Biology subjects

Rimbault, I.

Publications and source records attributed to Rimbault, I..

3 recordsLinked to original sources

bioRxiv2023

Culturable approach to rice-root associated bacteria in Burkina Faso: diversity, plant growth-promoting rhizobacteria properties and cross-comparison with metabarcoding data.

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity so as, to be able to assess the diversity of the collection based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected working collection isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the functional description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

microbiology↗

bioRxiv2022

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.

microbiology↗

bioRxiv2022

Differential genetic strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for root colonization of Oryza sativa ssp. japonica and ssp. indica, as revealed by Tn-seq

Burkholderia vietnamiensis LMG10929 (Bv) and Paraburkholderia kururiensis M130 (Pk) are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens while Paraburkholderia are mostly environmental and plant-associated species. Here, we compared the genetic strategies used by Bv and Pk to colonize two subspecies of their common host, Oryza sativa ssp. japonica (cv. Nipponbare) and ssp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes in Bv involved in rice roots colonization compared to Pk, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towards Bv compared to Pk. For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivars differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production in Bv and quorum sensing in Pk. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays. ImportanceBurkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

microbiology↗