A semi-selective medium to isolate and identify bacteria of the genus Pantoea

Kini, Kossi; Dossa, Rachelle; Dossou, Bernadin; Mariko, Mariame; Koebnik, Ralf; Silué, D.

doi:10.1007/s10327-019-00862-w

Cited by 16 publications

(15 citation statements)

References 23 publications

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“…Three out of the four species in the Pantoea species complex ( P. ananatis, P. agglomerans and P. stewartii subsp. indologenes ) are responsible for more than 80% of the reported cases of disease in onions [ 5 ]. Earlier, Mergaert et al [ 6 ] reclassified Eriwinia stewartii as P. stewartii and proposed two subspecies namely, P. stewartii subsp.…”

Section: Introductionmentioning

confidence: 99%

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

2021

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Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.

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Section: Introductionmentioning

confidence: 99%

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

2021

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“…The Pantoea genus is composed of several species characterized by their ubiquity and versatility in their interactions with living organisms and the environment [5] , [6] , [7] . Five species, namely P. ananatis, P. agglomerans, P. stewartii, P. allii and P. wallisii , have been widely reported as plant pathogens [8] , [9] , [10] , [11] with P. ananatis, P. agglomerans, P. stewartii on rice plants [12 , 13] and seeds [14] in Sub-Saharan Africa. Collectively, they cause various diseases and symptoms, such as leaf blight and dieback, red streak, black spot, necrosis, bacterial spot, tumors, rot center, stem necrosis, leaf rot, decay of seed and Stewart's wilt [11] .…”

Section: Introductionmentioning

confidence: 99%

“…New diagnostic tools have been developed, such as simplex and multiplex PCR schemes able of identifying the three major Pantoea species affecting rice plants [12] . A semi-selective medium for their isolation and identification has also been developed [13] . However, their use is complex, time consuming, expensive and cannot be deployed outside the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Development of two loop-mediated isothermal amplification (LAMP) genomics-informed diagnostic protocols for rapid detection of Pantoea species on rice

et al. 2021

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At least three species of Pantoea are responsible for bacterial blight disease and grain discoloration of rice in Sub-Saharan Africa. Thus, measures need to be taken to limit the pathogens' dispersion and robust diagnostic tools are required for rapid and cheap diagnosis in the field as well as for routine seed certification or control. Therefore, several diagnostic tools such as simplex and multiplex PCR schemes and a semi-selective medium have been developed and are being used. However, the use of these tools is time-consuming, expensive and therefore limited to laboratories that can afford the chemicals. We have therefore developed two isothermal loop amplification (LAMP) protocols, one of which detects all Pantoea species in the genus and another one that is specific for P. ananatis . The novel LAMP assays allow rapid and sensitive detection of these bacteria. They will help plant protection services in routine field and laboratory tests especially for monitoring the phytosanitary status of rice seeds.

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“…Three out of the four species in Pantoea complex, P. ananatis, P. agglomerans and P. stewartii subsp. indologenes are responsible for more than 80% of the reported cases of disease in onions [5]. Earlier, Mergaert et al [6] reclassified Eriwinia stewartii as P. stewartii and proposed two subspecies P. stewartii subsp.…”

Section: Introductionmentioning

confidence: 99%

Pan-genome of Novel <em>Pantoea stewartii</em> subsp. <em>indologenes</em> Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Agarwal¹,

Gitaitis²,

Dutta³

2021

Preprint

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Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onion and millets or on millets only, respectively. In the current study we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n= 4) and pv. setariae (n=13)]. The full spectrum of the pan-genome contained 7,030 genes. Among these, 3,546 (present in genomes of all 17 strains) were the core genes that were a subset of 3,682 soft-core genes (present in ≥16 strains). The accessory genome included 1,308 shell genes and 2,040 cloud genes (present in ≤ 2 strains). The pan-genome showed a clear liner progression with >6,000 genes, suggesting the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison to core genome SNP-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study including four other Pantoea species namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfers observed between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes including seven cluster of genes associated with the pathogenicity phenotype on onion. One of the clusters contain 11 genes with known functions and are found to be chromosomally located.

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A semi-selective medium to isolate and identify bacteria of the genus Pantoea

Cited by 16 publications

References 23 publications

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Development of two loop-mediated isothermal amplification (LAMP) genomics-informed diagnostic protocols for rapid detection of Pantoea species on rice

Pan-genome of Novel <em>Pantoea stewartii</em> subsp. <em>indologenes</em> Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

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