Pluri-annual sediment budget in a navigated river system: the Seine River (France)

Reduction of large vessel traffic improves water quality and alters fish habitat-use throughout a large river

Rivers are increasingly used as superhighways for the continental-scale transportation of freight goods, but the ecological impact of large vessel traffic on river ecosystems is difficult to study. Recently, the temporary maintenance closure of lock and dam systems on the Illinois Waterway (USA) brought commercial vessel traffic to a halt along the river's length, offering a rare opportunity to study the response of the ecosystem before, during, and after an extended pause of this persistent anthropogenic disturbance. We observed improvements in main- and side-channel water quality and a redistribution of fish habitat-use during a months-long, near-complete reduction of large vessel traffic. Over 3600 water quality and 1300 fish community samples indicate that large vessel traffic reduction coincided with a 33 % reduction in turbidity as well as increased use of sampling strata near vessel navigation corridors by sound-sensitive and rheophilic fishes. Gizzard shad (Dorosoma cepedianum), the most abundant species in the system, also expanded their use of these 'impact' areas. Though inland waterway transport is an economically- and climate-friendly alternative to trucking and rail for the shipment of freight, our data suggest that intense vessel traffic may have profound physical and biological impacts across a large river. Monitoring and mitigation of ecological impacts of the ongoing expansion of inland waterway transport around the world will be critical to balancing large rivers as both useful navigation corridors and functional ecosystems.

Data assimilation in surface water quality modeling: A review

Data assimilation (DA) techniques are powerful means of dynamic natural system modeling that allow for the use of data as soon as it appears to improve model predictions and reduce prediction uncertainty by correcting state variables, model parameters, and boundary and initial conditions. The objectives of this review are to explore existing approaches and advances in DA applications for surface water quality modeling and to identify future research prospects. We first reviewed the DA methods used in water quality modeling as reported in literature. We then addressed observations and suggestions regarding various factors of DA performance, such as the mismatch between both lateral and vertical spatial detail of measurements and modeling, subgrid heterogeneity, presence of temporally stable spatial patterns in water quality parameters and related biases, evaluation of uncertainty in data and modeling results, mismatch between scales and schedules of data from multiple sources, selection of parameters to be updated along with state variables, update frequency and forecast skill. The review concludes with the outlook section that outlines current challenges and opportunities related to growing role of novel data sources, scale mismatch between model discretization and observation, structural uncertainty of models and conversion of measured to simulated vales, experimentation with DA prior to applications, using DA performance or model selection, the role of sensitivity analysis, and the expanding use of DA in water quality management.

River Basin Visions: Tools and Approaches from Yesterday to Tomorrow

The aim of this chapter is to provide a critical assessment of the approaches and production of tools within the PIREN-Seine programme over the past 30 years, as well as their use for river basin management and river quality improvement, and to analyse the challenges for the future. Three types of tools used in the PIREN-Seine programme are presented: metrology and fieldwork; model construction, simulation and their use in scenarios; and participatory science tools. These tools have been gradually built by the PIREN-Seine researchers and often developed together with the partners of the research programme, the main managers of the Seine River basin. Three issues raised by scientists and their partners are identified: (1) for metrology, how it has been improved to measure the state of waterbodies and to avoid their degradation; (2) for models, what they currently do and do not do and how they share common knowledge with practitioners; and (3) the place of researchers in the use of participatory devices in territories and their view of the effects of these tools to improve the quality of rivers and aquifers.

Ecological Functioning of the Seine River: From Long-Term Modelling Approaches to High-Frequency Data Analysis

