Journal
GENES
Volume 12, Issue 1, Pages -Publisher
MDPI
DOI: 10.3390/genes12010111
Keywords
Rhizobium; species complex; bacterial taxonomy; core genes; housekeeping genes; average nucleotide identity; speciation; genospecies
Categories
Funding
- Innovation Fund Denmark [4105-00007A]
- European Community FP7 `Legumes for the Agriculture of Tomorrow' (LEGATO) [FP7-613551]
- Agence Nationale de la Recherche (GrasP)
- Rural and Environment Science and Analytical Services (RESAS, Scotland)
- 'Transition paths to sustainable legume based systems in Europe' (TRUE, EC Horizon 2020) [727973]
- RSF [17-76-30016, 19-16-00081, VA2I/463AC06, CLU-2018-04]
- SERB-DST, India [YSS/2015/000149]
- University of Otago
- CSIR, India [BSC0117]
- CSIR-HRDG, India [21(1023)/16/EMR-II]
- BBSRC [BB/L024209/1]
- Biotechnology and Biological Sciences Research Council [BB/L024209/1] Funding Source: researchfish
- Russian Science Foundation [19-16-00081] Funding Source: Russian Science Foundation
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The study identified 18 distinct genospecies within the Rhizobium leguminosarum complex (Rlc), each separated by a distinct gap in ANI values around 96%. The 16S ribosomal RNA sequence in the Rlc is diverse but not able to distinguish between genospecies. Single genes are not reliable guides to the true phylogeny of bacterial strains within the Rlc.
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, R. indicum and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
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