Nonperennial streams dominate global river networks and are increasing in occurrence across space and time. When surface flow ceases or the surface water dries, flow or moisture can be retained in the subsurface sediments of the hyporheic zone, supporting aquatic communities and ecosystem processes. However, hydrological and ecological definitions of the hyporheic zone have been developed in perennial rivers and emphasize the mixing of water and organisms from both the surface stream and groundwater. The adaptation of such definitions to include both humid and dry unsaturated conditions could promote characterization of how hydrological and biogeochemical variability shape ecological communities within nonperennial hyporheic zones, advancing our understanding of both ecosystem structure and function in these habitats. To conceptualize hyporheic zones for nonperennial streams, we review how water sources and surface and subsurface structure influence hydrological and physicochemical conditions. We consider the extent of this zone and how biogeochemistry and ecology might vary with surface states. We then link these components to the composition of nonperennial stream communities. Next, we examine literature to identify priorities for hydrological and ecological research exploring nonperennial hyporheic zones. Lastly, by integrating hydrology, biogeochemistry, and ecology, we recommend a multidisciplinary conceptualization of the nonperennial hyporheic zone as the porous subsurface streambed sediments that shift between lotic, lentic, humid, and dry conditions in space and time to support aquatic–terrestrial biodiversity. As river drying increases in extent because of global change, we call for holistic, interdisciplinary research across the terrestrial and aquatic sciences to apply this conceptualization to characterize hyporheic zone structure and function across the full spectrum of hydrological states.

Decades ago, Dr Noel Hynes eloquently summarized the inherent interconnectedness of a stream and its valley and made the case that human alteration of the valley would have direct negative consequences for freshwater systems. Currently, the freshwater biodiversity crisis extends across all continents and demands urgent attention from environmental planners, practitioners, and policymakers to protect streams and their valleys. As we work to slow losses of freshwater biodiversity and restore freshwater ecosystems, it is time to revisit the important messages from Hynes. One of the most obvious and immediate actions that could be undertaken is to “back off”—that is, to limit human activity and new development in floodplain and riparian areas immediately adjacent to freshwater systems, including streams, rivers, lakes, and wetlands, while minimizing impacts and risks in areas with existing development. From reducing erosion and flood damage to maintaining cool water temperatures, filtering pollutants, protecting critical habitats, and enabling lateral connectivity, intact riparian zones mitigate many of the threats that degrade freshwater ecosystems. There has been much research to identify optimal setbacks and buffer-strip widths to protect against harm. As such, in many areas, our ability to protect the stream and its valley is not limited by natural science but rather our failure to consistently apply floodplain and riparian regulations and the absence of political will. We are too quick to trade off the environment for short-term economic development. In areas that are already developed, solutions are more complicated but, in many cases, represent a key priority for healing damaged ecosystems and for addressing economic and social risks of vulnerable development. We need to redefine our relationship with freshwater ecosystems, and the first step is to back off and give freshwater ecosystems the opportunity to heal while ensuring that as-of-yet intact riparian areas continue to support freshwater resiliency. In doing so, we will also gain climate adaptive benefits, given that maintaining intact riparian areas is an effective nature-based solution.

Reaches are a fundamental unit for lotic biogeochemical characterization, yet a functional classification of nutrient processing at the reach scale is currently lacking. Here, we introduce nutrient processing domains (NPDs) to integrate routing (nutrient delivery) and local (benthic uptake and transformation) processes that dictate longitudinal patterns of lotic biogeochemical function. An NPD is defined as a realm in functional space occupied by reaches that share similar biogeochemical character. Occupation of a given NPD reflects characteristic net material balance (NMB), exchange potential, and availability, associated with changes in solute load, the extent of hydrologic gain or loss, and changes in concentration from the head to the base of a reach, respectively. Using a mass-balance approach, we represent NMB as the effective solute flux (F_eff, M L⁻² T⁻¹, where M = mass, L = length, and T = time), designating reaches as sources (+F_eff) or sinks (−F_eff). Discharge change along a reach is measured as the change in hydraulic load (ΔH_L, L/T), reflecting the potential for import and export to influence solute loads. Finally, the ratio of downstream-to-upstream concentration (C_dwn:up) represents the net effect that processes have on nutrient availability. Using a 20-y historical record for N and P in the Upper Clark Fork River, Montana, USA, we employed this approach to 3 consecutive reaches covering nearly 90 km of channel length to address spatial and temporal dynamics in NPD behavior in a nutrient-rich, productive river system. For total N and total P, reaches typically occupied compiler or enhancer NPDs, displaying load increases without or with concomitant increases in concentration, respectively. In contrast, reaches were NO₃⁻ consumers, acting as sinks for NO₃-N during summer and autumn. NO₃⁻ load reductions were typically accompanied by striking declines in concentration, despite positive exchange potential (i.e., +ΔH_L). Measured F_eff magnitudes for NO₃⁻ (−1.2 to −60.0 mg N m⁻² d⁻¹) were similar to those reported in the literature associated with autotrophic N demand. Individual reaches occupied contrasting NPDs for NO₃-N and soluble reactive P by simultaneously serving as a sink for one and a source for the other. Hence, alternating reaches acted as enhancers or consumers, sequentially along the river, reflecting geologic and biological influences with implications for whole river behavior. The NPD approach combines routing influences of material exchange and local biological stream processes to provide a biogeochemical taxonomy for stream reaches with application to theory and practice.

