Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Rhizobia: from saprophytes to endosymbionts

Key Points

  • Root secretion and plant immunity are key factors in controlling the assembly of root-associated microbiotas of which rhizobia are key members

  • Rhizobia exist in soil and compete with the general microbiota before infecting legumes, typically through root hairs, and forming N2-fixing bacteroids

  • Rhizobia have complex pan-genomes. Some strains also have large plasmids or symbiosis islands, which are crucial for fitness, nodulation and N2 fixation

  • Rhizobia have specific host plants, which makes them excellent models for studying the mechanisms, timing and location of root colonization in host and non-host plants

  • Some legumes, such as members of the invert repeat lacking clade, produce up to several hundred antimicrobial peptides to control bacteroid cell division and development

  • Bacteroids receive carbon as dicarboxylates from legumes, and in exchange, they fix N2 in a low O2 environment and secrete ammonia to the plant. Bacteroids must balance electron flow to nitrogenase, lipids, polyhydroxybutyrate and O2, and coordinate this process with reductant production by the tricarboxylic acid (TCA) cycle


Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Rhizobial genome organization.
Figure 2: Rhizobial attachment and colonization of legume roots.
Figure 3: Molecular mechanisms of plant–rhizobia signalling.
Figure 4: Nutrient exchange and regulation of bacteroid development.


  1. 1

    Philippot, L., Raaijmakers, J. M., Lemanceau, P. & van der Putten, W. H. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789–799 (2013).

    CAS  PubMed  Google Scholar 

  2. 2

    Herridge, D., Peoples, M. & Boddey, R. Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311, 1–18 (2008).

    CAS  Google Scholar 

  3. 3

    Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). This study is an attempt to look at the limits of production and consumption and their impact on a sustainable planet. It establishes planetary boundaries of consumption and production that should not be exceeded for key nutrients, CO 2 release and biodiversity loss.

    PubMed  Google Scholar 

  4. 4

    Gage, D. J. Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes. Microbiol. Mol. Biol. Rev. 68, 280–300 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Gibson, K. E., Kobayashi, H. & Walker, G. C. Molecular determinants of a symbiotic chronic infection. Annu. Rev. Genet. 42, 413–441 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6

    Relic, B. et al. Biological activity of rhizobium sp NGR234 nod-factors on Macroptilium atropurpureum. Mol. Plant. Microbe Interact. 6, 764–774 (1993).

    CAS  PubMed  Google Scholar 

  7. 7

    Cao, Y., Halane, M. K., Gassmann, W. & Stacey, G. The role of plant innate immunity in the legume-Rhizobium symbiosis. Annu. Rev. Plant Biol. 68, 535–561 (2017).

    CAS  PubMed  Google Scholar 

  8. 8

    Oldroyd, G. E., Murray, J., Poole, P. S. & Downie, J. A. The rules of engagement in the legume-rhizobial symbiosis. Annu. Rev. Genet. 45, 119–144. (2011).

    CAS  PubMed  Google Scholar 

  9. 9

    Oldroyd, G. E. & Downie, J. A. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu. Rev. Plant Biol. 59, 519–546 (2008).

    CAS  PubMed  Google Scholar 

  10. 10

    Poole, P. S. & Udvardi, M. Transport and metabolism in legume-rhizobia symbioses. Annu. Rev. Plant Biol. 64, 781–805 (2013).

    PubMed  Google Scholar 

  11. 11

    Zipfel, C. & Oldroyd, G. E. Plant signalling in symbiosis and immunity. Nature 543, 328–336 (2017).

    CAS  PubMed  Google Scholar 

  12. 12

    Turner, T. R. et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J. 7, 2248–2258 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Weinert, N. et al. PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS. Microbiol. Ecol. 75, 497–506 (2011).

    CAS  PubMed  Google Scholar 

  14. 14

    Griffiths, R. I. et al. The bacterial biogeography of British soils. Environ. Microbiol. 13, 1642–1654 (2011).

    PubMed  Google Scholar 

  15. 15

    Tkacz, A., Cheema, J., Chandra, G., Grant, A. & Poole, P. S. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 9, 2349–2359 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012). Together with reference 16, this study establishes the importance of the root-associated microbiota as the community most strongly influenced by the plant and leads to numerous studies on other plants.

    CAS  PubMed  Google Scholar 

  18. 18

    Haney, C. H., Samuel, B. S., Bush, J. & Ausubel, F. M. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature Plants 1, 1–9 (2015).

    Google Scholar 

  19. 19

    Mendes, R. et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100 (2011).

    CAS  PubMed  Google Scholar 

  20. 20

    Zgadzaj, R. et al. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc. Natl Acad. Sci. USA 113, E7996–E8005 (2016). This study shows that the common SYM pathway has a major influence on the microbiome of the model plant L. japonicus.

