Rhizobiaceae

Culture of Rhizobium leguminosarum, copyright Landcare Research.

Belongs within: Rhizobiales.

The Rhizobiaceae are soil-dwelling aerobic bacteria, many of which live in association with plant roots.

Friend and/or foe: separating Rhizobium and Agrobacterium
Published 11 November 2014
Roots of cowpea Vigna unguiculata with nodules containing Rhizobium, copyright Dave Whitinger.

For as far back as we have records to know, farmers have recognised the value of crop rotation: varying the crops grown on a particular patch of land in order to avoid exhausting the soil of nutrients. It also did not take these ancient farmers long to realise the value of one of these rotated crops being a legume, the group of plants including peas, beans, lentils and the like. What these pioneers of agriculture did not know was that the rejuvenating effect that legumes seemed to have on the soil was due to bacteria living in their roots, the organisms that we now know as Rhizobium.

The value of Rhizobium to agriculture comes from its ability to fix nitrogen. Nitrogen compounds are essential for all living organisms (proteins, for instance, contain nitrogen). But while nitrogen is also the most abundant element in our planet’s atmosphere, most of it exists in a form that cannot be used directly by most organisms. Nitrogen-fixing bacteria are the exception, able to extract the nitrogen directly from the atmosphere and ‘fix’ it into more tractable compounds. Rhizobium is not the only genus of bacteria able to fix nitrogen, but it is certainly one of the most predominant. One of the limitations of nitrogen fixation is that it generally involves enzymes that do not work well in the presence of oxygen. Rhizobium cells induce the growth of nodules on legume roots, within which they are sheltered from that polluting gas. Not all Rhizobium live in legumes, however: they may also be found in large numbers free in the soil, with concentrations of tens of millions of cells per gram of soil having been recorded (Kuykendall et al. 2005).

Crown gall caused by Agrobacterium tumefaciens, copyright Christoph Müller.

Rhizobium has been regarded as closely related to another bacterial genus called Agrobacterium, whose significance for agriculture has been seen somewhat less favourably. As classically distinguished, Agrobacterium species do not fix nitrogen like Rhizobium, but they do resemble Rhizobium in causing growths on plant roots. These might be tumours, as in Agrobacterium tumefaciens (which can also cause galls to form elsewhere on the plant), or an overabundance of small rootlets, as in A. rhizogenes. While not necessarily fatal to the host plant, these deformities do often stunt growth, causing a loss in yield. A third species, A. radiobacter, has been recognised for non-pathogenic Agrobacterium.

However, as microbiologists gained a better understanding of the underlying genetics of Rhizobium and Agrobacterium, the picture became more complicated. The ability of Rhizobium to fix nitrogen, and of Agrobacterium to cause root deformities, is due to particular sets of genes in each. These genes are not contained in the main chromosome of each bacterium, but are held in little ‘mini-chromosomes’ called plasmids. And plasmids can be readily transferred from one bacterial cell to another. Through the transfer of the right plasmids, an Agrobacterium might gain the ability to fix nitrogen, or a Rhizobium might start inducing tumours. Phylogenetic analyses of the genera also indicated that some ‘Rhizobium‘ were more closely related to ‘Agrobacterium‘, and vice versa. As a result, at least one group of researchers has proposed uniting the two genera into one, Rhizobium. But others have been loathe to abandon a name as long-used in both the microbiological and agricultural literature as Agrobacterium (Farrand et al. 2003). There are recognisably distinct phylogenetic lines within the family Rhizobiaceae that includes the two genera, and even differences in plasmids are not entirely uninformative: not all strains can utilise all plasmids.

Cells of Rhizobium trifolii on root hair of clover, copyright Frank Dazzo.

