Rhizobium leguminosarum 12

Genospecies C – Rhizobium ruizarguesonis

 

We first described genospecies A to E of the Rlc in our paper Kumar et al. 2015 (http://dx.doi.org/10.1098/rsob.140133) from just one square metre of soil, but later found the same five genospecies across sites in northern Europe (Cavassim et al. 2020, https://doi.org/10.1099/mgen.0.000351). We have covered gsE, gsD, gsA and gsB so far, so that just leaves gsC. I left it until last because this is the largest and most complex of these genospecies. It was quite a squeeze to fit the phylogeny onto the screen for this extract.

 

 

 

The ANI plot looks like this, using UPM1133 as the reference.

Strain UPM1133 is marked with a green “T”. There are no other strains very close to UPM1133. The closest is CZP2H1 (ANI 98.50), closely followed by 144 more strains down to 97.67; these are the strains marked with a dark green arrow in both figures. The clade marked in mid green (17 strains) has ANI values 96.90-97.22. The light green clade (5 strains) has ANI 96.07-96.54. The dark grey clade has ANI 94.80-94.94. The light grey clade has ANI below 94, similar to the values for strains of other genospecies that are not shown here.

 

I conclude that all three of the green clades should be included within gsC, as these strains all have ANI above 96 to the type strain. The light green clade includes SM132, which Cavassim et al. considered to be gsC, so that is consistent. On the other hand, the two grey clades are definitely too distant to include in gsC.

 

Why did I use UPM1133 as the reference? Recently, the species Rhizobium ruizarguesonis was described, with UPM1133 as its type strain (Jorrin et al. 2020, https://doi.org/10.1016/j.syapm.2020.126090). This species was named in honour of Tomás Ruiz-Arguëso, an excellent rhizobium researcher and good friend who sadly succumbed to COVID-19 in Madrid earlier this year. Since this strain is clearly right in the heart of gsC, it follows that gsC already has a name – it is Rhizobium ruizarguesonis. The species was described with just four strains, but now it has 168 strains, all with genome sequences. Like gsB, these include many European strains from three large recent studies: sv. trifolii strains from Cavassim et al. 2020 (https://doi.org/10.1099/mgen.0.000351), and sv. viciae strains from Boivin et al. 2020 (https://doi.org/10.1111/nph.16392) and unpublished work at the James Hutton Institute (JHI strains). There are also strains from other sources: Vf2, Vc2, Lp8, Vh3, Vf5, Ps8 from our study of symbionts of wild and cultivated Viceae in York (Mutch & Young 2004, https://doi.org/10.1111/j.1365-294X.2004.02259.x),  GB29, GB30 and P2.5 from pea in Poland,  L116 from lentil in France, RCAM1026 from pea in Kazakhstan, A1 from pea in Russia, 31B from red clover in Russsia, TA1 from Trifolium spumosum in Australia, and, of course, the four UPM strains from pea in Italy and Germany in the original description of R. ruizarguesonis. Strains from different studies, including both symbiovars viciae and trifolii, are well mixed thoughout the phylogeny. This implies two things: Strains of gsC have high geographic mobility, and symbiosis genes are highly mobile within the genospecies.

What about those two grey clades? The three strains in the dark grey clade are all viciae from wild legumes: Vaf-64 from Vavilovia formosa in Armenia, JHI1093 and  JHI1096 from Lathyrus linifolius Scotland. The JHI strains both have ANI of 97.66 to Vaf-46, so we can treat this clade as a genospecies. The next closest strain by ANI is UPM1134, which is in gsC. The light grey clade has SRDI565 (a trifolii strain isolated in Australia) and five GPTR strains from unspecified root nodules in Spain. The GPTR strains are labelled R. laguerreae, but they are definitely not R. laguerreae, which is in a distant part of the Rlc and will be discussed in the next post. The GPTR strains have ANI of 97.75-97.92 to SRDI565, so they are all the same genospecies. No other genome has ANI to SRDI565 above 94.64. We can conclude that we have two more genospecies here. Let’s call the dark grey clade gsL and the light grey on gsM.

A complete list of strains in gsC is going to be long, but the phylogeny is hard to read so I think the list will be helpful. Here goes – ranked by ANI to UPM1133.