Freshwater salinization is a global ecological concern because of the alarming biodiversity declines associated with increases in major ion concentrations. Loss of mayfly diversity appears to be a common ecological response to anthropogenic salinization worldwide. Remarkably few regulatory standards exist to protect aquatic life from major ions, and antiquated approaches for setting such standards rely on traditional laboratory toxicity tests, which do not address sensitivities of mayflies at different larval stages. The lab-reared mayfly Neocloeon triangulifer (McDunnough, 1931) has emerged as one of the very few useful aquatic insect models for studying the effects of environmental stressors, including salinity, in the laboratory. Here, we asked if different larval life stages are differentially sensitivity to ion concentrations by conducting traditional 96-h toxicity tests with NaCl, CaCl₂, and Ca/MgSO₄. We used a general linear model to determine if survivorship differed among larval stages as well as ion type and concentration. We also calculated median lethal concentrations (LC₅₀) for each larval stage. Larval sensitivity to NaCl decreased slightly with age (2–6, 9–13, and 17–21 d, with LC₅₀ values of 401, 441, and 570 mg/L, respectively, when expressed as Na concentrations). Similarly, larval sensitivity to Ca/MgSO₄ differed slightly among age groups (LC₅₀ = 748, 1503, and 1439 mg/L, respectively, when expressed as SO₄ concentrations). Reliable confidence intervals on LC₅₀ values for CaCl₂ could not be calculated because of high survivorship. However, our general linear model revealed that age played a moderate role in survival (p = 0.0065) across all salts of interest. To assess the potential changes in ion flux between larval stages, we used radiotracers (²²Na, ³⁵SO₄, or ⁴⁵Ca) in 18- and 25-d-old larvae and found no strong differences in ion uptake rates. We also qualitatively examined morphological differences between larval life stages, including the appearance of gills and number of ionocytes. Our results indicate that younger N. triangulifer larvae may be more sensitive to major ions than mature larvae. These results should be considered when experimentally using larger, late-stage N. triangulifer larvae to study the physiological effects and acute toxicity of salinity.

Beta diversity patterns have been frequently used to investigate metacommunity structure. The metacommunity concept has focused primarily on the spatial beta component, but part of the unaccounted variation is likely associated with temporal beta patterns. Here, we examined the effect of seasonal variation in water availability on the spatiotemporal assembly of microcrustaceans living in temporary pools. Specifically, we sampled microcrustaceans in 5 pools monthly for 12 mo and tested how temporal fluctuations in physicochemical variables affected beta diversity. We also investigated whether species showed synchronous responses in tracking dry or wet conditions. Our study revealed that only those microcrustacean species associated with the wet season had temporally synchronous population dynamics. However, we did not find population synchrony in the dry season and in those comparisons including all microcrustacean species. Physicochemical variables such as pH, dissolved oxygen, and water transparency explained part of the spatial variation in beta diversity. These results suggest a strong influence of species sorting on metacommunity structure both in space and in time. Extreme climatic conditions, such as water scarcity, could affect population dynamics; thus, linking spatial and temporal patterns will be necessary to disentangle the effects of stochastic processes and environmental filtering on metacommunity dynamics.