    CAS  PubMed  Google Scholar 

  21. 21

    Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Jones, F. P. et al. Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes — a genome comparison. Sci. Rep. 6, 25858 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    diCenzo, G., Milunovic, B., Cheng, J. & Finan, T. M. The tRNAarg gene and engA are essential genes on the 1.7-Mb pSymB megaplasmid of Sinorhizobium meliloti and were translocated together from the chromosome in an ancestral strain. J. Bacteriol. 195, 202–212 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol. 18, 141–148 (2010).

    CAS  PubMed  Google Scholar 

  25. 25

    Young, J. P. et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 7, R34 (2006).

    PubMed  PubMed Central  Google Scholar 

  26. 26

    Amadou, C. et al. Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 18, 1472–1483 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    Moulin, L. et al. Complete genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Stand. Genom. Sci. 9, 763–774 (2014).

    Google Scholar 

  28. 28

    Brewer, R. J. M., Haskett, T. L., Ramsay, J. P., O'Hara, G. W. & Terpolilli, J. J. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae WSM1497, an efficient nitrogen-fixing microsymbiont of the forage legume Biserrula pelecinus. Genome Announc. 5, e00902-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  29. 29

    Haskett, T. et al. Complete genome sequence of Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum. Genome Announc. 4, e00516-16 (2016).

    PubMed  PubMed Central  Google Scholar 

  30. 30

    Kaneko, T. et al. Complete genome sequence of the soybean symbiont Bradyrhizobium japonicum strain USDA6T. Genes 2, 763–787 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31

    Kaneko, T. et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189–197 (2002).

    PubMed  Google Scholar 

  32. 32

    Zheng, H. et al. The quorum sensing regulator CinR hierarchically regulates two other quorum sensing pathways in ligand-dependent and -independent fashions in Rhizobium etli. J. Bacteriol. 197, 1573–1581 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Tun-Garrido, C., Bustos, P., Gonzalez, V. & Brom, S. Conjugative transfer of p42a from Rhizobium etli CFN42, which is required for mobilization of the symbiotic plasmid, is regulated by quorum sensing. J. Bacteriol. 185, 1681–1692 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    He, X. et al. Quorum sensing in Rhizobium sp. strain NGR234 regulates conjugal transfer (tra) gene expression and influences growth rate. J. Bacteriol. 185, 809–822 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Danino, V. E., Wilkinson, A., Edwards, A. & Downie, J. A. Recipient-induced transfer of the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae is regulated by a quorum-sensing relay. Mol. Microbiol. 50, 511–525 (2003).

    CAS  PubMed  Google Scholar 

  36. 36

    Perez Carrascal, O. M. et al. Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris. Environ. Microbiol. 18, 2660–2676 (2016).

    CAS  PubMed  Google Scholar 

  37. 37

    Kumar, N. et al. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol. 5, 140133 (2015). Two (references 36 and 37) studies of sympatric populations of rhizobia reveal greater genetic diversity on rhizobial chromosomes and accessory plasmids than on symbiosis plasmids, suggesting that symbiosis genes are frequently exchanged in the natural environment between different rhizobial genotypes.

    PubMed  PubMed Central  Google Scholar 

  38. 38

    Sugawara, M. et al. Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies. Genome Biol. 14, R17 (2013).

    PubMed  PubMed Central  Google Scholar 

  39. 39

    Epstein, B. et al. Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet. 8, e1002868 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40

    Bailly, X. et al. Population genetics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME J. 5, 1–13 (2011).

    Google Scholar 

  41. 41

    Nelson, M. S., Chun, C. L. & Sadowsky, M. J. Type IV effector proteins involved in the Medicago-Sinorhizobium symbiosis. Mol. Plant. Microbe Interact. 30, 28–34 (2017).

    CAS  PubMed  Google Scholar 

  42. 42

    Ramsay, J. P., Sullivan, J. T., Stuart, G. S., Lamont, I. L. & Ronson, C. W. Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol. Microbiol. 62, 723–734 (2006).

    CAS  PubMed  Google Scholar 

  43. 43

    Haskett, T. L. et al. Assembly and transfer of tripartite integrative and conjugative genetic elements. Proc. Natl Acad. Sci. USA 113, 12268–12273 (2016). In some rhizobia, ICEs encoding symbiosis genes exist as three separate chromosomal regions that undergo recombination, assembling into a single circular ICE for conjugative transfer.

    CAS  PubMed  Google Scholar 

  44. 44

    Ling, J. et al. Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island. Proc. Natl Acad. Sci. USA 113, 13875–13880 (2016). This is the first report of symbiosis ICE transfer being enhanced by legume root exudates.

