A deep learning-based novel approach to generate continuous daily stream nitrate concentration for nitrate data-sparse watersheds

Artificial Intelligence in Aquatic Biodiversity Research: A PRISMA-Based Systematic Review

Freshwater ecosystems are increasingly threatened by climate change and anthropogenic activities, necessitating innovative and scalable monitoring solutions. Artificial intelligence (AI) has emerged as a transformative tool in aquatic biodiversity research, enabling automated species identification, predictive habitat modeling, and conservation planning. This systematic review follows the PRISMA framework to analyze AI applications in freshwater biodiversity studies. Using a structured literature search across Scopus, Web of Science, and Google Scholar, we identified 312 relevant studies published between 2010 and 2024. This review categorizes AI applications into species identification, habitat assessment, ecological risk evaluation, and conservation strategies. A risk of bias assessment was conducted using QUADAS-2 and RoB 2 frameworks, highlighting methodological challenges, such as measurement bias and inconsistencies in the model validation. The citation trends demonstrate exponential growth in AI-driven biodiversity research, with leading contributions from China, the United States, and India. Despite the growing use of AI in this field, this review also reveals several persistent challenges, including limited data availability, regional imbalances, and concerns related to model generalizability and transparency. Our findings underscore AI's potential in revolutionizing biodiversity monitoring but also emphasize the need for standardized methodologies, improved data integration, and interdisciplinary collaboration to enhance ecological insights and conservation efforts.

Enhancing prediction and inference of daily in-stream nutrient and sediment concentrations using an extreme gradient boosting based water quality estimation tool - XGBest

Estimating constituent loads in streams and rivers is a crucial but challenging task due to low-frequency sampling in most watersheds. While predictive modeling can augment sparsely sampled water quality data, it can be challenging due to the complex and multifaceted interactions between several sub-watershed eco-hydrological processes. Traditional water quality prediction models, typically calibrated for individual sites, struggle to fully capture these interactions. This study introduces XGBest, a machine learning-based tool, that integrates hydrological data, land cover, and physical watershed attributes at a regional scale to predict daily concentrations of Total Nitrogen (TN), Total Phosphorus (TP), and Total Suspended Solids (TSS). XGBest leverages 29 environmental variables, including daily and antecedent discharge, temporal features, and landscape characteristics, to comprehensively evaluate water quality dynamics across a large hydrologic region. To explore the robustness of the developed tool, XGBest was validated using observed water quality data in three different hydrologic regions in the eastern United States, encompassing 499 water quality monitoring sites characterized by diverse hydro-climatic conditions and watershed attributes. This study also employed the legacy United States Geological Survey (USGS) tools - LOADEST and WRTDS as benchmarks to evaluate the performance of XGBest in these regions. The results demonstrated that XGBest outperformed LOADEST and WRTDS in predictive accuracy and revealed critical insights into the spatial and temporal variability of nutrient and sediment loads. In addition, SHapley Additive exPlanations (SHAP) values highlighted the importance of integrating static and dynamic watershed attributes, such as land cover, antecedent discharge, and seasonality, in capturing the complex concentration-discharge (C-Q) relationships. This study positions XGBest as a robust and scalable water quality prediction tool that bridges the gap between hydrology and broader environmental management. By combining multiple environmental factors into a unified predictive framework, XGBest enhances our understanding of water quality and supports more effective environmental monitoring and management strategies.

Explainable deep learning identifies patterns and drivers of freshwater harmful algal blooms

The escalating magnitude, frequency, and duration of harmful algal blooms (HABs) pose significant challenges to freshwater ecosystems worldwide. However, the mechanisms driving HABs remain poorly understood, in part due to the strong regional specificity of algal processes and the uneven data availability. These complexities make it difficult to generalize HAB dynamics and effectively predict their occurrence using traditional models. To address these challenges, we developed an explainable deep learning approach using long short-term memory (LSTM) models combined with explanation techniques that can capture complex patterns and provide explainable insights into key HAB drivers. We applied this approach for algal density modeling at 102 sites in China's lakes and reservoirs over three years. LSTMs effectively captured daily algal dynamics, achieving mean and maximum Nash-Sutcliffe efficiency coefficients of 0.48 and 0.95 during testing phase. Moreover, water temperature emerged as the primary driver of HABs both nationally and in over 30% of localities, with stronger water temperature sensitivity observed in mid-to low-latitudes. We also identified regional similarities that allow for the successful transferability in modeling algal dynamics. Specifically, using fine-tuned transfer learning, we improved the prediction accuracy in over 75% of poorly gauged areas. Overall, LSTM-based explainable deep learning approach effectively addresses key challenges in HAB modeling by tackling both regional specificity and data limitations. By accurately predicting algal dynamics and identifying critical drivers, this approach provides actionable insights into the mechanisms of HABs, ultimately aids in the implementation of effective mitigation measures for nationwide and regional freshwater ecosystems.

