Role of indigenous microorganisms and organics in the release of iron and trace elements from sediments impacted by iron mine tailings from failed Fundão dam.

After Fundão Dam failure in 2015, most of Gualaxo do Norte River in Doce River Basin in Brazil became silted by iron mining tailings consisting mainly of fine-grained quartz, hematite, and goethite. Previous work pointed to the possibility of reductive dissolution of iron and manganese from tailings, leading to mobilization of iron, manganese and trace elements. Several microorganisms were shown to reduce Fe(III) to Fe(II) and Mn(III, IV) to Mn(II) "in vitro", but their roles in mobilization of Fe and trace elements from freshwater sediments are poorly understood. In this work, bottom sediments and water collected in Gualaxo do Norte River were used to build anoxic microcosms amended with acetate, glucose or yeast extract, in order to access if heterotrophic microorganisms, either fermenters or dissimilatory Fe reducers, could reduce Fe(III) from minerals in the sediments to soluble Fe(II), releasing trace elements. The Fe(II) concentrations were measured over time, and trace elements concentrations were evaluated at the end of the experiment. In addition, minerals and biopolymers in bottom sediments were quantified. Results showed that organic substrates, notably glucose, fuelled microbial reduction of iron minerals and release of Fe(II), Mn, Ba, Al and/or Zn from sediments. In general, higher concentrations of organic substrates elicited mobilization of larger amounts of Fe(II) and trace elements from sediments. The results point to the possibility of mobilization of huge amounts of iron and trace elements from sediments to water if excess biodegradable organic matter is released in rivers affected by iron mine tailings.

Stream Hydrology Controls the Longitudinal Bioreactive Footprint of Urban-Sourced Fine Particles.

The relevance of wastewater treatment plant (WWTP) effluents in fluvial networks is increasing as urbanization grows in catchments. Urban-sourced fine particles from WWTP effluents deposit and accumulate in the streambed sediment of receiving streams over time and can fuel respiration rates, which can thus potentially increase rates of biogeochemical reactions and CO2 emissions to the atmosphere. We aimed to provide a quantitative assessment of the influence of WWTP-sourced fine particles deposited in the streambed sediment on stream metabolic activity for 1 year in an intermittent Mediterranean stream. More nutrient-rich and metabolically active fine particle standing stocks were observed downstream of the WWTP, propagating to the end of the 820 m study reach, especially during the dry period (i.e., when the dilution capacity of the stream to WWTP inputs is <40%). Based on the longitudinal patterns of fine particle standing stocks and their metabolic activity, we estimated that the in-stream bioreactive capacity associated with these fine particles could potentially lead to substantial carbon dioxide emissions to the atmosphere (3.1 g C/m2/d). We show the importance of incorporating fine particle standing stocks downstream of point source inputs, particularly WWTPs in intermittent streams, into carbon budgets.

Physical habitat in conterminous US streams and rivers, Part 1: Geoclimatic controls and anthropogenic alteration.

Anthropogenic alteration of physical habitat structure in streams and rivers is increasingly recognized as a major cause of impairment worldwide. As part of their assessment of the status and trends in the condition of rivers and streams in the U.S., the U.S. Environmental Protection Agency's (USEPA) National Aquatic Resource Surveys (NARS) quantify and monitor channel size and slope, substrate size and stability, instream habitat complexity and cover, riparian vegetation cover and structure, anthropogenic disturbance activities, and channel-riparian interaction. Like biological assemblages and water chemistry, physical habitat is strongly controlled by natural geoclimatic factors that can obscure or amplify the influence of human activities. We developed a systematic approach to estimate the deviation of observed river and stream physical habitat from that expected in least-disturbed reference conditions. We applied this approach to calculate indices of anthropogenic alteration of three aspects of physical habitat condition in the conterminous U.S. (CONUS): streambed sediment size and stability, riparian vegetation cover, and instream habitat complexity. The precision and responsiveness of these indices led the USEPA to use them to evaluate physical habitat condition in CONUS rivers and streams. The scores of these indices systematically decreased with greater anthropogenic disturbance at river and stream sites in the CONUS and within ecoregions, which we interpret as a response of these physical habitat indices to anthropogenic influences. Although anthropogenic activities negatively influenced all three physical habitat indices in the least-disturbed sites within most ecoregions, natural geoclimatic and geomorphic factors were the dominant influences. For sites over the full range of anthropogenic disturbance, analyses of observed/expected sediment characteristics showed augmented flood flows and basin and riparian agriculture to be the leading predictors of streambed instability and excess fine sediments. Similarly, basin and riparian agriculture and non-agricultural riparian land uses were the leading predictors of reduced riparian vegetation cover complexity in the CONUS and within ecoregions. In turn, these reductions in riparian vegetation cover and complexity, combined with reduced summer low flows, were the leading predictors of instream habitat simplification. We conclude that quantitative measures of physical habitat structure are useful and important indicators of the impacts of human activities on stream and river condition.