    CAS  PubMed  Google Scholar 

  45. 45

    Ramsay, J. P. et al. Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element. Proc. Natl Acad. Sci. USA 112, 4104–4109 (2015).

    CAS  PubMed  Google Scholar 

  46. 46

    Servin-Garciduenas, L. E. et al. Complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, isolated from field nodules of the enigmatic wild bean Phaseolus microcarpus. Genome Announc. 4, e00126-16 (2016).

    PubMed  PubMed Central  Google Scholar 

  47. 47

    Albareda, M. et al. Factors affecting the attachment of rhizospheric bacteria to bean and soybean roots. FEMS Microbiol. Lett. 259, 67–73 (2006).

    CAS  PubMed  Google Scholar 

  48. 48

    Ramachandran, V. K., East, A. K., Karunakaran, R., Downie, J. A. & Poole, P. S. Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol. 12, R106 (2011). By comparing gene expression in several plant rhizospheres, this study establishes the basis for specificity in interaction with host and non-host plants.

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49

    Garcia-Fraile, P. et al. Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant Soil 390, 251–264 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    Perry, B. J. & Yost, C. K. Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae. BMC Microbiol. 14, 298 (2014).

    PubMed  PubMed Central  Google Scholar 

  51. 51

    Perry, B. J., Akter, M. S. & Yost, C. K. The use of transposon insertion sequencing to interrogate the core functional genome of the legume symbiont Rhizobium leguminosarum. Front. Microbiol. 7, 1873 (2016).

    PubMed  PubMed Central  Google Scholar 

  52. 52

    Wheatley, R. M. et al. The role of O2 in the growth of Rhizobium leguminosarum bv. viciae 3841 on glucose and succinate. J. Bacteriol. 199, e00572-16 (2017).

    PubMed  Google Scholar 

  53. 53

    diCenzo, G. C. et al. Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. Nat. Comms. 7, 12219 (2016). Through the use of a genome-scale metabolic model, this study shows metabolic reprogramming in rhizobia when they switch from one niche to another, and these adaptations are supported mainly by the secondary replicon.

    CAS  Google Scholar 

  54. 54

    Vanderlinde, E. M., Hynes, M. F. & Yost, C. K. Homoserine catabolism by Rhizobium leguminosarum bv. viciae 3841 requires a plasmid-borne gene cluster that also affects competitiveness for nodulation. Environ. Microbiol. 16, 205–217 (2014).

    CAS  PubMed  Google Scholar 

  55. 55

    Mauchline, T. H. et al. Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome. Proc. Natl Acad. Sci. USA 103, 17933–17938 (2006). This is a high-throughput transcriptional induction study that aims to identify the solutes transported by nearly all the transporters of S. meliloti . This study shows the metabolic plasticity of soil-dwelling rhizobia to adapt and survive in a wide variety of niches.

    CAS  PubMed  Google Scholar 

  56. 56

    Frederix, M. et al. Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. Mol. Microbiol. 93, 464–478 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Zheng, H. et al. Flagellar-dependent motility in Mesorhizobium tianshanense is involved in the early stage of plant host interaction: study of an flgE mutant. Curr. Microbiol. 70, 219–227 (2015).

    CAS  PubMed  Google Scholar 

  58. 58

    Miller, L. D., Yost, C. K., Hynes, M. F. & Alexandre, G. The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation. Mol. Microbiol. 63, 348–362 (2007).

    CAS  PubMed  Google Scholar 

  59. 59

    Breakspear, A. et al. The root rair “Infectome” of Medicago truncatula uncovers changes in cell cycle genes and reveals a requirement for auxin signaling in rhizobial infection. Plant Cell 26, 4680–4701 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Pini, F. et al. Bacterial biosensors for in vivo spatiotemporal mapping of root secretion. Plant Physiol. 174, 1289–1306 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61

    Li, B. et al. Root exudates drive interspecific facilitation by enhancing nodulation and N2 fixation. Proc. Natl Acad. Sci. USA 113, 6496–6501 (2016).

    CAS  PubMed  Google Scholar 

  62. 62

    Maimaiti, J. et al. Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environ. Microbiol. 9, 435–444 (2007).

    CAS  PubMed  Google Scholar 

  63. 63

    Madsen, L. H. et al. The molecular network governing nodule organogenesis and infection in the model legume Lotus japonicus. Nat. Comms. 1, 10 (2010).

    Google Scholar 

  64. 64

    Wang, E. et al. A common signaling process that promotes mycorrhizal and oomycete colonization of plants. Curr. Biol. 22, 2242–2246 (2012).

    CAS  PubMed  Google Scholar 

  65. 65

    Gobbato, E. et al. A GRAS-type transcription factor with a specific function in mycorrhizal signaling. Curr. Biol. 22, 2236–2241 (2012).

