The genus Burkholderia consists of some 35 bacterial species, most of which are soil saprophytes and phytopathogens that occupy a wide range of environmental niches. Several of these species, referred to as the Burkholderia cepacia complex (Bcc), are characterized by unusually high inter-species DNA-DNA hybridization values. Species within this group are further distinguished by being opportunistic human pathogens, particularly problematic in persons with cystic fibrosis (CF).

Burkholderia ambifaria is generally found as the dominant Burkholderia cepacia complex species in natural environments where it is often associated with plant roots. Burkholderia ambifaria strain MC40-6 was found to occur in soil associated with maize roots (i.e., maize rhizosphere) at a density of 10,000 to 100,000 cells per g (A. Ramette et al. unpublished), in Michigan State University research field, Michigan, USA in August 2004. The fact that large populations of Burkholderia ambifaria also exist in pristine, native ecosystems such as the tall grass prairies (A. Ramette, unpublished) suggests a broader beneficial effect than previously thought and perhaps indicates the original niche of this species.

Interestingly, strain MC40-6 is able to directly fix atmospheric nitrogen, as determined by isotopic techniques and acetylene reduction activity (J. J. Pena-Cabriales, unpublished). Despite its frequent occurrence on plant roots, the strain does not show any pathogenicity towards onion (inoculation test of the strain in onion leave tissues; J. Jacobs et al., unpublished), a plant on which plant-pathogenic Burkholderia cepacia strains show maceration or chlorosis symptoms.

Given B. ambifaria's close association with plants, it is not surprising that the strain harbors many dioxygenases and oxygenases that may metabolize complex aromatic compounds associated with root exudates, and may as such be a key part of effective phytoremediation systems. By tapping into the diversity of these key enzymes, industrial applications may potentially be foreseen in bioremediation and in catalytic systems for conversion of biomass into energy.

The strain was determined to belong to sequence type ST-293 by multi-locus sequence typing (A. Baldwin et al. unpublished). Noticeably, this sequence type forms a distinct cluster from B. ambifaria AMMD, the latter biological control agent against plant pathogens also being sequenced by JGI. Therefore strain MC40-6 offers another genome sequence to investigate the broad metabolic diversity present across B. ambifaria that is required to colonize different rhizospheres and natural environments. Moreover, the availability of genomes of several strains within the B. ambifaria species will offer resolution at the sub-species level, which is needed to better understand the ecology and evolution of the Burkholderiacaea.

B. ambifaria MC40-6 has been deposited at American Type Culture Collection, the Belgium Bacterial Collection as LMG 24309 (Laboratorium voor Microbiologie Gent, Universiteit Gent, Ghent), and is also known under the designation BCC1212 in other collections (Esh Mahenthiralingam, Cardiff University, Wales, UK).