Machine learning predicts ecological risks of nanoparticles to soil microbial communities

Advances and applications of machine learning and deep learning in environmental ecology and health

Machine learning (ML) and deep learning (DL) possess excellent advantages in data analysis (e.g., feature extraction, clustering, classification, regression, image recognition and prediction) and risk assessment and management in environmental ecology and health (EEH). Considering the rapid growth and increasing complexity of data in EEH, it is of significance to summarize recent advances and applications of ML and DL in EEH. This review summarized the basic processes and fundamental algorithms of the ML and DL modeling, and indicated the urgent needs of ML and DL in EEH. Recent research hotspots such as environmental ecology and restoration, environmental fate of new pollutants, chemical exposures and risks, chemical hazard identification and control were highlighted. Various applications of ML and DL in EEH demonstrate their versatility and technological revolution, and present some challenges. The perspective of ML and DL in EEH were further outlined to promote the innovative analysis and cultivation of the ML-driven research paradigm.

Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome

Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.

Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation

Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.

Elucidating nitrogen removal performance and response mechanisms of anammox under heavy metal stress using big data analysis and machine learning

In this study, machine learning algorithms and big data analysis were used to decipher the nitrogen removal rate (NRR) and response mechanisms of anammox process under heavy metal stresses. Spearman algorithm and Statistical analysis revealed that Cr⁶⁺ had the strongest inhibitory effect on NRR compared to other heavy metals. The established machine learning model (extreme gradient boost) accurately predicted NRR with an accuracy greater than 99%, and the prediction error for new data points was mostly less than 20%. Additionally, the findings of feature analysis demonstrated that Cu²⁺ and Fe³⁺ had the strongest effect on the anammox process, respectively. According to the new insights from this study, Cr⁶⁺ and Cu²⁺ should be removed preferentially in anammox processes under heavy metal stress. This study revealed the feasible application of machine learning and big data analysis for NRR prediction of anammox process under heavy metal stress.

Applying Convolutional Neural Network to Predict Soil Erosion: A Case Study of Coastal Areas

The development of ecological restoration projects is unsatisfactory, and soil erosion is still a problem in ecologically restored areas. Traditional soil erosion studies are mostly based on satellite remote sensing data and traditional soil erosion models, which cannot accurately characterize the soil erosion conditions in ecological restoration areas (mainly plantation forests). This paper uses high-resolution unmanned aerial vehicle (UAV) images as the base data, which could improve the accuracy of the study. Considering that traditional soil erosion models cannot accurately express the complex relationships between erosion factors, this paper applies convolutional neural network (CNN) models to identify the soil erosion intensity in ecological restoration areas, which can solve the problem of nonlinear mapping of soil erosion. In this study area, compared with the traditional method, the accuracy of soil erosion identification by applying the CNN model improved by 25.57%, which is better than baseline methods. In addition, based on research results, this paper analyses the relationship between land use type, vegetation cover, and slope and soil erosion. This study makes five recommendations for the prevention and control of soil erosion in the ecological restoration area, which provides a scientific basis and decision reference for subsequent ecological restoration decisions.

Prediction models on biomass and yield of rice affected by metal (oxide) nanoparticles using nano-specific descriptors

The use of in silico tools to investigate the interactions between metal (oxide) nanoparticles (NPs) and plant biological responses is preferred because it allows us to understand molecular mechanisms and improve prediction efficiency by saving time, labor, and cost. In this study, four models (C5.0 decision tree, discriminant function analysis, random forest, and stepwise multiple linear regression analysis) were applied to predict the effect of NPs on rice biomass and yield. Nano-specific descriptors (size-dependent molecular descriptors and image-based descriptors) were introduced to estimate the behavior of NPs in plants to appropriately represent the wide space of NPs. The results showed that size-dependent molecular descriptors (e.g., E-state and connectivity indices) and image-based descriptors (e.g., extension, area, and minimum ferret diameter) were associated with the behavior of NPs in rice. The performance of the constructed models was within acceptable ranges (correlation coefficient ranged from 0.752 to 0.847 for biomass and from 0.803 to 0.905 for yield, while the accuracy ranged from 64% to 77% for biomass and 81% to 89% for yield). The developed model can be used to quickly and efficiently evaluate the impact of NPs under a wide range of experimental conditions and sufficient training data.