    CAS  PubMed  Google Scholar 

  66. 66

    Gutjahr, C. et al. Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway. Plant Cell Online 20, 2989–3005 (2008).

    CAS  Google Scholar 

  67. 67

    Liang, Y. et al. Nonlegumes respond to rhizobial Nod factors by suppressing the innate immune response. Science 341, 1384–1387 (2013).

    CAS  PubMed  Google Scholar 

  68. 68

    Lopez-Gomez, M., Sandal, N., Stougaard, J. & Boller, T. Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. J. Exp. Bot. 63, 393–401 (2012).

    CAS  PubMed  Google Scholar 

  69. 69

    Lebeis, S. L. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).

    CAS  PubMed  Google Scholar 

  70. 70

    Wan, J. et al. A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell 20, 471–481 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71

    Miya, A. et al. CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis. Proc. Natl Acad. Sci. USA 104, 19613–19618 (2007).

    CAS  PubMed  Google Scholar 

  72. 72

    Miyata, K. et al. The bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice. Plant Cell Physiol. 55, 1864–1872 (2014).

    CAS  PubMed  Google Scholar 

  73. 73

    Zhang, X. et al. The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling. Plant J. 81, 258–267 (2015).

    CAS  PubMed  Google Scholar 

  74. 74

    Miyata, K. et al. Evaluation of the role of the LysM receptor-ilke kinase, OsNFR5/OsRLK2 for AM symbiosis in rice. Plant Cell Physiol. 57, 2283–2290 (2016).

    CAS  PubMed  Google Scholar 

  75. 75

    Limpens, E., van Zeijl, A. & Geurts, R. Lipochitooligosaccharides modulate plant host immunity to enable endosymbioses. Annu. Rev. Phytopathol. 53, 311–334 (2015).

    CAS  PubMed  Google Scholar 

  76. 76

    Kawaharada, Y. et al. Receptor-mediated exopolysaccharide perception controls bacterial infection. Nature 523, 308–312 (2015).

    CAS  PubMed  Google Scholar 

  77. 77

    Schmeisser, C. et al. Rhizobium sp strain NGR234 possesses a remarkable number of secretion systems. Appl. Environ. Microbiol. 75, 4035–4045 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78

    Okazaki, S., Kaneko, T., Sato, S. & Saeki, K. Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system. Proc. Natl Acad. Sci. USA 110, 17131–17136 (2013).

    CAS  PubMed  Google Scholar 

  79. 79

    Okazaki, S. et al. Rhizobium-legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS. ISME J. 10, 64–74 (2016).

    CAS  PubMed  Google Scholar 

  80. 80

    Williams, A. et al. Glucomannan-mediated attachment of Rhizobium leguminosarum to pea root hairs is required for competitive nodule infection. J. Bacteriol. 190, 4706–4715 (2008). This study demonstrates the polar localization and attachment of rhizobia on the root hair, which is mediated by glucomannan. The authors also show the effect of pH (acid and alkaline) on known attachment factors involved in rhizobial attachment and colonization of legume roots.

    CAS  PubMed  PubMed Central  Google Scholar 

  81. 81

    Smit, G., Kijne, J. W. & Lugtenberg, B. J. Involvement of both cellulose fibrils and a Ca2+-dependent adhesin in the attachment of Rhizobium leguminosarum to pea root hair tips. J. Bacteriol. 169, 4294–4301 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82

    Laus, M. C., van Brussel, A. A. & Kijne, J. W. Role of cellulose fibrils and exopolysaccharides of Rhizobium leguminosarum in attachment to and infection of Vicia sativa root hairs. Mol. Plant. Microbe Interact. 18, 533–538 (2005).

    CAS  PubMed  Google Scholar 

  83. 83

    Downie, J. A. The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol. Rev. 34, 150–170 (2010).

    CAS  PubMed  Google Scholar 

  84. 84

    Finnie, C., Zorreguieta, A., Hartley, N. M. & Downie, J. A. Characterization of Rhizobium leguminosarum exopolysaccharide glycanases that are secreted via a type I exporter and have a novel heptapeptide repeat motif. J. Bacteriol. 180, 1691–1699 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85

    Ausmees, N., Jacobsson, K. & Lindberg, M. A unipolarly located, cell-surface-associated agglutinin, RapA, belongs to a family of Rhizobium-adhering proteins (Rap) in Rhizobium leguminosarum bv. trifolii. Microbiol. 147, 549–559 (2001).

    CAS  Google Scholar 

  86. 86

    Russo, D. M, et al. Proteins exported via the PrsD-PrsE type i secretion system and the acidic exopolysaccharide are involved in biofilm formation by Rhizobium leguminosarum. J. Bacteriol. 188, 4474–4486 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Krehenbrink, M. & Downie, J. A. Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae. BMC Genomics 9, 55 (2008).

