Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules

Comparative microbiome diversity in root-nodules of three Desmodium species used in push-pull cropping system

Background

Desmodium species used as intercrops in push-pull cropping systems are known to repel insect-pests, suppress Striga species weeds, and shift soil microbiome. However, the mechanisms through which Desmodium species impact the soil microbiome, either through its root exudates, changes in soil nutrition, or shading microbes from its nodules into the rhizosphere, are less understood. Here, we investigated the diversity of root-nodule microbial communities of three Desmodium species- Desmodium uncinatum (SLD), Desmodium intortum (GLD), and Desmodium incanum (AID) which are currently used in smallholder maize push-pull technology (PPT).

Methods

Desmodium species root-nodule samples were collected from selected smallholder farms in western Kenya, and genomic DNA was extracted from the root-nodules. The amplicons underwent paired-end Illumina sequencing to assess bacterial and fungal populations.

Results

We found no significant differences in composition and relative abundance of bacterial and fungal species within the root-nodules of the three Desmodium species. While a more pronounced shift was observed for fungal community compositions compared to bacteria, no significant differences were observed in the general diversity (evenness and richness) of fungal and bacterial populations among the three Desmodium species. Similarly, beta diversity was not significantly different among the three Desmodium species. The root-nodule microbiome of the three Desmodium species was dominated by Bradyrhizobium and Fusarium species. Nevertheless, there were significant differences in the proportion of marker gene sequences responsible for energy and amino acid biosynthesis among the three Desmodium species, with higher sequence proportions observed in SLD.

Conclusion

There is no significant difference in the microbial community of the three Desmodium species used in PPT. However, root-nodule microbiome of SLD had significantly higher marker gene sequences responsible for energy and amino acid biosynthesis. Therefore, it is likely that the root-nodules of the three Desmodium species host similar microbiomes and influence soil health, consequently impacting plant growth and agroecosystem functioning.

Graphene oxide affects the symbiosis of legume-rhizobium and associated rhizosphere rhizobial communities

The large-scale production and utilization of graphene oxide (GO) have raised concerns regarding its environmental exposure and potential risks. However, existing research on GO toxicity has primarily focused on individual organisms. Little attention has been given to the interaction between GO and the nitrogen-fixing symbiosis of legume-rhizobium. In this study, we focused on alfalfa (Medicago sativa L.), a typical leguminous nitrogen-fixing plant, to investigate the effects of GO on various aspects of this symbiotic relationship, including root nodulation, rhizobial viability, nodule nitrogen fixation, DNA damage, and the composition of the rhizobial community in the rhizosphere. As the dosage of GO increased, a significant inhibition in nodulation development was observed. Exposure to GO resulted in decreased growth and viability of rhizobia, as well as induced DNA damage in nodule cells. Furthermore, with increasing GO dosage, there were significant reductions in nitrogenase activity, leghemoglobin level, and cytoplasmic ammonia content within the root nodules. Additionally, the presence of GO led to notable changes in the rhizobial community in the rhizosphere. Our findings support the existence of the damage promoted by GO in the symbiosis of nitrogen fixing rhizobia with legumes. This underscores the importance of careful soil GO management.

Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development

De novo purine biosynthesis is required for the incorporation of fixed nitrogen in ureide exporting nodules, as formed on soybean [Glycine max (L.) Merr.] roots. However, in many cases, the enzymes involved in this pathway have been deduced strictly from genome annotations with little direct genetic evidence, such as mutant studies, to confirm their biochemical function or importance to nodule development. While efforts to develop large mutant collections of soybean are underway, research on this plant is still hampered by the inability to obtain mutations in any specific gene of interest. Using a forward genetic approach, as well as CRISPR/Cas9 gene editing via Agrobacterium rhizogenes-mediated hairy root transformation, we identified and characterized the role of GmUOX (Uricase) and GmXDH (Xanthine Dehydrogenase) in nitrogen fixation and nodule development in soybean. The gmuox knockout soybean mutants displayed nitrogen deficiency chlorosis and early nodule senescence, as exemplified by the reduced nitrogenase (acetylene reduction) activity in nodules, the internal greenish-white internal appearance of nodules, and diminished leghemoglobin production. In addition, gmuox1 nodules showed collapsed infected cells with degraded cytoplasm, aggregated bacteroids with no discernable symbiosome membranes, and increased formation of poly-β-hydroxybutyrate granules. Similarly, knockout gmxdh mutant nodules, generated with the CRISPR/Cas9 system, also exhibited early nodule senescence. These genetic studies confirm the critical role of the de novo purine metabolisms pathway not only in the incorporation of fixed nitrogen but also in the successful development of a functional, nitrogen-fixing nodule. Furthermore, these studies demonstrate the great utility of the CRISPR/Cas9 system for studying root-associated gene traits when coupled with hairy root transformation.

Characteristics and Research Progress of Legume Nodule Senescence

Delaying the nodule senescence of legume crops can prolong the time of nitrogen fixation and attenuate the lack of fertilizer in the later stage of legume crop cultivation, resulting in improved crop yield and reduced usage of nitrogen fertilizer. However, effective measures to delay the nodule senescence of legume crops in agriculture are relatively lacking. In the present review, we summarized the structural and physiological characteristics of nodule senescence, as well as the corresponding detection methods, providing technical support for the identification of nodule senescence phenotype. We then outlined the key genes currently known to be involved in the regulation of nodule senescence, offering the molecular genetic information for breeding varieties with delayed nodule senescence. In addition, we reviewed various abiotic factors affecting nodule senescence, providing a theoretical basis for the interaction between molecular genetics and abiotic factors in the regulation of nodule senescence. Finally, we briefly prospected research foci of nodule senescence in the future.

Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules

The transcriptional activity of Bradyrhizobium diazoefficens isolated from soybean nodules was monitored over the period from symbiosis to late plant nodule senescence. The bacteria retained a near constant level of RNA throughout this period, and the variation in genes demonstrating increased, decreased, and/or patterned transcriptional activity indicates that the bacteria are responding to the changing environment within the nodule as the plant cells progress from an organized cellular structure to an unorganized state of internal decay. The transcriptional variation and persistence of the bacteria suggest that the bacteria are adapting to their environment and acting similar to hemibiotrophs, which survive both as saprophytes on live plant tissues and then as necrophytes on decaying plant tissues. The host plant restrictions of symbiosis make B. diazoefficiens a highly specialized, restricted hemibiotroph.