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Molecular Phylogenetic Analysis of Salt-Tolerance-Related Genes in Root-Nodule Bacteria Species Sinorhizobium meliloti
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Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects

Anna V. Tsyganova
* and
Viktor E. Tsyganov
Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg 196608, Russia
Authors to whom correspondence should be addressed.
Agronomy 2022, 12(11), 2857;
Submission received: 13 October 2022 / Revised: 13 November 2022 / Accepted: 14 November 2022 / Published: 15 November 2022
(This article belongs to the Special Issue Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects)
The production of high-value, environmentally friendly and healthy food has been the major global focus of sustainable agriculture in recent years [1,2]. Further progress in this area requires the development, testing and introduction of new agricultural technologies that would minimise environmental risks, help maintain or even improve the fertility of soils and support the creation of new types of agricultural products. To fulfil these conditions, new approaches are needed, including better use of genetic resources such as plants and microorganisms. The use of microorganisms will dramatically increase the diversity of genetic resources and contribute to increasing the resilience of agricultural systems [3].
Numerous studies show that during evolution, plants have used certain features of microorganisms to enhance their own adaptive capacities. For example, the plant genome incorporated some genetic factors that help create new ecological niches for microorganisms, wherein the genes providing the expression of adaptation remained in the genomes of microorganisms. Recent studies have shown that the symbiotic signalling pathways in plant species that form intracellular symbioses (including arbuscular mycorrhiza, ericoid and orchid mycorrhizae in angiosperms; ericoid-like mycorrhiza in bryophytes; legume–rhizobial and actinorhizal symbioses) is conserved [4]. The fact that symbiotic signalling has been conserved over 450 million years of evolution indicates the great importance of these associations for the successful spreading of land plants.
One of the best demonstrations of how the adaptive capacity of plants is expanded through co-evolution with microorganisms is the formation of symbiotic nitrogen-fixing nodules on the roots of legumes. Numerous genes in legumes are involved in the formation of the nodule. More than 40 regulatory symbiotic genes have been identified in the garden pea [5], while the process of nitrogen fixation is controlled by bacterial genes [6]. Therefore, the use of plant–microbe systems which are based on a nitrogen-fixing symbiosis between legumes and rhizobia is of significant interest for developing new approaches in sustainable agriculture [3,7,8,9]. The widespread use of legumes in sustainable agriculture will increase biological nitrogen fixation, reduce energy costs, improve the physical properties of the soil and increase soil microbial biodiversity [10,11]. In addition, legumes are important food and feed crops and are staples in some regions of the world [12].
The nitrogen-fixing nodule is a unique ecological niche for rhizobia in which micro-aerobic conditions enable the functioning of the main enzyme of nitrogen fixation, nitrogenase, which is highly sensitive to oxygen [13]. In the symbiotic nodule, specialised infected plant cells, which are increased in size due to endoreduplication, provide shelter to thousands of bacteria [14]. Bacteria are isolated from the cytoplasm of the plant cell through a membrane of plant origin, which has inclusions of bacterial proteins: the so-called symbiosome membrane. Within the symbiosome membrane, bacteria differentiate into a specialised form, bacteroids capable of nitrogen fixation, and together with the surrounding symbiosome membrane form a symbiosome [14]. The infected cells of the symbiotic nodule can be seen as a unique system in legumes that have appeared during their evolution to enable the adaptation of the plants to a lack of nitrogen in the soil and providing them with symbiotrophic nutrition. Therefore, it could be concluded that that the plant cell infected by rhizobia providing accommodation to numerous symbiosomes is the central component of nitrogen fixation. At the same time, it should be noted that the mechanisms that ensure the ability of plant cells to be filled by numerous symbiosomes, which are temporary cellular organelles of microbial origin, remain poorly understood.
In the current Special Issue, “Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects”, we gathered seven articles with recent insights from studies into the development of legume–rhizobial symbiosis. These studies looked at both macro- and microsymbionts, with specific focus on how this knowledge could be applied in agriculture.
