Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species

• Published in: FEMS microbiology letters 2006-06, Vol.259 (1), p.126-132
• Main Authors: Payne, George W., Ramette, Alban, Rose, Helen L., Weightman, Andrew J., Jones, T. Hefin, Tiedje, James M., Mahenthiralingam, Eshwar
• Format: Article
• Language: English
• Subjects: Aldehydes; Bacterial Typing Techniques; Bacteriology; Biological and medical sciences; Burkholderia; Burkholderia - classification; Burkholderia - genetics; Burkholderia - isolation & purification; Burkholderia cepacia complex - classification; Burkholderia cepacia complex - genetics; Burkholderia cepacia complex - isolation & purification; Corn; Cultivation; cultivation‐independent analysis; DNA, Bacterial; Fundamental and applied biological sciences. Psychology; Genes; Genetic Variation; Genetics; Microbiology; Molecular Sequence Data; Natural environment; PCR; Phylogeny; Plant Roots - microbiology; Rec A Recombinases - genetics; RecA protein; Rhizosphere; rhizosphere diversity; Sequence Analysis, DNA; Soil Microbiology; Species; Species diversity; Systematics; Zea mays - microbiology
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2006.00257.x

Abstract Burkholderia species are widely distributed in the natural environment. We evaluated the use of the recA gene in a cultivation-independent approach to examine the Burkholderia diversity associated with the maize rhizosphere. Two types of recA gene library were constructed, one with broad-specificity recA primers (BUR1 and BUR2) and a second from the products of nested PCRs using Burkholderia-specific primers (BUR3 and BUR4). The broad-specificity primer set provided near full-length recA sequences (869 bp) suitable for the creation of robust environmental sequence data sets; however, the nested PCR approach demonstrated the greatest specificity (84%) for detection of Burkholderia species recA genes. In addition, the screening approach was able to identify recA phylotypes matching Burkholderia cepacia complex species previously cultivated from the maize samples and discriminate these from other Burkholderia. The ecological benefit of Burkholderia species cultivated from maize rhizosphere is well documented, however, the fact that the majority of Burkholderia recA genes detected in this study (90%) were suggestive of novel taxa indicates that a wealth of potentially important interactions with uncultivated Burkholderia species remain unstudied in this habitat.