 

gcC (dark green clade)

R._sp._UPM1133_UPM1133.fna

R._leguminosarum_CZP2H1.fna

R._leguminosarum_GB29.fna

R._leguminosarum_P2.5.fna

R._leguminosarum_GB30.fna

R._leguminosarum_CZF1B5.fna

R._leguminosarum_SM71_gsC.fna

R._leguminosarum_CZF5G8.fna

R._leguminosarum_CZF5B4.fna

R._leguminosarum_SEF4H7.fna

R._leguminosarum_JHI788.fna

R._leguminosarum_JHI387.fna

R._leguminosarum_JHI1253.fna

R._leguminosarum_CZP2D2.fna

R._leguminosarum_CZP3H6.fna

R._leguminosarum_JHI1592.fna

R._leguminosarum_SM169_gsC.fna

R._leguminosarum_JHI388.fna

R._leguminosarum_VF5.fna

R._leguminosarum_L116.fna

R._leguminosarum_JHI370.fna

R._leguminosarum_SM44_gsC.fna

R._leguminosarum_SM58_gsC.fna

R._leguminosarum_SM53_gsC.fna

R._leguminosarum_SM55_gsC.fna

R._leguminosarum_SM66_gsC.fna

R._leguminosarum_SM137A_gsC.fna

R._leguminosarum_RCAM_1026.fna

R._leguminosarum_SM50_gsC.fna

R._leguminosarum_SM127_gsC.fna

R._leguminosarum_SM43_gsC.fna

R._leguminosarum_SM118_gsC.fna

R._leguminosarum_SM67_gsC.fna

R._leguminosarum_SM68_gsC.fna

R._leguminosarum_SM61_gsC.fna

R._leguminosarum_SM70_gsC.fna

R._leguminosarum_JHI787.fna

R._leguminosarum_31B.fna

R._leguminosarum_SM106_gsC.fna

R._leguminosarum_SM69_gsC.fna

R._leguminosarum_SM60_gsC.fna

R._leguminosarum_SM63_gsC.fna

R._leguminosarum_SM46_gsC.fna

R._leguminosarum_JHI24.fna

R._leguminosarum_SM76_gsC.fna

R._leguminosarum_SM150_gsC.fna

R._leguminosarum_SEF4B9.fna

R._sp._UPM1135_UPM1135.fna

R._leguminosarum_SM57_gsC.fna

R._leguminosarum_SM80_gsC.fna

R._leguminosarum_SM42_gsC.fna

R._leguminosarum_SM102_gsC.fna

R._leguminosarum_SM82_gsC.fna

R._leguminosarum_SM73_gsC.fna

R._leguminosarum_SM59_gsC.fna

R._leguminosarum_SM161_gsC.fna

R._leguminosarum_SM49_gsC.fna

R._leguminosarum_SM47_gsC.fna

R._leguminosarum_SM56_gsC.fna

R._leguminosarum_SM41_gsC.fna

R._leguminosarum_SM77_gsC.fna

R._leguminosarum_SM164C_gsC.fna

R._leguminosarum_JHI985.fna

R._leguminosarum_SM112_gsC.fna

R._leguminosarum_SM54_gsC.fna

R._leguminosarum_SM95_gsC.fna

R._leguminosarum_SM88_gsC.fna

R._leguminosarum_SM164A_gsC.fna

R._leguminosarum_SM119_gsC.fna

R._leguminosarum_SM74_gsC.fna

R._leguminosarum_SM143_gsC.fna

R._leguminosarum_JHI782.fna

R._leguminosarum_JHI783.fna

R._leguminosarum_SM87_gsC.fna

R._leguminosarum_SM105_gsC.fna

R._leguminosarum_SEF5C12.fna

R._leguminosarum_SM125_gsC.fna

R._leguminosarum_SM103_gsC.fna

R._leguminosarum_SM108_gsC.fna

R._leguminosarum_JHI979.fna

R._leguminosarum_SM170B_gsC.fna

R._leguminosarum_JHI1442.fna

R._leguminosarum_JHI1418.fna

R._leguminosarum_SM111_gsC.fna

R._leguminosarum_SM89_gsC.fna

R._leguminosarum_SM107_gsC.fna

R._leguminosarum_SM86_gsC.fna

R._leguminosarum_SM104_gsC.fna

R._leguminosarum_SM122B_gsC.fna

R._leguminosarum_SM98_gsC.fna

R._leguminosarum_TA1.fna

R._leguminosarum_SM81_gsC.fna

