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

2008 ◽  
Vol 74 (10) ◽  
pp. 3121-3129 ◽  
Author(s):  
Janette L. Jacobs ◽  
Anthony C. Fasi ◽  
Alban Ramette ◽  
James J. Smith ◽  
Raymond Hammerschmidt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Burkholderia Cepacia ◽  
Burkholderia Cepacia Complex ◽  
Organic Soils ◽  
Rrna Gene ◽  
Pseudomonas Cepacia ◽  
Gene Probe ◽  
Polymorphism Analysis ◽  
Complex Species

ABSTRACT Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source of B. cenocepacia.

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

2007 ◽  
Vol 73 (22) ◽  
pp. 7259-7267 ◽  
Author(s):  
Rodrigo Mendes ◽  
Aline A. Pizzirani-Kleiner ◽  
Welington L. Araujo ◽  
Jos M. Raaijmakers
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Burkholderia Cepacia ◽  
Endophytic Bacteria ◽  
Pathogenic Bacteria ◽  
Biochemical Characterization ◽  
Burkholderia Cepacia Complex ◽  
Rrna Gene ◽  
Endophytic Bacterial Community

ABSTRACT Bacteria were isolated from the rhizosphere and from inside the roots and stems of sugarcane plants grown in the field in Brazil. Endophytic bacteria were found in both the roots and the stems of sugarcane plants, with a significantly higher density in the roots. Many of the cultivated endophytic bacteria were shown to produce the plant growth hormone indoleacetic acid, and this trait was more frequently found among bacteria from the stem. 16S rRNA gene sequence analysis revealed that the selected isolates of the endophytic bacterial community of sugarcane belong to the genera of Burkholderia, Pantoea, Pseudomonas, and Microbacterium. Bacterial isolates belonging to the genus Burkholderia were the most predominant among the endophytic bacteria. Many of the Burkholderia isolates produced the antifungal metabolite pyrrolnitrin, and all were able to grow at 37°C. Phylogenetic analyses of the 16S rRNA gene and recA gene sequences indicated that the endophytic Burkholderia isolates from sugarcane are closely related to clinical isolates of the Burkholderia cepacia complex and clustered with B. cenocepacia (gv. III) isolates from cystic fibrosis patients. These results suggest that isolates of the B. cepacia complex are an integral part of the endophytic bacterial community of sugarcane in Brazil and reinforce the hypothesis that plant-associated environments may act as a niche for putative opportunistic human pathogenic bacteria.

scholarly journals Pantoea allii sp. nov., isolated from onion plants and seed

2011 ◽  
Vol 61 (4) ◽  
pp. 932-937 ◽  
Author(s):  
Carrie L. Brady ◽  
Teresa Goszczynska ◽  
Stephanus N. Venter ◽  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Gene Sequence

Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).

scholarly journals Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)

2005 ◽  
Vol 55 (4) ◽  
pp. 1649-1656 ◽  
Author(s):  
Hong Kim ◽  
Sun-Hyun Kim ◽  
Tae-Sun Shim ◽  
Mi-na Kim ◽  
Gill-Han Bai ◽  
...  
Keyword(s):  
Heat Shock ◽  
16S Rrna ◽  
Heat Shock Protein ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Direct Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
16S Rrna Gene Analysis

The nucleotide sequences (604 bp) of partial heat-shock protein genes (hsp65) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an XhoI PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.

scholarly journals Naturally Occurring Class A ß-Lactamases from the Burkholderia cepacia Complex

2008 ◽  
Vol 53 (3) ◽  
pp. 876-882 ◽  
Author(s):  
Laurent Poirel ◽  
José-Manuel Rodriguez-Martinez ◽  
Patrick Plésiat ◽  
Patrice Nordmann
Keyword(s):  
Burkholderia Cepacia ◽  
Regulatory Protein ◽  
Amino Acid Identity ◽  
Burkholderia Cepacia Complex ◽  
Pseudomonas Cepacia ◽  
Cloning And Sequencing ◽  
Complex Species ◽  
Class A ◽  
Naturally Occurring ◽  
Hydrolysis Activity

ABSTRACT Chromosomally encoded ß-lactamases from the Burkholderia cepacia complex species (formerly Pseudomonas cepacia) were characterized. Cloning and sequencing identified an Ambler class A ß-lactamase (PenB) from B. cenocepacia. It shares 82% amino acid identity with the PenA ß-lactamases previously identified from B. multivorans 249. Its expression was dependent upon a LysR-type regulatory protein. Its narrow-spectrum hydrolysis activity mostly included penicillins but also included expanded-spectrum cephalosporins and aztreonam at lower levels. In that study, Pen-like ß-lactamases (PenC, PenD, PenE, PenF) that shared 63 to 92% identity with PenB from B. cenocepacia were identified from other Burkholderia species. The corresponding ß-lactamase genes might be used as genetic tools for accurate Burkholderia species identification.

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