Recently, it was discovered that relict legumes could be considered as a source for new symbiotic genes. In current study, Safronova et al. [15] tested the effects of the co-inoculation of alfalfa (Medicago varia Martyn), common vetch (Vicia sativa L.) and red clover (Trifolium pratense L.) with commercial strains of Sinorhizobium meliloti and Rhizobium leguminosarum and with the strains of Mesorhizobium japonicum, Bradyrhizobium sp. or M. kowhaii isolated from the relict legumes Oxytropis popoviana Peschkova and Astragalus chorinensis Bunge. In some combinations, an increase in nodule number, plant weight and nitrogenase activity was reported. The authors attribute the positive effects on nodule development to the effect of rhizobial synergy, which occurs due to the presence of strains isolated from relict legumes with additional symbiotic genes, i.e., genes for the biosynthesis of phytohormones and genes encoding elements of the secretion systems. This study opens up new perspectives on the development of microbial biopreparations for the inoculation of legumes.
The studies presented by Zhukov et al. [16] revealed that in pea, the responses to double inoculation with rhizobial and arbuscular mycorrhizal fungi are increased in genotypes carrying the recessive allele le (Le encodes gibberellin 3-beta-dioxygenase). The increased responses are manifested by an increase in individual seed weight. This observation points out that the use of double inoculation could be a promising approach adopted in the cultivation of most modern pea varieties that carry the allele le. It could provide an important contribution for the development of sustainable agricultural technologies.
Given that legumes are a very large family, the number of species for which nodule development has been studied in detail is still limited. Therefore, studies of the development of symbiotic nodules in new legume species are of great interest. Glycyrrhiza uralensis Fisch. ex DC. is a well-known legume species, which is actively used in the pharmaceutical and food industries. Tsyganova et al. [17] conducted a detailed analysis of the development of nodules in this species (including tubulin cytoskeleton organization). In contrast to nodules of the other studied legumes, the walls of the infection threads are different from the cell wall in density and fibrillarity. A striking feature is the formation of indeterminate nodules in which infected cells are filled with multibacteroid symbiosomes, which is typical for nodules of a determinate type.
Medicago lupulina L. (black medic or hop clover) is another interesting legume species which is able to grow in adverse conditions. Roumiantseva et al. [18] performed a comprehensive analysis of the genome of its symbiont, Ensifer (Sinorhizobium) meliloti, strain L6-AK89. It revealed 53 nod/noe/nol/nif/fdx/fix genes and 32 genes involved in stress tolerance.
In recent years, the description of the transcriptional activity not only in the whole nodule but also in its individual zones has attracted increasing interest. Kusakin et al. [19] presented an analysis of differential gene expression in different zones of a symbiotic pea nodule isolated using laser microdissection. The maximum amount of differentially expressed genes was associated with the nitrogen fixation zone, with new genes involved in the nodule development being revealed.
Legume–rhizobium symbiosis is sensitive to various stresses, including salinity, which is one of the most widespread stress factors for plants. In this issue, two papers are dedicated to the study of genetic factors that may be involved in resistance to saline stress in rhizobia. Belfquih et al. [20] conducted a study of the Ensifer aridi strain isolated from the Moroccan Merzouga desert and demonstrating increased tolerance to drought and saline stresses. The authors did not confirm the expected involvement of the alternative sigma factor RpoE2 in adaptation to saline stress. Therefore, revealing the alternative mechanisms of salt tolerance of this species of rhizobia requires further research. Muntyan and Roumiantseva [21] performed molecular phylogenetic analysis of salt-tolerance-related genes in 26 Sinorhizobium meliloti strains and revealed that megaplasmid pSymA carries not only genes of nitrogen fixation but also genes involved in salt tolerance. It means that pSymA is required for the formation of a stress-related gene pool in addition to genes regulating the nitrogen fixation function.
In conclusion, it should be noted that a detailed understanding of the molecular, genetic and cellular mechanisms of legume–rhizobial symbiosis is required for engineering new associations of non-legume plants with bacteria, which will acquire the ability to fix nitrogen [22,23].