A hybrid deep learning approach to predict hourly riverine nitrate concentrations using routine monitored data

With high-frequency data of nitrate (NO3-N) concentrations in waters becoming increasingly important for understanding of watershed system behaviors and ecosystem managements, the accurate and economic acquisition of high-frequency NO3-N concentration data has become a key point. This study attempted to use coupled deep learning neural networks and routine monitored data to predict hourly NO3-N concentrations in a river. The hourly NO3-N concentration at the outlet of the Oyster River watershed in New Hampshire, USA, was predicted through neural networks with a hybrid model architecture coupling the Convolutional Neural Networks and the Long Short-Term Memory model (CNN-LSTM). The routine monitored data (the river depth, water temperature, air temperature, precipitation, specific conductivity, pH and dissolved oxygen concentrations) for model training were collected from a nested high-frequency monitoring network, while the high-frequency NO3-N concentration data obtained at the outlet were not included as inputs. The whole dataset was separated into training, validation, and testing processes according to the ratio of 5:3:2, respectively. The hybrid CNN-LSTM model with different input lengths (1d, 3d, 7d, 15d, 30d) displayed comparable even better performance than other studies with lower frequencies, showing mean values of the Nash-Sutcliffe Efficiency 0.60-0.83. Models with shorter input lengths demonstrated both the higher modeling accuracy and stability. The water level, water temperature and pH values at monitoring sites were main controlling factors for forecasting performances. This study provided a new insight of using deep learning networks with a coupled architecture and routine monitored data for high-frequency riverine NO3-N concentration forecasting and suggestions about strategies about variable and input length selection during preprocessing of input data.

Deep learning for water quality

Understanding and predicting the quality of inland waters are challenging, particularly in the context of intensifying climate extremes expected in the future. These challenges arise partly due to complex processes that regulate water quality, and arduous and expensive data collection that exacerbate the issue of data scarcity. Traditional process-based and statistical models often fall short in predicting water quality. In this Review, we posit that deep learning represents an underutilized yet promising approach that can unravel intricate structures and relationships in high-dimensional data. We demonstrate that deep learning methods can help address data scarcity by filling temporal and spatial gaps and aid in formulating and testing hypotheses via identifying influential drivers of water quality. This Review highlights the strengths and limitations of deep learning methods relative to traditional approaches, and underscores its potential as an emerging and indispensable approach in overcoming challenges and discovering new knowledge in water-quality sciences.

A coupled model to improve river water quality prediction towards addressing non-stationarity and data limitation

Accurate predictions of river water quality are vital for sustainable water management. However, even the powerful deep learning model, i.e., long short-term memory (LSTM), has difficulty in accurately predicting water quality dynamics owing to the high non-stationarity and data limitation in a changing environment. To wiggle out of quagmires, wavelet analysis (WA) and transfer learning (TL) techniques were introduced in this study to assist LSTM modeling, termed WA-LSTM-TL. Total phosphorus, total nitrogen, ammonia nitrogen, and permanganate index were predicted in a 4 h step within 49 water quality monitoring sites in a coastal province of China. We selected suitable source domains for each target domain using an innovatively proposed regionalization approach that included 20 attributes to improve the prediction efficiency of WA-LSTM-TL. The coupled WA-LSTM facilitated capturing non-stationary patterns of water quality dynamics and improved the performance by 53 % during testing phase compared to conventional LSTM. The WA-LSTM-TL, aided by the knowledge of source domain, obtained a 17 % higher performance compared to locally trained WA-LSTM, and such improvement was more impressive when local data was limited (+66 %). The benefit of TL-based modeling diminished as data quantity increased; however, it outperformed locally direct modeling regardless of whether target domain data was limited or sufficient. This study demonstrates the reasoning for coupling WA and TL techniques with LSTM models and provides a newly coupled modeling approach for improving short-term prediction of river water quality from the perspectives of non-stationarity and data limitation.

