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River landscapes are increasingly viewed as a collection of nested geomorphic features, the hydrological effects of which juxtapose to create a mosaic of aquatic habitat conditions. We examined how the combined hydrological influences of stream reaches and gravel bars affect the composition of hyporheic invertebrate assemblages along the longitudinal and vertical dimensions of river landscapes. We worked in 12 braided-river valley segments of tributaries to the Rhône River, France. Valley segments were bounded downstream by geological knickpoints so that bedform-induced exchange flows beneath gravel bars and riffles were predictably embedded in exchange flows occurring at the valley-segment scale. In upstream reaches (UR) and downstream reaches (DR) of each valley segment, we collected invertebrates at the heads and tails of gravel bars in the hyporheic zone and at the upstream and downstream ends of riffles in surface channels adjacent to the bars. Patterns of vertical hydraulic gradient and specific conductance and the resulting spatial heterogeneity of temperature, dissolved O2, and particulate organic C suggested that DR were points of flow convergence and water mixing. Specific conductance increased and temperature decreased more steeply along gravel bars in DR, indicating that water from long hyporheic flow paths or lateral aquifers was discharging at the tails of bars in DR. Density hotspots for insect larvae corresponded to hyporheic patches at the heads of bars in DR, which received the highest organic matter inputs from localized downwelling of surface water and were not affected by inputs of cold water from hyporheic flow paths or lateral aquifers. Density of epigean taxa at the tails of bars decreased more steeply with depth in DR than in UR, and density of hypogean taxa increased more steeply. Viewing local hyporheic assemblages as the outcome of a series of environmental filters operating over multiple exchange flows induced by nested geomorphic features provides a general framework that may foster our understanding of biodiversity patterns in river landscapes.

Decomposition of allochthonous organic matter is an essential process in headwater streams. Damming of streams alters decomposition rates in the benthic zone downstream, but little is known about the effects on hyporheic decomposition. We examined the effects of dams on hyporheic and benthic organic matter decomposition, using the cotton-strip assay over five seasons, in two forest mountain streams in western Japan. The decomposition rates in the hyporheic zone were lower downstream of the dams than at the unregulated reach in spring, rainy season and fall, but they did not differ in winter and summer. Hyporheic decomposition rates were comparable to the benthic rates in one river and were lower in the other river. Decomposition rates did not differ between coarse- and fine-mesh bags in many seasons at all sites, and the densities of macroinvertebrates were low, suggesting that the contribution of macroinvertebrate to decomposition in the hyporheic zone was small. These results showed that the hyporheic zone is an important zone for decomposition and that presence of dams altered the hyporheic decomposition in some seasons. Thus, it is crucial to examine both the benthic and hyporheic zones when addressing the effects of dams and reservoirs on stream ecosystem processes.

Anthropogenic deterioration of streams and rivers has affected their surface-subsurface linkages. This has led to the degradation of hyporheic zones, a sensitive interface between a stream channel and its surrounding sediments, responsible for transforming pollutants, natural solutes and supporting benthic communities. Several authors have reported the influence of stream restoration measures on hyporheic exchanges and have called for the inclusion of hyporheic zone restorations in stream management. Engineered Hyporheic Zones (EHZ) are the creation of artificial transition areas due to induced hyporheic flows, brought about by some feature modifications done to the stream channel or its subsurface. These feature modifications and their implications have been investigated through lab experiments, outdoor flumes, modelling and field studies for several years. This paper attempts to summarize the endeavours made in the study of EHZ and its applications in water quality improvement and habitat restoration. A comprehensive review of up-to-date literature with specific focus on the influence of engineered structures on hyporheic exchanges is presented, followed by the comparison of preferences opted for different studies and their limitations. The paper ends with suggestive future scope in EHZ studies and its potential as a low cost alternative treatment technology for river restoration.