    PubMed  PubMed Central  Google Scholar 

  88. 88

    Finnie, C., Hartley, N. M., Findlay, K. C. & Downie, J. A. The Rhizobium leguminosarum prsDE genes are required for secretion of several proteins, some of which influence nodulation, symbiotic nitrogen fixation and exopolysaccharide modification. Mol. Microbiol. 25, 135–146 (1997).

    CAS  PubMed  Google Scholar 

  89. 89

    Mongiardini, E. J. et al. The rhizobial adhesion protein RapA1 is involved in adsorption of rhizobia to plant roots but not in nodulation. FEMS. Microbiol. Ecol. 65, 279–288 (2008).

    CAS  PubMed  Google Scholar 

  90. 90

    Mongiardini, E. J. et al. Overproduction of the rhizobial adhesin RapA1 increases competitiveness for nodulation. Soil Biol. Biochem. 41, 2017–2020 (2009).

    CAS  Google Scholar 

  91. 91

    Nigmatullina, L. R., Lavina, A. M., Vershinina, Z. R. & Baimiev, A. Role of bacterial adhesin RAPA1 in formation of efficient symbiosis of Rhizobium leguminosarum with bean plants. Mikrobiologiia 84, 705–711 (2015).

    CAS  PubMed  Google Scholar 

  92. 92

    Abdian, P. L., Caramelo, J. J., Ausmees, N. & Zorreguieta, A. RapA2 is a calcium-binding lectin composed of two highly conserved cadherin-like domains that specifically recognize Rhizobium leguminosarum acidic exopolysaccharides. J. Biol. Chem. 288, 2893–2904 (2013).

    CAS  PubMed  Google Scholar 

  93. 93

    Janczarek, M. & Rachwal, K. Mutation in the pssA gene Involved in exopolysaccharide synthesis leads to several physiological and symbiotic defects in Rhizobium leguminosarum bv. trifolii. Int. J. Mol. Sci. 14, 23711–23735 (2013).

    PubMed  PubMed Central  Google Scholar 

  94. 94

    Janczarek, M. & Skorupska, A. The Rhizobium leguminosarum bv. trifolii RosR: transcriptional regulator involved in exopolysaccharide production. Mol. Plant. Microbe Interact. 20, 867–881 (2007).

    CAS  PubMed  Google Scholar 

  95. 95

    Janczarek, M., Kutkowska, J., Piersiak, T. & Skorupska, A. Rhizobium leguminosarum bv. trifolii rosR is required for interaction with clover, biofilm formation and adaptation to the environment. BMC Microbiol. 10, 284 (2010).

    PubMed  PubMed Central  Google Scholar 

  96. 96

    Robledo, M. et al. Role of Rhizobium endoglucanase CelC2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces. Microb. Cell Fact. 11, 125 (2012).

    CAS  PubMed  Google Scholar 

  97. 97

    Russo, D. M. et al. Lipopolysaccharide O-chain core region required for cellular cohesion and compaction of in vitro and root biofilms developed by Rhizobium leguminosarum. Appl. Environ. Microbiol. 81, 1013–1023 (2015).

    PubMed  PubMed Central  Google Scholar 

  98. 98

    Vanderlinde, E. M. et al. Rhizobium leguminosarum biovar viciae 3841, deficient in 27-hydroxyoctacosanoate-modified lipopolysaccharide, is impaired in desiccation tolerance, biofilm formation and motility. Microbiol. 155, 3055–3069 (2009).

    CAS  Google Scholar 

  99. 99

    Lang, C. & Long, S. R. Transcriptomic analysis of Sinorhizobium meliloti and Medicago truncatula symbiosis using nitrogen fixation-deficient nodules. Mol. Plant. Microbe Interact. 28, 856–868 (2015).

    CAS  PubMed  Google Scholar 

  100. 100

    Roux, B. et al. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J. 77, 817–837 (2014).

    CAS  PubMed  Google Scholar 

  101. 101

    Massalha, H., Korenblum, E., Malitsky, S., Shapiro, O. & Aharoni, A. Live imaging of root-bacteria interactions in a microfluidics set-up. Proc. Natl Acad. Sci. USA 114, 4549–4554 (2017).

    CAS  PubMed  Google Scholar 

  102. 102

    Pessi, G. et al. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Mol. Plant Micro. Interact. 20, 1353–1363 (2007).

    CAS  Google Scholar 

  103. 103

    Barnett, M. J., Tolman, C. J., Fisher, R. F. & Long, S. R. A dual-genome symbiosis chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc. Natl Acad. Sci. USA 101, 16636–16641 (2004).

