Environmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA-based species detection in streams and rivers may be influenced by sampling season and other key factors such as water temperature and discharge. Research linking these factors and also informing on the potential of eDNA metabarcoding to detect shifts in ecological signatures, such as species phenology and functional feeding groups across seasons, is missing. To address this gap, we collected water samples every two weeks for 15 months at a long-term ecological research (LTER) site and at three different positions in the river’s cross section, specifically the water surface, riverbed, and riverbank. For these 102 samples, we analyzed macroinvertebrate species and molecular Operational Taxonomic Unit (OTU) richness and temporal community turnover across seasons based on COI metabarcoding data. Using Generalized Additive Models, we found a significant influence of sampling season on species richness. Community turnover followed a cyclic pattern, reflecting the continuous change of the macroinvertebrate community throughout the year (‘seasonal clock’). Although water temperature had no influence on the inferred species richness, higher discharge reduced the number of Annelida and Ephemeroptera species detectable with eDNA. Most macroinvertebrate taxa showed the highest species richness in spring, in particular merolimnic species with univoltine life cycles. Further, we detected an increase in proportion of shredders in winter and of parasites in summer. Our results show the usefulness of highly resolved eDNA metabarcoding time series data for ecological research and biodiversity monitoring in streams and rivers.

A document by Behnam Balouchi. Click on the document to view its contents.

Streambank erosion impacts rivers and reservoirs due to bank erosion. However, little information of stream bank is available due to the need for advanced planning. Dendrogeomorphology offers a post-hoc method to calculate streambank erosion providing information about past erosion events and processes. Bank retreat can be calculated by dendrogeomorphology where the distance from a channel bank of an exposed live root shows anatomical changes that are dated from the root’s growth rings. We estimated bank erosion for three different sized southern U.S. watersheds ranging in area from 4 to 3781 km 2 using dendrogeomorphology compared to modeled erosion based on critical velocity required for sediment transport. Erosion values ranging from 3.8 to 13.5 cm/yr for the smaller drainages with no difference found between root and modeled erosion rates. The large sub-basin had erosion ranging from 33.6 to 196.4 cm/yr with high variance associated with two prior 2-year flow events with significant differences found between root and modeled values. We also found distance to bank strongly and positively correlated with root exposure in straight sections of the channel in contrast to roots collected in meander bends attributed to erosion processes (i.e., scour, mass wasting) occurring at these locations. When compared with other erosion studies across the southern U.S. prairie, our values were similar in magnitude but with low correlation to drainage area indicating site specificity of erosion mechanisms. We confirm dendrogeomorphology provides reasonable estimate of bank erosion across multiple spatial scales, important for watershed management in areas lacking intentional and persistent monitoring.

Blue sucker ( Cycleptus elongatus) occurs in the Mississippi River and Gulf of Mexico drainages of North America and is negatively affected by habitat fragmentation and flow regime alteration caused by dams. During fish assemblage surveys in August of 2022, we collected five specimens of juvenile blue sucker (312-428 mm total length) in the Angelina River upstream of Sam Rayburn Reservoir in east Texas (46,335-hectare surface area) where the occurrence of the species was previously unconfirmed. Given this unexpected finding, we (1) analyzed blue sucker mesohabitat associations to compare habitats we sampled with reports in the literature, and (2) reviewed blue sucker occurrence in state, national, and global databases across historical (1950-1980) and contemporary (1981-2022) periods to assess occurrence across gradients of habitat fragmentation and streamflow regulation. The blue sucker population in the Angelina River upstream of Sam Rayburn Reservoir was previously unconfirmed but is within the native range of the species. Mesohabitats occupied by blue sucker were consistent with literature reports, including fast velocity, shallow depth, and coarse substrates. The low degree of regulation (19% of natural runoff stored by upstream reservoirs) and a high degree of habitat connectivity (287 rkm of mainstem habitat) for the Angelina River upstream of Sam Rayburn Reservoir matched range-wide patterns of persistence within relatively intact (unfragmented and unregulated) or remnant (fragmented but unregulated) riverscapes. Our review reveals that blue sucker populations might persist (1) in remnant river fragments where local habitat templates are appropriate and (2) where effects of habitat fragmentation and flow regulation are not coupled.