Author Contributions

Both authors had an equal contribution to the writing of this Editorial. All authors have read and agreed to the published version of the manuscript.


The article was made with the support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement № 075-15-2022-320 date 20 April 2022 on providing a grant in the form of subsidies from the Federal budget of Russian Federation. The grant was provided for state support for the creation and development of a World-class Scientific Center “Agrotechnologies for the Future”.


It is with great pleasure that we thank all the contributors to this Special Issue, as well as the academic editors and anonymous reviewers. We thank Liliya Serazetdinova (Earlham Institute, Norwich Research Park, UK) for her critical reading of the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.


  1. Lal, R. Soils and sustainable agriculture. A review. Agron. Sustain. Dev. 2008, 28, 57–64. [Google Scholar] [CrossRef]
  2. Conway, G.R.; Barbier, E.B. After the Green Revolution: Sustainable Agriculture for Development; Routledge: London, UK, 2013. [Google Scholar]
  3. Tikhonovich, I.; Provorov, N. Microbiology is the basis of sustainable agriculture: An opinion. Ann. Appl. Biol. 2011, 159, 155–168. [Google Scholar] [CrossRef]
  4. Radhakrishnan, G.V.; Keller, J.; Rich, M.K.; Vernié, T.; Mbadinga Mbadinga, D.L.; Vigneron, N.; Cottret, L.; Clemente, H.S.; Libourel, C.; Cheema, J.; et al. An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages. Nat. Plants 2020, 6, 280–289. [Google Scholar] [CrossRef] [PubMed]
  5. Tsyganov, V.E.; Tsyganova, A.V. Symbiotic regulatory genes controlling nodule development in Pisum sativum L. Plants 2020, 9, 1741. [Google Scholar] [CrossRef] [PubMed]
  6. Cooper, J. Early interactions between legumes and rhizobia: Disclosing complexity in a molecular dialogue. J. Appl. Microbiol. 2007, 103, 1355–1365. [Google Scholar] [CrossRef] [PubMed]
  7. Das, A.; Ghosh, P. Role of legumes in sustainable agriculture and food security: An Indian perspective. Outlook Agric. 2012, 41, 279–284. [Google Scholar] [CrossRef]
  8. De Vries, F.T.; Bardgett, R.D. Plant–microbial linkages and ecosystem nitrogen retention: Lessons for sustainable agriculture. Front. Ecol. Environ. 2012, 10, 425–432. [Google Scholar] [CrossRef]
  9. Rubiales, D.; Mikic, A. Introduction: Legumes in sustainable agriculture. CRC Crit. Rev. Plant. Sci. 2015, 34, 2–3. [Google Scholar] [CrossRef] [Green Version]
  10. Courty, P.E.; Smith, P.; Koegel, S.; Redecker, D.; Wipf, D. Inorganic nitrogen uptake and transport in beneficial plant root-microbe interactions. CRC Crit. Rev. Plant. Sci. 2015, 34, 4–16. [Google Scholar] [CrossRef]
  11. Peix, A.; Ramírez-Bahena, M.H.; Velázquez, E.; Bedmar, E.J. Bacterial associations with legumes. CRC Crit. Rev. Plant. Sci. 2015, 34, 17–42. [Google Scholar] [CrossRef]
  12. Vaz Patto, M.C.; Amarowicz, R.; Aryee, A.N.; Boye, J.I.; Chung, H.-J.; Martín-Cabrejas, M.A.; Domoney, C. Achievements and challenges in improving the nutritional quality of food legumes. CRC Crit. Rev. Plant. Sci. 2015, 34, 105–143. [Google Scholar] [CrossRef]
  13. Oldroyd, G.E. Speak, friend, and enter: Signalling systems that promote beneficial symbiotic associations in plants. Nat. Rev. Microbiol. 2013, 11, 252–263. [Google Scholar] [CrossRef] [PubMed]