Abstract Biota in disturbance‐prone landscapes have evolved a variety of strategies to persist long term, either locally ( resistance ) or by regional recolonization ( resilience ). Habitat fragmentation and isolation can limit the availability of recolonization pathways, and thus the dynamics of post‐disturbance community reestablishment. However, empirical studies on how isolation may control the mechanisms that enable community recovery remain scarce. Here, we studied a pristine intermittent stream (Chalone Creek, Pinnacles National Park, California) to understand how isolation (distance from a perennial pool) alters invertebrate community recolonization after drying. We monitored benthic invertebrate reestablishment during the rewetting phase along a ~2‐km gradient of isolation, using mesh traps that selected for specific recolonization pathways (i.e., drift, flying, swimming/crawling, and vertical migration from the hyporheic). We collected daily emigration samples, surveyed the reestablished benthic community after 6 weeks, and compared assemblages across trap types and sites. We found that isolation mediated migration dynamics by delaying peak vertical migration from the hyporheic by ca. 1 day on average per 250 m of dry streambed. The relative importance of reestablishment mechanisms varied longitudinally–with more resistance strategists (up to 99.3% of encountered individuals) in the upstream reaches, and increased drift and aerial dispersers in the more fragmented habitats (up to 17.2% and 18%, respectively). Resistance strategists persisting in the hyporheic dominated overall (88.2% of individuals, ranging 52.9%–99.3% across sites), but notably most of these organisms subsequently outmigrated downstream (85.6% on average, ranging 52.1%–96% across sites). Thus, contrary to conventional wisdom, resistance strategists largely contributed to downstream resilience as well as to local community recovery. Finally, increased isolation was associated with a general decrease in benthic invertebrate diversity, and up to a 3‐fold increase in the relative abundance of drought‐resistant stoneflies. Our results advance the notion that understanding spatial context is key to predicting post‐disturbance community dynamics. Considering the interaction between disturbance and fragmentation may help inform conservation in ecosystems that are subject to novel environmental regimes.

This study investigated temporal changes in the vertical distribution of invertebrates during periods of low flows in the Tafna wadi, a semi-arid Mediterranean river characterised by a general decline in average flows. The hyporheos was sampled along a 130-m stretch at depths of 0.3, 0.6 and 1 m in a pool-riffle sequence and a lateral gravel bar. Benthic fauna was collected on each sampling occasion from different locations in the studied sections. Sampling was conducted in two consecutive years (2014 and 2015) at the end of the spring (high waters) and over a 2-month period during the low summer flow. The results indicated that high surface water temperatures may initiate the movement of some taxa into the interstitial habitat, thus supporting the hyporheic refuge hypothesis. In the hyporheic zone, the low oxygen rates recorded deeper in the sediment and in the last low-flow months caused significant declines in taxonomic richness, and lower pH values resulted in a reduction in invertebrate abundances. In the benthic zone, high flow velocities increased richness but decreased invertebrate abundances. A large number of taxa were found in the gravel bar section reflecting the more suitable living conditions in this habitat compared with the river reach (high DO rates).

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. The authors use a novel multimetric bioassay that is able to disentangle the contribution by Prokaryota, Protozoa and eumetazoan invertebrates to litter breakdown. The study reveals new insights into how organic matter breakdown is partitioned across biota and streambed compartments.

Drying disturbances are the primary determinant of aquatic community biodiversity in dynamic river ecosystems. Research exploring how communities respond to disturbance has focused on benthic invertebrates in surface sediments, inadequately representing a connected community that extends into the subsurface. We compared subsurface and benthic invertebrate responses to drying, to identify common and context‐dependent spatial patterns. We characterized community composition, alpha diversity and beta diversity across a gradient of drying duration. Subsurface communities responded to drying, but these responses were typically less pronounced than those of benthic communities. Despite compositional changes and in contrast to reductions in benthic alpha diversity, the alpha diversity of subsurface communities remained stable except at long drying durations. Some primarily benthic taxa were among those whose subsurface frequency and abundance responded positively to drying. Collectively, changing composition, stable richness and taxon‐specific increases in occurrence provide evidence that subsurface sediments can support persistence of invertebrate communities during drying disturbances. Beta‐diversity patterns varied and no consistent patterns distinguished the total diversity, turnover or nestedness of subsurface compared to benthic communities. In response to increasing drying duration, beta diversity increased or remained stable for benthic communities, but remained stable or decreased for subsurface communities, likely reflecting contrasts in the influence of mass effects, priority effects and environmental filtering. Dissimilarity between subsurface and benthic communities remained stable or increased with drying duration, suggesting that subsurface communities maintain distinct biodiversity value while also supporting temporary influxes of benthic taxa during drying events. As temporary rivers increase in extent due to global change, we highlight that recognizing the connected communities that extend into the subsurface sediments can enable holistic understanding of ecological responses to drying, the key determinant of biodiversity in these dynamic ecosystems.

