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Aminobacter huakuii

August 30, 2012

The first complete rhizobial genome to be published was that of Aminobacter huakuii symbiovar loti strain MAFF303099.  “What?”, I hear you say, “I thought it was Mesorhizobium loti!”.

Well, for a start, core gene sequences of MAFF303099 are not close to those of the type strain of M. loti; they are closer to those of M. huakuii.  On the other hand, MAFF303099 nodulates Lotus (unlike the type strain of M. huakuii, which nodulates Astragalus), and its nodA gene is similar to those of M. loti strains that also nodulate Lotus (Turner et al. 2002).  Since strains that nodulate the same hosts and have closely related nodulation genes are said to belong to the same symbiovar (Rogel et al. 2011), MAFF303099 could be called M. huakuii symbiovar loti.

In 2003, Willems et al. proposed the amalgamation of the genera Sinorhizobium and Ensifer.  They suggested using Sinorhizobium as the name for the combined genus, but under the rules of precedent, Ensifer has to be used for the combined genus because this name was published earlier (Judicial Commission 2008).

In 2004, in a talk at the North American Rhizobium Conference in Bozeman, Montana, I pointed out that a similar situation existed for the genera Mesorhizobium and Aminobacter, since the 16S SSU sequence of A. aminovorans fell inside the clade of Mesorhizobium sequences (Sawada et al. 2003).  A combined genus would, under the rules of precedent, be called Aminobacter, so I suggested that MAFF303099 might become Aminobacter huakuii biovar loti.

I was half joking, and certainly not keen to see it become official, but it seems that we are now a step further down that road.  Maynaud et al. (2012) have described a new species of Aminobacter that nodulates Anthyllis.  They say it represents “the first occurrence of legume symbionts in the genus Aminobacter“.  Their core gene phylogenies certainly show the symbiotic strains to be close to Aminobacter species, but they do not show a convincing separation between Aminobacter and Mesorhizobium.  I feel it is only a matter of time before some taxonomist spots the opportunity for a quick publication and proposes the amalgamation of the genera.

Remember, you read it here first!

 

Peter

 

Judicial Commission of the International Committee on Systematics of Prokaryotes (2008) The genus name Sinorhizobium Chen et al. 1988 is a later synonym of Ensifer Casida 1982 and is not conserved over the latter genus name, and the species name ‘Sinorhizobium adhaerens‘ is not validly published. Opinion 84. International Journal of Systematic and Evolutionary Microbiology 58: 1973. http://dx.doi.org/10.1099/ijs.0.2008/005991-0

Maynaud, G., Willems, A., Soussou, S., Vidal, C., Mauré, L., Moulin, L. et al. Molecular and phenotypic characterization of strains nodulating Anthyllis vulneraria in mine tailings, and proposal of Aminobacter anthyllidis sp. nov., the first definition of Aminobacter as legume-nodulating bacteria. Systematic and Applied Microbiology 35: 65-72. http://dx.doi.org/10.1016/j.syapm.2011.11.002

Rogel, M.A., Ormeño-Orrillo, E., and Martinez Romero, E. (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Systematic and Applied Microbiology 34: 96-104. http://dx.doi.org/10.1016/j.syapm.2010.11.015

Sawada, H., Kuykendall, L.D., and Young, J.M. (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. The Journal of General and Applied Microbiology 49: 155-179. http://dx.doi.org/10.2323/jgam.49.155

Turner, S.L., Zhang, X.X., Li, F.D., and Young, J.P.W. (2002) What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti. Microbiology 148: 3330-3331.

Willems, A., Fernandez-Lopez, M., Muñoz-Adelantado, E., Goris, J., De Vos, P., Martinez-Romero, E. et al. (2003) Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb. nov. Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology 53: 1207-1217. http://dx.doi.org/10.1099/ijs.0.02264-0

 

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From → Papers, Taxonomy

5 Comments
  1. I competely missed that information about your Aminobacter huakuii half joke proposal. How fun is our field 😉 Now we are again in trouble with these names switch!
    I’m wondering if all the photosynthetic Bradyrhizobium should not be called Photorhizobium for the same reason!

  2. Photorhizobium? Now there’s one I’d forgotten! In 1989-1990, the Boyce Thompson folks were bandying it about as a possible name for their magic strain BTAi1 (BTAi stands for Boyce Thompson Aeschynomene indica). Fortunately, it was never published as a valid name. In any case, Bradyrhizobium was proposed in 1982 so would take priority. Rhodopseudomonas, on the other hand, goes back as far as 1937, so you could destroy Bradyrhizobium by amalgamating it with Rhodopseudomonas. It is close enough to be worth a try!

    Peter

  3. Ana permalink

    Interesting article! Just wanted to point out that the first report of Aminobacter as a legume symbiont was in 2009: Estrella, M. J., S. Muñoz, M. J. Soto, O. Ruiz, and J. Sanjuán. 2009. Genetic diversity and host range of rhizobia nodulating Lotus tenuis in typical soils of the Salado River Basin (Argentina). Appl. Environ. Microbiol. 75:1088-1098.
    Later in 2010 the group from Granada found more Aminobacter species associated with Lotus: Lorite M, Muñoz S, Olivares J, Soto M, Sanjuán J. Characterization of Strains unlike Mesorhizobium loti That Nodulate Lotus spp. in Saline Soils of Granada, Spain. Appl Environ Microbiol. 2010 June; 76(12): 4019–4026.

    • Thanks, Ana, for pointing out those prior papers that I was unaware of. The strange thing is that Maynaud et al. did know about the Estrella (2009) paper, and even cited it as an example of symbiotic Aminobacter, and yet still felt able to claim in their title that they were reporting “the first definition of Aminobacter as legume-nodulating bacteria”.

      To make life easy for others who would like to look at these articles, here are the URLs:
      http://aem.asm.org/content/75/4/1088.short
      http://aem.asm.org/content/76/12/4019.short

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