Bacterial halo blight of coffee crop: aggressiveness and genetic diversity of strains

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Abstract

ABSTRACT Bacterial halo blight, caused by Pseudomonas syringae pv. garcae, is an important disease of coffee crop occurring in Brazil and other countries. In recent years, outbreaks of this disease have damaged several coffee crops in Brazil. Aggressiveness and genetic diversity of 25 strains of P. s. pv. garcae, obtained between the years 1958 and 2011, in 23 cities of São Paulo and Minas Gerais states, as well as three strains from Kenya were evaluated in this study. The strains were inoculated on coffee seedlings cultivar Mundo Novo, and their genetic diversity was evaluated by ERIC-PCR, REP-PCR, and their combination. All the strains were pathogenic to the coffee seedlings; the results of pathogenicity tests, in both experiments, could be divided in four aggressiviness classes (highly aggressive; aggressive; moderately aggressive and less aggressive). The Kenyan strains grouped separately from the Brazilian strains with ERIC-PCR and the combination of ERIC- and REP-PCR. The Brazilian strains could be grouped in two sub-clusters, the first including the older strains, obtained from 1958 to 1978, and the other comprising the remaining strains. With a few exceptions, strains isolated from 1997 to 2011, grouped mainly by their region of origin, were predominantly isolated from higher altitude regions, above 800 m. This probably occurred because the climatic conditions that prevail in these regions, characterized by milder temperatures and regular rainfall, are favorable for the coffee crop and for the production of high quality coffee beverage, but can be also favorable to bacterial halo blight.

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Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR.

F. J. Louws, D. Fulbright, C. Stephens … (1994)

DNA primers corresponding to conserved motifs in bacterial repetitive (REP, ERIC, and BOX) elements and PCR were used to show that REP-, ERIC-, and BOX-like DNA sequences are widely distributed in phytopathogenic Xanthomonas and Pseudomonas strains. REP-, ERIC, and BOX-PCR (collectively known as rep-PCR) were used to generate genomic fingerprints of a variety of Xanthomonas and Pseudomonas isolates and to identify pathovars and strains that were previously not distinguishable by other classification methods. Analogous rep-PCR-derived genomic fingerprints were generated from purified genomic DNA, colonies on agar plates, liquid cultures, and directly from lesions on infected plants. REP, ERIC, and BOX-PCR-generated fingerprints of specific Xanthomonas and Pseudomonas strains were found to yield similar conclusions wtih regard to the identity of and relationship between these strains. This suggests that the distribution of REP-, ERIC, and BOX-like sequences in these strains is a reflection of their genomic structure. Thus, the rep-PCR technique appears to be a rapid, simple, and reproducible method to identify and classify Xanthomonas and Pseudomonas strains, and it may be a useful diagnostic tool for these important plant pathogens.

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Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system.

K Kersters, B Hoste, L Vauterin … (2000)

The genus Xanthomonas contains a large number of strains, which have been characterized by a variety of phenotypic and genotypic classification methods. The Xanthomonas collection constitutes one of the largest groups of bacteria that have been characterized phylogenetically by DNA-DNA homology studies and genomic fingerprinting. Presently, a total genomic DNA-DNA homology value of 70% represents an internationally accepted criterion to define bacterial species levels. However, the complexity of DNA-DNA reassociation kinetics methods precludes the rapid analysis of large numbers of bacterial isolates, which is imperative for molecular microbial diversity studies. Therefore, the aim of this study was to compare more facile PCR-based genomic fingerprinting techniques, such as repetitive-sequence-based (rep)-PCR and AFLP genomic fingerprinting, to DNA-DNA hybridization studies. Using three different primer sets, rep-PCR genomic fingerprint patterns were generated for 178 Xanthomonas strains, belonging to all 20 previously defined DNA-DNA homology groups, and one Stenotrophomonas maltophilia strain. In addition, AFLP genomic fingerprints were produced for a subset of 80 Xanthomonas strains belonging to the 20 DNA-DNA homology groups and for the S. maltophilia strain. Similarity values derived from rep-PCR- and AFLP-generated fingerprinting analyses were calculated and used to determine the correlation between rep-PCR- or AFLP-derived relationships and DNA-DNA homology values. A high correlation was observed, suggesting that genomic fingerprinting techniques truly reveal genotypic and phylogenetic relationships of organisms. On the basis of these studies, we propose that genomic fingerprinting techniques such as rep-PCR and AFLP can be used as rapid, highly discriminatory screening techniques to determine the taxonomic diversity and phylogenetic structure of bacterial populations.