A new study in the journal Open Biology suggests that bacteria are as individual as people. The results of the genomic sequencing study of isolates of the bacterium Rhizobium leguminosarum showed that while the core genes remained largely conserved, variation in ecological properties arose from horizontal gene transfer of accessory genes. Prof Peter Young in the University of York, who led the research team said: "Bacteria are like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by horizontal gene transfer)."
NeighborNet phylogeny of the isolates and related sequenced bacteria based on 305 conserved genes. Symbol colour indicates symbiovar: red, viciae; blue, trifolii; green, phaseoli. The new isolates (unlabelled symbols) are identified in electronic supplementary material, figure S3. Named species are represented by their type strains. Round symbols indicate genome sequences obtained in this study; square symbols indicate published genome data. Background colours indicate R. leguminosarum as currently defined (grey), and the five genospecies A–E are identified within R. leguminosarum (coloured).
The study focused on 72 Rhizobium leguminosarum isolates obtained from one square metre of roadside verge on the University of York campus. The results showed that all the strains had core 16S rRNA ‘housekeeping’ genes typical of Rhizobium leguminosarum, while the criterion of average nucleotide identity supported the division of the strains into five ‘genospecies’. However, variation in ecological properties such as symbiotic host range and carbon-source utilization occurs across these genospecies due to the existence of mobile genes. Thus when the DNA sequence of each of the 72 strains was analysed, it was shown that each strain is unique, containing different genes and with the ability to grow on different food sources.
While bacteria reproduce by binary fission in which they make two identical daughters, they pass packages of genes from one cell to another by the process of horizontal gene transfer. This is the process that resulted in every rhizobium being unique. Prof Young explained: "We can think of the bacterial genome as having two parts. The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world.”
Bacterial communities play vital roles, whether it is in our intestine or in the roots of plants. In many cases, standard core genes are used for compiling lists of the species in a bacterial community, but research such as this study suggests that this is not sufficient. The researchers suggest that “a more consistent taxonomic framework” is needed to recognise the facts that “many bacterial species share adaptive modules by horizontal gene transfer” and that bacterial “population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes.” They suggest designation of ‘bioavars’ to recognise significant phenotypes conferring different ecological properties within a species defined by a core gene phylogeny.
Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Kumar N et al. Open Biology, January 14 2015. DOI: 10.1098/rsob.140133.