Pseudomonas, Ralstonia and Burkholderia: HGT buddies

Wednesday 28 October 2015

Pseudomonas, Ralstonia and Burkholderia: HGT buddies

Recently I was reminded of an interesting thing that intrigued me: Ralstonia and Burkholderia were formerly classed as Pseudomonas spp. and now are from different proteobacterial classes, but they share several close genes. One hypothesis that can be made is that a series of horizontal gene transfer events occurred at some point and the phenotypes of the three species became so close that they were mistakenly grouped together.

I came across the quirk while doing research for a paper from Dr. Monica Gerth and Prof. Paul Rainey:
Gerth ML, Ferla MP, Rainey PB. The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1. Environ Microbiol. 2012 Aug;14(8):1929-40. doi: 10.1111/j.1462-2920.2011.02691.x. Epub 2012 Jan 9. PubMed PMID: 22225844.

The Ralstonia and Burkholderia are in different families within the Burkholderiales (Betaproteobacteria), while the Pseudomonas is in the Gammaproteobacteria. The taxonomic genus Burkholderia was coined when 7 Pseudomonas spp. were moved in 1993, while Ralstonia was created when two Burkholderia spp. were moved in 1996. The two are not sister genera.
In addition to the hut operon these three species are phylogenetically close to each other for many protein.

Using the Darkhorse server set to genus level detail, the top hits for Pseudomonas aeruginosa are

  1. Azotobacter vinelandii, a bona fide pseudomonad, but given its own genus for silly reasons —okay, technically it is the Pseudomonas genus should be split.
  2. Ralstonia metallidurans
  3. Bermanella marisrubri
  4. Chromohalobacter salexigens
  5. Burkholderia xenovorans
  6. Burkholderia thailandensis
With Pseudomonas fluorescens B. xenovorans is in third place. With Pseudomonas putida it's in second place, while R. metallidurans in fourth. While Ralstonia and Burkholderia pick each other up. The results for Ralstonia eutropha indicate that 2/3 of its large genome are from Cupriavidus taiwanensis (sister species of Burkholderia), which in reality means that there is some phylogenetic issue afoot.
Nevertheless, it does not explain the pseudomonad link, which is probably because the ancestors of Pseudomonas and of Burkholderia/Ralstonia got to know each other well and as a result today we have:

  • Burkholderia spp. have two chromosomes and lots of plasmids, R. eutropha has over six and half thousand genes and pseudomonads are gene collectors too.
  • They all have weird relationship with their sister genera or families.
  • The seem to have similar lifestyles.
  • The share lots of genes
  • They were mistaken as pseudomonads morphologically.
This is just a mix of speculation and quick checks, but there is nevertheless a link. Which is not only curiosity, it finds data in mistakes from the past and potentially tells of dangers that may assail genome-concatenation studies.

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