Culture-Based and Non-Growth-Dependent Detection of the Burkholderia cepacia Complex in Soil Environments

Abstract

Burkholderia cepacia complex (Bcc) bacteria reside in soil, plant rhizospheres, and water, but their prevalence and distribution in outdoor environments is not clear. We sampled a variety of soil and rhizosphere environments with which people may have contact: playgrounds, athletic fields, parks, hiking trails, residential yards, and gardens. A total of 91 sites was sampled in three large U.S. cities. In the first phase of the study, putative Bcc isolates were recovered on Burkholderia cepacia selective agar and trypan blue tetracycline medium and subsequently examined for biochemical reactivity and growth at 32 and 22°C. Isolates were further examined by PCR assays targeting Bcc-specific ribosomal DNA and recA gene sequences. Among the 1,013 bacterial isolates examined, 68 were identified as Bcc; 14 (15%) of 91 sampled sites yielded Bcc isolates. In the second phase, DNA was extracted directly from soil samples and examined with PCR assays targeting Bcc 16S rRNA gene sequences. Either 82 or 93% of the soil samples were positive for at least one Bcc genomovar, depending on the PCR assay system used. Cloning and sequencing were performed to check the specificity of the PCR assays. Sequence analysis of the 463-bp 16S rRNA inserts from eight clones indicated that all were from members of the Bcc. The four soil samples from which these clones were generated did not yield isolates identified as Bcc. Based on PCR detection, Bcc appears to be prevalent in soil from urban and suburban environments. Culture-based recovery of Bcc may underestimate environmental populations.

Infection Prevention and Control Guideline for Cystic Fibrosis: 2013 Update

“…Other species, particularly Burkholderia ambifaria, exist within the rhizospheres of certain plants, while B. multivorans is infrequently recovered from the environment. [292][293][294][295][296] Several investigations since the publication of the 2003 Infection Control Guideline for CF have enhanced our understanding of the potential role played by the natural environment in the acquisition of CF pathogens and possible strain-specific reservoirs.…”

Multivariate Analyses of Burkholderia Species in Soil: Effect of Crop and Land Use History

“…Recently, the diversity of the Burkholderia community associated with woodland rhizospheres was also assessed (27). However, these reports were based on culture-dependent techniques, which are likely to underestimate the natural bacterial population (23). In order to overcome this problem, we developed a method, based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE), which allows the direct analysis of the diversity of Burkholderia species in environmental samples (30).…”

The Tomato Rhizosphere, an Environment Rich in Nitrogen-Fixing Burkholderia Species with Capabilities of Interest for Agriculture and Bioremediation

“…Although the complete genome of B. xenovorans LB400 T was recently sequenced (12), it is noteworthy that the four extant B. xenovorans strains described in diverse studies have been randomly recovered from different environments and widely distant geographical regions, and there are no studies on the distribution of this PCB-degrading, nitrogen-fixing species or its association with plants. Emphasis has been given to studies of the isolation, taxonomy, and distribution of Burkholderia species related to human opportunistic pathogens, especially the B. cepacia complex species found in cystic fibrosis patients (33,45,52; for reviews, see references 15 and 42). In contrast, few studies have been performed on the overall diversity of the genus Burkholderia (61,63), even though nonpathogenic Burkholderia species are frequently recovered from different environments (6,40,70), and despite their biotechnological potential in bioremediation and other applications (34,70; for a review, see reference 48).…”