There are also some significant genomic differences involved. Some of you may have learnt in biology class that the normal arrangement for bacterial cells is to have the bulk of the genome contained in a single circular chromosome, possibly with a scattering of small plasmids. The difference between the two is that the cell can function without the plasmids, but not without the chromosome. Rhizobium leguminosarum, the type species of Rhizobium, keeps to this arrangement, as do most other Rhizobium (though the plasmid containing the nitrogen-fixation genes is a bit of a whopper by usual standards). However, Agrobacterium tumefaciens*, the type species of its genus, is more unusual in having not one but two chromosomes: some of its vital genes have been transferred to what was originally a large plasmid (Slater et al. 2009). What is more, this second chromosome is not formed as a circle like other bacterial chromosomes, but is linear like the chromosomes of eukaryotes. Another ‘Agrobacterium‘ species, A. vitis, has the second chromosome like A. tumefaciens but it remains circular. The type strain of A. rhizogenes, on the other hand, has only a single circular chromosome, and appears to be closer to Rhizobium.

*The type strains of ‘Agrobacterium tumefaciens‘ and ‘A. radiobacter‘ are close enough that the two names should be synonymised into a single species. However, there seems to be an on-going dispute over which of the two names should be used for the combined taxon. I’m using A. tumefaciens for convenience, but I wouldn’t be able to judge which of the sides is correct.

Phylogenetic analysis also supports the recognition of a further genus of Rhizobiaceae, Ensifer, sitting outside the clade including Rhizobium and Agrobacterium. The type species of Ensifer, E. adhaerens, is a soil-dwelling bacterium that can live as a predator of other bacteria. It attaches to them end-wise (when multiple E. adhaerens attach to a single target cell, they may form a palisade) and causes them to burst open. Ensifer adhaerens is not an obligate predator—when suitable prey is not available, it can survive on free nutrients in the soil—and when analysed it turns out to be related to a clade of nitrogen-fixing bacteria previously recognised as the genus ‘Sinorhizobium‘. Indeed, one species of this genus turned out to be simply a non-parasitic form of E. adhaerens (Young 2003).

Systematics of Rhizobiaceae
<==Rhizobiaceae
    |--+--Allorhizobium undicolaCG03
    |  `--AgrobacteriumCG03
    |       |--A. radiobacterZ92
    |       |--A. rhizogenesTG88
    |       |--A. rubiK92
    |       `--A. tumefaciens [=Bacterium tumefaciens]S01
    `--Rhizobium Frank 1889CG03, S01
         |--R. etliYK99
         |--R. galegaeE92
         |--R. indigoferae Wei et al. 2002JC08
         |--R. larrymorei (Bouzar & Jones) Young 2004 [=Agrobacterium larrymorei Bouzar & Jones 2001]Y04
         |--R. leguminosarumTG88
         |--R. lotiGH01b
         |--R. lupiniZ92
         |--R. melilotiTG88
         |--R. phaseoliTG88
         |--R. trifoliiTG88
         `--R. vitisCG03
Rhizobiaceae incertae sedis:
  Ensifer Casida 1982 [incl. Sinorhizobium Chen et al. 1988]Y03
    |--*E. adhaerens Casida 1982 (see below for synonymy)Y03
    |--E. arboris (Nick et al.) Young 2003 [=Sinorhizobium arboris Nick et al. 1999]Y03
    |--E. fredii (Scholla & Elkan) Young 2003Y03 (see below for synonymy)
    |--E. kostiensis (Nick et al.) Young 2003 [=Sinorhizobium kostiense Nick et al. 1999]Y03
    |--E. kummerowiae (Wei et al.) Young 2003 [=Sinorhizobium kummerowiae Wei et al. 2002]Y03
    |--E. medicae (Rome et al.) Young 2003 [=Sinorhizobium medicae Rome et al. 1996]Y03
    |--E. meliloti (Dangeard 1926) Young 2003 [=Sinorhizobium meliloti]Y03
    |--E. saheli (de Lajudie et al.) Young 2003 [=Sinorhizobium saheli de Lajudie et al. 1994]Y03
    |--E. terangae (de Lajudie et al.) Young 2003 [=Sinorhizobium terangae de Lajudie et al. 1994]Y03
    `--E. xinjiangensis (Chen et al.) Young 2003 [=Sinorhizobium xinjiangense Chen et al. 1988]Y03
  CarbophilusGH01a
  Photobacterium thompsonumE92

