Role of the rhizosphere microbiome in providing soil nutrients to the plant : Plant iron nutrition as a study case
Résumé
Understanding and valuing beneficial interactions between plants and soil borne microorganisms is a major issue in agroecology. Importance of some rhizosphere microorganisms in plant nutrition has been known for a very long time. Nitrogen-fixing bacteria, mycorrhizal fungi that enhance phosphate uptake, or phosphate solubilizing rhizosphere bacteria have long been studied. This is also the case for bacteria that display beneficial effect on plant growth and iron status1. However, these microorganisms have been mostly studied without taking into consideration the fact that they are part of a complex plant microbiome recruited by the plant. This probably accounts for the limitation of the use of microbial tools in agriculture often related to low efficacy and inconsistent performance in the field and stresses the importance of using microbiome-based approaches in soil ecology. As a micronutrient, iron might seem to be of minor importance compared to macronutrients. However, iron is vital for living organisms being part of many essential molecules and reactions such as cellular respiration or chlorophyll synthesis in plant. But, although it is present in large amount in soils, iron is mainly in insoluble forms which are not bioavailable to plant and microorganisms. Thus there is a strong competition for iron between organisms ; it is already well known that competition for iron can drive phytopathogen control by rhizosphere bacteria. Promotion of plant iron nutrition is important for many reasons : (i) iron deficiency can reduce yield while needs are to increase yield for food safety, (ii) iron is a limiting factor of legume nitrogen fixation which has to be promoted in agroecological systems - it is also involved in nitrogen assimilation, (iii) iron is required in biotic and abiotic stress resistance which is essential to resist and adapt to climate change. Moreover, increasing the iron content of plant productions and more particularly of legumes, is needed to promote the replacement of animal proteins by plant proteins. The results of many studies made in our team tend to indicate that iron dynamics could be an important driver of biotic interactions in the rhizosphere. Therefore the microbiome could be an important lever to promote plant iron nutrition without increasing the use of inputs. Additional results obtained recently reinforce this hypothesis showing that genes involved in iron dynamics are well represented in the functional rhizosphere microbiota. In a context of agroecological transition, our objectives are to increase legume yields and grain quality taking advantage of the plant microbiome through the identification bacterial traits, plant traits and cultural practices that promote biotic interactions beneficial to plant iron nutrition. We studied the effect of the plant genotype on the rhizosphere microorganisms and, in return, of the microorganisms on the plant in order to identify microbial and plant traits associated to positive interactions. Two pea cultivars, one sensitive (S), and the other tolerant (T), to iron deficiency chlorosis were studied in first place in order to draw hypotheses from their comparison. Two reseach approaches have been followed. On the one hand, research has been undertaken with a priori on a bacterial group known for its positive influence on plant growth and health associated with siderophore production, pseudomonads. On the other hand, rhizosphere bacterial populations and communities have been studied without a priori. The results of the two approaches highlighted differences in the root microbiota depending on the pea genotype. In return, we demonstrated that these differences may impact the plant iron status and modulate the expression of plant genes. These results suggest that greater tolerance to iron chlorosis in certain pea varieties could be linked to a better capacity of these plants to use iron mobilized by microbial siderophores2. In addition, it has been shown that a cultural practice, intercropping, impacts plant nutrition in relationship with changes in Pseudomonas spp. and Enterobacterales abundances3. Moreover, additional information concerning the mechanisms involved in the improvement of plant iron nutrition by pseudomonads has been obtained. Arabidopsis thaliana and a model siderophore produced by a Pseudomonas strain were used to explore these mechanisms. The results obtained support a direct involvement of iron chelates of microbial origin in plant iron uptake and homeostasis4. Altogether, our findings confirm the contribution of the rhizosphere microbiota to plant nutrition and underline the importance of taking into account the plant microbiome in crop science.
