Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan

Sarfraz, Sohaib; Riaz, Kashif; Oulghazi, Saïd; Cigna, Jérémy; Sahi, Shahbaz Talib; Khan, S. H.; Faure, Denis

doi:10.1099/ijsem.0.003029

Cited by 63 publications

(39 citation statements)

References 20 publications

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“…Out of the 136 strains isolated from potatoes, 31 were isolated from the stem or leaf and 33 from the tuber, and, unfortunately, it was not clearly documented for the remaining 71 strains ( Table 3). The 31 strains isolated from the stem or leaf belonged to six species: five of which-P. brasiliense, P. atrosepticum, P. parvum, P. parmentieri and P. punjabense-are well-known species triggering blackleg disease [4,23,26]. Interestingly, the newly described P. versatile species was also isolated from potato stems or leaves in the UK, Morocco and France from 1972 to 2016.…”

Section: Analysis Of Strains Isolated On Potato Plantsmentioning

confidence: 99%

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

et al. 2020

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Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp.

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Section: Analysis Of Strains Isolated On Potato Plantsmentioning

confidence: 99%

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

et al. 2020

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“…Previously known as Erwinia species (Winslow et al 1920), the taxonomic reclassifications based on genetic differences within this genus led to the recognition of the genus Pectobacterium (Hauben et al 1998) which was later separated into Pectobacterium and Dickeya (Samson et al 2005). Pectobacterium currently includes ten formally described species and three subspecies (Gardan et al 2003;Nabhan et al 2013;Khayi et al 2016) with several recently described species including Pectobacterium polaris (Dees et al 2017b), Pectobacterium peruviense (Waleron et al 2017), Pectobacterium punjabense (Sarfraz et al 2018), Pectobacterium zantedeschiae (Waleron et al in press) and Candidatus Pectobacterium maceratum (Shirshikov et al 2018) being proposed. The genus Dickeya currently includes eight species and two subspecies (Samson et al 2005;Brady et al 2012;Parkinson et al 2014;Tian et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Pectobacterium and Dickeya species detected in vegetables in Northern Ireland

et al. 2019

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Destructive soft rot Pectobacteriaceae affect a number of vegetable crops and cause high economic loses in the field and storage. The diversity of Pectobacterium and Dickeya causing soft rot of vegetables in Northern Ireland is unknown. This study provides details of Pectobacterium and Dickeya spp. detected in vegetables from several locations in Northern I r e l a n d i n t h e y e a r s 2 0 1 5-2 0 1 7. S o f t r o t Pectobacteriaceae were identified based on DNA sequences. Thirty three strains were selected for further phylogenetic analysis based on the recA gene region. Results from the testing of over 3456 potato samples for plant health statutory purposes in the years 2005-2017 demonstrated that Dickeya spp. is not the major pathogen causing soft rot or blackleg in Northern Ireland. The most predominant species causing soft rot of vegetables in Northern Ireland were Pectobacterium atrosepticum and Pectobacterium carotovorum subsp. carotovorum. Pectobacterium atrosepticum was also detected on hosts other than potato. Testing of bacteria isolated from carrots led to the detection of P. carotovorum and Dickeya sp. This is the first study to provide knowledge about Pectobacterium and Dickeya spp. diversity causing soft rot of vegetables in Northern Ireland confirmed by real-time PCR and DNA sequences. This is also the first report of the detection of D. aquatica from a source other than water.

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“…The level of diversity in SRE species so vary greatly that it is attributed to the unique taxon in the group (Seo et al 2002), with a range of different phenotypic, biochemical, host range, and genetic characteristic (Toth et al 2003). The genus Pectobacterium comprises the following species: Pectobacterium carotovorum, Pectobacterium atrosepticum, Pectobacterium betavasculorum, Pectobacterium cacticida, Pectobacterium aroidearum (Nabhan et al 2013), Pectobacterium wasabiae, Pectobacterium parmentieri (Khayi et al 2016), Pectobacterium polaris (Dees et al 2017), Pectobacterium peruviense (Waleron et al 2018), and Pectobacterium punjabense (Sarfraz et al 2018). In addition, Pectobacterium zantedeschiae (Waleron et al 2019a), Pectobacterium aquaticum (Pedron et al 2019), Pectobacterium fontis (Oulghazi et al 2019), Pectobacterium polonicum (Waleron et al 2019b), and the new genomospecies, Candidatus Pectobacterium maceratum (Shirshikov et al 2018;Waleron et al 2019c) are recently added to the genus.…”

Section: Introductionmentioning

confidence: 99%

A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

2019

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Abstract. Joko T, Soffan A, Muhammad Saifur Rohman MS. 2019. A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense. Biodiversitas 20: 3042-3048. Pectobacterium carotovorum subsp. brasiliense is one of the major causative bacterial pathogens of the soft rot disease in various crops. It has a high virulence and a wide range of hosts in the tropics and the subtropics. Most often, conventional methods are not able to accurately distinguish P. carotovorum subsp. brasiliense from other subspecies. Thus, this study aimed to design a specific gyrase B gene (gyrB) -based primers for the detection and identification of soft rot pathogen. The specific primers design was based on the alignment using gyrB gene sequence data from P. carotovorum subsp. brasiliense and other data from the GenBank. The primers comprised of F-gyr-Pcb (5’-CAC AGG CAC CGC TGG CTG TT-3’) and R-gyr-Pcb (5’-CGT CGT TCC ACT GCA ATG CCA-3’) with an amplicon of 336 base pairs. The specificity of the primers pair was verified both in silico and in polymerase chain reaction (PCR) assays, where the primers could only detect P. carotovorum subsp. brasiliense. Primers’ sensitivity was determined by qualitative PCR with a detection limit of less than 0.5 ng/µL of genomic DNA. Hence, the proposed detection tool can be beneficial to advance further studies on the ecology and epidemiology of soft rot diseases.

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Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan

Cited by 63 publications

References 20 publications

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

Pectobacterium and Dickeya species detected in vegetables in Northern Ireland

A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

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