1.Large wood (LW) is a natural element of river environments and an integral component of many river restoration schemes to promote biodiversity. It is an important habitat in itself, but it also induces a wide range of hydraulic, hydrological, geomorphological, and chemical conditions that influence the ecological community. However, the effects of hydro‐geomorphological processes induced by LW on local benthic and hyporheic invertebrates have not been well characterized. 2.A functional approach was applied to invertebrate data collected in a field survey at sites with LW and without LW (control), to investigate the response of hyporheic and benthic invertebrates’ trait profiles in response to local LW‐induced processes. 3.We hypothesized LW sites to be associated with different trait modalities than control sites in relation to wood‐induced processes and conditions (i.e. hyporheic exchange flow, oxygen availability, temporal stability, organic matter, denitrification, hydraulic conductivity). Multivariate analyses and Partial Least Squares (PLS) Path Modelling were used to detect the differences in trait profiles between LW and control sites and to study the variation of traits as a function of hydrological, sedimentological, physical and chemical variables. 4.Biological (i.e. aquatic stages, reproduction), physiological (i.e. dispersal, feeding habits) and behavioural (i.e. substrate preferences) trait utilization by the hyporheic meiofauna differed between LW and control sites. At LW sites, the hyporheic meiofaunal assemblage was significantly associated with aquatic active dispersal, aquatic eggs and hard substrate preferences. This trait category selection was linked to changes in physical‐sedimentological processes at LW sites when compared to control sites. Macrofaunal benthic and hyporheic functional traits did not differ significasignificantly between wood and control sites, suggesting similar functioning of these assemblages at the surface‐subsurface interface. 5.This study found that LW affects invertebrate traits by altering fluvial processes to produce, locally, a mosaic of habitats. Hyporheic meiofauna trait responses to LW‐processes have suggested (i) the crucial role of LW in supporting river benthic zone functioning, and thus (ii) a possible benefit to river restoration by enhancing functional interactions among different ecological niches.

Surface and subsurface sediments in river ecosystems are recognized as refuges that may promote invertebrate survival during disturbances such as floods and streambed drying. Refuge use is spatiotemporally variable, with environmental factors including substrate composition, in particular the proportion of fine sediment (FS), affecting the ability of organisms to move through interstitial spaces. We conducted a laboratory experiment to examine the effects of FS on the movement of Gammarus pulex Linnaeus (Crustacea: Amphipoda) into subsurface sediments in response to surface water loss. We hypothesized that increasing volumes of FS would impede and ultimately prevent individuals from migrating into the sediments. To test this hypothesis, the proportion of FS (1–2 mm diameter) present within an open gravel matrix (4–16 mm diameter) was varied from 10 to 20% by volume in 2.5% increments. Under control conditions (0% FS), 93% of individuals moved into subsurface sediments as the water level was reduced. The proportion of individuals moving into the subsurface decreased to 74% at 10% FS, and at 20% FS no individuals entered the sediments, supporting our hypothesis. These results demonstrate the importance of reducing FS inputs into river ecosystems and restoring FS-clogged riverbeds, to promote refuge use during increasingly common instream disturbances.

In intermittent streams, aquatic organisms use various strategies to face dry phases, but the relative contribution of these strategies to persist during dry phase remains unclear. Here, we investigated the in situ persistence of benthic invertebrates in the saturated hyporheic sediments and the “invertebrate seedbank” that persists in dry sediments across six Mediterranean intermittent streams. Taxonomic and functional responses within hyporheic and seedbank assemblages were compared with those in the benthic assemblages under connected flow conditions by combining field and mesocosms data. The dry phase duration in each stream was calculated to assess the responses of hyporheic and seedbank assemblages. Taxonomic composition and abundance-weighted traits related to resistance and resilience to face the dry phase in each assemblage type (benthic, hyporheic, seedbank) were determined. Taxonomic (richness and diversity) and functional (richness and dispersion) metrics were also calculated. We found that seedbank and hyporheic assemblages supported up to 16% and 40% of the benthic taxa, respectively. Only taxonomic and functional richness differed between assemblage types. Contrary to previous research, no clear relationship was established between diversity or the abundance of resistance traits and the duration of dry phase; however, a negative linear relationship was identified between the abundance of resilience traits and the duration of the dry phase. The increase in the frequency and duration of drying events due to climate change will reduce water availability in both saturated and unsaturated streambed sediments, compromising the persistence of aquatic biodiversity in intermittent streams.