Over the past ∼15 y, unconventional oil and gas (UOG) production utilizing hydraulic fracturing and horizontal drilling has increased dramatically in the Marcellus Shale in the Appalachian region of the USA. The area also has a long history of conventional oil and gas (COG) production as well as coal mining, and the 3 extractive activities (UOG, COG, and coal mining) often occur in the same watersheds. Produced water and wastewater from oil and gas (OG) extraction can have very high concentrations of dissolved metals, radionuclides, and other solutes. Previous studies have documented streamwater pollution associated with spills and releases of these fluids, but it remains unclear whether OG development has broad regional effects on streamwater quality. This study assessed whether COG and UOG well densities in watersheds were associated with water-quality metrics, including specific conductance, dissolved metals, nutrients, radium isotopes, and anions, when controlling for coal mining and land cover. Water quality was measured at 120 stream sites with non-nested watersheds in the Marcellus Shale region. Linear modeling revealed that COG well density was associated with higher concentrations of Mg and Cl⁻, and UOG well density was associated with higher ²²⁸Ra:²²⁴Ra ratios, suggesting that this ratio might be a useful indicator of UOG development in watersheds. Adding OG well density to linear models explaining the concentrations of water-quality variables improved R² by ≤0.04, indicating little increase in explanatory power. However, linear regression coefficients indicated that an increase in COG well density from 0 to 11 wells/km² (the maximum well density observed in our study area) could be associated with 35× increases in Mg and Cl⁻ concentrations, although the SE of these estimates was large. This research suggests that OG well density may have small but measurable effects on streamwater quality; however, the effects of other human activities and land uses, such as coal extraction and urban development, are likely larger and more environmentally relevant.

Decision triggers, used in adaptive management frameworks to decide when a specific management action will be implemented, are often informed by monitoring data. The identification and application of decision triggers is highly relevant to endangered fishes migrating through regulated rivers, as examined in the current study. The main goal was to determine whether seasonal patterns of behavioral, physical, and physiological indices of juveniles were related to subsequent smolt-to-adult return (SAR) survival and, if so, to determine whether these indices could be used to guide decisions related to the mitigation strategy of the juvenile fish transportation program in the Federal Columbia River Power System (Pacific Northwest, USA). Hatchery yearling Chinook Salmon (Oncorhynchus tshawytscha Walbaum in Artedi, 1792) were collected over the migration season at 3 dams in the hydrosystem and measured for fork length, wet mass, Fulton’s K (or condition factor), Na⁺/K⁺-ATPase (NKA) activity (or smoltification index), and % dry mass (or index of energetic reserves and smoltification). We estimated SAR survival from passive integrated transponder-tagged fish representative of our field samples and assessed its relationship to our fish indices, as well as indices of transported vs run-of-river passage and distance of sampling site to ocean. SAR survival was associated to interaction effects between juvenile fish transportation and % dry mass or NKA activity. Transported hatchery Chinook Salmon with dry mass <23% of whole fish wet mass and NKA activity >7 µmol ADP mg protein⁻¹ h⁻¹ showed greater SAR survival than their run-of-river counterparts. Fish with the highest predicted SAR survival had been transported and had fish indices consistent with smolts that were more developed (i.e., lower % dry mass and higher NKA activity). Furthermore, our results on % dry mass provided support for the hypothesis that greater lipid content increases fish buoyancy leading to greater susceptibility to predation. The buoyancy effect is expected to be greatest in hatchery fish. Overall, this study shows that decision triggers based on biological indices of migrating fish are potentially useful tools for in-season management.

One of the major goals in microbial ecology is to understand whether the empirical biogeographic patterns of macroorganisms also apply to microorganisms. Here, we used morphological data from live organisms, along with molecular data, to investigate the importance of spatial factors and environmental variables in influencing ciliate composition from floodplain lakes. Our main goal was to use 2 different approaches (morphological and molecular) to compare ciliate diversity and distribution patterns as well as to compare how these methods differ in their ability to detect distribution patterns and the roles of spatial and environmental factors that shape ciliate assemblages in the 4 largest floodplains in Brazil. Planktonic water samples were gathered from 33 lakes associated with 4 different river floodplain systems in Brazil. We analyzed ciliates in vivo and sequenced surface water DNA using a metabarcoding approach with general eukaryotic primers. We showed that the diversity of operational taxonomic units was much higher than that of morphospecies. Regardless of the method of identification, we found a consistent spatial assembly pattern of ciliate assemblages across the 4 floodplain systems. We also found that environmental filters had a stronger association with the morphological than with the molecular site-by-site dissimilarities. Meanwhile, biogeographic factors and the distance among sites limited the distribution of molecular-based composition, resulting in strong differences among the floodplain lakes analyzed. This finding suggests that ecological research and biomonitoring activities should find an equilibrium between morphological and molecular approaches because each approach provides unique insights.

