DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA.

Abstract

The present study was aimed at reducing the time and labour used to perform DNA-DNA hybridizations for classification of bacteria at the species level. A micro-well-format DNA hybridization method was developed and validated. DNA extractions were performed by a small-scale method and DNA was sheared mechanically into fragments of between 400 and 700 bases. The hybridization conditions were calibrated according to DNA similarities obtained by the spectrophotometric method using strains within the family Pasteurellaceae. Optimal conditions were obtained with 300 ng DNA added per well and bound by covalent attachment to NucleoLink. Hybridization was performed with 500 ng DNA, 5 % (w/w) of which was labelled with photoactivatable biotin (competitive hybridization) for 25 h at 65 SC in 2iSSC followed by stringent washing with 2iSSC at the same temperature. The criteria for acceptance of results were a maximum of 15 % standard deviation, calculated as a percentage of the mean for four replicate micro-wells, and that DNA similarities were not significantly different in at least two independent experiments. The relationship between DNA similarities obtained by the microwell method (y) and by the spectrophotometric method (x) was y l 0534xM306, when these criteria had been applied to 23 pairs of strains of Actinobacillus species, avian [Pasteurella] haemolytica-like bacteria and Mannheimia species. The correlation (Pearson) between DNA similarities obtained by interchange of strains used for covalent binding and hybridization was 0794. Significantly lower DNA similarities were observed by the spectrophotometric compared with the micro-well method for three pairs of hybridizations. After removal of these data, the relationship between DNA similarities obtained by the micro-well and spectrophotometric methods improved to y l 0855xM110. It was found that the accuracy and precision of the micro-well method was at the same level as that of the spectrophotometric method, but the labour and analysis time were reduced significantly. The use of hybridization in the micro-well format will allow DNA-DNA hybridizations to be carried out between all strains selected for a particular taxonomic study, in order to construct complete data matrices and improve species definition.

Tessaracoccus rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis

“…DNA-DNA hybridization was performed between the novel strain and T. flavescens DSM 18582 T by the fluorometric micro-well method (Ezaki et al, 1989;Christensen et al, 2000;He et al, 2005). The experiments were set with three replications at the optimal hybridization temperature (47 8C).…”

Streptomyces artemisiae sp. nov., isolated from surface-sterilized tissue of Artemisia annua L.

“…All other representatives of the genus Streptomyces exhibited lower sequence similarity to strain YIM 63135 T (,97.0 %). In view of the high level of 16S rRNA gene sequence similarity between isolate YIM 63135 T and S. armeniacus NBRC 12555 T , DNA-DNA relatedness between them was studied according to the fluorometric microwell method (Ezaki et al, 1989;Christensen et al, 2000;He et al, 2005). Fluorescence intensities were measured using a fluorescence microplate reader (Spectra Max Gemini xps).…”

Micrococcus yunnanensis sp. nov., a novel actinobacterium isolated from surface-sterilized Polyspora axillaris roots

“…The topology of the phylogenetic tree was evaluated by using the bootstrap resampling method of Felsenstein (1985) with 1000 replicates. DNA-DNA relatedness was studied using the fluorometric micro-well method (Ezaki et al, 1989;Christensen et al, 2000;He et al, 2005). Fluorescence intensities were measured using a fluorescence microplate reader (SpectraMax Gemini XPS; Molecular Devices).…”