    CAS  PubMed  Google Scholar 

  104. 104

    Karunakaran, R. et al. Transcriptomic analysis of Rhizobium leguminosarum b.v. viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J. Bacteriol. 191, 4002–4014 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. 105

    Becker, A. et al. Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol. Plant Micro. Interact. 17, 292–303 (2004).

    CAS  Google Scholar 

  106. 106

    Mergaert, P. et al. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol. 132, 161–173 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. 107

    Guefrachi, I. et al. Extreme specificity of NCR gene expression in Medicago truncatula. BMC Genomics 15, 712 (2014).

    PubMed  PubMed Central  Google Scholar 

  108. 108

    Van de Velde, W. et al. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 327, 1122–1126 (2010).

    CAS  PubMed  Google Scholar 

  109. 109

    Mergaert, P. et al. Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis. Proc. Natl Acad. Sci. USA 103, 5230–5235 (2006). This breakthrough paper establishes that members of the IRLC legumes produce up to hundreds of NCR peptides that take control of the bacterial cell cycle and development.

    CAS  PubMed  Google Scholar 

  110. 110

    Penterman, J. et al. Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis. Proc. Natl Acad. Sci. USA 111, 3561–3566 (2014).

    CAS  PubMed  Google Scholar 

  111. 111

    Pini, F. et al. Cell cycle control by the master regulator CtrA in Sinorhizobium meliloti. PLoS Genet. 11, e1005232 (2015).

    PubMed  PubMed Central  Google Scholar 

  112. 112

    Wang, D. et al. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science 327, 1126–1129 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. 113

    Montiel, J. et al. Morphotype of bacteroids in different legumes correlates with the number and type of symbiotic NCR peptides. Proc. Natl Acad. Sci. USA 114, 5041–5046 (2017).

    CAS  PubMed  Google Scholar 

  114. 114

    Farkas, A. et al. Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms. Proc. Natl Acad. Sci. USA 111, 5183–5188 (2014).

    CAS  PubMed  Google Scholar 

  115. 115

    Bittner, A. N., Foltz, A. & Oke, V. Only one of five groEL genes is required for viability and successful symbiosis in Sinorhizobium meliloti. J. Bacteriol. 189, 1884–1889 (2007).

    CAS  PubMed  Google Scholar 

  116. 116

    Kim, M. et al. An antimicrobial peptide essential for bacterial survival in the nitrogen-fixing symbiosis. Proc. Natl Acad. Sci. USA 112, 15238–15243 (2015).

    CAS  PubMed  Google Scholar 

  117. 117

    Horváth, B. et al. Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant. Proc. Natl Acad. Sci. USA 112, 15232–15237 (2015).

    PubMed  Google Scholar 

  118. 118

    Wang, Q. et al. Host-secreted antimicrobial peptide enforces symbiotic selectivity in Medicago truncatula. Proc. Natl Acad. Sci. USA 114, 6854–6859 (2017).

    CAS  PubMed  Google Scholar 

  119. 119

    Yang, S. et al. Microsymbiont discrimination mediated by a host-secreted peptide in Medicago truncatula. Proc. Natl Acad. Sci. USA 114, 6848–6853 (2017).

    CAS  PubMed  Google Scholar 

  120. 120

    Price, P. A. et al. Rhizobial peptidase HrrP cleaves host-encoded signaling peptides and mediates symbiotic compatibility. Proc. Natl Acad. Sci. USA 112, 15244–15249 (2015).

    CAS  PubMed  Google Scholar 

  121. 121

    Haag, A. F. et al. Protection of Sinorhizobium against host cysteine-rich antimicrobial peptides is critical for symbiosis. PLoS Biol. 9, e1001169 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. 122

    Karunakaran, R. et al. BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. J. Bacteriol. 192, 2920–2928 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 123

    Ishihara, H. et al. Characteristics of bacteroids in indeterminate nodules of the leguminous tree Leucaena glauca. Microbes. Environ. 26, 156–159 (2011).

    PubMed  Google Scholar 

  124. 124

    Crespo-Rivas, J. C. et al. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis. Environ. Microbiol. 18, 2392–2404 (2016).

    CAS  PubMed  Google Scholar 

  125. 125

    Oono, R. & Denison, R. F. Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids. Plant Physiol. 154, 1541–1548 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. 126

    Hakoyama, T. et al. Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation. Nature 462, 514–518 (2009). This study shows that most rhizobia cannot make a functional nitrogenase because they lack homocitrate synthase (NifV) and the ability to synthesize homocitrate. Instead, they rely on the plant to make homocitrate via the product of Fen1.

    CAS  PubMed  Google Scholar 

  127. 127

    Terpolilli, J. J., Hood, G. A. & Poole, P. S. What determines the efficiency of N2-fixing Rhizobium-legume symbioses? Adv. Microb. Physiol. 60, 325–389 (2012).

