Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency

ZHENG Lei; ZHENG Qiteng; ZHANG Tianjiao; DUAN Kun; ZHANG Ruifu

doi:10.12211/2096-8280.2025-075

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Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency

Invited Review | 更新时间：2025-11-12

- Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency
- Synthetic Biology Journal Vol. 6, Issue 5, Pages: 1058-1071(2025)
- 作者机构：
  
  南京农业大学资源与环境科学学院，江苏南京 210095
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2025-075
  CLC： S182;Q81
- Received：21 July 2025，
  
  Revised：2025-09-09，
  
  Published：31 October 2025
- 稿件说明：
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郑雷，郑棋腾，张天骄，段鲲，张瑞福. 构建根际合成微生物菌群促进作物养分高效吸收利用［J］. 合成生物学， 2025， 6（5）： 1058-1071

ZHENG Lei， ZHENG Qiteng， ZHANG Tianjiao， DUAN Kun， ZHANG Ruifu. Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency［J］. Synthetic Biology Journal， 2025， 6（5）： 1058-1071
郑雷，郑棋腾，张天骄，段鲲，张瑞福. 构建根际合成微生物菌群促进作物养分高效吸收利用［J］. 合成生物学， 2025， 6（5）： 1058-1071 DOI： 10.12211/2096-8280.2025-075.

ZHENG Lei， ZHENG Qiteng， ZHANG Tianjiao， DUAN Kun， ZHANG Ruifu. Engineering rhizosphere synthetic microbial communities to enhance crop nutrient use efficiency［J］. Synthetic Biology Journal， 2025， 6（5）： 1058-1071 DOI： 10.12211/2096-8280.2025-075.

摘要

现代农业发展正面临养分利用效率低下和环境负担持续加剧的双重挑战。近年研究表明，根际微生物组（rhizosphere microbiome）作为植物的“第二基因组”，通过调控土壤氮、磷、铁等关键养分的生物地球化学循环，在植物高效获取养分过程中发挥核心驱动作用。合成生物学（synthetic biology）的快速发展为根际微生物组的精准解析与功能设计提供了创新性工具，通过模块化基因编辑、人工群落构建及宿主-微生物互作调控等策略显著提升植物养分利用效率，为突破传统农业依赖化肥、缓解资源浪费和环境压力提供全新的技术途径。本文系统综述了合成生物学驱动下根际微生物组工程在植物养分高效利用领域的研究进展，重点包括根际微生物组参与土壤养分循环的作用机制解析，合成生物学工具在单菌功能强化，群落协同调控、宿主-微生物互作优化等方面的关键作用以及当前技术发展中面临的微生物组复杂性限制、工程菌田间定植稳定性不足、跨作物普适性受限和潜在生态安全风险等诸多瓶颈。并展望了合成微生物组在可持续农业发展中的应用潜力，未来通过定向功能设计、智能响应系统构建及“植物-微生物-环境”协同调控，有望实现作物养分利用效率与可持续生产力的显著提升，从而为推动农业绿色转型提供关键科学技术支撑。

Abstract

Modern agriculture confronts the dual challenge of suboptimal nutrient use efficiency (NUE) and the escalating chain of environmental burdens. These include increased greenhouse gas emissions

widespread soil degradation

and rising water eutrophication due to excessive fertilizer runoff. In this context

the rhizosphere microbiome

an indispensable symbiotic partner to plants throughout their life cycle

has been shown to critically regulate the transformation

mobilization

and supply of key soil nutrients. This occurs through core ecological mechanisms such as associative nitrogen fixation (

e.g

performed by genera including

Azospirillum

)

organic acid secretion-mediated dissolution of insoluble phosphorus (as commonly observed in

Pseudomonas

)

and siderophore-chelated iron mobilization

which enhance nutrient accessibility for plant uptake. Recent breakthroughs in synthetic biology have significantly advanced the engineering of stable and efficient Synthetic Microbial Communities (SynComs)

propellin

g this approach into a burgeoning frontier of agricultural biotechnology. SynComs integrate functionally diverse microbial strains to overcome well-documented limitations of single-strain inoculants

such as inconsistent performance and low resilience under field conditions. These designed communities form more stable and robust functional modules within the rhizosphere

leading to improved nutrient cycling and root system health. Beyond their application as agronomic biofertilizers

SynComs also serve as a powerful toolset for deciphering complex microbe-microbe interactions and elucidating synergistic mechanisms between microorganisms and host plants. Despite the considerable promise of SynComs technology

several critical barriers impede its real-world deployment. These include poor colonization stability of artificially constructed communities

limited environmental adaptability across varying agroecosystems with divergent soil properties and climatic conditions

and an insufficient mechanistic understanding of multi-trophic plant-microbe interactions. Additionally

commercialization faces further challenges due to prohibitive costs linked to large-scale production

formulation

and field application

as well as undefined long-term ecological risks such as potential disruption of native microbial communities or horizontal gene transfer. To realize the full potential of SynComs

coordinated multidisciplinary efforts are essential. Research should focus on engineering adaptively intelligent consortia capable of responding to dynamic environmental conditions

creating field-applicable tools for real-time monitoring and precision regulation

advancing scalable deployment strategies amenable to existing farming systems

and establishing rigorous ecological risk assessment protocols. An in-depth understanding of rhizosphere microbiome functions

coupled with the active development of SynCom technologies

represents a pivotal opportunity to address pressing agricultural nutrient management challenges. Such advances

can significantly reduce inputs of synthetic fertilizers while enhancing nutrient use efficiency

ultimately promoting a transition toward resource-efficient and ecologically sustainable agricultural systems. Collectively

these efforts posses theoretical value and substantial industrial potential.

关键词

Keywords

references

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