ANALYSIS OF AGROBACTERIUM POPULATIONS ISOLATED FROM TUNISIAN SOILS: GENETIC STRUCTURE, AVIRULENT-VIRULENT RATIOS AND CHARACTERIZATION OF TUMORIGENIC STRAINS

The aim of this work is to assess the presence of agrobacterial populations in a variety of Tunisian soils to provide information regarding the diversity of strains occurring in agricultural soils. Twenty five soil samples were collected from seven different regions, which had or didn’t have a history of crown gall. Agrobacterium spp. members were dominant in Tunisian soils, isolated from 23 samples and assigned to the genomospecies G4, G7 and G9 by specific primers. The majority of samples yielded strains belonging to more than one genomospecies and showed a predominance of G4 and/or G7 members. Partial recA gene sequencing revealed new alleles and a high allelic diversity at both local and country scales. BOX-PCR fingerprinting of non-tumorigenic strains from dominant alleles did not show a clear correlation with geographic origin/soil plantation type, or a clear clonal spread of Agrobacterium strains in Tunisian soils. Ti plasmid-containing strains were only recovered from soils of fields with evidence of crown gall disease, and were exclusively allocated to the genomospecies G4. Tumorigenic strains isolated from soils with galled grapevines were distinct from tumorigenic strains isolated from soils with galled stone fruit trees, based on recA sequences, Ti plasmid type, sensitivity to the strain K84 and L-tartrate utilization.

[1]  A. Obradović,et al.  Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. , 2015, Systematic and applied microbiology.

[2]  A. Willems,et al.  Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. , 2015, Systematic and applied microbiology.

[3]  L. Paulin,et al.  Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. , 2014, Systematic and applied microbiology.

[4]  G. Urek,et al.  Isolation of non-pathogenic Agrobacterium spp. biovar 1 from agricultural soils in Slovenia , 2014 .

[5]  V. Daubin,et al.  Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. , 2014, Molecular phylogenetics and evolution.

[6]  X. Nesme,et al.  Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR. , 2013, Systematic and applied microbiology.

[7]  A. Rhouma,et al.  OCCURRENCE OF CROWN GALL OF THE GRAPEVINE IN TUNISIA AND CHARACTERIZATION OF TUNISIAN AGROBACTERIUM VITIS AND A. TUMEFACIENS STRAINS , 2013 .

[8]  A. Willems,et al.  Rhizobium nepotum sp. nov. isolated from tumors on different plant species. , 2012, Systematic and applied microbiology.

[9]  C. Rensing,et al.  Genome Sequence and Mutational Analysis of Plant-Growth-Promoting Bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a Zinc-Lead Mine Tailing , 2012, Applied and Environmental Microbiology.

[10]  X. Nesme,et al.  Rapid and Efficient Methods to Isolate, Type Strains and Determine Species of Agrobacterium spp. in Pure Culture and Complex Environments , 2012 .

[11]  B. Duffy,et al.  DETECTION AND IDENTIFICATION METHODS AND NEW TESTS AS DEVELOPED AND USED IN THE FRAMEWORK OF COST873 FOR BACTERIA PATHOGENIC TO STONE FRUITS AND NUTS Tumorigenic Agrobacterium spp. , 2012 .

[12]  J. Puławska,et al.  Phylogenetic relationship and genetic diversity of Agrobacterium spp. isolated in Poland based on gyrB gene sequence analysis and RAPD , 2011, European Journal of Plant Pathology.

[13]  K. Rymuza,et al.  BOX-PCR is an adequate tool for typing of clinical Pseudomonas aeruginosa isolates. , 2012, Folia histochemica et cytobiologica.

[14]  K. Lindström,et al.  International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium: minutes of the meeting, 7 September 2010, Geneva, Switzerland. , 2011, International journal of systematic and evolutionary microbiology.

[15]  Sabrine Saïdi,et al.  Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia. , 2011, Systematic and applied microbiology.

[16]  J. Puławska Crown gall of stone fruits and nuts, economic significance and diversity of its causal agents: tumorigenic Agrobacterium spp. , 2010 .

[17]  X. Nesme,et al.  Rapid and Efficient Identification of Agrobacterium Species by recA Allele Analysis , 2010, Microbial Ecology.

[18]  M. Ferreira,et al.  Low genetic diversity among pathogenic strains of Erwinia psidii from Brazil , 2009, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology].

[19]  M. López,et al.  Chromosomal and Ti plasmid characterization of tumorigenic strains of three Agrobacterium species isolated from grapevine tumours , 2009 .

[20]  Julio A. Rozas Liras,et al.  DnaSP v 5 : a software for comprehensive analysis of DNA polymorphism data , 2009 .