Watersheds in the Great Plains region of the United States are dominated by agriculture, interspersed with remnant or restored prairie vegetation. The pulse-shunt concept predicts these coexisting land uses likely have opposing effects on seasonal biogeochemical and hydrological controls of organic C (OC) fates in freshwater ecosystems, but few studies have focused on temporal patterns of OC fates in streams that are influenced by agriculture and tallgrass prairie. We estimated stream metabolism and OC spiraling in a stream (Glacier Creek, Omaha, Nebraska, USA) draining a mixed land-use watershed with restored tallgrass prairie and agriculture to answer: 1) Does a mixed land-use stream exhibit seasonal patterns of ecosystem metabolism? and 2) Does the balance between active OC processing vs passive OC transport change across seasons and years as predicted by the pulse-shunt concept? We hypothesized that the stream would be net heterotrophic, rapidly mineralize OC (V_f-OC), and exhibit short spiraling lengths (S_OC) at baseflow, and that these functions would be modulated in opposing directions by seasonal patterns of nutrient availability and turbidity. Mean gross primary production was 0.30 g O₂ m⁻² d⁻¹, mean ecosystem respiration was −1.25 g O₂ m⁻² d⁻¹, and Glacier Creek was net heterotrophic throughout the study (mean net ecosystem production = −0.94 g O₂ m⁻² d⁻¹; mean production:respiration = 0.19). Peak gross primary production and ecosystem respiration occurred in the spring driven by discharge and light. High-resolution OC-spiraling estimates revealed a continuum of OC processing and transport consistent with pulse-shunt fluxes. OC-spiraling lengths spanned 2 orders of magnitude (1–934 km), but most S_OC ranged between distances of 4 to 15 km at baseflow. S_OC was shorter with higher nutrient concentrations and longer with higher turbidity, consistent with the inverse pattern for V_f-OC. Our study confirms that the metabolic regime of a prairie stream was seasonal, while underscoring that factors that are modified by land-use change, such as nutrients and turbidity, can influence OC processing.

Climate change predictions for Southern Europe indicate an increase in the frequency and duration of summer low flows and water scarcity in streams. Droughts can cause substantial changes in aquatic communities and biogeochemical processes because they modify stream environmental conditions. Among the many physical, chemical, and biological variables that influence stream metabolism, nutrients may affect algae and heterotrophic microorganisms, and nutrient concentrations may vary with reduction in water discharge. We experimentally manipulated stream discharge and used a before–after control–impact paired design to assess how reduction of stream discharge affected metabolism (i.e., ecosystem respiration [ER] and gross primary production [GPP]). The study was done in 2 lowland forested streams in northwestern Spain with contrasting nutrient concentrations (i.e., mesotrophic: Caselas stream; eutrophic: Pego stream). In the 2 streams, metabolism was estimated before and after discharge manipulation. Prior to discharge reduction, the 2 streams were heterotrophic (i.e., GPP∶ER < 1), and GPP and ER were related in the eutrophic Pego. Discharge reduction increased GPP at the impacted reaches of the mesotrophic Caselas and decoupled GPP and ER at the Pego. An information-theoretic approach was used to assess which combinations of physical, chemical, and biological variables were most important to explain the variation in ER and GPP under the different hydrologic conditions. The observed differences between the 2 streams suggest that the metabolic response to stream drought can be modulated by the interplay between nutrient availability and the density of consumers feeding on resources, among other environmental variables. We show that longer summer periods and reduced stream discharge have the potential to increase daily hypoxia in nutrient-rich lowland stream ecosystems. Increased hypoxia can threaten biodiversity of stream ecosystems and reduce consumer pressure on basal instream resources, such as algae, bacteria, and fungi, which may, in turn, favor instream GPP. In addition, drying conditions seemed to favor autotrophic over heterotrophic activity under moderate nutrient availability (i.e., increase in the GPP∶ER ratio in the impacted Caselas reaches). Therefore, drought conditions not only affect overall daily rates of metabolic activity, but also the relative importance of different energy sources and organic matter for instream function. Our results show that discharge reduction caused by increased water scarcity, due to both climate change and water demand by human activities, can influence energy flow and organic matter dynamics through effects on the metabolism of forested lowland streams.

