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16S rRNA gene‐based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia
Author(s) -
Schönmann Susan,
Loy Alexander,
Wimmersberger Céline,
Sobek Jens,
Aquino Catharine,
Vandamme Peter,
Frey Beat,
Rehrauer Hubert,
Eberl Leo
Publication year - 2009
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2008.01800.x
Subject(s) - biology , burkholderia , 16s ribosomal rna , phylogenetic tree , gene chip analysis , genetics , microarray , microbiology and biotechnology , ribosomal rna , microarray analysis techniques , gene , computational biology , 23s ribosomal rna , dna microarray , bacteria , gene expression , rna , ribosome
Summary For cultivation‐independent and highly parallel analysis of members of the genus Burkholderia , an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene‐targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia , Pandoraea , Ralstonia and Limnobacter . Hybridization patterns based on presence/absence of probe signals were interpreted semi‐automatically using the novel likelihood‐based strategy of the web‐tool PhyloDetect. Eighty‐eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmium‐contaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.