through depth. However, only a few studies have assessed the contribution of the hyporheos to whole system production, and they have focused only on the fraction of relatively large organisms. 4) The bioreactor ability of the HZ to transform nutrients and pollutants is an important ecosystem service sustained by the life activities of hyporheos. Biofilms have the key role in this process due to their capacity to metabolize a wide range of dissolved 3 compounds, including emerging pollutants. However, the residence time of water in pore sediments (resulting from hyporheic exchange flow) and the rest of the community (constantly reworking the sediments and grazing biofilms) are indirectly involved.

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A current controversy in ecology is whether biological communities are discrete biological entities or simply study units created for convenience; a debate that becomes even more heated when delimiting communities along ecotones. Here, we report an interdisciplinary study designed to address the interplay between environmental drivers and community ecology in a typical ecotone ecosystem: the streambed. Environmental filtering at a micro-scale determined how diversity, productivity and composition of the whole streambed assemblage varied with depth and with the direction of vertical water exchange. Biomass and production decreased with increasing depth, and were lower under upwelling than downwelling conditions. However, the rate at which biomass and production decreased with increasing depth differed significantly for different taxonomic groups. Using quantitative biocenosis analysis, we also showed that benthic and hyporheic zone assemblages (assemblages in close juxtaposition) could be clearly distinguished as discrete communities with individual integrity. Vertical hydrodynamic conditions also influenced the demarcation between both communities; the benthic community reached greater depths in downwelling than in upwelling zones.

Litter breakdown in the streambed is an important pathway in organic carbon cycling and energy transfer in the biosphere that is mediated by a wide range of streambed organisms. However, most research on litter breakdown to date has focused on a small fraction of the taxa that drive it (e.g. microbial vs. macroinvertebrate‐mediated breakdown) and has been limited to the benthic zone (BZ). Despite the importance of the hyporheic zone (HZ) as a bioreactor, little is known about what, or who, mediates litter breakdown in this compartment and whether breakdown rates differ between the BZ and HZ.Here, we explore the relationship between litter breakdown and the variation in community structure of benthic and hyporheic communities by deploying two standardized bioassays (cotton strips and two types of commercially available tea bags) in 30 UK streams that encompass a range of environmental conditions. Then, we modelled these assays as a response of the streambed compartment and the biological features of the streambed assemblage (Prokaryota, Protozoa and Eumetazoa invertebrates) to understand the generality and efficiency of litter processing across communities.Litter breakdown was much faster in the BZ compared with the HZ (around 5 times higher for cotton strips and 1.5 times faster for the tea leaves). However, differences in litter breakdown between the BZ and the HZ were mediated by the biological features of the benthos and the hyporheos. Biomass of all the studied biotic groups, α‐diversity of Eumetazoa invertebrates and metabolic diversity of Prokaryota were important predictors that were positively related to breakdown coefficients demonstrating their importance in the functioning of the streambed ecosystem.Our study uses a novel multimetric bioassay that is able to disentangle the contribution by Prokaryota, Protozoa and Eumetazoa invertebrates to litter breakdown. In doing so, our study reveals new insights into how organic matter decomposition is partitioned across biota and streambed compartments.

We present the results of a study of the food web of a Mediterranean river in the four seasons of the year. A high-resolution taxonomic description has been produced to characterise the different community components. We have also determined the trophic relationships among organisms by analysing their gut contents. From the network topology, we extracted several descriptors of structural complexity of the comunity in terms of number of nodes and links. We found a positive relationship between connectance and diversity (both biological and functional). Moreover, we developed and applied a quantitative approach to estimate the link strength, which showed that not all links constituting the network are equally important. In the present paper, we show that the strength of the food-web links vary over time, but there is a natural tendency to keep a small set of strong links throughout the year. However, the existence of two consecutive strong links is not common, meaning that trophic cascades are not promoted.

In this work we present the results of a one-year study on the macroinvertebrate community in an intermittent stream in southern Spain. We have studied the taxonomic composition, diversity and food web monthly in order to consider temporal variability in these parameters. More than 60 macroinvertebrate taxa have been recorded in the stream, but they do not cohabit at the same time. Many of them join the community at the beginning of the wet period. Afterwards, some new taxa incorporate but some others disappear. This leads to huge fluctuations in the diversity of the community and in the food web of different sampling dates. These variations are linked to environmental disturbances, mainly to flow peaks and minimums. From a relatively well structured, but simple, food web at the beginning of the wet period, it can be seen how several trophic levels disappear with time, and how several organisms change or extend their trophic function within it. We relate these variations to the intermediate disturbance hypothesis and discuss the resilience of the community of this intermittent stream.

Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.