Freshwater mussels live partially or fully buried in river sediments, and burrowing by mussels causes bioturbation, increases benthic complexity, provides niche partitioning among other mussel species, and may reduce the chance of mussel dislodgment during high flows. However, there remains a need to better understand what influences the burrow position of mussels and how burrow position modifies physical and hydraulic habitat. In this study, we examined how mussel burrow position varied across species in 2 gravel-bedded rivers in the northeastern USA and how burrow position modified benthic habitat. We quantified the amount of benthic habitat mussels contributed to the riverbed and determined the contribution of burrow position to bed roughness and near-bed flow patterns. We found that burrow position varied by species, which was likely influenced by shell morphology, sculpture type, and river characteristics. We observed that the amount of shell exposed into the water column was similar to the coarse-sized sediment where mussels were found. We also found that mussel shells were exposed at a height greater than the median grain size and could, therefore, influence near-bed flows. Moreover, because larger grain sizes control sediment stability, the similar exposed length of burrowed mussels as coarse sediment could contribute to enhanced bed stability and reduce the risk of dislodgement. Better understanding of how mussel burrow position influences these important biophysical processes may help identify important Allee effects or minimum viable population indices, which may aid conservation and restoration efforts.

Species introductions are common in freshwater environments and have the potential to transform community and ecosystem structure. Predatory centrarchid fishes and American Bullfrogs (Lithobates catesbeianus Shaw, 1802 previously Rana catesbeiana) are both widespread aquatic invaders implicated in native amphibian declines. In lowland ecosystems, co-occurrence between native and nonnative amphibian and fish taxa is common; however, the mechanisms that facilitate their co-occurrence are poorly studied. Stable isotope analysis offers a tool to examine trophic interactions among native and nonnative taxa, including predation, competition, and shifting food resource availability, which may provide mechanistic insight into the drivers of co-occurrence. In this study, we used stable isotopes (δ¹³C and δ¹⁵N) to determine how the trophic structure of native fishes and amphibians differs between waterbodies with and without nonnative centrarchid fishes and bullfrogs across a floodplain in southwestern Washington, USA. We hypothesized that native species alter their feeding strategies to reduce niche overlap with nonnative taxa. In the presence of nonnative taxa, Three-spine Stickleback (Gasterosteus aculeatus Linnaeus, 1758), all native larval salamander species (Ambystoma gracile Baird, 1859 and Ambystoma macrodactylum Baird, 1850), and 1 of 2 native larval frog species (Rana aurora Baird and Girard, 1852) exhibited shifts in food resources or trophic position. Despite trophic differences, only 1 species (A. macrodactylum) had a smaller niche size in the presence of nonnatives. The observed trophic shifts reflect changes in habitat or food resources, which may reduce competition or predation and promote co-occurrence between nonnative and native taxa. Our results suggest that the co-occurrence of native and nonnative amphibians and fishes in lowland floodplain habitats may be facilitated by a broad range of food resources and complex habitat structure.

Terrestrial and stream ecosystems are interconnected, with changes in one system cascading to affect the other. Tree mortality related to nonnative pest infestation has increased, yet we do not understand the effects that riparian tree species losses will have on the structural characteristics of stream ecosystems. We compared riparian canopy cover, algal standing crop, and diatom assemblage composition in 8 southern Appalachian headwater stream reaches within the Coweeta Hydrologic Laboratory in North Carolina, USA, before and after a massive die-off of riparian eastern hemlock (Tsuga canadensis [L.] Carr.) related to the introduction of hemlock woolly adelgid (Adelges tsugae Annand), an invasive insect. We analyzed historical preserved algal samples collected prior to hemlock die-off, in both summer (September 2005) and winter (January 2006), and used multivariate analyses to compare them to samples collected in the same 8 reaches and seasons 13 y following hemlock die-off (2018–2019). We predicted that increased canopy openness following hemlock death would change light availability and lead to higher standing crop and increases in the relative biovolume of high-profile diatoms. Contrary to our expectations, we found little difference in canopy cover and lower algal standing crop 13 y post-hemlock die-off, likely due to increased basal area of the understory shrub, Rhododendron maximum L., that replaced shade cover formerly provided by hemlock. Diatom assemblages were dominated by acidophilic taxa (e.g., Eunotia spp.) across all stream reaches before and after hemlock die-off. We observed some shifts in diatom assemblage composition, but the relative biovolume of a majority of the top 20 most abundant taxa, including Eunotia incisa W. Sm. ex W. Greg., Nupela lapidosa (Krasske) Lange-Bert., and Meridion alansmithii Brant (an endemic taxon), remained relatively unchanged 13 y after hemlock mortality. Diatom assemblages differed post-hemlock die-off in summer but not winter due to a decrease in the relative biovolume of Eunotia metamondon complex and an increase in the relative biovolume of Eunotia rhomboidea complex. Our study highlights the relative stability of diatom assemblage composition in southern Appalachian streams and the importance of long-term studies following a major riparian disturbance.