Centuries of human development have altered the connectivity of rivers, adversely impacting ecosystems and the services provided. Significant investments in natural resource projects are made annually with the goal to restore function to degraded rivers and floodplains and protect freshwater resources. Yet restoration projects often fall short of their objectives, in part, due to the lack of systems-based, strategic planning. To evaluate channel-floodplain (dis)connectivity and erosion/incision hazard at the regional scale, we calculate Specific Stream Power (SSP), an estimate of the energy of a river, using a topographically-based, low-complexity hydraulic model. Other basin-wide SSP modeling approaches neglect reach-specific geometric information embedded in Digital Elevation Models. Our approach leverages this information to generate reach-specific SSP-flow curves. We extract measures from these curves that describe (dis)connected floodwater storage capacity and erosion hazard at individual design storm flood stages and demonstrate how these measures may be used to identify watershed-scale patterns in connectivity. We show proof-of-concept using 25 reaches in the Mad River watershed in central Vermont and demonstrate that the SSP results have acceptable agreement with a well-calibrated process-based model (2D Hydraulic Engineering Center’s River Analysis System) across a broad range of design events. While systems-based planning of regional restoration and conservation activities has been limited largely due to computational and human resource requirements, measures derived from low complexity models can provide an overview of reach-scale conditions at the regional level and aid planners in identifying areas for further restoration and/or conservation assessments.

Floodplain restoration can enhance capacity for carbon sequestration by facilitating higher water tables, deposition of fine sediment, and increased input and residence time of organic matter. We measured floodplain soil organic carbon stocks in nine stream restoration projects across the western United States and compared them to nearby degraded and reference condition floodplains. Degraded floodplains had the lowest soil mean carbon stocks in the majority of floodplains measured (range 161-894 Mg C/ha), and reference stocks had the highest stocks (range 391-904 Mg C/ha) of those with statistically significant differences between the three categories. Across all sites measured, stream restoration sites, referred to as treatment sites, had stocks (range 203-1028 Mg C/ha) similar to degraded condition floodplains but the largest range. When modeled under degraded conditions, four out of nine of the treatment sites had significantly higher OC stocks than predicted. Climate and geologic variables are most influential in predicting carbon stocks, and floodplains in the interior western USA have the highest carbon stocks. As the demand for carbon sequestration increases due to climate change, ecologically responsible floodplain restoration provides a significant opportunity for carbon storage. However, despite the statistically significant relationships we observed in this dataset, the variations within the data in relation to degraded/treatment/reference categories illustrate the uncertainties in quantifying the effects of restoration on floodplain carbon stocks.

Salt dilution is a well-established streamflow measurement method in creeks, which works particularly well downstream of turbulent flow sections as mixing of the salt tracer is enhanced. Usually salt dilution measurements are performed manually, which considerably limits the observations of rare peak flow events. However, these events are particularly important for constructing robust rating curves and avoiding large uncertainties in the extrapolation of river discharge values. An additional challenge is the variability of the river cross-section, especially after larger discharge events, leading to non-stationary rating curves. Therefore, discharge measurements well distributed over time are needed to both construct a reliable streamflow-water level relationship and to detect changes caused by erosion and deposition processes. To overcome these two issues, we used an automated streamflow measuring systems at three different sites in the Alps for event-based discharge measurements. This system allowed us to measure close to the highest peak flows at all three sites in the observation period (2020-2021) and to detect abrupt changes in the rating curve. Based on a very large data set of almost 300 measurements, we were able to evaluate the reliability of the system and to identify the main sources of uncertainty in the experimental setup. One key aspect was the site selection for the downstream electrical conductivity sensors as measurement location strongly controls the signal-to-noise ratio (SNR) in the recorded breakthrough curves.

Mapping fluvial hydromorphology is an important part of defining river habitat. Mapping via field sampling or hydraulic modelling is however time consuming, and mapping hydromorphology directly from remote sensing data may offer an efficient solution. Here we present a system for automated classification of fluvial hydromorphology based on a deep learning classification scheme applied to aerial orthophotos. Using selected rivers in Norway, we show how surface flow patterns (smooth or rippled surfaces versus standing waves) can be classified in imagery using a trained convolutional neural network. We show how integration of these classified surface flow patterns with information on channel gradient, obtained from airborne topographic LiDAR data, can be used to compartmentalize the rivers into hydromorphological units that represent the dominant flow features. Automated classifications were consistent with those produced manually. They were found to be discharge-dependent, showing the temporally dynamic aspect of hydromorphology. The proposed system is quick, flexible, generalizable, and free from researcher-subjectivity. The deep learning approach used here can be customized to provide more detailed information on flow features, such as delineating between standing waves and advective diffusion of air bubbles/foam, to provide a more refined classification of surface flow patterns, and the classification approach can be further advanced by inclusion of additional remote sensing methods that provide further information on hydromorphological features.

