Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco

Number: 6 Publisher: Multidisciplinary Digital Publishing InstituteInternational audienceDickeya 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

Identifying a candidate gene for the broad-spectrum resistance qtl to <em>Phytophthora</em> root rot and blight in pepper

International audienc

Identifying a candidate gene for the broad-spectrum resistance qtl to <em>Phytophthora</em> root rot and blight in pepper

International audienc

Marinitoga aeolica sp. nov., a novel thermophilic anaerobic heterotroph isolated from a shallow hydrothermal field of Panarea Island in the Aeolian archipelago, Italy

A novel thermophilic strain, designated BP5-C20A T , was isolated from the shallow hydrothermal field of the Panarea island in the Aeolian archipelago close to Sicily, Italy. Cells are motile rods surrounded with a ‘toga’, Gram-stain-negative and display a straight to curved morphology during the exponential phase. Strain BP5-C20A T is thermophilic (optimum 55 °C), moderately acidophilic (optimum pH 5.6) and halotolerant (optimum 25 g l −1 NaCl). It can use yeast extract, peptone and tryptone. It uses the following carbohydrates: cellobiose, fructose, glucose, maltose, starch, sucrose and xylan. Elemental sulphur is used as an electron acceptor and reduced to hydrogen sulphide. The predominant cellular fatty acid is C 16 : 0 . Phylogenetic analysis showed that strain BP5-C20A T shared 97.3 % 16S rRNA gene sequence identity with the closest related species Marinitoga lauensis LG1 T . The complete genome of strain BP5-C20A T is 2.44 Mb in size with a G+C content of 27.3 mol%. The dDDH and ANI values between the genomes of strains BP5-C20A T and M. lauensis LG1 T are 31.0 and 85.70% respectively. Finally, from its physiological, metabolic and genomic characteristics, strain BP5-C20A T (=DSM 112332 T =JCM 39183 T ) is proposed as representative of a novel species of the genus Marinitoga named Marinitoga aeolica sp. nov. and belonging to the order Petrotogales , in the phylum Thermotogota

Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato

International audienceAbstract The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%

Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity

International audienceDNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the Mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of Mycoplasma agalactiae , an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers

Alkalicella caledoniensis gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from ‘La Crouen’ alkaline thermal spring, New Caledonia

International audienceA novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated strain LB2 T , grew at 25–50 °C (optimum, 37 °C) and pH 8.2–10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0–1 %) but was tolerated up to 7 %. Strain LB2 T utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C 15 : 0 and C 16 : 0 . The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Proteinivoraceae , order Clostridiales within the phylum Firmicutes . Strain LB2 T was most closely related to the thermophilic Anaerobranca gottschalkii LBS3 T (93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA–DNA hybridization of strain LB2 T with A. gottschalkii LBS3 T showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2 T is proposed to represent the first species of a novel genus, for which the name Alkalicella caledoniensis gen. nov., sp. nov. is proposed (type strain LB2 T =DSM 100588 T =JCM 30958 T )