Project description:Acid environments are worldwide distributed due to their natural conditions or by the inappropriate use of the intensive agriculture. The moderately low pHs from the soils are an important barrier in the plant-rhizobia interaction. These low pHs affect the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect in the rhizobia-legume is mainly due the low acid-tolerance of the bacteria. Here, we described and identified relevant factors in the acid tolerance of Rhizobium. favelukesii, using RNA-Seq. A total of 1924 genes were differentially expressed under acidic condition, with ca. 60% underexpressed. Remarkably, 60% of the CDS of the symbiotic plasmid were also underexpressed. The in silico functional analysis showed that R. favelukesii acid response involves both general and specific response. Regarding the general response, it includes mainly changes in energetic metabolism and protein turnover, while the specific response is a combination of mechanisms that would contribute to the general phenotype of acid-tolerant in R. favelukesii. GABA and Histidine metabolism, cell envelope changes and reverse proton efflux were significant. Moreover, we confirmed a phenotype acid sensible of a mutant in braD, this gene showed a higher expression under acid stress. Remarkably, we evidenced that a strain without pSym presented an improved performance in acidic condition. Hence, this work supply relevant information in the characterization of genes associated with tolerance or adaptation to abiotic stresses of R. favelukesii LPU83 using transcriptomic tools.
Project description:Acid soils constitute a severe problem for leguminous crops mainly through a disturbance in rhizobia-legume interactions. Rhizobium favelukesii—an acid-tolerant rhizobium able to nodulate alfalfa—is highly competitive for nodule occupation under acid conditions, but inefficient in biologic nitrogen fixation. In this work, we obtained a general description of the acid-stress response of R. favelukesii LPU83 by means of proteomics by comparing the total proteome profiles in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. Thus, a total of 336 proteins were identified with a significant differential expression, 136 of which species were significantly overexpressed and 200 underexpressed in acidity. An in-silico functional characterization with those respective proteins revealed a complex and pleiotropic response by these rhizobia involving components of oxidative phosphorylation, glutamate metabolism, and peptidoglycan biosynthesis, among other pathways. Furthermore, a lower permeability was evidenced in the acid-stressed cells along with several overexpressed proteins related to γ-aminobutyric-acid metabolism, such as the gene product of livK, which was mutated. This mutant exhibited an acid-sensitive phenotype in agreement with the proteomics results. We conclude that both γ-aminobutyric-acid metabolism and a modified cellular envelope could be relevant to acid tolerance in R. favelukesii.
Project description:We report an small RNA sequencing (sRNA-seq) approach to identify host sRNAs involved in the nitrogen fixing symbiosis between Mesoamerican Phaseolus vulgaris and Rhizobium etli strains with different degrees in nodulation efficiency. This approach identified conserved and known microRNAs (miRNAs) differentially accumulated in Mesoamerican P. vulgaris roots in response to a highly efficient strain, to a less efficient one or to both strains.