    CAS  PubMed  Google Scholar 

  128. 128

    Prell, J. et al. Role of symbiotic auxotrophy in the Rhizobium-Legume symbioses. PLoS One 5, e13933 (2010).

    PubMed  PubMed Central  Google Scholar 

  129. 129

    Prell, J. et al. Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc. Natl Acad. Sci. USA 106, 12477–12482 (2009). This study demonstrates that bacteroids shut down many nutrient synthesis pathways, such as branched-chain amino acid synthesis, and become symbiotic auxotrophs dependent on the plant.

    CAS  PubMed  Google Scholar 

  130. 130

    Lodwig, E. M. et al. Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature 422, 722–726 (2003).

    CAS  PubMed  Google Scholar 

  131. 131

    Tian, C. F., Garnerone, A.-M., Mathieu- Demazière, C., Masson-Boivin, C. & Batut, J. Plant-activated bacterial receptor adenylate cyclases modulate epidermal infection in the Sinorhizobium melilotiMedicago symbiosis. Proc. Natl Acad. Sci. USA 109, 6751–6756 (2012).

    CAS  PubMed  Google Scholar 

  132. 132

    Murphy, P. J. et al. Synthesis of an opine-like compound, a rhizopine, in alfalfa nodules is symbiotically regulated. Proc. Natl Acad. Sci. USA 85, 9133–9137 (1988).

    CAS  PubMed  Google Scholar 

  133. 133

    King, B. J. et al. Regulation of O2 concentration in soybean nodules observed by in situ spectroscopic measurement of leghemoglobin oxygenation. Plant Physiol. 87, 296–299 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. 134

    Cherfils, J., Gibrat, J. F., Levin, J., Batut, J. & Kahn, D. Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition. J. Mol. Recognit. 2, 114–121 (1989).

    CAS  PubMed  Google Scholar 

  135. 135

    de Philip, P., Batut, J. & Boistard, P. Rhizobium meliloti Fix L is an oxygen sensor and regulates R. meliloti nifA and fixK genes differently in Escherichia coli. J. Bacteriol. 172, 4255–4262 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. 136

    David, M. et al. Cascade regulation of nif gene-expression in Rhizobium meliloti. Cell 54, 671–683 (1988).

    CAS  PubMed  Google Scholar 

  137. 137

    Ditta, G., Virts, E., Palomares, A. & Kim, C. H. The nifA gene of Rhizobium meliloti is oxygen regulated. J. Bacteriol. 169, 3217–3223 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  138. 138

    Boesten, B. & Priefer, U. B. The C-terminal receiver domain of the Rhizobium leguminosarum bv. viciae FixL protein is required for free-living microaerobic induction of the fnrN promoter. Microbiol. 150, 3703–3713 (2004).

    CAS  Google Scholar 

  139. 139

    Patschkowski, T., Schluter, A. & Priefer, U. B. Rhizobium leguminosarum bv viciae contains a 2nd fnr/fixK-like gene and an unusual FixL homolog. Mol. Microbiol. 21, 267–280 (1996).

    CAS  PubMed  Google Scholar 

  140. 140

    Martinez, M., Palacios, J. M., Imperial, J. & Ruiz-Argueso, T. Symbiotic autoregulation of nifA expression in Rhizobium leguminosarum bv. viciae. J. Bacteriol. 186, 6586–6594 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  141. 141

    Lindemann, A. et al. New target genes controlled by the Bradyrhizobium japonicum two-component regulatory system RegSR. J. Bacteriol. 189, 8928–8943 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. 142

    Sullivan, J. T., Brown, S. D. & Ronson, C. W. The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator. PLoS One 8, e53762 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  143. 143

    Mitsch, M. J., diCenzo, G. C., Cowie, A. & Finan, T. M. Succinate transport is not essential for symbiotic nitrogen fixation by Sinorhizobium meliloti nor Rhizobium leguminosarum. Appl. Environ. Microbiol. 84, e01561-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  144. 144

    Geddes, B. A. & Oresnik, I. J. Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacterium Sinorhizobium meliloti. Can. J. Microbiol. 60, 491–507 (2014).

    CAS  PubMed  Google Scholar 

  145. 145

    Mulley, G. et al. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol. Microbiol. 80, 149–167 (2011).

    CAS  PubMed  Google Scholar 

  146. 146

    Patriarca, E. J., Tate, R. & Iaccarino, M. Key role of bacterial NH4+ metabolism in Rhizobium-plant symbiosis. Microbiol. Mol. Biol. Rev. 66, 203–222 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. 147

    Terpolilli, J. J. et al. Lipogenesis and redox balance in nitrogen-fixing pea bacteroids. J. Bacteriol. 198, 2864–2875 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. 148

    Gubler, M., Zurcher, T. & Hennecke, H. The Bradyrhizobium japonicum fixBCX operon: identification of fixX and of a 5' mRNA region affecting the level of the fixBCX transcript. Mol. Microbiol. 3, 141–148 (1989).

