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 species, with the reassurance that it is clearly defined. This would save a lot of trouble, because people with new isolates would just have to check that they were in this clade. If they were, they could safely call them R. leguminosarum, as we always did in the past, and need not enquire further. Job done!
The problem is that this broadly-defined group has too much diversity to fit comfortably within one species. As we showed in our first genome-based survey, ANI values between strains in this group can be as low as 93%, and the strains clustered in a number of tighter clades that corresponded more closely to the species that people were defining in other bacteria – we called them genospecies A to E (Kumar et al. 2015, http://dx.doi.org/10.1098/rsob.140133).
In response to these low ANI values (or the antiquated DNA-DNA hybridisation that ANI has replaced), a number of crews have already moved in and carved off chunks of the R. leguminosarum species complex (Rlc), setting them up as separate species. First we had R. laguerreae (Saïdi et al. 2014, https://doi.org/10.1099/ijs.0.052191-0), then R. sophorae (Jiao et al. 2015, https://doi.org/10.1099/ijs.0.068916-0), and this year we have already had R. ruizarguesonis (Jorrin et al. 2020, https://doi.org/10.1016/j.syapm.2020.126090) and R. indicum (Rahi et al. 2020, https://doi.org/10.1016/j.syapm.2020.126127). All these new species are perfectly justifiable and were well described in accordance with the conventions of bacterial taxonomy. In each case, there were several (3 to 6) strains assigned to the new species. The remnants of R. leguminosarum are not really a viable taxonomic unit without these chunks, though, so there is now a strong motivation to sort the situation out.
The standard approach to bacterial taxonomy is what I call “flag sticking”. Back in the bad old days of European imperialism, sea captains ranged over the oceans without proper maps and when they found a piece of coastline that hadn’t been claimed (by other Europeans), they stuck their national flag on it and gave it a name. Often, they didn’t really know how big the territory was that they were claiming – was it Brazil, or was it just Bermuda? Similarly, bacterial taxonomists happen upon a strain that hasn’t been “claimed”, because its similarity to all published type strains is less than the magic number, so they make it the type strain of a new species. There is no obligation, or even expectation, that they will attempt to define the boundaries of the territory that they are claiming. The better studies include several strains, but the rules allow a species to be based on a single isolate. Typical bacterial taxonomy is, in fact, the taxonomy of bacterial type strains. The result is a map on which the capital cities are clearly marked, but the international borders are very hazy.
What we really need is a satellite image of the entire landscape, so that we can see where the landmasses are, and whether there are clear natural boundaries between them. Now that we have hundreds of genomes, we are beginning to see such an image. Of course, it has some serious limitations because the genomes that have been sequenced were selected from a limited range of sources. There are undoubtedly parts of the landscape that are blank because no satellite has yet passed over them. However, as we will see in the following posts, there are some clearly defined territories (genospecies) within the Rlc, and some are much larger (represented by more genomes) than others. We will discover that R. ruizarguesonis is Brazil, while R. sophorae is Bermuda and R. laguerreae is Indonesia.
In the next post, I’ll have a look at what ANI (Average Nucleotide Identity) can tell us about the Rlc.
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