To split or not to split: an opinion on dividing the genus Burkholderia

Abstract

The genus Burkholderia is a large group of species of bacteria that inhabit a wide range of environments. We previously recommended, based on multilocus sequence analysis, that the genus be separated into two distinct groups-one that consists predominantly of human, plant, and animal pathogens, including several opportunistic pathogens, and a second, much larger group of species comprising plant-associated beneficial and environmental species that are primarily known not to be pathogenic. This second group of species is found mainly in soils, frequently in association with plants as plant growth-promoting bacteria. They also possess genetic traits that bestow them with an added potential for agriculture and soil restoration, such as nitrogen fixation, phosphate solubilization, iron sequestration, and xenobiotic degradation, and they are not pathogenic. In this review, we present an update of current information on this second group of Burkholderia species, with the goal of focusing attention on their use in agriculture and environmental remediation. We describe their distribution in the environment, their taxonomy and genetic features, and their relationship with plants as either associative nitrogen-fixers or legume-nodulating/nitrogen-fixing bacteria.We also propose that a concerted and coordinated effort be made by researchers on Burkholderia to determine if a definitive taxonomic split of this very large genus is justified, especially now as we describe here for the first time intermediate groups based upon their 16S rRNA sequences. We need to learn more about the plant-associated Burkholderia strains regarding their potential for pathogenicity, especially in those strains intermediate between the two groups, and to discover whether gene exchange occurs between the symbiotic and pathogenic Burkholderia species. The latter studies will require both field and laboratory analyses of gene loss and gain.

Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato

“…Various previous studies have pointed out that these species should be excluded from Burkholderia sensu stricto, Caballeronia and/or Paraburkholderia (e.g., Estrada-de los Santos et al, 2013, 2016; Dobritsa and Samadpour, 2016). In fact, they have been suggested to represent new genera (Estrada-de los Santos et al, 2013; Dobritsa and Samadpour, 2016).…”

International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016

“…However, many strains, particularly rhizobial and plant beneficial strains from Clade III, show great potential as biofertilizers and bioremediants in sustainable agricultural systems. Research efforts directed towards robust characterization and taxonomy of Burkholderia sensu lato species can help in realizing this agricultural potential [13]. Clearly, large-scale phylogenomic study is required for resolving these taxa.…”

Engineering root microbiomes for healthier crops and soils using beneficial, environmentally safe bacteria

“…Because of their potential health risk, the use of the Burkholderia cepacia complex (Bcc) in the field has been restricted (US Environmental Protection Agency 2003; see also Chiarini et al 2006 for a description of the Bcc). Eberl and Vandamme (2016) discussed these topics in great depth with reference to Burkholderia, and efforts are being made to separate the pathogenic Burkholderia species from the beneficial ones (see Estrada-de los Santos et al 2016, 2018 based not only on phylogeny but also on physiology and the absence or presence of factors associated with virulence. Earlier, Gyaneshwar et al (2011) showed that the plant-associated and nodulating Burkholderia (now Paraburkholderia, Sawana et al 2014) has a lower G + C content than the pathogenic species.…”