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Predicting microbial extracellular electron transfer activity in paddy soils with soil physicochemical properties using machine learning

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Abstract

Soil extracellular electron transfer (EET) is a pivotal biological process within the realm of soil. Unfortunately, EET suffers from a lack of predictive models. Herein, an intricately crafted machine learning model has been developed for the purpose of predicting soil EET by using the physicochemical properties of soil as independent input variables and the EET capabilities in terms of current density (jmax) and Coulombic charge (Cout) as dependent output variables. An autoencoder ensemble stacking (AES) model was developed to address the aforementioned issue by integrating support vector machine, multilayer perceptron, extreme gradient boosting, and light gradient boosting machine algorithms as the stacking algorithms. With 10-fold cross-validation, the AES model exhibited notable improvements in predicting jmax and Cout, with average test R2 values of 0.83 and 0.84, respectively, surpassing those of single machine learning (ML) models and the basic ensemble model. By utilizing partial correlation plots (PDPs), Shapley Additive explanations (SHAP) values, and SHAP decision plots, we quantitatively explained the impact and contribution of the input molecules on the AES model’s predictions of jmax and Cout. In the context of the SHAP method for the AES model, total carbon (TC) was identified as the most correlated descriptor for jmax, while total organic carbon (TOC) stood out as the most relevant descriptor for Cout. In the prediction tasks of jmax and Cout within the AES model, employing a multitask ML approach allowed the model to benefit from the shared information of input variables, thereby enhancing its overall generalizability. This study provides a feasible tool for the prediction of soil EET from soil physiochemical properties and an advanced understanding of the relationship between soil physiochemical properties and EET capability.

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Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. School of Automation, Guangdong University of Technology, Guangzhou, 510006, China

    JiaJun Ou

  2. Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China

    XiaoShan Luo, JunYang Liu, LinYan Huang & Yong Yuan

  3. School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China

    LiHua Zhou

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  1. JiaJun Ou
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  6. Yong Yuan
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Corresponding author

Correspondence to Yong Yuan.

Additional information

This work was supported by Guangdong Basic and Applied Basic Research Foundation (Grant No. 2023B1515040022) and the National Natural Science Foundation of China (Grant Nos. 42177270 and 42207340).

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The supporting information is available online at tech.scichina.com and link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.

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Supplementary materials: Predicting microbial extracellular electron transfer activity in paddy soils with soil physicochemical properties using machine learning

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Ou, J., Luo, X., Liu, J. et al. Predicting microbial extracellular electron transfer activity in paddy soils with soil physicochemical properties using machine learning. Sci. China Technol. Sci. 67, 259–270 (2024). https://doi.org/10.1007/s11431-023-2537-y

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