Rhizobium anhuiense
Before we get stuck into the Rhizobium leguminosarum species complex (Rlc), let us have a quick look at its sister species, R. anhuiense. So far, this is a very compact clade that is on a long branch and clearly forms a single species, with all strains having ANI > 98 with the type strain. Here is an excerpt from the 120-gene phylogeny:
Here is the list of genomes that are included in R. anhuiense, with their ANI to the type strain:
|
R._anhuiense_CCBAU_23252_GCF_003985145.1.fna |
100.00 |
|
R._anhuiense_S10_GCF_002531655.1.fna |
98.92 |
|
R._anhuiense_J3_GCF_002531645.1.fna |
98.91 |
|
R._sp._BK398_BK398_GCF_004343265.1.fna |
98.88 |
|
R._anhuiense_Y27_GCF_002531615.1.fna |
98.87 |
|
R._anhuiense_JX3_GCF_002531635.1.fna |
98.87 |
|
R._anhuiense_CCBAU43229_GCF_012276505.1.fna |
98.82 |
|
R._anhuiense_C15_GCF_002531695.1.fna |
98.81 |
|
R._anhuiense_WYCCWR10015_GCF_001632995.1.fna |
98.79 |
|
R._tropici_CF286_GCF_000800135.1.fna |
98.43 |
|
R._leguminosarum_CF307_GCF_000799945.1.fna |
98.40 |
This homogeneity is surprising given their diverse origins. The type strain, CCBAU23252, is a symbiont of Vicia faba, as is CCBAU43229, whereas WYCCWR10015 nodulates Trifolium repens, and C15, S10, J3, JX3, Y27 are all Phaseolus vulgaris symbionts. They are all from China, but represent three symbiovars. Strains CF286 and CF307 were isolated by the JGI from Populus root endosphere, presumably in the USA. They were published before R. anhuiense was defined, but it is not clear why they were assigned to different species when they are so similar. The origin of BK398 is unspecified, but it is probably also from Populus. There are also three assemblies from a JGI study of single cells from Arabidopsis roots that fall in the R. anhuiense clade, but the genomes are very incomplete and error-prone, so they are not shown in the phylogeny.
R. anhuiense seems to be widespread as a legume symbiont across China, with various symbiovars, but I am not aware of any reports of symbionts from outside China. Has anyone else seen it? The fact that it keeps cropping up in non-legume rhizospheres in the USA suggests that it might have a much wider distribution.
From now on, we will turn our attention to the Rlc itself.
Dear Peter,
ReplyDeleteWe are enthusiastic about the idea of clarifying/defining the boundaries of the leguminosarum complex species. This will certainly help the community. There is no doubt that you are the best expert to solve this question. We will be pleased to help, if necessary, although we are specialists in systematic.
We read you posts with great interest. Thank you to give us the historical perspective and for initiating the debate for a new rationale organization of R leguminosarum , based on our current knowledge.
In your first tree you suggest to restrict Rlc to the large green clade. What do you think about extending this complex to the Anhuiense Gs and more generally to all related bacteria that nodulate clover, pea, fababean and bean that share closely related symbiotic clusters on symbiotic plasmid? The general objective might be to define a large leguminosarum complex gathering all “leguminosarum” symbiovars? We know, for example, that bacteria of the symbiovar viciae may belong to R anuihense R pisi or R binae… It is apparently the same story for symbiovars trifoli or phaseoli… To our understanding, Anhuiense Gs were defined as separate species only because their ANI with R leguminosarum Gs are lowers than the arbitrary limit. But, up to now there is little evidence suggesting that their symbiotic characteristics may strongly differ from the other leguminosarum (ie nodulating clover, pea, faba etc and possibly associated as PGP with non legume plants). To our knowledge, there is no clear rule and/or ANI threshold to define a complex species boundaries. Is this aim completely heterodox or unrealistic?
Best regards,
Stephane Boivin and Marc Lepetit