Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco

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.

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

“…In fact, Pbr has been reported in potato in Brazil since 2004 [ 11 ], followed by its detection in North America [ 66 , 67 , 68 ], Europe [ 12 , 13 , 14 , 69 , 70 ], Africa [ 7 , 9 , 71 , 72 ], Asia [ 62 , 73 , 74 , 75 , 76 ], and New Zealand [ 77 ]. Generally, Pbr causes blackleg and soft rot in potato leaves, stems, and tubers [ 8 , 10 , 66 , 68 , 74 ]. Tomatoes have been reported to be also infected by Pbr, resulting in a large loss for producers.…”

“…Several molecular method have been employed for the characterization of Pbr, including conventional polymerase chain reaction (PCR) [ 8 , 9 ], real-time qPCR [ 103 ], PCR-restriction fragment length polymorphism (PCR-RFLP) [ 10 ], pulsed-field gel electrophoresis (PFGE), MLSA [ 62 ] and HTS [ 8 ], with conventional PCR and real-time PCR commonly used in laboratories for robust confirmation of Pbr in the samples [ 9 , 103 ] ( Table 2 ).…”

“…The most recommended method for differentiation of Pbr from other SRP are MLSA and HTS enable to confirm phylogenetic position within Pectobacterium genus [ 8 , 34 ]. Additionally, among other reported detection methods ( Table 2 ), MLSA is widely used due the availability of the data in the public data base (NCBI).…”

“…Additionally, among other reported detection methods ( Table 2 ), MLSA is widely used due the availability of the data in the public data base (NCBI). Also, it was used for taxonomic information [ 34 , 111 ] and the study of the diversity of Pbr with the related species [ 8 , 9 ]. Most recently, several housekeeping genes were reported to differentiate Pbr in MLSA schemes [ 8 , 9 , 34 , 50 ].…”

“…Pectobacterium brasiliense (Pbr) is a worldwide-distributed bacterial plant pathogen causing soft rot of a wide range of economically important crops. Pbr has been reported in Eurasia: from Western European countries to Russia and China [ 4 , 5 , 6 ], in Africa: South Africa, Morocco, Algeria and Kenya [ 7 , 8 , 9 , 10 ]. Pbr has been constantly reported since 2004 causing significant losses particularly of potato ( Solanum tuberosum L.) [ 11 , 12 , 13 , 14 ] and posing a threat to worldwide potato gross production value which is estimated to be $63914 million in 2018 [ 15 ].…”