根际化学与生物多样性的表征方法:组学技术的机遇与挑战

Characterization methods of rhizosphere chemo- and biodiversity: Opportunities and challenges of omics technology

根际是联结植物、土壤和微生物的重要界面,是化学与生物过程耦合最活跃的区域.根际环境影响土壤中有机和无机污染物的行为,而研究方法的完善与提升有助于阐释根际中复杂的过程与作用机制.本文从传统的化学和生物学方法到新兴的组学技术对根际科学的方法学研究进展进行了综述,重点讨论了当今组学技术在根际研究中应用机遇与挑战,同时展望了今后需要关注的科学问题.根际化学组分的传统分析方法涵盖了光谱、色谱、质谱和色质联用等技术,主要聚焦于低分子量有机酸等小分子的定性定量测定,导致对根际化学多样性的认知偏差;传统的根际微生物研究依赖于培养技术,对微生物多样性的描述存在很大的局限.揭示根际异质性和复杂性,亟需采用高端的技术,组学方法显示出极大的优势,显著提高了研究者对根际科学的认识.基于靶向和非靶向代谢组学有利于深入研究根际复杂的化学多样性过程;基于宏基因组学、转录组学和蛋白组学等组学工具能够提供微生物组基因和蛋白的表达、功能特性等更详细的信息,可以全面地揭示根际微生物的多样性.应该强调的是,未来多组学整合分析更是表征根际化学与生物多样性的一个强有力工具,但需要更多的模型、框架和计算基础来实现根际基因、蛋白、转录和代谢水平的多层次关联,以助于挖掘根-微生物-土壤界面大量尚未揭示的关键过程、机理及生态环境效应.

Rhizosphere is an important interface between plants,soil,microorganisms,and their environment.It is the most active area of biochemical coupling processes.Rhizosphere environment can affect the behaviors of organic and inorganic pollutants in the soil.Research methods should be further improved to explain the complex biochemical mechanisms in the rhizosphere.This paper reviews the progress of methodological research in the rhizosphere science,from traditional chemical and biological methods to emerging omics technologies,focuses on the application and challenges of omics technology in rhizosphere research so far,and looks forward to the scientific issues that need attention in the future.The traditional analysis methods of chemical components in the rhizosphere include spectroscopy,chromatography,and their combination with mass spectrometry.These methods simply pay attention to the qualitative and quantitative determination of small molecules,such as low molecular weight organic acids,which leads to a deviation in the understanding of the rhizosphere chemical diversity.The traditional research on rhizosphere microorganisms relies on the cultivation techniques,and there are great limitations in the investigation of microbial diversity.Research on heterogeneity and complexity of rhizosphere requires the use of advanced techniques.Omics technologies show great advantages and can significantly improve our understanding of rhizosphere science.Targeted and non-targeted metabolomics methods facilitate insight into the complex chemically diversity processes in the rhizosphere.Based on metagenomics,transcriptomics,proteomics,and other omics methods,it can provide more detailed information on the expression and functional characteristics of microbiome genes and proteins,and comprehensively reveal the diversity of rhizosphere microorganisms.In the future,it should be emphasized that the integrated multi-omics analysis will be a more powerful tool to characterize the chemistry and biodiversity in the rhizosphere.However,more models,frameworks and computational foundations are needed to achieve multi-associations at gene,protein,transcriptional and metabolic levels,to uncover many yet-to-be-revealed key processes,mechanisms,and eco-environmental effects in the root-microbe-soil interface.