Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium

Oulghazi, Saïd; Cigna, Jérémy; Lau, Yin Yin; Moumni, Mohiéddine; Chan, Kok‐Gan; Faure, Denis

doi:10.1099/ijsem.0.003180

Cited by 53 publications

(32 citation statements)

References 26 publications

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“…For "P. zantedeschiae", the three strains hosted at CIRM-CFBP were all isolated from Araceae plants, as the other strains described for this species [27]. Concerning the recently described freshwater environmental species P. aquaticum [17], P. fontis [21] and P. polonicum [25] and the strain CFBP 8739, we were surprised that these species had either no representative in the CIRM-CFBP or only strains deposited following the recent description of the species. The fact that no strain representative of these species was isolated from crop plants and ornamentals along the 75-year period that covered our analysis strongly suggests that these species are not an important threat for crop plants and ornamentals.…”

Section: Analysis Of Species Host Range and Geographic Distributionmentioning

confidence: 97%

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 Species Host Range and Geographic Distributionmentioning

confidence: 97%

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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“…In addition, new Pectobacterium species were progressively described, most of them recently on the basis of whole genome sequence analysis. Today, the Pectobacterium genus encompasses 17 recognized species Pectobacterium actinidiae [15], Pectobacterium aquaticum [17], Pectobacterium aroidearum [18], Pectobacterium atrosepticum [14], Pectobacterium betavasculorum [14], Pectobacterium brasiliense [15], Pectobacterium cacticida [9,19], Pectobacterium carotovorum [8,15,20], Pectobacterium fontis [21], Pectobacterium odoriferum [15], Pectobacterium parmentieri [22], Pectobacterium parvum [23], Pectobacterium polaris [24], Pectobacterium polonicum [25], Pectobacterium punjabense [26], Pectobacterium versatile [15] and Pectobacterium wasabiae [14] and 2 proposed species not yet validated by had hoc committees:…”

Section: Introductionmentioning

confidence: 99%

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

Portier¹,

Pédron²,

Taghouti³

et al. 2020

Preprint

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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. To solve this difficulty, we analyzed 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 non-host environments. MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. Results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species to the exception of P. polonicum. Yet, 6 strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, the P. versatile species, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. Analysis of P. versatile strains revealed that this species is endemic all over the world on various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from fresh water environment. Our work also revealed new host plants for several Pectobacterium spp.

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“…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. P. carotovorum isolates are subsequently divided into three different subspecies viz.…”

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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Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium

Cited by 53 publications

References 26 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

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

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

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