Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population

Abstract

In a comparative study, the PCR‐based RAPD and ERIC fingerprint methods were evaluated for their resolving power to discriminate among 21 isolates of a natural Rhizobium meliloti population. PCR fingerprint patterns were analysed by using an automated laser fluorescent (ALF) DNA sequencer, thus allowing the automated on‐line storage of data. Results obtained were compared to a classification system using insertion sequence (IS) fingerprinting. Both PCR fingerprint methods were comparable in their ability to resolve differences amongst Rh. meliloti isolates. Grouping of strains on the basis of their RAPD as well as their ERIC fingerprints correlated with grouping of strains according to their IS fingerprints. Moreover, strains displaying identical PCR patterns could be further differentiated according to their IS fingerprints, thus allowing a detailed insight into phylogenetic relationship among strains. The automated evaluation of strain‐specific fingerprint patterns has the potential to become a valuable tool for studies of bacterial population genetics. Moreover, the rapid identification of single strains, e.g. pathogens in epidemiological studies seems feasible.

Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.

“…Genomic DNA was extracted from strains using an alkali extraction method (Niemann et al, 1997) and stored at 220 u C until further use. Almost-complete 16S rRNA gene sequences were determined for representative strains from each DNA HG, LMG 5345 T , LMG 2781 T , LMG 5343 T , LMG 24534 T , and the type strain of Pectobacterium cypripedii, LMG 2657 T , using the primers and conditions described by Coenye et al (1999).…”

Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator

“…Genomic DNA was prepared according to the protocol of Niemann et al (1997). 16S rRNA gene amplification, purification and sequencing were performed as described by Vancanneyt et al (2004) except that 16S rRNA gene amplicons were purified using a NucleoFast 96 PCR Cleanup kit (Macherey-Nagel).…”

Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988

“…Genomic DNA was prepared according to the protocol of Niemann et al (1997). 16S rDNA was amplified by using oligonucleotide primers that were complementary to highly conserved regions of bacterial 16S rRNA genes.…”