[21]  X. Nesme,et al.  POTENTIAL EFFECT OF RHIZOBACTERIA IN THE MANAGEMENT OF CROWN GALL DISEASE CAUSED BY AGROBACTERIUM TUMEFACIENS BIOVAR 1 , 2008 .

[22]  B. Mohapatra,et al.  Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments. , 2008, Water science and technology : a journal of the International Association on Water Pollution Research.

[23]  J. Ley,et al.  The host range of crown gall , 1976, The Botanical Review.

[24]  Calum R. Wilson,et al.  Diversity and detection of Korean Erwinia pyrifoliae strains as determined by plasmid profiling, phylogenetic analysis and PCR , 2007 .

[25]  A. Brandelli,et al.  Phenotypic and genotypic characterization of Salmonella Enteritidis isolates , 2007 .

[26]  X. Nesme,et al.  Plasmid and Chromosomal Diversity of a Tunisian Collection of Agrobacterium tumefaciens Strains , 2007 .

[27]  R. Simon,et al.  Wildlife identified as major source of Escherichia coli in agriculturally dominated watersheds by BOX A1R-derived genetic fingerprints. , 2007, Journal of environmental management.

[28]  B. Engelen,et al.  Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments. , 2006, Environmental microbiology.

[29]  W. Ruppitsch,et al.  Characterization of Erwinia amylovora strains from different host plants using repetitive‐sequences PCR analysis, and restriction fragment length polymorphism and short‐sequence DNA repeats of plasmid pEA29 , 2006, Journal of applied microbiology.

[30]  S. Pennycook,et al.  Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an opinion. , 2006, International journal of systematic and evolutionary microbiology.

[31]  E. Szegedi,et al.  Characterization of Agrobacterium tumefaciens strains isolated from grapevine , 2005 .

[32]  X. Nesme,et al.  Susceptibility of Some Stone and Pome Fruit Rootstocks to Crown Gall , 2005 .

[33]  Gerald R. Dickens,et al.  Distributions of Microbial Activities in Deep Subseafloor Sediments , 2004, Science.

[34]  H. Sawada,et al.  Detection of tumorigenic Agrobacterium strains from infected apple saplings by colony PCR with improved PCR primers , 2004, Journal of General Plant Pathology.

[35]  A. Raio,et al.  Physiological, Biochemical and Molecular Analyses of an Italian Collection of Agrobacterium tumefaciens strains , 2003, European Journal of Plant Pathology.

[36]  C. Manceau,et al.  Multiphasic Approach for the Identification of the Different Classification Levels Of Pseudomonas savastanoi Pv. Phaseolicola , 2000, European Journal of Plant Pathology.

[37]  P. Oger,et al.  Agrobacterium is a definable genus of the family Rhizobiaceae. , 2003, International journal of systematic and evolutionary microbiology.

[38]  J. Thioulouse,et al.  Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil , 2003, Applied and Environmental Microbiology.

[39]  X. Nesme,et al.  Seasonal Fluctuations and Long-Term Persistence of Pathogenic Populations of Agrobacterium spp. in Soils , 2002, Applied and Environmental Microbiology.

[40]  X. Nesme,et al.  Novel Tellurite-Amended Media and Specific Chromosomal and Ti Plasmid Probes for Direct Analysis of Soil Populations of Agrobacterium Biovars 1 and 2 , 2001, Applied and Environmental Microbiology.

[41]  Y. Dessaux,et al.  Characterization of Plasmid-Borne and Chromosome-Encoded Traits of Agrobacterium Biovar 1, 2, and 3 Strains from France , 2000, Applied and Environmental Microbiology.

[42]  Jan LW Rademaker,et al.  Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. , 2000, International journal of systematic and evolutionary microbiology.

[43]  P. Cobanov,et al.  Tartrate utilization genes promote growth of Agrobacterium spp. on grapevine , 1998 .

[44]  P. Sobiczewski Etiology of crown gall on fruit trees in Poland , 1996 .

[45]  P. Mcmanus,et al.  Genetic fingerprinting of Erwinia amylovora strains isolated from tree-fruit crops and Rubus spp. , 1995 .

[46]  F. D. de Bruijn,et al.  Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR , 1994, Applied and environmental microbiology.

[47]  P Simonet,et al.  Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction , 1992, Applied and environmental microbiology.

[48]  A. Kerr,et al.  Agrobacterium vitis sp. nov. for Strains of Agrobacterium biovar 3 from Grapevines , 1990 .

[49]  M. López,et al.  Opine utilization by Spanish isolates of Agrobacterium tumefaciens , 1988 .

[50]  H. V. Vuuren,et al.  Biotypes and phenotypic groups of strains of Agrobacterium in South Africa , 1984 .

[51]  N. Schaad,et al.  Laboratory guide for identification of plant pathogenic bacteria , 1988 .

[52]  J. Ley,et al.  A Biochemical Test for Crown Gall Bacteria , 1963, Nature.