Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera ( Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4⁻7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into , , and is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in (which also includes all the N₂-fixing legume symbionts) and , while most of the human and animal pathogens are retained in sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related and , which are both symbionts of the fungal phytopathogen . The second group comprises the -nodulating bacterium , the phytopathogen , and the soil bacteria and . In order to clarify their positions within sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera gen. nov. and gen. nov. The newly proposed combinations are comb. nov., comb. nov., comb. nov., comb. nov., comb. nov., and comb. nov. Given that the division between the genera that comprise s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits-diazotrophy and/or symbiotic nodulation, and pathogenesis-were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in via-à-vis other were determined, and the possibility of pathogenesis in and was tested by performing infection experiments on plants and the nematode . It is concluded that (1) and genes fit within the wider -nodulating but appear in separate clades and that genes are basal to the free-living s.l. strains, while with regard to pathogenesis (2) none of the and strains tested are likely to be pathogenic, except for the known phytopathogen .