Biodiversity-based enhancement of rhizosphere microbiome functionality

Abstract

The rhizosphere microbiome is the unseen engine driving agricultural systems. However, intensive agricultural systems, especially the high inputs of fertilizers and pesticides, have caused a widespread loss of microbiome diversity, and decoupled the rhizosphere microbiome from plant fitness and performance. Restoring the microbiome’s ability to stimulate plant growth, while keeping diseases under control, may therefore represent a powerful strategy towards enabling higher crop yields while reducing agrochemical inputs. For this, this thesis focuses on biodiversity-based enhancement of rhizosphere microbiome functionality. A general introduction and an outline of the thesis are described in Chapter 1. In Chapter 2, I addressed the build-up process of rhizosphere microbiome: the early stage rhizosphere microbiome contains lower bacterial density and their assembly process is totally stochastic. Based on the individual bacterial trait test, we found an increase in functional diversity during the plant development indicating a rhizosphere microbiome niche differentiation. The matured plant rhizosphere contains high bacterial density and the individual bacterial members hold the higher potential to resist abiotic and biotic stresses. Especially, pathogen suppression ability was low at the early stage rhizosphere, which shows the vulnerability of early stage rhizosphere microbiome. In Chapter 3, biodiversity-ecosystem relationships were used to guide the development of multispecies consortia efficiently promoting microbiome ability to withstand pathogen invasion. I particularly found that increasing the diversity of inoculated bacterial consortia enhances community survival in the rhizosphere microbiome, leading to increased pathogen suppression via intensified resource competition and interference with the pathogen, implying that ecology-based community assembly rules could thus play a key role for engineering functionally reliable microbiome applications. Chapter 4 applied a similar approach to address whether inoculum diversity also affected other traits linked to plant growth, including the phosphate, potassium and iron concentration in plant tissues. I found a high correlation between bacterial trait expression in vitro and the effect of inoculation on plants, for instance siderophore production has a positive correlation with the assimilation of iron in plant tissues. Taken together, these results suggest that the richness of multispecies consortia could have increased the plant growth and nutrient assimilation via upregulation of important plant-growth promoting traits. Chapter 5 examined the effect of microbial introduction on the resident microbiome composition and the resulting level of soil multifunctionality, defined as the ability to simultaneously deliver multiple functions needed for vigorous plant growth and health. The functionality of the original soil was low, which was expected given its intensive land use history. Inoculation with one microbial species generally led to the enhancement of a single soil function, whereas introduction of 8 microbial species together improved all measured soil functions with the exception of soil nitrogen. I then examined the degree to which enhanced microbiome multifunctionality was due to shifts in the indigenous microbial community composition as opposed to the individual traits of the inoculated strains. In contrast to the expectations generated by Chapter 4, which highlighted the importance of specific bacterial traits, we found inoculation-dependent alteration of the resident microbiome to have the largest impact on microbiome multifunctionality.