Physical habitat in conterminous US streams and Rivers, part 2: A quantitative assessment of habitat condition.

Rigorous assessments of the ecological condition of water resources and the effect of human activities on those waters require quantitative physical, chemical, and biological data. The U.S. Environmental Protection Agency's river and stream surveys quantify river and stream bed particle size and stability, instream habitat complexity and cover, riparian vegetation cover and structure, and anthropogenic disturbance activities. Physical habitat is strongly controlled by natural geoclimatic factors that co-vary with human activities. We expressed the anthropogenic alteration of physical habitat as O/E ratios of observed habitat metric values divided by values expected under least-disturbed reference conditions, where site-specific expected values vary given their geoclimatic and geomorphic context. We set criteria for good, fair, and poor condition based on the distribution of O/E values in regional least-disturbed reference sites. Poor conditions existed in 22-24% of the 1.2 million km of streams and rivers in the conterminous U.S. for riparian human disturbance, streambed sediment and riparian vegetation cover, versus 14% for instream habitat complexity. Based on the same four indicators, the percentage of stream length in poor condition within 9 separate U.S. ecoregions ranged from 4% to 42%. Associations of our physical habitat indices with anthropogenic pressures demonstrate the scope of anthropogenic habitat alteration; habitat condition was negatively related to the level of anthropogenic disturbance nationally and in nearly all ecoregions. Relative risk estimates showed that streams and rivers with poor sediment, riparian cover complexity, or instream habitat cover conditions were 1.4 to 2.6 times as likely to also have fish or macroinvertebrate assemblages in poor condition. Our physical habitat condition indicators help explain deviations in biological conditions from those observed among least-disturbed sites and inform management actions for rehabilitating impaired waters and mitigating further ecological degradation.

Sediment transport, turbidity, and dissolved oxygen responses to annual streambed drawdowns for downstream fish passage in a flood control reservoir.

Sediment transport, turbidity, and dissolved oxygen were evaluated during six consecutive water years (2013-2018) of drawdowns of a flood control reservoir in the upper Willamette Valley, Oregon, USA. The drawdowns were conducted to allow volitional passage of endangered juvenile chinook salmon through the dam's regulating outlets by lowering the reservoir elevation to a point where the historical streambed was exposed and transported water and sediment through the reservoir dam. Sediment loads during the drawdown were highest in the first year of monitoring, with a computed value of 40,200 metric tons over a 5-day drawdown, followed by 5 years of lower sediment loads and lower sediment transport rates, suggesting that much of the stored sediment within the reservoir thalweg was transported out of the reservoir in the early years of the consecutive drawdowns. Suspended sediment concentrations (SSC) computed using turbidity and streamflow data resulted in maximum SSC at the onset of the drawdowns, with the highest computed values occurring during the water year 2017 drawdown at 17,500 mg/L (turbidity = 2,990 FNU), and average drawdown SSC values ranging from 654 to 3,950 mg/L for the six years of monitoring. Computed SSC were on the lower range of concentrations that could be harmful to out-migrating juvenile salmon published in other studies. High amounts of particulate organic matter and sand-sized material in drawdown SSC samples affected relations between turbidity and SSC, requiring the use of multiple surrogate regression models over short time frames. Dissolved oxygen minimum values were recorded in two of the monitoring years, with a minimum value of 0.71 and 3.4 mg/L recorded at the onset of the drawdowns in water years 2016 and 2018, respectively. Dissolved oxygen values below 4 mg/L lasted for 1 h, suggesting a rapidly expressed chemical oxygen demand. The response of suspended sediment loads and SSC highlight the site-specific nature of reservoir drawdowns, and the need for evaluation of expected sediment responses for drawdowns being considered at other locations.