At the start of the PIREN-Seine program, organic pollution by the effluent of the Parisian conurbation was responsible for episodic anoxia in the lower Seine River, while nutrients from both point and diffuse sources are used to cause eutrophication, a nuisance for drinking water production from surface water and biodiversity. The implementation of the EU Water Framework Directive led to a drastic decrease of organic carbon, phosphorus and ammonium concentrations in surface waters starting in the early 2000s and to a reduction of the frequency and the amplitude of phytoplankton blooms. However, nitrate contamination from fertiliser-intensive agriculture continued to increase or at best levelled off, threatening groundwater resources and causing unbalanced nutrient ratios at the coastal zone where eutrophication still results in harmful algal blooms. High-frequency O2 data combined with models, which have been developed for 30 years, can help discriminate the contribution of auto- vs. heterotrophic metabolism in the CO2 supersaturation observed in the Seine River. Despite the impressive improvement in water quality of the Seine River, episodic crises such as summer low-flow conditions still threaten the good ecological status of both river and coastal waters. Modelling scenarios, including further wastewater treatments and structural changes in agriculture and future changes in hydrology under climate changes, provide the basis for a future vision of the ecological functioning of the Seine River network.

Trajectories of the Seine River Basin

The Seine River basin in France (76,238 km2, 17 million (M) people) has been continuously studied since 1989 by the PIREN-Seine, a multidisciplinary programme of about 100 scientists from 20 research units (hydrologists, environmental chemists, ecologists, biogeochemists, geographers, environmental historians). Initially PIREN-Seine was established to fill the knowledge gap on the river functioning, particularly downstream of the Paris conurbation (12 M people), where the pressure and impacts were at their highest in the 1980s (e.g. chronic summer hypoxia). One aim was to provide tools, such as models, to manage water resources and improve the state of the river. PIREN-Seine gradually developed into a general understanding and whole-basin modelling, from headwater streams to the estuary, of the complex interactions between the hydrosystem (surface water and aquifers), the ecosystem (phytoplankton, bacteria, fish communities), the agronomic system (crops and soils), the river users (drinking water, navigation), and the urban and industrial development (e.g. waste water treatment plants). Spatio-temporal scales of these interactions and the related state of the environment vary from the very fine (hour-meter) to the coarser scale (annual – several dozen km). It was possible to determine the trajectories (drivers-pressures – state-responses) for many issues, over the longue durée time windows (50–200 years), in relation to the specific economic and demographic evolution of the Seine basin, the environmental awareness, and the national and then European regulations. Time trajectories of the major environmental issues, from the original organic and microbial pollutants in the past to the present emerging contaminants, are addressed. Future trajectories are simulated by our interconnected modelling approaches, based on scenarios (e.g. of the agro-food system, climate change, demography, etc.) constructed by scientists and engineers of major basin institutions that have been supporting the programme in the long term. We found many cumulated and/or permanent hereditary effects on the physical, chemical, and ecological characteristics of the basin that may constrain its evolution. PIREN-Seine was launched and has been evaluated since its inception, by the National Centre for Scientific Research (CNRS), today within its national Zones Ateliers (ZA) instrument, part of the international Long-Term Socio-Economic and Ecosystem Research (LTSER) network.

Oxygen data assimilation for estimating micro-organism communities' parameters in river systems

The coupling of high frequency data of water quality with physically based models of river systems is of great interest for the management of urban socio-ecosystems. One approach to exploit high frequency data is data assimilation which has received an increasing attention in the field of hydrology, but not for water quality modeling so far. We present here a first implementation of a particle filtering algorithm into a community-centered hydro-biogeochemical model to assimilate high frequency dissolved oxygen data and to estimate metabolism parameters in the Seine River system. The procedure is designed based on the results of a former sensitivity analysis of the model (Wang et al., 2018) that allows for the identification of the twelve most sensible parameters all over the year. Those parameters are both physical and related to micro-organisms (reaeration coefficient, photosynthetic parameters, growth rates, respiration rates and optimal temperature). The performances of the approach are assessed on a synthetic case study that mimics 66 km of the Seine River. Virtual dissolved oxygen data are generated using time varying parameters. This paper aims at retrieving the predefined parameters by assimilating those data. The simulated dissolved oxygen concentrations match the reference concentrations. The identification of the parameters depends on the hydrological and trophic contexts and more surprisingly on the thermal state of the river. The physical, bacterial and phytoplanktonic parameters can be retrieved properly, leading to the differentiation of two successive algal blooms by comparing the estimated posterior distribution of the optimal temperature for phytoplankton growth. Finally, photosynthetic parameters' distributions following circadian cycles during algal blooms are discussed.

