Rhizobium leguminosarum 7

 

Genospecies E – Rhizobium leguminosarum sensu stricto

Genospecies E includes the type strain of Rhizobium leguminosarum, so it is, by definition, the true R. leguminosarum in the narrow sense.

The last time I looked (25/07/2020), there were 68 gsE genomes in GenBank. The same set of genomes is found in the group with ANI > 97% to the type strain and in a well-separated clade in the phylogeny. They are, in alphabetical order:

R._gallicum_R602sp

R._indigoferae_CCBAU_71042

R._leguminosarum_128C53

R._leguminosarum_23B

R._leguminosarum_3B

R._leguminosarum_4292

R._leguminosarum_4B

R._leguminosarum_ATCC_14479

R._leguminosarum_BIHB_1217

R._leguminosarum_CB1

R._leguminosarum_CC283b

R._leguminosarum_CZF1F8

R._leguminosarum_CZP1G1

R._leguminosarum_CZP1G4

R._leguminosarum_CZP1G9

R._leguminosarum_CZP1H7

R._leguminosarum_CZP3C9

R._leguminosarum_CZP3G7

R._leguminosarum_CZP3H7

R._leguminosarum_FRF1A1

R._leguminosarum_FRF3E2

R._leguminosarum_FRP2D7

R._leguminosarum_FRP3A12

R._leguminosarum_FRP3E11

R._leguminosarum_FRP3E5

R._leguminosarum_FRP3G5

R._leguminosarum_FRP4D11

R._leguminosarum_FRP4H3

R._leguminosarum_FRP5A4

R._leguminosarum_FRP5C5

R._leguminosarum_FRP5D3

R._leguminosarum_FRP5H7

R._leguminosarum_GB51

R._leguminosarum_GD25

R._leguminosarum_IAUb11

R._leguminosarum_JHI1084

R._leguminosarum_JHI944

R._leguminosarum_L113

R._leguminosarum_L125

R._leguminosarum_L324

R._leguminosarum_LCS0306

R._leguminosarum_OV152

R._leguminosarum_P1.14

R._leguminosarum_P2.59

R._leguminosarum_P221

R._leguminosarum_RSP1E11

R._leguminosarum_Rt24.2

R._leguminosarum_SEP2G2

R._leguminosarum_SEP3F1

R._leguminosarum_SEP4B10

R._leguminosarum_SEP5D11

R._leguminosarum_SEP5D7

R._leguminosarum_SM126A_gsE

R._leguminosarum_SM135A_gsE

R._leguminosarum_SM135B_gsE

R._leguminosarum_SM141B_gsE

R._leguminosarum_SM149A_gsE

R._leguminosarum_SM159_gsE

R._leguminosarum_SM160_gsE

R._leguminosarum_SM168A_gsE

R._leguminosarum_SM168B_gsE

R._leguminosarum_SM45_gsE

R._leguminosarum_SM52_gsE

R._leguminosarum_UPM1137

R._leguminosarum_UPM791

R._leguminosarum_UPM988

R._leguminosarum_USDA_2370_GCF_003058385.1

R._leguminosarum_USDA_2370_GCF_002008365.1

The last two entries are two genomes for the type strain, sequenced by different groups. Fortunately, they are more or less identical (ANI 99.9981). More problematic are the first two entries on the list, which are labelled as different species altogether. R. indigoferae CCBAU 71042 is a well known problem. The type strain of this species, which should be related to R. gallicum according to the original publication, has been lost and replaced by a strain of R. leguminosarum. This has been discussed by the Taxonomy Subcommittee (https://doi.org/10.1099/ijsem.0.002974 minute 18). Now we have a complete genome sequence to prove that the available culture is R. leguminosarum, not R. indigoferae! The R. gallicum genome seems to be a different kind of mistake. This genome (GCF_000373025.1) was published by JGI, who seem to have got hold of the wrong strain. Fortunately, the real R. gallicum type strain R602 has been sequenced by CCG UNAM and is available as GCF_000816845.1.

That leaves genome sequences of 65 different known strains of genospecies E. The majority of these are symbiovar viciae, although the SM strains are sv. trifolii from our Danish project (Cavassim et al. 2020, https://doi.org/10.1099/mgen.0.000351). Since we already know the genospecies of all strains from that study, this has been appended to their names to reassure us that we are looking at the right genospecies.

Genospecies E is shown below in an extract from the phylogeny based on 120 genes. It is clearly defined by a long, well supported branch. There is a very tight group around the type strain (USDA2370), and some looser groups, matching the pattern of the ANI values that we saw in the previous post. I think the strains in the tight group are all symbiovar viciae, except for 4292 (phaseoli), but they are from many different places. There is a clade of trifolii strains at the bottom, mostly Danish but a couple from Russia. The other strains are a mix of viciae, trifolii and phaseoli, and sometimes closely related strains are of different symbiovars, e.g. 23B (trifolii) and P1.14 (viciae), SM45 (trifolii) and UPM1137 (viciae).

 

Despite their diverse geographic origins and various symbiovars, the strains in gsE form a tight group, easily distinguished by phylogeny and ANI from any other strains. Whatever the mechanisms that created and maintained it, genospecies E is a real biological entity that deserves recognition. If the rest of the Rlc is as clear as this, our job will soon be done! Next time, I’ll look at gsD.