Headwater streams can constitute up to 80% of river channel length and are vulnerable to anthropogenic pressures due to their high connectivity to adjacent land, large relative catchment size and low dilution capacity. In these environments unrestricted cattle access is a potential significant cause of water quality deterioration, resulting from increases in stream bank erosion, riparian damage and sediment deposition among others. Several studies have reported improvements in physico-chemical and hydromorphological conditions of streams following elimination of cattle access; few, however, have focussed on the ecological impacts of such management practices. Here, such impacts are assessed. We look at the short-term effects by comparing habitat condition, sediment deposition, and instream macroinvertebrate communities upstream and downstream of cattle access points prior to, and one year following exclusion via fencing. The long-term effects are also measured by reassessing a small stream catchment entirely fenced off from cattle access in 2008 under a concerted management effort. In the short term, cattle exclusion led to reduction in deposited sediment downstream of cattle access points and a related homogenisation of macroinvertebrate community structure between upstream and downstream sampling points. Increased abundances of specific indicator taxa ( Ancylus fluviatilis, Glossosomatidae and Elmidae) in the fenced catchment following 9 years of exclusion highlight the long-term ecological benefits of such mitigation practices. These findings highlight the importance of incentivised agri-environment schemes in reducing the negative impacts of cattle access to these vulnerable ecosystems.

Over the last decade, rapid vegetation colonization and changes in channel morphology have been observed in the Naeseongcheon Stream in South Korea, which were linked to short-term hydrological fluctuations under a changing monsoon climate. The surface area covered by vegetation has been increasing; this increase intensified after the 2014–2015 drought, which provided a window of opportunity for vegetation establishment. During the drought, pioneer herbaceous vegetation densely colonized the lower floodplains, including bare sandbars and temporarily exposed riverbed. Although the colonized lower floodplain and river banks were partially rejuvenated by several subsequent floods, succession to woody vegetation continued, resulting in stable vegetation cover in areas that had previously been bare. Moreover, sediment carried by flood water was deposited on and around the vegetated areas, and the low-water channel was incised, causing vertical development of river topography. In addition, the main channel width decreased in previously relatively wide sites, and secondary channels formed. The results of this study show that river rejuvenation by floods may decrease owing to systemic changes in the river system. Therefore, we concluded that the Naeseongcheon watershed was primed by human-induced changes, which made the river system more susceptible to changes in rainfall and discharge due to climate change. Furthermore, after the initial vegetation colonization, changes in nutrients and temperature created a positive feedback loop, which reinforced vegetation establishment.

The Clarence River (New South Wales, Australia) was the main transport corridor for the sugar cane industry operating in the area from the 1860s to the 1970s. Using archaeological, documentary and oral historical resources we explore some of the anthropogenic impacts of this industry upon river channels and hydrology, in particular through the deliberate abandonment of obsolete vessels. These deliberately discarded former cane barges have been used as erosion control devices in several areas around the Harwood Island sugar mill, resulting in the accumulation of sediments and the establishment of mangrove environments in what were degraded areas.

