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