Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development

• Published in: Environmental microbiology Vol. 22; no. 12; pp. 5005 - 5018
• Main Authors: Hu, Jie, Wei, Zhong, Kowalchuk, George A., Xu, Yangchun, Shen, Qirong, Jousset, Alexandre
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.12.2020; Wiley Subscription Services, Inc; Society for Applied Microbiology and Wiley-Blackwell
• Subjects: Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Biodiversity and Ecology; Community composition; community structure; Complementarity; Composition; Consortia; Environmental Sciences; functional diversity; Invasive species; Life history; Lycopersicon esculentum - growth & development; Lycopersicon esculentum - microbiology; microbiology; microbiome; Microbiomes; Microbiota - genetics; Microorganisms; Niches; Pathogens; phenotype; Phenotyping; plant development; Plant Development - physiology; Plant growth; Plant Roots - microbiology; Rhizosphere; Soil Microbiology; Species
• ISSN: 1462-2912; 1462-2920; 1462-2920
• DOI: 10.1111/1462-2920.15097

Summary The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community‐level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high‐density, functionally complementary climax communities at later stages. During plant growth, fast‐growing species were further replaced by antagonistic and stress‐tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of ‘climax’ microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life‐history strategies prevail at different plant growth stages and that community‐level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.