Carbon dioxide, methane and nitrous oxide emissions from the human-impacted Seine watershed in France

Greenhouse gas (GHG) emissions from rivers and lakes have been shown to contribute significantly to global carbon and nitrogen cycling. In temperate and human-impacted regions, simultaneous carbon dioxide, methane and nitrous oxide emissions from aquatic systems are poorly documented. We estimated carbon dioxide (CO₂) concentrations in the Seine hydrosystem (71,730 km², France) using direct measurements, and calculations of CO₂ partial pressures from 14 field campaigns conducted between 2010 and 2017, and compared them to methane (CH₄) and nitrous oxide (N₂O) concentrations. In the main stem of the Seine River, CO₂ showed the same spatial gradient as N₂O and CH₄ with peaks in concentration downstream from the arrival of effluents from wastewater treatment plants enriched in organic matter, thus favoring mineralization. It is likely that high CO₂ concentrations upstream were due to organic carbon inputs from soils and enriched CO₂ groundwater discharges, whereas high N₂O and CH₄ upstream values were likely due to denitrification in riparian wet areas and anoxic decomposition of organic matter-rich wetlands, respectively. In addition, seasonal variations in all three GHGs were observed with higher concentrations in summer when higher temperatures promote mineralization and low water reduces the dilution of organic matter mainly originating from WWTP effluents. GHG emissions were calculated and compared with agricultural and nonagricultural (urban, transport) fluxes in the basin. In the Seine River network, CO₂ emissions dominated riverine GHG emissions, reaching 95.3%, while N₂O and CH₄ emissions accounted for 4.4% and 0.3%, respectively. These indirect emissions from the hydrosystem were estimated to account for 3.7% of the total GHG emissions from the basin that amounted to 61,284 Gg CO₂eq yr^-1. Comparatively, direct agricultural and nonagricultural GHG emissions were estimated at 23.3% and 73.0%., respectively.

Time-dependent global sensitivity analysis of the C-RIVE biogeochemical model in contrasted hydrological and trophic contexts

Dissolved oxygen within water column is a key variable to characterize the water quality. Water quality modeling has been extensively developed for decades. However, complex biogeochemical cycles are described using a high number of parameters. Hence, parameters' uncertainty constitutes a major problem in the application of these models. Sensitivity analysis allows the identification of the most influential parameters in a model and a better understanding of the governing processes. This paper presents a time-dependent sensitivity analysis for dissolved oxygen using Morris and Sobol methods combined with a functional principal components analysis for dimension reduction. The aim of this study is to identify the most important parameters of C-RIVE model in different trophic contexts and to understand the biogeochemical functioning of river systems. The results indicate that the maintenance respiration of phytoplankton and the photosynthetic parameters (i.e. photosynthetic capacity, the maximal photosynthesis rate and light extinction coefficients) are the most influential parameters during algal blooms. When the river system becomes heterotrophic, the bacterial activities (moderate and high temperature) and the reaeration coefficients (low temperature) affect the most the dissolved oxygen concentration in the water column. An anthropogenic effect (ship navigation) on variation of dissolved oxygen concentration has been identified and the role of this anthropogenic effect evolves with hydrological and trophic conditions.

Estimating ecosystem metabolism from continuous multi-sensor measurements in the Seine River

Large rivers are important components of the global C cycle. While they are facing an overall degradation of their water quality, little remains known about the dynamics of their metabolism. In the present study, we used continuous multi-sensors measurements to assess the temporal variability of gross primary production (GPP) and ecosystem respiration (ER) rates of the anthropized Seine River over an annual cycle. Downstream from the Paris urban area, the Seine River is net heterotrophic at the annual scale (-226 gO₂ m^-2 year^-1 or -264 gC m^-2 year^-1). Yet, it displays a net autotrophy at the daily and seasonal scales during phytoplankton blooms occurring from late winter to early summer. Multivariate analyses were performed to identify the drivers of river metabolism. Daily GPP is best predicted by chlorophyll a (Chla), water temperature (T), light, and rainfalls, and the coupling of daily GPP and Chla allows for the estimation of the productivity rates of the different phytoplankton communities. ER rates are mainly controlled by T and, to a lesser extent, by Chla. The increase of combined sewer overflows related to storm events during the second half of the year stimulates ER and the net heterotrophy of the river. River metabolism is, thus, controlled at different timescales by factors that are affected by human pressures. Continuous monitoring of river metabolism must, therefore, be pursued to deepen our understanding about the responses of ecosystem processes to changing human pressures and climate.

Estimation of the water quality of a large urbanized river as defined by the European WFD: what is the optimal sampling frequency?

Assessment of the quality of freshwater bodies is essential to determine the impact of human activities on water resources. The water quality status is estimated by comparing indicators with standard thresholds. Indicators are usually statistical criteria that are calculated on discrete measurements of water quality variables. If the time step of the measured time series is not sufficient to fully capture the variable's variability, the deduced indicator may not reflect the system's functioning. The goal of the present work is to assess, through a hydro-biogeochemical modeling approach, the optimal sampling frequency for an accurate estimation of 6 water quality indicators defined by the European Water Framework Directive (WFD) in a large human-impacted river, which receives large urban effluents (the Seine River across the Paris urban area). The optimal frequency depends on the sampling location and on the monitored variable. For fast varying compounds that originate from urban effluents, such as PO[Formula: see text], NH[Formula: see text] and NO[Formula: see text], a sampling time step of one week or less is necessary. To be able to reflect the highly transient character of bloom events, chl a concentrations also require a short monitoring time step. On the contrary, for variables that exert high seasonal variability, as NO[Formula: see text] and O ₂, monthly sampling can be sufficient for an accurate estimation of WFD indicators in locations far enough from major effluents. Integrative water quality variables, such as O ₂, can be highly sensitive to hydrological conditions. It would therefore be relevant to assess the quality of water bodies at a seasonal scale rather than at annual or pluri-annual scales. This study points out the possibility to develop smarter monitoring systems by coupling both time adaptative automated monitoring networks and modeling tools used as spatio-temporal interpolators.

Synthetic and non-synthetic anthropogenic fibers in a river under the impact of Paris Megacity: Sampling methodological aspects and flux estimations

Processed fibers are highly present in our daily life and can be either natural, artificial (regenerated cellulose) and synthetic (made with petrochemicals). Their widespread use lead inevitably to a high contamination of environment. Previous studies focus on plastic particles regardless of their type or shape as long as they are comprised between 330μm and 5mm. On the contrary, this study focuses exclusively on fibers using a smaller mesh size net (80μm) to sample freshwater. Moreover, all processed organic fibers are considered, irrespective to their nature. First, the short term temporal variability of the fibers in the environment was assessed. While exposing the sampling net during 1min a coefficient of variation of approx. 45% (with n=6) was determined. It was of only 26% (n=6) when the exposure was of 3min. The assessment of the distribution through the section showed a possible difference in concentrations between the middle of the water surface and the river banks which could be attributed to the intense river traffic within the Paris Megacity. The vertical variability seems negligible as turbulence and current conditions homogenize the distribution of the fibers. A monthly monitoring showed concentrations of 100.6±99.9fibers·m^-3 in the Marne River and of: 48.5±98.5, 27.9±26.3, 27.9±40.3 and 22.1±25.3fibers·m^-3 from the upstream to downstream points in the Seine River. Once these concentrations are converted into fluxes, it seems that the impact generated by the Paris Megacity cannot be distinguished. Investigations on the role of sedimentation and deposition on the banks are required. This study helped fill some major knowledge gaps regarding the fibers in rivers, their sampling, occurrence, spatial-temporal distribution and fluxes. It is encouraged that future studies include both synthetic and none synthetic fibers.