*Ensifer adhaerens Casida 1982 [=Sinorhizobium adhaerens (Casida) Willems et al. 2003 (nom. illeg.); incl. Sinorhizobium morelense Wang, Tan et al. 2002]Y03

Ensifer fredii (Scholla & Elkan) Young 2003Y03 [=Sinorhizobium fredii Scholla & Elkan 1984Y03, Rhizobium frediiZ92]

*Type species of generic name indicated

References

[CG03] Cho, J.-C., & S. J. Giovannoni. 2003. Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order ‘Rhizobiales’. International Journal of Systematic and Evolutionary Microbiology 53: 1853–1859.

[E92] Eady, R. R. 1992. The dinitrogen-fixing bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 534–553. Springer-Verlag: New York.

Farrand, S. K., P. B. van Berkum & P. Oger. 2003. Agrobacterium is a definable genus of the family Rhizobiaceae. International Journal of Systematic and Evolutionary Microbiology 53 (5): 1681–1687.

[GH01a] Garrity, G. M., & J. G. Holt. 2001a. The road map to the Manual. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[GH01b] Garrity, G. M., & J. G. Holt. 2001b. Phylum BIX. Deferribacteres phy. nov. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 465–471. Springer.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

[K92] Kado, C. I. 1992. Plant pathogenic bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 659–674. Springer-Verlag: New York.

Kuykendall, L. D., J. M. Young, E. Martínez-Romero & H. Sawada. 2005. Genus I. Rhizobium Frank 1889, 337AL. In: Garrity, G., D. J. Brenner, N. R. Krieg & J. T. Staley (eds) Bergey’s Manual of Systematic Bacteriology vol. 2. The Proteobacteria pt C. Springer.

Slater, S. C., B. S. Goldman, B. Goodner, J. C. Setubal, S. K. Farrand, E. W. Nester, T. J. Burr, L. Banta, A. W. Dickerman, I. Paulsen, L. Otten, G. Suen, R. Welch, N. F. Almeida, F. Arnold, O. T. Burton, Z. Du, A. Ewing, E. Godsy, S. Heisel, K. L. Houmiel, J. Jhaveri, J. Lu, N. M. Miller, S. Norton, Q. Chen, W. Phoolcharoen, V. Ohlin, D. Ondrusek, N. Pride, S. L. Stricklin, J. Sun, C. Wheeler, L. Wilson, H. Zhu & D. W. Wood. 2009. Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. Journal of Bacteriology 191 (8): 2501–2511.

[S01] Sneath, P. H. A. 2001. Bacterial nomenclature. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 83–88. Springer.

[TG88] Tepfer, D., A. Goldmann, N. Pamboukdjian, M. Maille, A. Lepingle, D. Chevalier, J. Dénarié & C. Rosenberg. 1988. A plasmid of Rhizobium meliloti 41 encodes catabolism of two compounds from root exudate of Calystegium sepium. Journal of Bacteriology 170 (3): 1153–1161.

[YK99] Yamada, Y., H. Kawasaki, Y. Nagatsuka, K. Mikata & T. Seki. 1999. The phylogeny of the cactophilic yeasts based on the 18S ribosomal RNA gene sequences: the proposals of Phaffomyces antillensis and Starmera caribaea, new combinations. Bioscience, Biotechnology, and Biochemistry 63: 827–832.

[Y03] Young, J. M. 2003. The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology 53: 2107–2110.

[Y04] Young, J. M. 2004. Renaming of Agrobacterium larrymoorei Bouzar and Jones 2001 as Rhizobium larrymoorei (Bouzar and Jones 2001) comb. nov. International Journal of Systematic and Evolutionary Microbiology 54: 149.

[Z92] Zumpft, W. G. 1992. The denitrifying prokaryotes. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 554–582. Springer-Verlag: New York.

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