Remote sensing-enabled machine learning for river water quality modeling under multidimensional uncertainty

Two fundamental problems have inhibited progress in the simulation of river water quality under climate (and other) uncertainty: 1) insufficient data, and 2) the inability of existing models to account for the complexity of factors (e.g., hydro-climatic, basin characteristics, land use features) affecting river water quality. To address these concerns this study presents a technique for augmenting limited ground-based observations of water quality variables with remote-sensed surface reflectance data by leveraging a machine learning model capable of accommodating the multidimensionality of water quality influences. Total Suspended Solids (TSS) can serve as a surrogate for chemical and biological pollutants of concern in surface water bodies. Historically, TSS data collection in the United States has been limited to the location of water treatment plants where state or federal agencies conduct regularly-scheduled water sampling. Mathematical models relating riverine TSS concentration to the explanatory factors have therefore been limited and the relationships between climate extremes and water contamination events have not been effectively diagnosed. This paper presents a method to identify these issues by utilizing a Long Short-Term Memory Network (LSTM) model trained on Moderate Resolution Imaging Spectroradiometer (MODIS) satellite reflectance data, which is calibrated to TSS data collected by the Ohio River Valley Water Sanitation Commission (ORSANCO). The methodology developed enables a thorough empirical analysis and data-driven algorithms able to account for spatial variability within the watershed and provide effective water quality prediction under uncertainty.

Fe-loaded biochar thin-layer capping for the remediation of sediment polluted with nitrate and bisphenol A: Insight into interdomain microbial interactions

The information on the collaborative removal of nitrate and trace organic contaminants in the thin-layer capping system covered with Fe-loaded biochar (FeBC) is limited. The community changes of bacteria, archaea and fungi, and their co-occurrence patterns during the remediation processes are also unknown. In this study, the optimized biochar (BC) and FeBC were selected as the capping materials in a batch experiment for the remediation of overlying water and sediment polluted with nitrate and bisphenol A (BPA). The community structure and metabolic activities of bacteria, archaea and fungi were investigated. During the incubation (28 d), the nitrate in overlying water decreased from 29.6 to 11.0 mg L-1 in the FeBC group, 2.9 and 1.8 times higher than the removal efficiencies in Control and BC group. The nitrate in the sediment declined from 5.03 to 0.75 mg kg-1 in the FeBC group, 1.3 and 1.1 times higher than those in Control and BC group. The BPA content in the overlying water in BC group and FeBC group maintained below 0.4 mg L-1 during incubation, signally lower than in the Control group. After capping with FeBC, a series of species in bacteria, archaea and fungi could collaboratively contribute to the removal of nitrate and BPA. In the FeBC group, more metabolism pathways related to nitrogen metabolism (KO00910) and Bisphenol degradation (KO00363) were generated. The co-occurrence network analysis manifested a more intense interaction within bacteria communities than archaea and fungi. Proteobacteria, Firmicutes, Actinobacteria in bacteria, and Crenarchaeota in archaea are verified keystone species in co-occurrence network construction. The information demonstrated the improved pollutant attenuation by optimizing biochar properties, improving microbial diversity and upgrading microbial metabolic activities. Our results are of significance in providing theoretical guidance on the remediation of sediments polluted with nitrate and trace organic contaminants.

Explainable AI approach with original vegetation data classifies spatio-temporal nitrogen in flows from ungauged catchments to the Great Barrier Reef

Transfer of processed data and parameters to ungauged catchments from the most similar gauged counterpart is a common technique in water quality modelling. But catchment similarities for Dissolved Inorganic Nitrogen (DIN) are ill posed, which affects the predictive capability of models reliant on such methods for simulating DIN. Spatial data proxies to classify catchments for most similar DIN responses are a demonstrated solution, yet their applicability to ungauged catchments is unexplored. We adopted a neural network pattern recognition model (ANN-PR) and explainable artificial intelligence approach (SHAP-XAI) to match all ungauged catchments that flow to the Great Barrier Reef to gauged ones based on proxy spatial data. Catchment match suitability was verified using a neural network water quality (ANN-WQ) simulator trained on gauged catchment datasets, tested by simulating DIN for matched catchments in unsupervised learning scenarios. We show that discriminating training data to DIN regime benefits ANN-WQ simulation performance in unsupervised scenarios ( p< 0.05). This phenomenon demonstrates that proxy spatial data is a useful tool to classify catchments with similar DIN regimes. Catchments lacking similarity with gauged ones are identified as priority monitoring areas to gain observed data for all DIN regimes in catchments that flow to the Great Barrier Reef, Australia.