In riparian forests, clear-cutting causes long-lasting changes in both riparian and aquatic biota. In this work, we examined if past clear-cutting events occurred at different times have imprints on riparian forests in a Mediterranean river in central Italy. We carried out a randomized, plot-based vegetation survey of riparian forests in systematically sampled 500 m-long sectors along the whole river, dividing the riparian zone into two internal and two external strips. From historical aerial photos, past clear-cutting events within plots were detected and classified in age classes: i) cut in the past 8 years (recent); ii) cut between 8 and 19 years ago (intermediate); iii) no signs of clear-cutting in the last 19 years (distant). We analyzed the responses of vegetation to clear-cutting and strip position. Alien species richness increased and woody species richness decreased in recently clear-cut areas compared to those with a distant clear-cutting event. Moreover, recently cut woods showed an increase in alien and synanthropic species. Intermediate clear-cut areas had higher levels of invasion by alien species compared to areas with distant cut. Riparian forests of internal strips are impacted by clear-cutting, but seem to recover in 8-19 years thanks to their natural resilience. Conversely, recent or intermediate clear-cutting events did not affect any of the investigated vegetation attributes in the external strips since such forests were already invaded by Robinia pseudoacacia after human disturbance. Our results confirm that clear-cutting events can have long-lasting effects on Mediterranean riparian forests, confirming the vulnerability of river ecosystems to clear-cutting and suggesting the need for more caution in management practices to improve the conservation status of riparian forests.

Widespread hydrologic alterations have simplified in-stream habitats in rivers globally, driving population declines and local extirpations of many native fishes. Here, we examine how rapid geomorphic change in a historically degraded desert river has influenced habitat diversification and ecosystem persistence. In 2010, a large reach of the degraded and simplified lower San Rafael River (SRR), Utah, was impacted by the formation of a valley plug and began to shift from a homogenous, single-thread channel to a complex, multi-threaded riverscape. We combined field measurements and drone-collected imagery to document habitat changes due to the valley plug. Our results demonstrate that in 2021, the valley plug reach was more diverse than any other stream reach along the SRR, containing 641% more diverse habitat (e.g., pools, riffles, backwaters) than what was measured in 2015. The plug reach also retained water for periods beyond what was expected during seasonal drying, with the total extent of inundation within the riverscape increasing by over 2,800%. Since the formation of the valley plug, riparian habitat has increased by 230% and channel networks have expanded to more than 50 distinct channels throughout the zone of influence. Our results provide evidence of successful self-restoration in a formerly highly degraded reach of desert river, and encourage new methods of desert river restoration. We aim to inform the use of large-scale, disruptive restoration actions like intentional channel occlusions, with the goal of mitigating the impacts of simplification and increasing habitat persistence in the face of exacerbated aridity in the desert Southwest.

Although the dispersal is important for riparian plants, few studies have evaluated the patterns in species richness and composition of propagules deposited by different dispersal types. In the present study we evaluate the temporal and spatial patterns in the diversity of propagules deposited by hydrochory and by other types of dispersal along mountain rivers. To do this, we sampled the propagules deposited in the riparian zone in a distance gradient with respect to the site of origin of the rivers in two seasons. Regarding the temporal analyses, we found no differences in the number of propagules between seasons. In the rainy season we observed a greater number of species deposited by hydrochory, while for other types of dispersal there was a greater number of species in the dry season. Differences in composition were observed for hydrochory but not for other types of dispersal. Regarding the spatial analyses, there were no changes in the number of propagules deposited along the river by hydrochory, while for other types of dispersal an increase was observed in the dry season. A lower number of species deposited by hydrochory along the river in the rainy season was observed. Finally, we observed that turnover increases by other types of dispersal in the dry season but not for hydrochory. The results underline the importance of types of dispersal other than hydrochory in the contribution of propagules dispersed and the temporal and spatial particularities of the hydrochory in mountain rivers.

Global changes and local pressures related to the exploitation of water resources are significantly reducing streams' biodiversity and threatening their ecological balance. This trend concerns both the lowland rivers flowing in densely populated areas, and the alpine headwaters, where the effects of global change are dramatically evident and often accompanied by alterations in river hydro-morphology. In mountainous river stretches, regulation and morphological alterations such as bank reinforcement, water abstractions, dams, and weirs are increasing. In the Alps, protected areas and especially large National Parks constitute an effective strategy to face the loss of biodiversity, but little is known about their effectiveness regarding lotic environments. To examine the recent trend in aquatic communities in Alpine protected areas, we carried out biological samplings and hydro-morphological evaluation in twelve high-altitude streams within the oldest Italian National Park, the Gran Paradiso Park, located in the heart of the Western Alps, and we compared results with a previous survey performed in 2005, keeping the same experimental design. Our results detected minimal changes in the hydro-morphology of the studied watercourses. Biomonitoring indices associated with benthic communities likewise do not evidence significant differences. Concerning diatom flora, we found however in 2020 a greater uniformity in species composition compared to communities of 2005, and a slight turnover between species. In conclusion, our findings underline the effectiveness of protected areas for the conservation of running water environments because they limit hydro-morphological alterations thus increasing the resilience of aquatic communities to climate change.

