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October 26, 2011

Some history

Once upon a time, over a hundred years ago, there was only one species of legume root-nodule bacterium, Rhizobium leguminosarum, the root-dweller of the legumes1.  Nearly fifty years later,  people had noticed that isolates differed stably in the range of host plants they could nodulate2, and used this as a basis for a classification based on “cross-inoculation groups”.  R. leguminosarum (now just the symbiont of peas and vetches) was joined by R. trifolii (the clover rhizobium), R. phaseoli (the bean rhizobium), R. lupini (the lupin rhizobium), R. japonicum (the Japanese rhizobium, which nodulated soybeans) and R. meliloti (the sweetclover rhizobium).  After that, nothing happened in rhizobial taxonomy for another fifty years. Then Carl Jordan really shook things up with his idea that general bacteriological similarity would be a better basis for taxonomy than host range alone.  He split off a new genus Bradyrhizobium for rhizobia that grew slowly in culture3, and he amalgamated R. leguminosarum, R.  trifolii and R. phaseoli into a single species4.  Henceforth, they became mere biological varieties (biovars) of the single species, R. leguminosarum.  Since then, there has been an explosion in the description of new rhizobial taxa, and several distinct species have been sliced off the edges of Jordan’s monolithic R. leguminosarum, but the concept of biovars has proved useful, and has been extended to other rhizobial species as well.

 Core and accessory genomes

Now that we have genomic data, the basis of biovars is clearer.  Host specificity is determined by “nodulation” genes that form part of the accessory, or shell, genome, often carried on plasmids5.  By contrast, a stable taxonomy can be based on core genes involved in “housekeeping” processes, and these genes are usually on the chromosome.  Hence, bacteria of the same species (core) can have different host specificity (accessory).


Of course, bacteria have large accessory genomes and these can confer many important properties besides nodulation.  For example, the host range of a plant pathogen may be characterised as its “pathovar”, whereas the antigenic properties of the cell surface of a bacterium determine its “serovar”.  By contrast with these examples, the term “biovar” is very bland and does not convey any notion of the particular property that is being described.  The term “symbiotic variety”, or “symbiovar” would be much more precise, and this would be helpful in the future as more properties conferred by the accessory genomes of bacteria are described.  A recent paper by Rogel et al. makes just this proposal6, and I suggest that we all adopt the term “symbiovar” from now on.  The Rogel paper provides a very useful summary of the occurrence of symbiovars in different rhizobial species.

  1. Frank, B. (1889). Über die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7, 332-346.
  2. Fred EB, Baldwin IL, McCoy E (1932) Root nodule bacteria and leguminous plants University of Wisconsin.  Digitized19 Feb 2008
  3. Jordan DC (1982) Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. International Journal of Systematic Bacteriology 32, 136-139.  doi: 10.1099/00207713-32-1-136
  4. Jordan, D. C. (1984). Family III. Rhizobiaceae Conn 1938, 321 AL .In  Bergey’s  Manual  of  Systematic  Bacteriology,  vol.  1,  pp.234±254.  Edited  by  N. R.  Krieg  &  J. G.  Holt.  Baltimore: Williams & Wilkins.
  5. Young JPW, Crossman L, Johnston A, et al. (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biology 7, R34.  doi: 10.1186/gb-2006-7-4-r34
  6. Rogel MA, Ormeño-Orrillo E, Martinez Romero E (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Systematic and Applied Microbiology 34, 96-104.  doi: 10.1016/j.syapm.2010.11.015

From → Taxonomy

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