  14. Tsyganova, A.V.; Kitaeva, A.B.; Tsyganov, V.E. Cell differentiation in nitrogen-fixing nodules hosting symbiosomes. Funct. Plant. Biol. 2018, 45, 47–57. [Google Scholar] [CrossRef]
  15. Safronova, V.; Sazanova, A.; Kuznetsova, I.; Belimov, A.; Guro, P.; Karlov, D.; Yuzikhin, O.; Chirak, E.; Verkhozina, A.; Afonin, A.; et al. Increasing the legume–rhizobia symbiotic efficiency due to the synergy between commercial strains and strains isolated from relict symbiotic systems. Agronomy 2021, 11, 1398. [Google Scholar] [CrossRef]
  16. Zhukov, V.A.; Zhernakov, A.I.; Sulima, A.S.; Kulaeva, O.A.; Kliukova, M.S.; Afonin, A.M.; Shtark, O.Y.; Tikhonovich, I.A. Association study of symbiotic genes in pea (Pisum sativum L.) cultivars grown in symbiotic conditions. Agronomy 2021, 11, 2368. [Google Scholar] [CrossRef]
  17. Tsyganova, A.V.; Kitaeva, A.B.; Gorshkov, A.P.; Kusakin, P.G.; Sadovskaya, A.R.; Borisov, Y.G.; Tsyganov, V.E. Glycyrrhiza uralensis nodules: Histological and ultrastructural organization and tubulin cytoskeleton dynamics. Agronomy 2021, 11, 2508. [Google Scholar] [CrossRef]
  18. Roumiantseva, M.L.; Vladimirova, M.E.; Saksaganskaia, A.S.; Muntyan, V.S.; Kozlova, A.P.; Afonin, A.M.; Baturina, O.A.; Simarov, B.V. Ensifer meliloti L6-AK89, an effective inoculant of Medicago lupulina varieties: Phenotypic and deep-genome screening. Agronomy 2022, 12, 766. [Google Scholar] [CrossRef]
  19. Kusakin, P.G.; Serova, T.A.; Gogoleva, N.E.; Gogolev, Y.V.; Tsyganov, V.E. Laser microdissection of Pisum sativum L. nodules followed by RNA-Seq analysis revealed crucial transcriptomic changes during infected cell differentiation. Agronomy 2021, 11, 2504. [Google Scholar] [CrossRef]
  20. Belfquih, M.; Sakrouhi, I.; Ait-Benhassou, H.; Dubois, E.; Severac, D.; Filali-Maltouf, A.; Le Quere, A. Ensifer aridi LMR001T symbiosis and tolerance to stress do not require the alternative sigma factor RpoE2. Agronomy 2021, 11, 1787. [Google Scholar] [CrossRef]
  21. Muntyan, V.S.; Roumiantseva, M.L. Molecular phylogenetic analysis of salt-tolerance-related genes in root-nodule bacteria species Sinorhizobium meliloti. Agronomy 2022, 12, 1968. [Google Scholar] [CrossRef]
  22. Pankievicz, V.C.S.; Irving, T.B.; Maia, L.G.S.; Ané, J.-M. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol. 2019, 17, 99. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Haskett, T.L.; Paramasivan, P.; Mendes, M.D.; Green, P.; Geddes, B.A.; Knights, H.E.; Jorrin, B.; Ryu, M.-H.; Brett, P.; Voigt, C.A.; et al. Engineered plant control of associative nitrogen fixation. Proc. Natl. Acad. Sci. USA 2022, 119, e2117465119. [Google Scholar] [CrossRef] [PubMed]
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Tsyganova, A.V.; Tsyganov, V.E. Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects. Agronomy 2022, 12, 2857.

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Tsyganova AV, Tsyganov VE. Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects. Agronomy. 2022; 12(11):2857.

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Tsyganova, Anna V., and Viktor E. Tsyganov. 2022. "Rhizobial Symbiosis in Crop Legumes: Molecular and Cellular Aspects" Agronomy 12, no. 11: 2857.

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