Increasing complexity of riverine management is driving the need for more participatory approaches in which a wide range of stakeholders inform management actions. The foundational conditions of successful stakeholder engagement in participatory riverine management include the stakeholders’ familiarity with, trustworthiness of, shared vision with, and perceived competence of agencies involved in riverine management. We employ an embedded experimental mixed-methods approach to gain insight into two key stakeholder group’s (agricultural producers and non-farm households) perceptions of foundational conditions of successful stakeholder engagement in participatory riverine management in watersheds of two geographically and regulatorily disparate states. Overall, ratings for familiarity were often contrary to ratings of other three conditions. Contrary to previous research our findings suggest that familiarity does not necessarily lead to stakeholder perceived trustworthiness, shared vision, and competence of those involved in riverine management. These findings are important for participatory processes; for example, trust and shared vision without familiarity may inhibit the active involvement of diverse stakeholders in participatory processes that is needed for improving management of complex riverine systems. Our findings suggest agencies and groups involved in riverine management prioritize developing stronger relationships with agricultural producers to improve on these foundational conditions. Agencies and groups involved in riverine management rated low on familiarity should consider campaigns to increase stakeholders’ familiarity with them to leverage the generally high ratings on the other three foundational conditions. Future research should explore these contrary findings and their relationships to active involvement in participatory riverine management.

Most studies exploring land use impacts have focused on taxonomic metrics, but interest in the functional approach has increased because it helps to understand the relationships between community structure and functioning of aquatic ecosystems. We evaluated how functional and taxonomic approaches contribute to assessing the effects of land use on macroinvertebrate assemblages of lowland streams. We also studied the relationships between both approaches. We sampled benthic macroinvertebrates in 17 sites with different land uses (agricultural, peri-urban, and extensive livestock). We computed the taxonomic metrics and biotic indexes as well as functional richness (FRic), divergence (FDiv), dispersion (FDis), and Rao diversity indexes for each site. We performed general linear mixed models to compare land-uses and also performed correlation analysis between taxonomic and functional indexes. Taxonomic richness was significantly higher in extensive livestock than in the other two land uses, while Shannon diversity was significantly different between land uses (extensive livestock>peri-urban>agriculture). FRic and FDiv were significantly lower in peri-urban land use than in agricultural and extensive livestock sites. Only taxonomic richness showed a significant and positive relationship with FRic, FDis, and Rao, but they fit better to a logarithmic function. Therefore, an increase in taxonomic richness and Shannon diversity did not necessarily imply an increase in the functional aspects of the macroinvertebrate assemblage. Using only one of these approaches could lead to partial evaluations and loss of information. Combining them could improve bioindication and predictive potential and help assess the effects of multiple stressors on freshwater ecosystems to improve biomonitoring.

A poor understanding of factors leading to species decline can result in inefficient or ineffective species restoration. Endangered Colorado Pikeminnow ( Ptychocheilus lucius) was nearly extirpated from the San Juan River, NM, USA and recent efforts to reestablish the species via hatchery augmentation of juveniles has yet to reach the targeted number of adults in the system. To assess how changes to the river’s food web could be limiting reestablishment of this top predator, we used stable isotope (δ 13C and δ 15N) signatures of the fish community pre- (museum specimens) and post river regulation with coincident extirpations and invasions. Following river regulation, four of five community-wide trophic structure metrics used to quantify resource use diversity were reduced and species turnover likely had little effect per se. For species sampled in both time periods, shared trophic resources generally increased (mean niche overlap = +35.7%). However, Colorado Pikeminnow experienced a large decrease in niche breadth (-72%) and diet mixing models suggested a shift from piscivory towards insectivory in contemporary collections. Our results suggested an overall reduction in basal resource availability after river regulation. We suggest increased reliance on similar resources may be limiting fish prey for Colorado Pikeminnow, ultimately contributing to the slow and limited reestablishment in the San Juan River. This study adds to the growing body of knowledge provided by museum specimens and stable isotope analyses to identify food-web dynamics that are a departure from historical conditions which can provide novel information critical to imperiled species management in modified systems.