Effects of ship-induced waves on aquatic ecosystems

Most larger water bodies worldwide are used for navigation, and the intensity of commercial and recreational navigation is expected to further increase. Navigation profoundly affects aquatic ecosystems. To facilitate navigation, rivers are trained and developed, and the direct effects of navigation include chemical and biological impacts (e.g., inputs of toxic substances and dispersal of non-native species, respectively). Furthermore, propagating ships create hydrodynamic alterations, often simply summarized as waves. Although ship-induced waves are recognized as influential stressors, knowledge on their effects is poorly synthesized. We present here a review on the effects of ship-induced waves on the structure, function and services of aquatic ecosystems based on more than 200 peer reviewed publications and technical reports. Ship-induced waves act at multiple organizational levels and different spatial and temporal scales. All the abiotic and biotic components of aquatic ecosystems are affected, from the sediment and nutrient budget to the planktonic, benthic and fish communities. We highlight how the effects of ship-induced waves cascade through ecosystems and how different effects interact and feed back into the ecosystem finally leading to altered ecosystem services and human health effects. Based on this synthesis of wave effects, we discuss strategies for mitigation. This may help to develop scientifically based and target-oriented management plans for navigational waters that optimize abiotic and biotic integrity and their ecosystem services and uses.

The role of environmental land use conflicts in soil fertility: A study on the Uberaba River basin, Brazil

In the Uberaba River basin (state of Minas Gerais, Brazil), pastures for livestock production have invaded areas of native vegetation (Cerrado biome), while already existing pastures were invaded by crop agriculture, with an expansion of sugar cane plantations in the most recent years. In some areas of the basin, these land use changes were classified as environmental land use conflicts because the new uses were not conforming to land capability, i.e. the soil's natural use. Where the areas in conflict became dense, some soil properties have changed significantly, namely the organic matter content and the exchangeable potassium concentration, which have decreased drastically (5kg/m(3) per 10% increase in the conflict area) threatening the fertility of soil. Besides, these changes may have triggered a cascade of other environmental damages, specifically the increase of soil erosion and the degradation of water quality with negative impacts on aquatic biodiversity, related to a disruption of soil organic matter structural functions. Because half the Uberaba catchment has been considered is a state of accentuated environmental degradation, not only caused by environmental land use conflicts, conservation measures have been proposed and requested for immediate implementation across the watershed.

Modelling the fate of nitrite in an urbanized river using experimentally obtained nitrifier growth parameters

Maintaining low nitrite concentrations in aquatic systems is a major issue for stakeholders due to nitrite's high toxicity for living species. This study reports on a cost-effective and realistic approach to study nitrite dynamics and improve its modelling in human-impacted river systems. The implementation of different nitrifying biomasses to model riverine communities and waste water treatment plant (WWTP)-related communities enabled us to assess the impact of a major WWTP effluent on in-river nitrification dynamics. The optimal kinetic parameters and biomasses of the different nitrifying communities were determined and validated by coupling laboratory experiments and modelling. This approach was carried out in the Seine River, as an example of a large human-impacted river with high nitrite concentrations. The simulation of nitrite fate was performed at a high spatial and temporal resolution (Δt = 10 min, dx¯ = 500 m) including water and sediment layers along a 220 km stretch of the Seine River for a 6-year period (2007-2012). The model outputs were in good agreement with the peak of nitrite downstream the WWTP as well as its slow decrease towards the estuary. Nitrite persistence between the WWTP and the estuary was mostly explained by similar production and consumption rates of nitrite in both water and sediment layers. The sediment layer constituted a significant source of nitrite, especially during high river discharges (0.1-0.4 mgN h(-1) m(-2)). This points out how essential it is to represent the benthic layer in river water quality models, since it can constitute a source of nitrite to the water-column. As a consequence of anthropogenic emissions and in-river processes, nitrite fluxes to the estuary were significant and varied from 4.1 to 5.5 TN d(-1) in low and high water discharge conditions, respectively, over the 2007-2012 period. This study provides a methodology that can be applied to any anthropized river to realistically parametrize autochthonous and WWTP-related nitrifier communities and simulate nitrite dynamics. Based on simulation analysis, it is shown that high spatio-temporal resolution hydro-ecological models are efficient to 1) estimate water quality criteria and 2) forecast the effect of future management strategies. Process-based simulations constitute essential tools to complete our understanding of nutrient cycling, and to decrease monitoring costs in the context of water quality and eutrophication management in river ecosystems.