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Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments

Garbeva, P.V. and Voesenek, K. and Elsas van, J.D. (2004) Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments. Soil Biology & Biochemistry, 36, 1453-1463. ISSN 0038-0717.

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Official URL: http://dx.doi.org/10.1016/j.soilbio.2004.03.009

Abstract

The prevalence of antibiotic production loci in soil is a key issue of current research aimed to unravel the mechanisms underlying the suppressiveness of soil to plant pathogens. Pyrrolnitrin (PRN) is a key antibiotic involved in the suppression of a range of phytopathogenic fungi. Therefore, field soils from different agricultural regimes, including permanent grassland, arable land under common agricultural rotation and arable land under maize monoculture, were investigated in respect of the prevalence of pyrrolnitrin biosynthetic loci. Primers for detection of the prnD gene were used for initial PCR/hybridisation-based assessments. By this method, evidence was obtained for the contention that PRN production loci were most prevalent in grasslands, however, robust quantitative data were not achieved. To quantify the prevalence of PRN biosynthetic loci, we designed a TaqMan PCR system based on the prnD gene for the real-time quantitative detection of this production locus in soil. The system was found to be specific for prnD sequences from Pseudomonas, Serratia and Burkholderia species. Using pure culture DNA, the prnD gene was detectable down to a level of 60 fg, or approximately 10 gene copies, per amplification reaction. Application of the system to soil DNA spiked with different levels of Field soil samples obtained from the different agricultural regimes were then screened for the prevalence of prnD with the real-time PCR system. The quantitative data obtained suggested a strongly enhanced presence of prnD genes in grassland or grassland-derived plots, as compared to the prevalence of this biosynthetic locus in the arable land plots. The implications of these findings are placed in the context of the suppressiveness of soil to phytopathogens, notably Rhizoctonia solani AG3. [KEYWORDS: Pyrrolnitrin biosynthetic locus; Detection; Real-time PCR; Diversity; Soil]

Item Type:Article
Institutes:Nederlands Instituut voor Ecologie (NIOO)
ID Code:11519
Deposited On:23 Nov 2011 01:00
Last Modified:31 Mar 2014 10:06

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