    CAS  PubMed  Google Scholar 

  149. 149

    Earl, C. D., Ronson, C. W. & Ausubel, F. M. Genetic and structural analysis of the Rhizobium meliloti fixA, fixB, fixC, and fixX genes. J. Bacteriol. 169, 1127–1136 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. 150

    Buckel, W. & Thauer, R. K. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827, 94–113 (2013).

    CAS  PubMed  Google Scholar 

  151. 151

    Weghoff, M. C., Bertsch, J. & Müller, V. A novel mode of lactate metabolism in strictly anaerobic bacteria. Environ. Microbiol. 17, 670–677 (2014).

    PubMed  Google Scholar 

  152. 152

    Ledbetter, R. N. et al. The electron bifurcating FixABCX protein complex from Azotobacter vinelandii: generation of low-potential reducing equivalents for nitrogenase catalysis. Biochem 56, 4177–4190 (2017).

    CAS  Google Scholar 

  153. 153

    Scott, J. D. & Ludwig, R. A. Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation. Microbiol. 150, 117–126 (2004).

    CAS  Google Scholar 

  154. 154

    Poole, P. Shining a light on the dark world of plant root–microbe interactions. Proc. Natl Acad. Sci. USA 114, 4281–4283 (2017).

    CAS  PubMed  Google Scholar 

  155. 155

    Robledo, M. et al. Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots. Proc. Natl Acad. Sci. USA 105, 7064–7069 (2008).

    CAS  PubMed  Google Scholar 

  156. 156

    Ivanov, S. et al. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation. Proc. Natl Acad. Sci. USA 109, 8316–8321 (2012).

    CAS  PubMed  Google Scholar 

  157. 157

    Turner, T., James, E. & Poole, P. The plant microbiome. Genome Biol. 14, 209 (2013).

    PubMed  PubMed Central  Google Scholar 

  158. 158

    Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).

    CAS  PubMed  Google Scholar 

  159. 159

    Wetmore, K. M. et al. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. mBio 6, e00306-15 (2015).

    PubMed  PubMed Central  Google Scholar 

  160. 160

    Andrews, M. & Andrews, M. E. Specificity in legume-rhizobia symbioses. Int. J. Mol. Sci. 18, E705 (2017).

    PubMed  Google Scholar 

  161. 161

    Sprent, J. I., Ardley, J. & James, E. K. Biogeography of nodulated legumes and their nitrogen-fixing symbionts. New Phytol. 215, 40–56 (2017).

    CAS  PubMed  Google Scholar 

Download references


The authors thank T. Haskett and B. Jorrín for help with figures and A. East and A. Tkacz for comments on the manuscript. This work was supported by the Biotechnology and Biological Sciences Research Council [grant numbers BB/K001868/1, BB/K001868/2, BB/J007749/1, BB/J007749/2, BB/K006134/1, BB/L011484/1, BB/N003608/1, BB/N013387/1].

Author information




P.P., V.R. and J.T. substantially contributed to the discussion of content, wrote the article and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Philip Poole.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides


Root cortex

The outermost layer of the plant root that lies between the epidermal cells on the outside and vascular cells on the inside.


The complete set of genes present in the members of a certain group; for example, the sum of all genes found in bacterial strains belonging to a species.


Organisms that live on dead and decaying organic matter.

Oligotrophic lifestyle

The usage of a broad range of carbon sources in a nutritionally limited environment.


(LCO). Microbial signalling molecule with a 1,4-linked N-acetylglucosamine backbone that induces nodule formation. Species-dependent side decorations determine plant specificity.

Integrative and conjugative elements

(ICEs). ICEs are mobile genetic elements that can excise from the host chromosome to form a plasmid-like entity capable of catalysing its own transfer through conjugation. In recipient cells, ICEs integrate site-specifically into the chromosome, usually at conserved sites within an aminoacyl-tRNA gene.


Antimicrobial compounds produced by plants to protect them from pathogens.


Repeated cycles of DNA replication without cell division, which leads to extensive amplification of the entire genome.

Nodule senescence

Old nodules cease N2 fixation, and viable rhizobia are released back into the soil. In terminally differentiated rhizobia (for example, bacteroids from IRLC legumes), only undifferentiated bacteria from infection threads will be viable.

Exergonic reaction

A chemical reaction that releases free energy.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Poole, P., Ramachandran, V. & Terpolilli, J. Rhizobia: from saprophytes to endosymbionts. Nat Rev Microbiol 16, 291–303 (2018).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing