基于合成微生物组的土壤新污染物生物修复研究进展

Research progress on synthetic microbiome-based bioremediation of emerging contaminants in soil

摘要

土壤是新污染物在环境中的重要汇。持久性有机污染物、内分泌干扰物、抗生素、抗生素抗性基因以及微塑料等新污染物可通过污水灌溉、污泥和有机肥施用、农药化肥投入以及大气沉降等途径进入土壤环境，并对土壤生态功能和农产品安全造成威胁。传统的生物修复方法存在单菌代谢能力有限、外源菌定殖不稳定和中间产物积累等问题。基于合成微生物组的修复技术可根据污染物类型和降解过程，筛选功能菌株，并构建具有互补作用的合成菌群；同时结合多组学分析和模型辅助设计技术，使其对新污染物生物修复更具针对性。本文围绕功能菌筛选、合成菌群构建、多组学表征和模型辅助设计等内容，综述了合成微生物组在土壤新污染物生物修复中的进展，并结合实际案例，阐述了合成微生物组在重点管控新污染物修复中的作用效能，并归纳代谢分工、中间产物继续转化、营养互补和底物接触改善等主要作用机制。目前，已有研究主要关注合成微生物组的构建方法及一般环境应用，但针对土壤新污染物修复过程中菌群设计、污染物降解机制以及生态应用风险的总结仍然不足。因此，本文围绕土壤新污染物生物修复需求，系统梳理了合成微生物组的构建方法、技术支撑和应用进展。其中，重点总结了功能菌挖掘、合成菌群设计、多组学技术以及模型辅助优化在抗生素、微塑料、邻苯二甲酸酯和除草剂等典型新污染物去除中的应用，并总结其作用关键点、作用机制以及生态应用限制。未来需进一步优化菌群组成，加强植物在实际土壤中与根际微生物互作研究，并结合降解产物风险、土著微生物群落变化和土壤生态功能变化开展研究，以促进合成微生物组在实际土壤污染修复中的应用。

Abstract

Soils serves as an important sink for emerging contaminants in the environment. Emerging contaminants, including persistent organic pollutants, endocrine-disrupting chemicals, antibiotics, antibiotic resistance genes, and microplastics, can enter soil environments through various pathways, such as wastewater irrigation, sludge and organic fertilizer application, agricultural pesticide and fertilizer inputs, and atmospheric deposition, thereby posing threats to soil ecological functions and agricultural products safety. Traditional bioremediation approaches are limited by the restricted metabolic capabilities of individual strains, unstable colonization of introduced microorganisms, and accumulation of intermediate metabolites. Synthetic microbiome-based remediation technologies can select functional microorganisms according to pollutant types and degradation processes and construct synthetic consortia with complementary functions. Meanwhile, integration with multi-omics analyses and model-assisted design technologies enables more targeted bioremediation of emerging contaminants. This review focuses on functional microorganisms screening, synthetic consortium construction, multi-omics characterization, and model-assisted design, and summarizes the advances of synthetic microbiomes in the bioremediation of emerging contaminants in soil. Based on representative cases, the remediation performance of synthetic microbiomes toward priority emerging contaminants is discussed, and the major mechanisms, including metabolic division of labor, further transformation of intermediate metabolites, nutrient complementation, and enhanced substrate accessibility, are summarized. Currently, existing studies have mainly focused on synthetic microbiome construction strategies and their general environmental applications; however, comprehensive summaries of microbial consortium design, pollutant degradation mechanisms, and ecological application risks during soil emerging contaminant remediation remain insufficient. Therefore, this review systematically summarizes the construction strategies, technical support, and application progress of synthetic microbiomes for soil emerging contaminant remediation. In particular, the applications of functional microorganism discovery, synthetic consortium design, multi-omics technologies, and model-assisted optimization in the removal of typical emerging contaminants, including antibiotics, microplastics, phthalate esters, and herbicides, are highlighted. The key functional roles, underlying mechanisms, and ecological limitations associated with these applications are also summarized. Future research should further optimize consortium composition, strengthen investigations of plant-rhizosphere microbiome interactions under realistic soil conditions, and incorporate assessments of degradation product risks, alterations in indigenous microbial communities, and changes in soil ecological functions, thereby promoting the practical application of synthetic microbiomes in soil pollution remediation.

关键词

合成微生物组 / 土壤 / 新污染物 / 生物修复 / 合成菌群

Key words

synthetic microbiome / soil / emerging contaminants / bioremediation / synthetic microbial consortia

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基金资助

国家自然科学基金项目(42307031,U22A20590,42430703)

国家重点研发计划项目(2023YFC3708101)