Application of arecAgene-based identification approach to the maize rhizosphere reveals novel diversity inBurkholderiaspecies

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.

Diversity of Cultivated Endophytic Bacteria from Sugarcane: Genetic and Biochemical Characterization of Burkholderia cepacia Complex Isolates

“…Nevertheless, 16S rRNA gene and recA gene phylogenetic analyses suggest that the endophytic Burkholderia strains isolated from sugarcane are closely related to well-characterized B. cepacia complex type strains. To date, most studies on the occurrence of B. cepacia complex strains in natural habitats have focused on the maize rhizosphere (19,20,63,65). The results of our study indicate, for the first time, that B. cepacia complex-related isolates are an integral part of the endophytic bacterial community of sugarcane.…”

Identification and Onion Pathogenicity of Burkholderia cepacia Complex Isolates from the Onion Rhizosphere and Onion Field Soil

“…For example, the prevalence of each of the nine species in natural environmental settings remains to be determined by systematic study. Rhizosphere distribution studies have been conducted on maize and rice (15,38,55), both plant species that are not subject to infection by B. cepacia complex strains. In contrast, onion is a host of B. cepacia; however, only one study has examined the occurrence of B. cepacia populations associated with decayed onions and onion field soil (54), and this work was done prior to the current changes in the taxonomy of the species.…”

Diversidade da microbiota endofítica na cultura da palma (Opuntia spp. e Nopalea spp.) no Semiárido de Pernambuco

“…O gene recA permite melhor discriminação do que o gene 16S rDNA. Entretanto, as análises obtidas do gene recA não são exatamente semelhantes às obtidas pela filogenia da sequência do gene 16S rRNA, indicando maior grau de resolução entre espécies relacionadas (PAYNE et al, 2006).…”

“…Apenas o isolado isolAM20 (Gluconacetobacter diazotrophicus) apresentou uma baixa homologia, de 49%, com as sequências de bactérias diazotróficas endofíticas. Segundo Payne et al (2006) e Scholz et al (2008), o gene recA permite melhor discriminação 30 min. A presença do hormônio foi visualizada pela coloração rósea.…”