宏基因组结合机器学习揭示稻田土壤健康的微生物指示类群

Unveiling the role of soil microorganisms in indicating paddy soil health via metagenomics combined with machine learning

摘要

【1】The soil microbiome performs various ecological functions, making it a potentially vital component of soil health assessment; however, the indicator taxa of soil health remain unidentified.土壤微生物组执行多种生态功能，使其成为土壤健康评估中潜在的重要组成部分；然而，土壤健康的指示微生物类群尚未被确定。

【2】This study explored these taxa in paddy soils of the black soil region in Northeast China.本研究在中国东北黑土区的稻田土壤中探索了这些指示类群。

【3】First, the soil health index (SHI) was evaluated using representative physicochemical and biological parameters, revealing that approximately one-third of the soils had a low health level.首先，利用代表性的理化参数和生物学参数评估了土壤健康指数，结果显示约三分之一的土壤处于低健康水平。

【4】A Random Forest model was then developed based on microbial species' relative abundance to predict the SHI, achieving an R² value greater than 0.6.随后，基于微生物物种的相对丰度构建了随机森林模型来预测土壤健康指数，模型的R²值超过了0.6。

【5】Based on the SHapley Additive exPlanations values of this model, 40 microbial species were identified as potential indicator taxa of soil health, with 39 of these taxa occurring in more than 50% of the samples.基于该模型的SHAP值，鉴定出40个微生物物种作为土壤健康的潜在指示类群，其中39个类群在超过50%的样本中出现。

【6】Specifically, paddy soils with more abundant carbon- and nitrogen-fixing bacteria exhibited higher soil organic matter and total N contents, along with higher health levels.具体而言，固碳菌和固氮菌更为丰富的稻田土壤表现出更高的土壤有机质和全氮含量，以及更高的健康水平。

【7】Conversely, soils rich in denitrifying bacteria exhibited lower SHI values because of increased N loss.相反，富集反硝化细菌的土壤因氮损失增加而表现出更低的土壤健康指数值。

【8】Furthermore, C-fixing, N-fixing, and denitrifying genes showed functional relationships with the corresponding soil properties and SHI.此外，固碳基因、固氮基因和反硝化基因与相应的土壤性质和土壤健康指数表现出功能上的关联。

【9】In addition, halophilic, halotolerant, and eutrophic bacteria indicated soil health by reflecting salinity and nutrient status.此外，嗜盐菌、耐盐菌和富营养菌通过反映盐分和养分状况来指示土壤健康。

【10】 The potential of these indicator taxa was validated at multidecadal and regional spatial scales.这些指示类群的潜力在数十年尺度和区域空间尺度上得到了验证。

【11】 These results highlight the practical value of such indicator taxa, which elucidate the ecological processes associated with soil health and respond predictably to changes in soil health, thereby serving as rapid diagnostic tools for assessing soil health. 这些结果突显了此类指示类群的实用价值，它们能够阐明与土壤健康相关的生态过程，并对土壤健康的变化做出可预测的响应，从而作为评估土壤健康的快速诊断工具。