Identification and quantification of Fusarium oxysporum in plants and soil by means of an improved specific and quantitative PCR assay

• Published in: Applied soil ecology : a section of Agriculture, ecosystems & environment ecosystems & environment, 2010-11, Vol.46 (3), p.372-382
• Main Authors: Jimenez-Fernandez, Daniel, Montes-Borrego, Miguel, Navas-Cortes, Juan A, Jimenez-Diaz, Rafael M, Landa, Blanca B
• Format: Article
• Language: English
• Subjects: Cicer arietinum; Fusarium oxysporum
• ISSN: 0929-1393
• DOI: 10.1016/j.apsoil.2010.10.001

The proper identification and quantification of F. oxysporum populations inhabiting soil and plant rhizosphere niches are of importance for soil microbial ecology and plant pathology. In this study, we report the improvement of a PCR protocol for the specific identification of the F. oxysporum species complex and its conversion into a real-time qPCR assay for the quantification up to 1 pg of the fungus DNA in soil and different plant tissues. The amplification efficiency, sensibility and reproducibility of qPCR assays were not influenced by presence of non-target DNA from either plant or soil. The applicability of the newly developed qPCR protocol for F. oxysporum population studies was demonstrated using the technique for quantifying the fungus in different complex environmental samples. The use of the qPCR protocol allowed to accurately quantify up to 25 pg of F. oxysporum/g of naturally infested field soil, as well as to identify significant differences in the amount of F. oxysporum DNA in roots of different chickpea cultivars grown in a field soil infested with diverse pathogenic and nonpathogenic F. oxysporum populations. This qPCR protocol may be especially important for studies on soil microbial ecology and plant pathology since it provides a new opportunity for analyzing F. oxysporum populations and their interactions with the soil microflora, environment and plant host genotypes.