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Are there gamma-rhizobia?

November 13, 2011

Lionel Moulin has just raised an interesting question in a comment left on my post “What are rhizobia”.  He asks about the evidence for rhizobia in the class Gammaproteobacteria.  Lionel is particularly well placed to ask that question, of course, since it was he who brought us beta-rhizobia ten years ago (1).

My current view is that gamma-rhizobia probably do exist, but nobody has proved it yet.

Why do I think they exist?  Well, until ten years ago, all known rhizobia belonged to certain clades within the class Alphaproteobacteria, and it would have been perfectly rational to have speculated that the nodulation genes needed a specific genetic background, found only in this restricted bacterial group, in order to function.  The discovery of effective nodulation by the Betaproteobacteria  Burkholderia and Cupriavidus showed that this was not the case.

There are strong similarities between Betaproteobacteria like Burkholderia and Gammaproteobacteria like Pseudomonas.  Indeed, until 1992 (2), the bacteria we now know as Burkholderia were considered to be species of Pseudomonas. There are many similarities in phenotype and lifestyle, and mobile elements such as IncP plasmids move frequently between betas and gammas.  If Burkholderia can be a rhizobium, why not gammas like Pseudomonas or Xanthomonas?  They commonly interact with plants in other ways, so they have ample opportunities to pick up nodulation genes.

There is every reason, therefore, to think that gamma-rhizobia should be possible.  However, I agree with Lionel that none of the claims that I am aware of look convincing.  I think we should collect all the potential examples that we are aware of, and then evaluate them carefully.  Please send me references to publications that report potential gamma-rhizobia.  If you like, also tell us what you think about the evidence.  Please keep your comments polite, though – I will not publish abusive personal attacks!  Once we have a list of the potential evidence, we can discuss the current state of our knowledge, and perhaps decide how to look for definitive evidence.

Right now, I am at Manchester Airport on my way to Cuernavaca, Mexico, where the Centre for Genomic Sciences is celebrating 30 years.  This is a major rhizobium research centre, so I shall have more to say once I get there.

Peter

(1) Moulin L et al. Nature 411, 948-950 (2001) | doi:10.1038/35082070

(2) Yabuuchi E et al. Microbiol Immunol. 1992;36(12):1251-75.

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From → Papers, Taxonomy

9 Comments
  1. To me, the most advanced study for one strain being potentially a gamma-rhizobia is a paper in Syst. Appl. Microbiol., “Nodulation in black locust by the Gammaproteobacteria Pseudomonas sp. and the Betaproteobacteria Burkholderia sp” by Ayami Shiraishi, Norihisa Matsushita, Taizo Hougetsu. Volume 33, Issue 5, August 2010, Pages 269-274.
    There is nodulaiton tests on plant, reisolation of strains from the nodule and characterization by 16S rDNA sequencing, and nodulation genes sequencing. It seems at first sight pretty convincing. I just regret that some antibiotic tests were not done to select spontaneous mutant and test their nodulation ability. It is a way to be sure of a pure culture. There is always the problem of mixt cultures were 2 strains are very hard to separate, especially when one grows quickly and the other is quite slow. But overall, this pseudomonas strain might be the first one able to induce nodules. unfortunaltely, we have no idea if it fixes nitrogen symbiotically.

    • Thanks! I know there are other papers out there that appear to claim that they have found gamma-rhizobia, so please keep the suggestions coming in.

  2. Gilles Béna permalink

    But “what are rhizobia” is not the same question than “what is a rhizobia”? What would be the limit to accept a strain, isolate, as belonging to the rhizobia family? Rhizobia used to be only an alphaproteoacteria, used to be under the compulsory control of nod genes. They are not any more. So what is the lowest common denominator to design a bacteria as a rhizobia? Nodulation and Nitrogen fixation? If we want to push back the taxonomic frontiers of rhizobia, we should answer this question. This pseudomonas; or other gammaproteobacteria, could obviously be a rhizobia, but, for instance, is Frankia a rhizobia? It doesn’t harbor nod genes, but phytosynthetic bradyrhizobia don’t too, the nodule structure is different, but we have seen that it is also the case (I agree not so strongly) for other bacterial species. To me the answer is not that easy. Maybe you’ve got one??!

    • Most definitions in biology become unclear when one looks closely! I think of rhizobia as bacteria that cause the formation of root nodules in legumes and that fix nitrogen within those nodules. This would not include Frankia, but does include beta-rhizobia and the bradyrhizobia that make nodules without the classical nod genes. Of course, then you can ask what we will call bacteria that use nod genes only to cause nodules on nonlegumes, or archaea that make legume nodules, but we have not discovered such things yet, so they are not in need of names.

  3. I think we should mention in this topic the paper of Benhizia et al. (2004) that claimed to have found gamma-rhizobia in Hedysarum legume nodules. But in fact the story ended with this second paper by Muresu et al. (2008), that proved that in fact the real symbionts in Hedysarum were non-culturable Mesorhizobium (so classis rhizobia), with many endophytic bacteria in the nodules (but non-nodulating) belonging to the gamma proteobacteria class. So no gamma-rhizobia with this story!

    Lionel

    Benhizia Y, Benhizia H, Benguedouar A, Muresu R, Giacomini A, Squartini A., Gamma proteobacteria can nodulate legumes of the genus Hedysarum. Syst Appl Microbiol. 2004 Aug;27(4):462-8.

    Muresu R, Polone E, Sulas L, Baldan B, Tondello A, Delogu G, Cappuccinelli P, Alberghini S, Benhizia Y, Benhizia H, Benguedouar A, Mori B, Calamassi R, Dazzo FB, Squartini A.Coexistence of predominantly nonculturable rhizobia with diverse, endophytic bacterial taxa within nodules of wild legumes.. FEMS Microbiol Ecol. 2008 Mar;63(3):383-400. Epub 2008 Jan 9.

  4. Dr. Pooja Agrawal permalink

    Rhizobia means have the capacity either to fix nitrogen or nodule formation or both at same time

    • Hi Pooja –

      According to the definition I gave in one of my first blogs:
      “Rhizobia are legume root-nodule bacteria. They are soil bacteria that induce the formation of special structures (nodules) on the roots of their host plants. Inside these nodules, the rhizobia fix nitrogen.”

      According to my view, it is essential that a rhizobium is able to induce nodule formation. Other bacteria often get into nodules that a rhizobium has induced, but if they cannot themselves induce nodules then they are not rhizobia. Rhizobia normally fix nitrogen in nodules, but sometimes a bacterium induces a nodule, colonises it, but then does not fix any nitrogen because its fixation genes are defective or it is in an incompatible host plant. In such circumstances, I would be happy to call it a “non-fixing rhizobium” or “ineffective rhizobium”. So my answer is that a rhizobium must nodulate but need not fix.

      Peter

  5. Hukam S Gehlot permalink

    I agree with Peter. Some time rhizobia may nodulate host but lost nif gene and unable to fix N. So it is better to called ineffective rhizobia.

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