title: Detection of cultured and uncultured Burkholderia cepacia complex bacteria naturally occurring in the maize rhizosphere.
abstract: The species composition of a Burkholderia cepacia complex population naturally occurring in the maize rhizosphere was investigated by using both culture-dependent and culture-independent methods. B. cepacia complex isolates were recovered from maize root slurry on the two selective media Pseudomonas cepacia azelaic acid tryptamine (PCAT) and trypan blue tetracycline (TB-T) and subjected to identification by a combination of restriction fragment length polymorphism (RFLP) analysis and species-specific polymerase chain reaction (PCR) tests of the recA gene. DNA extracted directly from root slurry was examined by means of nested PCR to amplify recA gene with species-specific B. cepacia complex primers and to obtain a library of PCR amplified recA genes. Using the culture-dependent method the species Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia ambifaria and Burkholderia pyrrocinia were identified, whereas using the culture-independent method also the species Burkholderia vietnamiensis was detected. The latter method also allowed us to highlight a higher diversity within the B. cenocepacia species. In fact, by using the culture-independent method the species B. cenocepacia recA lineages IIIA and IIID besides B. cenocepacia recA lineage IIIB were detected. Moreover, higher heterogeneity of recA RFLP patterns was observed among clones assigned to the species B. cenocepacia than among B. cenocepacia isolates from selective media.
authors.affiliation: ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, UTS Biotecnologie - Protezione della Salute e degli Ecosistemi, Sezione Genetica e Genomica, Via Anguillarese 301, 00060 S. Maria di Galeria, Rome, Italy.
authors.forename: Luisa
authors.initials: L
authors.lastname: Pirone
authors.forename: Luigi
authors.initials: L
authors.lastname: Chiarini
authors.forename: Claudia
authors.initials: C
authors.lastname: Dalmastri
authors.forename: Annamaria
authors.initials: A
authors.lastname: Bevivino
authors.forename: Silvia
authors.initials: S
authors.lastname: Tabacchioni
mesh_terms: D001483:Base Sequence; D042602:Burkholderia cepacia complex / Q000235:genetics*; D016000:Cluster Analysis; D003470:Culture Media / Q000378:metabolism; D017931:DNA Primers; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D011938:Rec A Recombinases / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013045:Species Specificity; D003313:Zea mays / Q000382:microbiology*
chemical_list: D003470:Culture Media; D017931:DNA Primers; D011938:Rec A Recombinases