Comparing biotic drivers of litter breakdown across stream compartments.

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.

Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments.

Wastewater discharges introduce antibiotic residues and antibiotic-resistant bacteria (ARB) into surface waters. Both inputs directly affect the streambed resistome, either by exerting a selective pressure that favour the proliferation of resistant phenotypes or by enriching the resident communities with wastewater-associated ARB. Here, we investigated the impact of raw and treated urban wastewater discharges on epilithic (growing on rocks) and epipsammic (growing on sandy substrata) streambed biofilms. The effects were assessed by comparing control and impact sites (i) on the composition of bacterial communities; (ii) on the abundance of twelve antibiotic resistance genes (ARGs) encoding resistance to ß-lactams, fluoroquinolones, sulphonamides, tetracyclines, macrolides and vancomycin, as well as the class 1 integron-integrase gene (intI1); (iii) on the occurrence of wastewater-associated bacteria, including putative pathogens, and their potential linkage to target ARGs. We measured more pronounced effects of raw sewage than treated wastewater at the three studied levels. This effect was especially noticeable in epilithic biofilms, which showed a higher contribution of wastewater-associated bacteria and ARB than in epipsammic biofilms. Comparison of correlation coefficients obtained between the relative abundance of both target ARGs and operational taxonomic units classified as either potential pathogens or nonpathogens yielded significant higher correlations between the former category and genes intI1, sul1, sul2 and ermB. Altogether, these results indicate that wastewater-associated micro-organisms, including potential pathogens, contribute to maintain the streambed resistome and that epilithic biofilms appear as sensitive biosensors of the effect of wastewater pollution in surface waters.

Stream network geomorphology mediates predicted vulnerability of anadromous fish habitat to hydrologic change in southeast Alaska.

In rivers supporting Pacific salmon in southeast Alaska, USA, regional trends toward a warmer, wetter climate are predicted to increase mid- and late-21st-century mean annual flood size by 17% and 28%, respectively. Increased flood size could alter stream habitats used by Pacific salmon for reproduction, with negative consequences for the substantial economic, cultural, and ecosystem services these fish provide. We combined field measurements and model simulations to estimate the potential influence of future flood disturbance on geomorphic processes controlling the quality and extent of coho, chum, and pink salmon spawning habitat in over 800 southeast Alaska watersheds. Spawning habitat responses varied widely across watersheds and among salmon species. Little variation among watersheds in potential spawning habitat change was explained by predicted increases in mean annual flood size. Watershed response diversity was mediated primarily by topographic controls on stream channel confinement, reach-scale geomorphic associations with spawning habitat preferences, and complexity in the pace and mode of geomorphic channel responses to altered flood size. Potential spawning habitat loss was highest for coho salmon, which spawn over a wide range of geomorphic settings, including steeper, confined stream reaches that are more susceptible to streambed scour during high flows. We estimated that 9-10% and 13-16% of the spawning habitat for coho salmon could be lost by the 2040s and 2080s, respectively, with losses occurring primarily in confined, higher-gradient streams that provide only moderate-quality habitat. Estimated effects were lower for pink and chum salmon, which primarily spawn in unconfined floodplain streams. Our results illustrate the importance of accounting for valley and reach-scale geomorphic features in watershed assessments of climate vulnerability, especially in topographically complex regions. Failure to consider the geomorphic context of stream networks will hamper efforts to understand and mitigate the vulnerability of anadromous fish habitat to climate-induced hydrologic change.

Long-term monitoring of streambed sedimentation and scour in a dynamic stream based on streambed temperature time series.

