Advances in microbial-mediated numerical modeling of biogeochemical processes in groundwater
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摘要:
地下水污染是全球性的环境问题，严重威胁人类健康和生态环境。作为地下水生态系统的重要组成部分，微生物通过其代谢反应参与多种生物地球化学过程，控制着污染物的转化与迁移。数值模拟是定量描述和预测地下水污染物迁移转化行为的重要手段，而理解和掌握微生物代谢过程的建模方法将有助于进一步提升对地下水中污染物运移行为的模拟和预测精度。鉴于此，文章按照发展时间与应用尺度，系统总结了微生物代谢活动模拟方法的发展进程，重点探讨了新一代基因测序技术的进步对数值模拟研究的推动作用；同时，详细介绍了如何构建微生物代谢模型，以定量描述其参与的生物地球化学过程，并汇总了常用的微生物信息数据库和模拟软件；最后指出，当前微生物代谢模型的应用仍面临诸多挑战，包括模型验证困难、参数适用性不足、数据获取难度大以及计算需求高等问题。未来研究需进一步深入探索微生物代谢机制，优化建模方法，完善适用于不同需求的参数和经验方程，以提升模型的准确性和适用性；同时，还需着力解决模型构建中微生物相关数据的处理、计算精度与效率的问题。
Abstract:Groundwater contamination is a global environmental issue that seriously threatens human health and ecological environment. As an essential component of groundwater ecosystems, microorganisms are involved in a series of biogeochemical processes through their metabolic reactions, which control the transformation and transport of contaminants. Numerical simulation of the contaminants transport and transformation is an effective method to quantitatively describe and predict their behaviors. Understanding and handling the modeling of microbial metabolic processes can significantly improve the accuracy of simulation and prediction of contaminants behaviors in groundwater. Here, this review systematically summarizes the development process of microbial metabolic activities according to the development timeline and application scales, focusing on the advancement of next-generation gene sequencing technology to promote numerical simulation research. Meanwhile, this review analyzes how to construct microbial metabolism models to quantitatively describe the biogeochemical processes they are involved in, and summarizes the commonly used microbial information databases and simulation softwares. It is pointed out that the current application of microbial metabolism modeling still faces many challenges, including verification difficulty, low parameter applicability, data acquisition difficulty, and high computational demands. Future research should further explore microbial metabolic mechanisms, optimize microbial metabolic modeling methods, and improve parameters and empirical equations under different demands, to enhance the accuracy and applicability of models, as well as to solve the issues of microbial-related data processing and computational precision and efficiency in model establishment.
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表 1 微生物基因信息平台的基本信息
Table 1. Basic information of the microbial gene information platform
平台 网站 优势与限制 NCBI https://www.ncbi.nlm.nih.gov 全面性、
权威性、
更新快、
工具丰富MODEL SEED https://modelseed.org 专注于代谢
数据集成、
完整的建模工具KBase http://kbase.us 集成化平台、
用户友好界面、
云计算资源、
用户协作
下载: 导出CSV
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