Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation

Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of B. diazoefficiens USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of B. diazoefficiens USDA110 by computational approaches. Based on the comparison of interactomes between B. diazoefficiens USDA110 and other rhizobia, we inferred that the slow growth of B. diazoefficiens USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of B. diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.

Testing Whether Pre-Pod-Fill Symbiotic Nitrogen Fixation in Soybean Is Subject to Drift or Selection Over 100 Years of Soybean Breeding

Soybean [Glycine max (L.) Merr.] is the world's leading legume crop and the largest oilseed crop. It forms a symbiotic relationship with rhizobia bacteria residing in root nodules that provide fixed nitrogen to host plants through symbiotic nitrogen fixation (SNF). In soybean, it has been widely reported that the highest SNF occurs at the pod-filling stage, associated with the peak demand for nitrogen. However, the majority of seed nitrogen is derived from remobilizing root/shoot nitrogen, representing cumulative SNF from the seedling stage to the pre-pod-fill stage. Therefore, the question arises as to whether there has also been selection for improved SNF at these earlier stages, or whether pre-pod-fill SNF traits have drifted. To test this hypothesis, in this study, pre-pod SNF-related traits were evaluated in soybean cultivars that span 100 years of breeding selection in the Canadian Province of Ontario. Specifically, we evaluated SNF traits in 19 pedigree-related historical cultivars and 25 modern cultivars derived from the University of Guelph soybean breeding program. Field trials were conducted at Woodstock, Ontario, Canada in 2016 and 2017, and various SNF-related traits were measured at pre-pod-fill stages (R1-R3), including nitrogen fixation capacity. Considerable variation was observed among Canadian soybean cultivars released over the past 100 years for pre-pod-fill nitrogen fixation. The modern soybean cultivars had similar or moderately higher pre-pod-fill SNF compared to the historical lines in terms of the percentage of nitrogen derived from the atmosphere (%Ndfa) and total shoot fixed nitrogen. These findings suggest that, despite no direct selection by breeders, pre-pod-fill nitrogen fixation, and associated SNF traits have been maintained and possibly improved in modern soybean breeding. However, the low level of pre-pod-fill SNF in some modern cultivars, and generally wide variation observed in SNF between them, suggest some level of genetic drift for this trait in some pedigrees. Specific historical and modern soybean cultivars were identified as potential parents to enable targeted breeding for improved pre-pod-fill SNF. This retrospective study sheds light on our understanding of the impact of decades of recent selective breeding on pre-pod-fill nitrogen fixation traits in soybean in a temperate environment.

Performance of Mesoamerican bean (Phaseolus vulgaris L.) lines in an unfertilized oxisol

Introduction. Common beans (Phaseolus vulgaris L.) in Central America and the Caribbean are often produced on low fertility soils which reduces crop yield. Bean breeding programs need to identify genotypes that have superior adaptation to these conditions. Objective. Identify Mesoamerican bean germplasm lines with superior adaptation to low soil fertility. Materials and methods. The performance of twenty-seven Mesoamerican bean (Phaseolus vulgaris L.) lines from the Bean Abiotic Stress Evaluation (BASE) 120 panel were evaluated in an unfertilized oxisol at Isabela, Puerto Rico over five growing seasons (four-year period from 2015-2018). The lines were inoculated with a mixture of Rhizobium etli and R. tropici to promote symbiotic nitrogen fixation (SNF). Results. Four lines produced mean seed yields >1,200 kg ha-1 and had estimates of nitrogen derived from the atmosphere (NDFA) >50 %. Greater nodule number was positively correlated with % NDFA, later maturity and seed yield. The heat and drought tolerant small red cultivar ‘Rojo Chortí’ and the heat tolerant white cultivar ‘Verano’ had among the smallest apparent C isotope discrimination values suggesting greater water use efficiency. Among the elite lines in the trial, root rot damage was minimal and the basal root growth angles were intermediate (40-60 %), which favored the uptake of water and soil nutrients. Conclusion. Mesoamerican bean lines with superior seed yield and enhanced symbiotic nitrogen fixation in a low fertility soil were identified. Many of these lines also possess resistance to other biotic and abiotic factors that limit bean seed yield in Central America and the Caribbean.

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.