Finkel, O. M. | bioRxiv Science

bioRxiv2019

Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome

Plants grow within a complex web of species interacting with each other and with the plant. Many of these interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development. To understand how microbe-microbe interactions influence root development in Arabidopsis, we established a model system for plant-microbe-microbe-environment interactions. We inoculated seedlings with a 185-member bacterial synthetic community (SynCom), manipulated the abiotic environment, and measured bacterial colonization of the plant. This enabled classification of the SynCom into four modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying microbe-microbe interactions that determine root phenotypes. These interactions primarily involve a single bacterial genus, Variovorax, which completely reverts severe root growth inhibition (RGI) induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulate plant hormone levels to balance this ecologically realistic root communitys effects on root development. We identify a novel auxin degradation operon in the Variovorax genome that is necessary and sufficient for RGI reversion. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the roots developmental program. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising new ecological strategy towards the development of more resilient and productive crops.

microbiology↗

bioRxiv2019

The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response

Phosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms - the plant microbiota - are exposed to direct influence by the soils phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrations per se than bacteria, and less depended on the soil community composition.\n\nUsing a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genus Burkholderia is specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence of Burkholderia from the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plants P starvation.

microbiology↗