R._leguminosarum_SM170A_gsC.fna

R._leguminosarum_SM84_gsC.fna

R._leguminosarum_JHI42.fna

R._leguminosarum_SM110_gsC.fna

R._leguminosarum_SM48_gsC.fna

R._leguminosarum_SM93_gsC.fna

R._leguminosarum_SM117_gsC.fna

R._leguminosarum_SM121A_gsC.fna

R._leguminosarum_SM83_gsC.fna

R._leguminosarum_SM100_gsC.fna

R._leguminosarum_SM133B_gsC.fna

R._leguminosarum_JHI367.fna

R._leguminosarum_SM166A_gsC.fna

R._leguminosarum_SM101_gsC.fna

R._leguminosarum_Ps8.fna

R._leguminosarum_SM170C_gsC.fna

R._leguminosarum_JHI1259.fna

R._leguminosarum_SM129_gsC.fna

R._leguminosarum_SM99B_gsC.fna

R._leguminosarum_SM121B_gsC.fna

R._sp._UPM1134_UPM1134.fna

R._leguminosarum_SM147A_gsC.fna

R._leguminosarum_SM149C_gsC.fna

R._leguminosarum_SM151C_gsC.fna

R._leguminosarum_SM134A_gsC.fna

R._leguminosarum_UPM1134.fna

R._leguminosarum_A1.fna

R._leguminosarum_SM149B_gsC.fna

R._leguminosarum_SM134B_gsC.fna

R._sp._UPM1132_UPM1132.fna

R._leguminosarum_SM147C_gsC.fna

R._leguminosarum_JHI364.fna

R._leguminosarum_SM157C_gsC.fna

R._leguminosarum_A1_GCF_011128975.1.fna

R._leguminosarum_SM147B_gsC.fna

R._leguminosarum_JHI953.fna

R._leguminosarum_SM148A_gsC.fna

R._leguminosarum_VF2.fna

R._leguminosarum_SM165B_gsC.fna

R._leguminosarum_SM168C_gsC.fna

R._leguminosarum_SM165A_gsC.fna

R._leguminosarum_SM157B_gsC.fna

R._leguminosarum_SM122A_gsC.fna

R._leguminosarum_SM158_gsC.fna

R._leguminosarum_SM166B_gsC.fna

R._leguminosarum_SM157A_gsC.fna

R._leguminosarum_SM148C_gsC.fna

R._leguminosarum_SM148B_gsC.fna

R._leguminosarum_SM141A_gsC.fna

R._leguminosarum_SM153D_gsC.fna

R._leguminosarum_SM167_gsC.fna

R._leguminosarum_SM153A_gsC.fna

R._leguminosarum_SM153C_gsC.fna

R._leguminosarum_SM126B_gsC.fna

 

gsC (mid green clade)

R._leguminosarum_SM90_gsC.fna

R._leguminosarum_JHI1266.fna

R._leguminosarum_SM85_gsC.fna

R._leguminosarum_SM114_gsC.fna

R._leguminosarum_SM94_gsC.fna

R._leguminosarum_SM133A_gsC.fna

R._leguminosarum_SM97_gsC.fna

R._leguminosarum_SM92_gsC.fna

R._leguminosarum_SM91_gsC.fna

R._leguminosarum_SM109_gsC.fna

R._leguminosarum_SM116_gsC.fna

R._leguminosarum_SM120_gsC.fna

R._leguminosarum_SM115_gsC.fna

R._leguminosarum_SM113_gsC.fna

R._leguminosarum_SM96_gsC.fna

R._leguminosarum_JHI1422.fna

R._leguminosarum_FRF1H7.fna

 

gsC (light green clade)

R._leguminosarum_Vc2.fna

R._leguminosarum_Lp8.fna

R._leguminosarum_Vh3.fna

R._leguminosarum_JHI925.fna

R._leguminosarum_SM132_gsC.fna

 

gsL

R._leguminosarum_JHI1096.fna

R._leguminosarum_JHI1093.fna

R._leguminosarum_Vaf-46.fna

 

gsM

R._leguminosarum_SRDI565.fna

R._laguerreae_GPTR21.fna

R._laguerreae_GPTR08.fna

R._laguerreae_GPTR29.fna

R._laguerreae_GPTR19.fna

R._laguerreae_GPTR02.fna

 

As I said, those strains in gsM are not R. laguerreae, but next time we will look at the real R. laguerreae and her friends.