ISSN:
1573-0972
Keywords:
Azorhizobium caulinodans
;
DNA fingerprinting
;
genomic structure
;
nodules
;
PCR
;
phylogeny
;
repetitive DNA sequences
;
Rhizobium loti
;
Rhizobium meliloti
;
strain identification
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Process Engineering, Biotechnology, Nutrition Technology
Notes:
Abstract A rapid and reproducible method has been developed for genomic fingerprinting of rhizobia and other soil microbes interacting with plants. The method is based on the use of oligonucleotide primers, corresponding to conserved motifs in naturally occurring interspersed repetitive DNA elements in bacteria (rep-elements), and the polymerase chain reaction (rep-PCR). Rep-PCR results in the amplification of inter-element genomic DNA fragments of characteristic lengths and thereby generates a genomic fingerprint. These fingerprints resemble UPC bar code patterns, and can be used to identify bacteria at the sub-species and strain level, as well as for phylogenetic analyses. Here we show that highly characteristic and very reproducible rep-PCR generated genomic fingerprints can be obtained not only from purified genomic DNA, but also directly from rhizobial cells derived from liquid cultures or from colonies on plates, as well as from nodule tissue. We examine the effect of growth phase of the bacterial cells, serial subculturing and other parameters on the reproducibility of the rep-PCR fingerprinting protocol. Moreover, we describe the results of mixing experiments designed to determine if individual genomic fingerprints can be recognized in mixtures of strains. Lastly, we review the use of computer-based fragment detection and phylogentic analysis packages to analyse rep-PCR generated genomic fingerprints of a collection of Rhizobium loti and Bradyrhizobium strains nodulating different Lotus spp.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF00364681
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