Ecological Mechanisms Of Synthetic Pseudomonas Consortia Against Ralstonia Solanacearum Invasion In Rhizosphere

The rhizosphere microbiome is essential for plant growth and health and numerous studies have attempted to link microbiome functionality species and trait composition.However,to date little is known about the actual ecological processes shaping community,complicating attempts to steer microbiome functionality.Here,we assess the development of microbial life history and community-level species interaction patterns emerge during plant development.Crucially,microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance was used in this study.Plant-associated microbes play an important role in plant growth and development.While the introduction of beneficial microbes into the soil could improve plant production in low-input agricultural systems,real-world applications are still held back by poor survival and activity of the probiotic microbes.Plant growth depends on a range of functions provided by the rhizosphere microbiome,such as nutrient mineralization,hormone co-regulation and pathogen suppression.Improving microbiome ability to deliver all these functions is essential for robust and sustainable crop production systems.Here,we sought to enhance the native plant microbiome multifunctionality by targeted introduction of probiotic bacterial consortia consisting of up to eight plantassociated Pseudomonas species in the tomato plant rhizosphere.The work presented in this thesis seeks to deepen our understanding of the rhizosphere microbiome from an ecological perspective,building on the biodiversity-ecosystem functioning framework to lay the ecological foundation upon which future microbial strategies for improved plant growth and protection can be built.1.In chapter 2,a combination of culture dependent-and independent methods were used to scrutinize the processes underlying rhizosphere microbiome assembly.Rhizosphere bacteria were isolated from tomato plants at different growth stages and measured functional traits linked to pathogen suppression.Toxicity towards pathogens and resource complementarity between co-occurring species increase during plant growth,with microbial communities recovered from the flowering stage rhizosphere showing the highest potential to protect the plant against the pathogen infection.In contrast,the early rhizosphere microbiome showed a high vulnerability to pathogen invasion,calling for strategies to bolster the microbiome to speed up functionality buildup and protect young plants.2.In chapter 3,the importance of biodiversity ecosystem functioning relationships within bacterial communities was investigated.Microbial diversity often promotes microbiome functioning and may increase host protection against pathogen invasions.It is still,however,unclear which underlying factors lead to the beneficial effects of microbial biodiversity.To examine this relationship,we introduced defined Pseudomonas bacterial consortia of varying diversity into the rhizosphere of tomato plants grown in natural soil.We then measured the survival of the introduced consortia and their effects on microbiome ability to prevent infection by the bacterial pathogen Ralstonia solanacearum.The results show that higher inoculum diversity improved the persistence of the introduced species and led to a higher suppression of both pathogen growth and disease incidence.Our results further demonstrated that consortia consuming a broad range of plant-derived resources and producing high levels of antimicrobial compounds were the best at preventing disease.3.In chapter 4,the rhizosphere microbiome was amended with the same consortia of Pseudomonas spp.used in chapter 3,but in the absence of the pathogen.The connections between consortium diversity,in vitro characteristics and the effect of consortium introduction on plant nutrition,hormonal balance and pathogen suppression were examined.Pseudomonas bacterial consortia proved to be more effective than any single species in isolation.Furthermore,we found that the impact of bacterial diversity on plant biomass and nutrition was correlated with the production of plant beneficial traits such as phytohormones and siderophores in vitro.4.In chapter 5,the biodiversity ecosystem functioning framework was combined with DNA-based microbiome interrogation and plant host phenotyping to assess the impact of multispecies inoculation on resident community biodiversity,composition,and multifunctionality in terms of services provided to the plant.We demonstrate that multispecies inoculations have a positive effect on microbiome biodiversity,possibly due to the inhibition of dominant species in the resident community and the promotion of rare species.Thus,multispecies inoculants may improve plant growth thanks to their ability to shift the resident community composition by activating and inhibiting different microbial populations.In conclusion,the importance of stochastic and deterministic processes is examined with respect to rhizosphere microbiome assembly in this thesis.We also examine the best means to supplement the rhizosphere microbiome to improve function and provide enhanced services to the plant.In addition,a framework based on the biodiversity/ecosystem function relationship is proposed to design microbial inoculants that can be tested under greenhouse condition for promoting plant growth and protecting plant health.In total,the results from this thesis are examined in terms of how they can contribute to the design of more sustainable agricultural systems with a low input of chemicals yet high outputs in terms of crop yield.