Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

Martin, Jacques; Durand, Karine; Orgeur, Geoffrey; Balidas, Samuel; Fricot, Céline; Bonneau, Sophie; Quillevere, Anne; Audusseau, C.; Olivier, Valérie; Grimault, Valérie; Mathis, René

doi:10.1128/aem.02158-12

Cited by 85 publications

(103 citation statements)

References 74 publications

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“…Sequences were concatenated by following the alphabetic order of the genes. Multilocus sequence analysis (MLSA) was conducted as described by Jacques et al (37). Multilocus sequence typing (MLST) was performed according to the X. fastidiosa MLST website (http://pubmlst.org /xfastidiosa/).…”

Section: Methodsmentioning

confidence: 99%

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Jacques

Denancé

Legendre³

et al. 2016

Appl Environ Microbiol

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Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants.

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Section: Methodsmentioning

confidence: 99%

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Jacques

Denancé

Legendre³

et al. 2016

Appl Environ Microbiol

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“…Housekeeping Genes Another valuable method is the genetic analyses of the housekeeping genes such as rpoB (the RNA polymerase β subunit-encoding gene), rpoD, gyrB (gyrase subunit β gene), recA (encoding a protein involved in repairing damaged DNA in the SOS regulon) and multilocus sequence analysis MLSA (Dahllöf et al 2000;Kasai et al 2000;Maréchal et al 2000;St-Onge et al 2008;Bernèche-D'Amours et al 2011;Waleron et al 2011;Jacques et al 2012;Carro et al 2012;Xu et al 2012b). …”

Section: Genomic Fingerprinting Methodsmentioning

confidence: 99%

“…Also, attempts aiming to differentiate Clavibacter subspecies as well as to differentiate between saprophytes, non virulent and virulent Clavibacter strains have been performed by many researchers (Dreier et al 1995;Dreier et al 1997;Louws et al 1998;Pastrik and Rainey 1999;Smith et al 2001;Bach et al 2003;Waleron et al 2011;Jacques et al 2012;Zaluga et al 2013). Molecular methods include qualitative gene PCR (Dreier et al 1995;Li and de Boer 1995;Slack et al 1996;Waleron et al 2011;Jacques et al 2012) rep-PCR (Louws et al 1998;Smith et al 2001), Nested PCR (Lee et al 1997b), RAPD-PCR (de Leon et al 2009), SSR-PCR , RT-PCR (Bach et al 2003), rDNA sequencing (Kaneshiro et al 2006) and DNA hybridization (Slack et al 1996). For example, molecular studies allowed to establish that the subspeciation event between C. michiganensis subsp.…”

Section: A-order Micrococalesmentioning

confidence: 99%

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Diversity of Plant Associated Actinobacteria

Bouizgarne

Aouamar

2014

Sustainable Development and Biodiversity

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The phylum Actinobacteria encompasses Gram-positive bacteria with a high DNA G+C. In soils, they present multiple lifestyles: rhizosphere saprophytes, endophytes, facultative symbionts and obligate phytopathogens. They play either beneficial or adverse effects towards plants. Numerous studies focused on their taxonomy and preservation. Also, adequate strategies were developed to enable their isolation. Phenotypically, the Actinobacteria is one of the most diverse phyla within bacteria. Their presence was once monitored by classical culture dependent techniques and phenetic characterization. Development of culture independent methods including chemotaxonomic and genomic approaches such as 16S rRNA gene analysis allowed to detect the so called unculturable bacteria. Major works on their diversity combine culture dependant and independant techniques. This chapter focuses on the phenetic and genetic diversity of Actinobacteria in plant-soil systems. It begins with some knowledge of their biology and their taxonomy, followed by a brief overview of the methods that have facilitated advances in the understanding of their diversity. It also discusses diversity of ecologically important plant associated Actinobacteria (rhizosphere and phyllosphere colonizers, endophytes, symbionts and phytopathogens).

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“…They were isolated from five different tomato cultivars and seven different locations, in the period February 2010 till February 2012 (Table 1). Clavibacter -like isolates from tomato seed are phenotypically similar to Cmm in the common diagnostic semi-selective media and are identified as Cmm in the standard tests but are non-pathogenic to tomato [32,33]. They were isolated according to the current method for detection of Cmm in tomato seed recommended by International Seed Federation (ISF) [34].…”

Section: Methodsmentioning

confidence: 99%

Multilocus Variable-Number-Tandem-Repeats Analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium

Zaluga

Stragier

Vaerenbergh³

et al. 2013

BMC Microbiology

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BackgroundClavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains.ResultsA phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010–2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons.ConclusionsWe hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm.

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Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

Cited by 85 publications

References 74 publications

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Diversity of Plant Associated Actinobacteria

Multilocus Variable-Number-Tandem-Repeats Analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium

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