This study presented the monitoring and quantification of streambed sedimentation and scour in a stream with dynamically changing streambed based on measured phase and amplitude of the diurnal signal of sediment temperature time series. With the applied method, changes in streambed elevation were estimated on a sub-daily scale with 2-h intervals without continuous maintenance of the measurement system, thus making both high temporal resolution and long-term monitoring of streambed elevations possible. Estimates of streambed elevation showed that during base flow conditions streambed elevation fluctuates by 2-3 cm. Following high stream stages, scouring of 2-5 cm can be observed even at areas with low stream flow and weak currents. Our results demonstrate that weather variability can induce significant changes in the stream water and consequently sediment temperatures influencing the diurnal temperature signal in such an extent that the sediment thickness between paired temperature sensors were overestimated by up to 8 cm. These observations have significant consequences on the design of vertical sensor spacing in high-flux environments and in climates with reduced diurnal variations in air temperature.

Enrichment of stream water with fecal indicator organisms during baseflow periods.

Fecal indicator organisms (FIOs) are generally believed to be present in surface waters due solely to direct deposition of feces or through transport in runoff. However, emerging evidence points toward hyporheic exchange between sediment pore water and the overlying water column during baseflow periods as a source of FIOs is surface waters. The objective of this work was to (a) propose a mass balance-based technique for estimating changes of FIO concentrations in the same volume of water (or "slug") from the inlet to outlet of stream reaches in baseflow conditions and (b) to use such enumeration to estimate rate of the FIO release to stream water column. Concentrations of Escherichia coli (E. coli) and enterococci were measured in the slug while simultaneously monitoring the movement of a conservative tracer, Br that labeled the slug. Concentrations of E. coli in the slug were significantly larger (P = 0.035, P = 0.001, and P = 0.001, respectively) at the outlet reach in all three replications, while enterococci concentrations were significantly larger in two of three replications (P = 0.001, P < 0.001, and P = 0.602). When estimated without accounting for die-off in water column, FIO net release rates across replications ranged from 36 to 57 cells m-2 s-1 and 43 to 87 cells m-2 s-1 for E. coli and enterococci, respectively. These release rates were 5 to 20% higher when the die-off in water column was taken into account. No diurnal trends were observed in indicator concentrations. No FIO sources other than bottom sediment have been observed during the baseflow period. FIOs are released into stream water column through hyporheic exchange during baseflow periods.

Impact of trace metals from past mining on the aquatic ecosystem: a multi-proxy approach in the Morvan (France).

This study seeks to determine to what extent trace metals resulting from past mining activities are transferred to the aquatic ecosystem, and whether such trace metals still exert deleterious effects on biota. Concentrations of Cd, Cu, Pb and Zn were measured in streambed sediments, transplanted bryophytes and wild brown trout. This study was conducted at two scales: (i) the entire Morvan Regional Nature Park and (ii) three small watersheds selected for their degree of contamination, based on the presence or absence of past mining sites. The overall quality of streambed sediments was assessed using Sediment Quality Indices (SQIs). According to these standard guidelines, more than 96% of the sediments sampled should not represent a threat to biota. Nonetheless, in watersheds where past mining occurred, SQIs are significantly lower. Transplanted bryophytes at these sites consistently present higher trace metal concentrations. For wild brown trout, the scaled mass and liver indices appear to be negatively correlated with liver Pb concentrations, but there are no obvious relationships between past mining and liver metal concentrations or the developmental instability of specimens. Although the impact of past mining and metallurgical works is apparently not as strong as that usually observed in modern mining sites, it is still traceable. For this reason, past mining sites should be monitored, particularly in protected areas erroneously thought to be free of anthropogenic contamination.

Light over mechanics: microbial community structure and activity in simulated migrating bedforms are controlled by oscillating light rather than by mechanical forces.

