A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data

作者：Maria Berihu, Tracey Somera, Assaf Malik, Shlomit Medina, Edoardo Piombo, Ofir Tal, Matan J. Cohen, Alon Avraham Ginatt, Maya Ofek‐Lalzar, Adi Doron‐Faigenboim, Mark Mazzola, Shiri Freilich · 发表于：Microbiome · 年份：2023 · DOI：10.1186/s40168-022-01438-1 · 被引用次数：56 · 研究领域：Microbial Community Ecology and Physiology、Plant-Microbe Interactions and Immunity、Microbial Metabolic Engineering and Bioproduction

Abstract Background The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. Results This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from ‘sick’ vs ‘healthy/recovered’ rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The pot...