The nodD1 gene of Sinorhizobium fredii HH103 Restores Nodulation Capacity on Bean in a Rhizobium tropici CIAT 899 nodD1/nodD2 Mutant, but the Secondary Symbiotic Regulators nolR, nodD2 or syrM Prevent HH103 to Nodulate with This Legume

Rhizobial NodD proteins and appropriate flavonoids induce rhizobial nodulation gene expression. In this study, we show that the nodD1 gene of Sinorhizobium fredii HH103, but not the nodD2 gene, can restore the nodulation capacity of a double nodD1/nodD2 mutant of Rhizobium tropici CIAT 899 in bean plants (Phaseolus vulgaris). S. fredii HH103 only induces pseudonodules in beans. We have also studied whether the mutation of different symbiotic regulatory genes may affect the symbiotic interaction of HH103 with beans: ttsI (the positive regulator of the symbiotic type 3 protein secretion system), and nodD2, nolR and syrM (all of them controlling the level of Nod factor production). Inactivation of either nodD2, nolR or syrM, but not that of ttsI, affected positively the symbiotic behavior of HH103 with beans, leading to the formation of colonized nodules. Acetylene reduction assays showed certain levels of nitrogenase activity that were higher in the case of the nodD2 and nolR mutants. Similar results have been previously obtained by our group with the model legume Lotus japonicus. Hence, the results obtained in the present work confirm that repression of Nod factor production, provided by either NodD2, NolR or SyrM, prevents HH103 to effectively nodulate several putative host plants.

Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Microscopic and transcriptomic analyses of Dalbergoid legume peanut reveal a divergent evolution leading to Nod Factor dependent epidermal crack-entry and terminal bacteroid differentiation.

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS come from model legumes that exhibit a root-hair mode of bacterial infection in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step towards understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated a comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen scavenging mechanisms in the Papilionoid family. Finally, absence of cysteine-rich motif-1 containing-NCRs, but the recruitment of defensin like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobial symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.

A glutamate synthase mutant of Bradyrhizobium sp. strain ORS285 is unable to induce nodules on Nod factor-independent Aeschynomene species

The Bradyrhizobium sp. strain ORS285 is able to establish a nitrogen-fixing symbiosis with both Nod factor (NF) dependent and NF-independent Aeschynomene species. Here, we have studied the growth characteristics and symbiotic interaction of a glutamate synthase (GOGAT; gltD::Tn5) mutant of Bradyrhizobium ORS285. We show that the ORS285 gltD::Tn5 mutant is unable to use ammonium, nitrate and many amino acids as nitrogen source for growth and is unable to fix nitrogen under free-living conditions. Moreover, on several nitrogen sources, the growth rate of the gltB::Tn5 mutant was faster and/or the production of the carotenoid spirilloxanthin was much higher as compared to the wild-type strain. The absence of GOGAT activity has a drastic impact on the symbiotic interaction with NF-independent Aeschynomene species. With these species, inoculation with the ORS285 gltD::Tn5 mutant does not result in the formation of nodules. In contrast, the ORS285 gltD::Tn5 mutant is capable to induce nodules on NF-dependent Aeschynomene species, but these nodules were ineffective for nitrogen fixation. Interestingly, in NF-dependent and NF-independent Aeschynomene species inoculation with the ORS285 gltD::Tn5 mutant results in browning of the plant tissue at the site of the infection suggesting that the mutant bacteria induce plant defence responses.

The importance of Rhizobium, Agrobacterium, Bradyrhizobium, Herbaspirillum, Sinorhizobium in sustainable agricultural production

Rhizobia which are soil bacteria capable of symbiosis with legume plants in the root or stem nodules and perform nitrogen fixation. Rhizobial genera include Agrobacterium, Allorhizobium, Aminobacter, Azorhizobium, Bradyrhizobium, Devosia, Mesorhizobium, Methylobacterium, Microvirga, Ochrobacterum, Phyllobacterium, Rhizobium, Shinella and Ensifer (Sinorhizobium). Review of the literature was carried out using the keywords Rhizobium, Agrobacterium, Bradyrhizobium, Herbaspirillum and Sinorhizobium. Rhizobial nodulation symbioses steps are included flavonoid signaling, Nod factor induction, and Nod factor perception, root hair responses, rhizobial infection, cell division and formation of nitrogen-fixing nodule. Rhizobium improves sustainable production by boosting organic nitrogen content.

The Effect of a Preparation Containing Rhizobial Nod Factors on Pea Morphological Traits and Physiology

The aim of the study was to determine the possibility of increasing the pea yields by improving the symbiotic nitrogen fixation through the use of a preparation containing bacterial Nod factors (NFs). Two pea cultivars were included in the experiment: Wiato (with traditional foliage) and Model (afila type). Before sowing, the seeds were soaked in distilled water (control) and in a preparation of Nod factors at a concentration of 10−12 M dm−3 H2O. As a result, of the Nod factor preparation use, an acceleration of the date and uniformity of pea plant emergence was observed. The treatment had also a positive effect on the number and weight of root nodules, which resulted in a significant increase in the yield of vegetative and generative plant organs. A positive effect of seed soaking with NFs preparation was also observed in the dynamics of pea weight increase, chlorophyll content in leaves and the values of gas exchange parameters. Model cultivar of pea had generally higher values of the analysed traits than Wiato, but the response of both cultivars to Nod factors was similar. This means that application of the preparation containing NFs, may improve the growth, development, and yield of both types of pea.