Sandy sediments of lowland streams are transported as migrating ripples. Benthic microorganisms colonizing sandy grains are exposed to frequent moving-resting cycles and are believed to be shaped by two dominant environmental factors: mechanical stress during the moving phase causing biofilm abrasion, and alternating light-dark cycles during the resting phase. Our study consisted of two laboratory experiments and aimed to decipher which environmental factor causes the previously observed hampered sediment-associated microbial activity and altered community structure during ripple migration. The first experiment tested the effect of three different migration velocities under comparable light conditions. The second experiment compared migrating and stationary sediments under either constant light exposure or light oscillation. We hypothesized that microbial activity and community structure would be more strongly affected by (1) higher compared to lower migration velocities, and by (2) light oscillation compared to mechanical stress. Combining the results from both experiments, we observed lower microbial activity and an altered community structure in sediments exposed to light oscillation, whereas migration velocity had less impact on community activity and structure. Our findings indicate that light oscillation is the predominating environmental factor acting during ripple migration, resulting in an increased vulnerability of light-dependent photoautotrophs and a possible shift toward heterotrophy.

Streambed immobilization controls the transport of antibiotic resistance genes in flowing water.

Antibiotic resistance is a serious global health issue, resulting in at least 1.2 million deaths in 2019. The environment is a potentially important reservoir of antibiotic resistance; however, the fate of Antibiotic Resistance Genes (ARGs) in the environment remains poorly characterized. One important environmental source of ARGs is manure used as a soil amendment. ARGs from manure may then enter nearby flowing waterbodies, where the factors governing their downstream transport remain unknown. To address this, we conducted experiments by spiking cattle manure in an artificial stream to estimate removal rates (k; m-1) for three ARGs (mefA, tetQ, and tetW) and a ruminant fecal marker (bacR). We then used a Stochastic Mobile-Immobile Model (SMIM) to separate the overall removal into two components, rs, and rh, corresponding to immobilizations in the surface (i.e., water column) and subsurface (i.e., streambed), respectively. Finally, we applied the SMIM across four model streams to predict the downstream travel distance of ARGs and bacR. Our results showed measurable removal for all targets in all experimental replicates (n = 3) and no differences were found in the removal rates among replicates for any target (ANCOVA; p > 0.05). We found that the removal of bacR was significantly lower than tetW (p < 0.05) and slightly lower than mefA (p = 0.088), while tetQ removal was slightly different from tetW's (p = 0.072). We also found that rh values were orders of magnitude larger than rs for ARGs and bacR (t-test; p < 0.05). These findings suggest that ARGs and bacR are being removed from the water column through immobilization reactions occurring in the streambed. Additionally, we predicted that the 90 % removal (or D90) of targets occurs within the first 500 m in all model streams except in a slow-flow pastoral stream, which required 1400 m of downstream transport for 90 % removal. Our findings and model stand out as promising tools to predict the fate of ARGs in streams and will contribute to improving and managing agricultural practices that employ animal manure.

Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities.

Freshwater ecosystems are characterised by the co-occurrence of stressors that simultaneously affect the biota. Among these, flow intermittency and chemical pollution severely impair the diversity and functioning of streambed bacterial communities. Using an artificial streams mesocosm facility, this study examined how desiccation and pollution caused by emerging contaminants affect the composition of stream biofilm bacterial communities, their metabolic profiles, and interactions with their environment. Through an integrative analysis of the composition of biofilm communities, characterization of their metabolome and composition of the dissolved organic matter, we found strong genotype-to-phenotype interconnections. The strongest correlation was found between the composition and metabolism of the bacterial community, both of which were influenced by incubation time and desiccation. Unexpectedly, no effect of the emerging contaminants was observed, which was due to the low concentration of the emerging contaminants and the dominant impact of desiccation. However, biofilm bacterial communities modified the chemical composition of their environment under the effect of pollution. Considering the tentatively identified classes of metabolites, we hypothesised that the biofilm response to desiccation was mainly intracellular while the response to chemical pollution was extracellular. The present study demonstrates that metabolite and dissolved organic matter profiling may be effectively integrated with compositional analysis of stream biofilm communities to yield a more complete picture of changes in response to stressors.

Effects of a point source of phosphorus on the arsenic mobility and transport in a small fluvial system.

