Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.

Saïd Oulghazi,Denis Faure,Slimane Khayi,Mohieddine Moumni,Céline Lopez-Roques,Céline Vandecasteele,Kévin Robic,Sohaib Sarfraz

doi:10.3390/microorganisms8060895

Abstract

Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015–2017). Pathogens were characterized by sequence determination of both the gapA gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to P. versatile (19%), P. carotovorum (3%), P. polaris (5%), P. brasiliense (56%) and D. dianthicola (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, D. dianthicola isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of D. dianthicola LAR.16.03.LID was obtained and compared with other D. dianthicola genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a D. dianthicola strain isolated in Morocco that will be suitable for further epidemiological studies.

Highlights

Pectinolytic Pectobacterium and Dickeya spp. are causative agents of severe diseases in a wide range of plants of high economic value [1,2]
The main objectives of this study were: (i) to investigate the species composition of the Moroccan Dickeya and Pectobacterium populations, collected between 2015 and 2017 from diseased potato tubers and stems, (ii) to compare the aggressiveness of some identified pathogens belonging to different species, and (iii) to propose a complete genome of the emerging pathogen D. dianthicola in Morocco, that could be used for further studies as a reference genome
Out of 200 strains isolated from plant symptoms, 140 provoked cavities on the pectate-containing medium. These were tested by PCR to evaluate whether they belonged to the Pectobacterium and Dickeya genera: 119 isolates generated amplification signals for either the Y1/Y2 or ADE1/ADE2 primer couples

Summary

Introduction

Pectinolytic Pectobacterium and Dickeya spp. are causative agents of severe diseases in a wide range of plants of high economic value [1,2]. On potato tubers and stems, the diseases caused by pectinolytic pathogens are soft rot and blackleg, respectively. These pathogens produce a large set of extracellular enzymes that degrade the plant cell wall, resulting in plant tissue decay and maceration. This rotting process causes losses in the production of potato tubers sold both on the food market and as certified seed tubers [3]. The pathogens may be acquired by the host plants from soil and/or from contaminated seed tubers [4]. Pathogen populations remain at a low level in asymptomatic plant tissues, and may become destructive when environmental conditions favor their proliferation and the expression of virulence factors

Objectives

Methods

Results

Discussion

Conclusion