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

Microbiome

Research

Matan Cohen¹  Adi Doron-Faigenboim¹  Shlomit Medina¹  Maria Berihu¹  Alon Ginatt¹  Shiri Freilich¹  Ofir Tal²  Edoardo Piombo³  Tracey S. Somera⁴  Mark Mazzola⁵  Maya Ofek-Lalzar⁶  Assaf Malik⁶ 

[1] Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel;Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel;Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), P.O. Box 447, 49500, Migdal, Israel;Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy;Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007, Uppsala, Sweden;United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, 98801, Wenatchee, WA, USA;United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, 98801, Wenatchee, WA, USA;Department of Plant Pathology, Stellenbosch University, Private Bag X1, 7600, Matieland, South Africa;University of Haifa, Haifa, Israel;

关键词: Microbial community;    Metagenomics;    Shotgun sequencing;    Differential abundance;    Microbiome;    Rhizosphere;    Disease suppressive soils;    Rootstock;    Biostimulants;    Network;    Pathway;    Compound;    Functional annotation;    MAG;   

DOI  :  10.1186/s40168-022-01438-1

 received in 2022-04-14, accepted in 2022-11-28,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsThis 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 potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant’s potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2.ConclusionsThis research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems.E7XdzHk-x_xNr6tGiZLY1VVideo Abstract

【 授权许可】

CC BY   
© The Author(s) 2023

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