One of the leading causes of As release from streambed sediments into freshwater systems is competition with phosphate. Among important sources of P to the fluvial ecosystems are wastewater treatment plants (WWTP), estimated to account for 25-45% of all P in surface waters. In this paper, long-term effects of discharged phosphorus from a small WWTP on the arsenic mobility were studied in an As-enriched fluvial system (approx. 240 mg/kg) in central Czech Republic. After 7 years of elevated P (≤7.7 mg/L) in the stream water, the total As decreased by 25% and the total P increased by 40% in the sediments downstream (at a distance of 66 m). The results of the chemical extractions and mineralogical analyses indicated that the changes in the concentration were mostly due to the sorption processes in the Fe (oxyhydr)oxides (goethite and hematite). In the downstream samples, the As in these phases decreased two-fold, and P was significantly enriched by 45-140%. Phosphorus was also found precipitated as newly formed Ca phosphates. The stream water monitoring indicated that the discharged P was either sequestered when the levels of dissolved P were high (>2.3 mg/L) or released from the downstream sediments when these levels were low (<∼1.5 mg/L). Meanwhile, As was continuously mobilized from the downstream sediments likely due to (i) the ongoing As desorption from the exterior parts of the Fe (oxyhydr)oxides at high aqueous P levels and (ii) the dissolution of As-bearing Ca phosphates at low dissolved P levels. These findings clearly demonstrate that point sources of P to streams and rivers, such as WWTP, may result in the permanent and long-term release of As from contaminated streambed sediments.

Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange.

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.

Streambed pollution: A comprehensive review of its sources, eco-hydro-geo-chemical impacts, assessment, and mitigation strategies.

Streambeds are an integral part of the river ecosystem. They provide habitat to a vast array of aquatic and benthic organisms as well as facilitate the bio-degradation and transformation of organic matter and vital nutrients. Increasing anthropogenic influence introduces multiple stressors to the stream networks resulting in pollution of streambeds, which in turn, have detrimental effects on the overall stream ecosystem health. There is a huge gap in the current understanding of streambed pollution and its impacts, and the widely practiced streambed pollution mitigation strategies lack a holistic approach. In this comprehensive review, we first synthesize the state-of-the-art knowledge of conventional and emerging forms of contaminants, their overall impacts on stream ecosystem functions, and present future directions to comprehend the problem of streambed pollution. We highlight that fine sediments and plastics (found especially in urban streambeds) are among the major physical pollutants causing streambed pollution and the chemical pollutants generally comprise hydrophobic compounds including various legacy contaminants such as polychlorinated biphenyl (PCB), dichlorodiphenyltrichloroethane (DDT), a wide range of pesticides and a variety of heavy metals. Moreover, in recent years, highly polar and hydrophilic emerging contaminants such as micro-plastics, pharmaceutical waste and personal care products have been identified in riverbeds and streambeds across the world. We stress that the impacts of streambed pollution have been largely studied with discipline-driven perspectives amongst which the ecological impacts have received a lot of attention in the past. To present a comprehensive outlook, this review also synthesizes and discusses most of the understudied hydrological, geomorphological and biochemical impacts of different forms of streambed pollution. Subsequently, we also present a global inventory by compiling information from the published literature to highlight the status of streambed pollution around the globe. In the end, we endorse the positive and negative aspects of the current impact assessment methodologies and also highlight various physical, chemical and biological remediation measures that could be undertaken to alleviate streambed pollution.

Characterizing bioavailable phosphorus concentrations in an agricultural stream during hydrologic and streambed disturbances.

