Towards an understanding of Rhizobium leguminosarum
I have been trying to understand the diversity of Rhizobium leguminosarum for most of my career. When I first started work on R. leguminosarum in the 1980s, our concept of this species was in the...
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Finding the genome sequencesI downloaded all the genome sequences for Rhizobium (taxid 379) from NCBI. I used a very handy script called genbank_get_genomes_by_taxon.py that is distributed as part of...
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A preliminary genome-based phylogenyThe most usual way to make a genome-based phylogeny is to select a set of representative genes, concatenate their sequences, and apply standard phylogenetic methods....
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What’s in a name?Last time, we saw that Rhizobium leguminosarum, in the traditional sense, is a very clearly defined clade in the genomic phylogeny. We could just go on treating this as a single...
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Average Nucleotide IdentityIn recent years, genome-based ANI has taken over from the old laboratory technique of DNA-DNA hybridisation (DDH) as the main criterion for deciding whether two strains...
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Rhizobium anhuienseBefore 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...
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Genospecies E – Rhizobium leguminosarum sensu strictoGenospecies E includes the type strain of Rhizobium leguminosarum, so it is, by definition, the true R. leguminosarum in the narrow sense.The last...
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Genospecies DThe sister group of gsE looks like this:There is a tight clade that includes the 5 strains from clover in Denmark that were identified as genospecies D in the study by Cavassim et al....
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How do we define the Rhizobium leguminosarum species complex?Before continuing our tour of the Rhizobium leguminosarum species complex (Rlc), I want to pause to consider what we are trying to...
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Genospecies AHere is the part of the tree that includes genospecies A. The majority of the strains are SM strains isolated by Sara Moeskjær in our NCHAIN project, and we already know that these are...
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Genospecies B We are still working our way through the previously described genospecies of the Rlc, and have reached gsB. Here is the part of the phylogeny that includes this genospecies. In the...
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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...
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The F-clade – Rhizobium laguerreae and its relativesHere is the clade that is the sister group to gsB and its relatives, which were considered in an earlier post (Rhizobium leguminosarum 11). When we...
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The F-clade was the last large group that we need to consider, but there are a number of small clades left over that we need to look at before we have finished our dissection of the Rlc. Genospecies I...
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Colouring in the phylogeny Now it is time to put together all the fragments of the Rlc phylogeny that we have seen in recent posts, and see the whole picture. Here it is. Each of the 18 coloured...
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Average Nucleotide Identity So far, I have only shown ANI values using selected reference strains. Now that we have some potential genospecies that look reasonable in the phylogeny, it is time to see...
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Questions for you So far, I have identified the Rhizobium leguminosarum species complex (Rlc) as a clearly-defined cluster with over 400 genomes that can be split into 18 putative genospecies plus 7...
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No comment Last week, I asked my reader(s) for comments on what I had done so far, and ideas for further analysis. So far, I have received no response. Zero. It seems that nobody else is interested in...
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Some more information Many thanks to everyone who responded so quickly to my request for information on the country and host of origin, and especially to Marta Maluk who not only dealt with her own JHI...
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A 16S flashback In November 1991, Helen Downer and I were sequencing 16S genes of rhizobia. We used a recently-invented process called PCR (Saiki et al. 1988...
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16S: the full story The 16S ribosomal RNA sequences of the type strains of Rhizobiumlaguerreae, R. sophorae, R. ruizarguesonis and R. indicum are all identical to that of the type strain of R....
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The manuscript has been submitted The manuscript "Defining the Rhizobium leguminosarum species complex" was submitted to Genes on 11 December. It is available as a preprint at...
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Our paper is published!Our paper “Defining the Rhizobium leguminosarum species complex” was published today in Genes. You can download the PDF and the supplementary files from...
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The minutes of the annual meeting (2022) of our subcommittee can be found at https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005856.
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As we discussed in the 2022 annual meeting of the subcommittee (Minute13; Mousavi and Young, Int J Syst Evol Microbiol 2023; doi:10.1099/ijsem.0.005856),Esperanza Martinez-Romero and Alvaro Piex...
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