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1. Comparison of nodule endophyte composition, diversity, and gene content between Medicago truncatula genotypes

   https://doi.org/10.1094/PBIOMES-10-20-0077-R  

   Burns, Mannix; Epstein, Brendan; Burghardt, Liana (May 2021, Phytobiomes Journal)

   null (Ed.)

   Leguminous plants form symbiotic relationships with rhizobia. These nitrogen-fixing bacteria live in specialized root organs called nodules. While rhizobia form the most notable host relationship within root nodules, other bacterial endophytes also inhabit these root nodules and can influence host-rhizobia interactions as well as exert effects of their own, whether beneficial or detrimental. In this study, we investigate differences in nodule communities between genotypes (A17 and R108) of a single plant species, the model legume Medicago truncatula. While diversity of endophytes in nodules was similar across hosts, both nodule endophyte composition and gene functional groups differed. In contrast to the significant direct effect of host genotype, neither the presence nor identity of a host in the previous generation (either A17 or R108) had a significant effect on the nodule endophyte diversity or composition. However, whether or not a host was present altered gene functional groups. We conclude that genetic variation within a legume host species can play an important role in the establishment of nodule microbiomes. Further studies, including GWAS and functional assays, can open the door for engineering and optimizing nodule endophyte communities that promote growth or have other beneficial qualities. 

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2. Antagonism within mutualism: host control of symbionts through nodule-specific antimicrobial peptides

   https://doi.org/10.3389/fmicb.2025.1622262  

   Eaker, Ashton A; Rowe, Shawna L; Friesen, Maren L (September 2025, Frontiers in Microbiology)

   Legumes (Fabaceae) have developed a symbiotic relationship with nitrogen-fixing bacteria called rhizobia to meet their nitrogen needs. Legumes recruit rhizobia from the soil, house them in root organs called nodules, and manipulate bacterial metabolism, providing carbon and receiving bacterially fixed nitrogen in return. One mechanism of host control is through a family of antimicrobial peptides that only appears in the inverted repeat lacking clade (IRLC) of the legumes, though the Dalbergioid clade has similar peptides. They are named nodule-specific cysteine-rich (NCR) peptides due to their exclusive expression in the nodule during symbiosis and the shared 4 or 6 cysteine residue motif. These genes and subsequent proteins vary in number, sequence, and function, but evolutionary genomics research shows that they are adapted from the plant immune system for the new function of symbiont manipulation. In this review, we present the current understanding of NCR peptide biology, expression, and function. We examine NCR genomic and biochemical features and explore their roles in shaping symbiotic outcomes. Finally, we discuss emerging applications and key open questions. Understanding host manipulation of bacterial symbionts within plant tissues provides researchers with targets for engineering more efficient nitrogen-fixing symbioses. In addition, NCR peptides show promise as therapeutic agents with the potential to control both plant and animal pathogens. 

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3. The evolutionary genomics of incipient endosymbiosis in wild rhizobia bacteria

   https://doi.org/10.64898/2025.12.03.692210  

   Montoya, Angeliqua P; Jensen, Kyson; Griffitts, Joel S; Porter, Stephanie S (December 2025, bioRxiv)

   The advent of endosymbiosis underlies evolutionary innovation and ecosystem function. However, whether free-living partners tend to benefit or exploit each other during incipient endosymbiosis remains a dilemma. Rhizobia bacteria are plant endosymbionts capable of initiating root nodules and fixing nitrogen due to genes carried on mobile genetic elements (MGEs) such as the symbiosis island (SI). We conjugated marked SIs into the genomes of nonnodulating strains, which was sufficient to generatede novoroot nodule-forming endosymbionts. Most novel endosymbionts originated as commensals that incurred no detectable costs to host plants, in contrast to predictions of exploitation. In fact, a third of endosymbionts originated as nitrogen fixing mutualists. Consistent with phylogenetic limits to transfer of MGE function, novel endosymbionts derived from more closely related SI donor and recipient strains showed greater nitrogen fixation. However, we did not detect phylogenetic limits to SI transmission, which could reflect selfish selection for generalized horizontal transfer of this MGE. In fact, the SI was able to displace other genomic elements residing at its characteristic tRNA gene insertion site. We thus provide genetic, genomic, and functional evidence of how MGEs can potentiate and constrain major evolutionary transitions to expand bacterial niches, with cascading effects on host organisms. 

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4. Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules.

   https://doi.org/doi.org/10.1093/plphys/kiaa115  

   Dokwal, D; Romsdahl, TB; Kunz, DA; Alonso, AP; Dickstein, R (January 2021, Plant physiology)

   null (Ed.)

   In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization–mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization–mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule. 

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5. Partners in root nodule symbiosis respond uniquely to heavy metal stresses in a host genotype-dependent manner

   https://doi.org/10.1038/s41598-025-17827-z  

   Chakraborty, Sanhita; Sharma, Reena; Bhat, Aditi; Curtin, Shaun J; Wen, Jiangqi; Mysore, Kirankumar S; Paape, Timothy (December 2025, Scientific Reports)

   Abstract The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using theMedicago truncatula-Sinorhizobium melilotisymbiotic system. Phenotypes were measured in the wild-typeMedicago truncatulaand a mutant in anABCtransporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies. 

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