In freshwater ecosystems, phosphorus (P) is often considered a growth-limiting nutrient. The use of fertilizers on agricultural fields has led to runoff-driven increases in P availability in streams, and the subsequent eutrophication of downstream ecosystems. Isolated storms and periodic streambed dredging are examples of two common disturbances that contribute dissolved and particulate P to agricultural streams, which can be quantified as soluble reactive P (SRP) using the molybdate-blue method on filtered water samples, or total P (TP) measured using digestions on unfiltered water reflecting all forms of P. While SRP is often considered an approximation of bioavailable P (BAP), research has shown that this is not always the case. Current methods used to estimate BAP do not account for the role of biology (e.g., NaOH extractions) or require specialized platforms (e.g., algal bioassays). Here, in addition to routine analysis of SRP and TP, we used a novel yeast-based bioassay with unfiltered sample water to estimate BAP concentrations during two storms (top 80% and > 95% flow quantiles), and downstream of a reach where management-associated dredging disturbed the streambed. We found that the BAP concentrations were often greater than SRP, suggesting that SRP is not fully representative of P bioavailability. The SRP concentrations were similarly elevated during the two storms, but remained consistently low during streambed disturbance. In contrast, turbidity and TP were elevated during all events. The BAP concentrations were significantly related to turbidity during all disturbance events, but with TP only during storms. The novel yeast assay suggests that BAP export can exceed SRP, particularly when streams are not in equilibrium, such as the rising limb of storms or during active dredging.

Time-series temperature analyses indicate conduction and diffusion are dominant heat-transfer processes in fine sediment, low-flow streams.

Stream-groundwater exchange has been investigated in a wide range of hydrologic settings, though very few studies have focused on fine-sediment streambeds. Well-established thermal methods (i.e., analytical and numerical solution of time-series temperature depth-profiles) in combination with Darcy's and electrical resistivity (ER) evaluations were implemented to improve understanding of processes dominating flow and transport in a low permeability and low-flow coastal stream such as Oso Creek, Texas. The seasonal-trend decomposition using Loess (STL) is tested as a potential means to differentiate between advection and conduction and is validated against groundwater fluxes derived from the other well-established thermal methods. The numerical and analytical solutions indicate groundwater upward discharge was 9 mm d-1 for summer and 3.5 mm d-1 for winter, corresponding to the region's extreme drought conditions. These types of low flow conditions are usually accompanied by hyporheic flow, limiting the vertical flow assumption. While the numerical and analytical methods provide good insight into streambed hydrology for a low-permeability and low-flow stream in a semiarid coastal area, there are limitations associated with the STL method. The analytical and numerical thermal methods employed herein confirm that conduction and diffusion are the dominant processes of heat and solute transfer in fine-sediment streambeds, providing an improved understanding of process-based groundwater-stream interaction and water resources in this type of settings.

Agricultural land use changes stream dissolved organic matter via altering soil inputs to streams.

Agricultural land use leads to significant changes in both the quality (e.g., sources and compositions) and quantity of dissolved organic matter (DOM) exported from terrestrial to aquatic ecosystems. However, the effect of agricultural activities often interacts with those of hydroclimatic drivers, making it difficult to delineate agriculture-induced changes and identify associated mechanisms. Using partial least square path modeling (PLS-PM), we examined the relative importance of agricultural land use, stream order, precipitation, and temperature in mediating allochthonous versus autochthonous sources and pathways that influenced stream DOM quality and quantity. We analyzed stream water DOM from 15 small streams draining watersheds across a gradient of agricultural land use in Southeast USA for about one year. For DOM quantity, agricultural land use increased the export of DOC and various DOM pools (terrestrial humic, microbial humic, and protein-like DOM) from land to streams, and for DOM quality, agricultural streams showed greater proportions of microbial humic compounds than forested streams. The PLS-PM model for DOM quantity accounted for 75.5% of total variance and identified that agricultural land use increased stream water DOM quantity primarily through increasing allochthonous inputs, which can be attributed to shallower flow paths in agricultural watersheds that enabled the export of organic materials from the upper, organic-rich soil horizon. PLS-PM models for DOM quality only explained ~13% of the total variance, highlighting the complex dynamics between environmental drivers and stream water DOM. Relative to commonly used multivariate statistic modeling (e.g., redundancy analysis (RDA)), PLS-PM models offer the advantages of identifying the primary pathway by which agricultural lands alter freshwater DOM and quantifying the relative importance of interactive effects of agriculture and hydroclimatic drivers. Therefore, structural equation modeling is a powerful tool that should be more widely adopted to distinguish among multiple drivers and mechanisms regulating freshwater biogeochemistry.