From synthetic communities to synthetic ecosystems: exploring causalities in plant–microbe–environment interactions

2024/11/05 by Guillaume Chesneau, Johannes Herpell, Johannes B. Herpell +2 · 42 citations
Agricultural and Biological Sciences · #Biology #Bridging (networking) #Computational biology #Computer science #Ecology #Ecosystem #Mycorrhizal Fungi and Plant Interactions #Nematode management and characterization studies #Plant-Microbe Interactions and Immunity #Synthetic biology

paper · pdf · doi:10.1111/nph.20250

published in New Phytologist 245(2), 496-502 (Wiley)

openalex publication_date 2024/11/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04

Abstract

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning.

Cited by

• Functional team selection as a framework for local adaptation in plants and their belowground microbiomes
• Spatial structure: shaping the ecology and evolution of microbial communities
• Building microbial synthetic communities: get inspired by the design of synthetic plant communities
• Assembly and co-occurrence networks of nitrogen-fixing bacteria associated with epiphyllous liverworts in fragmented tropical forests
• Building microbial synthetic communities: get inspired by the design of synthetic plant communities. [europepmc]
• MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions. [europepmc]
• Effects and molecular mechanism of endophytic elicitors on the accumulation of secondary metabolites in medicinal plants. [europepmc]
• Functional team selection as a framework for local adaptation in plants and their belowground microbiomes. [europepmc]
• In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions. [europepmc]
• Assembly and co-occurrence networks of nitrogen-fixing bacteria associated with epiphyllous liverworts in fragmented tropical forests. [europepmc]
• Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere Microbiome and Metabolome. [europepmc]
• Spatial structure: shaping the ecology and evolution of microbial communities. [europepmc]
• Marine synthetic ecology: From microbial communities to ecosystems. [europepmc]
• Ecology-guided Bacillus SynCom from a rice-duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression. [europepmc]
• Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner. [europepmc]
• Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media. [europepmc]

Related

• Building microbial synthetic communities: get inspired by the design of synthetic plant communities
• The Use of Synthetic Microbial Communities to Improve Plant Health
• Plant-microbiome engineering: synergistic microbial partners for crop health and sustainability
• What is microbial community ecology?
• Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications