Detection and Identification of Potato Soft Rot <i>Pectobacterium carotovorum</i> Subspecies <i>carotovorum</i> by PCR Analysis of 16S rDNA in Jordan

Abstract

Various bacterial species are known to be agents causing soft rot of potatoes. The results of this study showed that potato soft rot is widely spread in different potato planting areas in Jordan. A survey was conducted through the years 2013-2015 to detect potato soft rot disease in Jordan, two hundred and four rotted potato samples were collected from different potato growing areas through different potato growing seasons. One hundred and thirty one bacterial isolates were isolated, purified on selective media and identified as Pectobacterium carotovorum subspecies carotovorum (Pcc) by different biochemical and physiological tests. Furthermore, 131 Pcc Jordanian (Jo) isolates were identified by PCR analysis of total DNA extracted from isolates that were biochemically identified as Pcc using universal primer Fd1/Rd1. Cloning and sequencing of representative PCR products, amplifying the 16S rDNA region were done. Phylogenetic analysis of the Pcc Jo-isolates revealed other than 90% similarity with different reference Pcc strains available at the GenBank. Different rot causal agents also were detected by PCR amplification and further sequences. The sequencing data revealed similarities to Pseudomonas fluorescence, Enterobacteriaceae genera such as Enterobacter spp., Serratia spp. and Klebsiella spp., in addition to Pectobacterium carotovorum subsp. carotovorum. This study indicated that using molecular techniques such as amplification of 16S rDNA region is a sensitive and specific method for detecting Pcc as potato soft rot causal agent. So far this is the first study where Pcc has been identified by using PCR and sequencing approaches in Jordan.

Pectobacterium carotovorum: agente fitopatógeno causante de la pudrición blanda en la papa (Solanum tuberosum)

“…Un método diagnóstico rápido para la detección e identificación de P. carotovorum es la reacción en cadena de la polimerasa (PCR), técnica caracterizada por ser rápida, específica y altamente sensible (Abu-Obeid et al, 2018;De Boer & Ward, 1995;Fraijee et al, 1997;Perombelon et al, 1995). Para esta metodología y sus variantes, tales como PCR anidada, PCR múltiple y PCR en tiempo real, se han seleccionado algunos marcadores moleculares para identificación y caracterización de Pectobacterium sp.…”

“…Para esta metodología y sus variantes, tales como PCR anidada, PCR múltiple y PCR en tiempo real, se han seleccionado algunos marcadores moleculares para identificación y caracterización de Pectobacterium sp. como los ITS 16S-23rRN y 16S rDNA (Abu-Obeid et al, 2018;Diallo et al, 2009;Nikitin et al, 2018;Potrykus et al, 2014). En la tabla 4 se pueden observar algunos primers empleados para la amplificación del gen 16 r DNA de P. carotovorum.…”