Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Genome Biology and Evolution - Tập 3 - Trang 762-781 - 2011
Florent Lassalle1,2, Tony Campillo1,3, Ludovic Vial1, Jessica Baude4,3, Denis Costechareyre1, David Chapulliot1, Malek Shams1, Danis Abrouk1, Céline Lavire1, Christine Oger‐Desfeux5, Florence Hommais4,3, Laurent Guéguen2, Vincent Daubin2, Daniel Müller1, Xavier Nesme1
1Université de Lyon; Université Lyon 1; CNRS; INRA; Laboratoire Ecologie Microbienne Lyon, UMR 5557, USC 1193, Villeurbanne, France
2Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
3Université de Lyon; Université Lyon 1; CNRS; INSA de Lyon; Bayer Crop Science; UMR 5240, Laboratoire Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
4INSA de Lyon
5Université de Lyon; Université Lyon 1; SFR Bio-Environnement et Santé; PRABI Pôle Rhône-Alpes de Bio-Informatique, Villeurbanne, France

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Achtman, 2008, Microbial diversity and the genetic nature of microbial species, Nat Rev Microbiol., 6, 439, 10.1038/nrmicro1872

Bouzar, 2001, Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina, Int J Syst Evol Microbiol., 51, 1023, 10.1099/00207713-51-3-1023

Braun, 2006, Gene regulation by transmembrane signaling, Biometals, 19, 103, 10.1007/s10534-005-8253-y

Breese, 1998, 4-Hydroxybenzoyl-CoA reductase (dehydroxylating) from the denitrifying bacterium Thauera aromatica—prosthetic groups, electron donor, and genes of a member of the molybdenum-flavin-iron-sulfur proteins, Eur J Biochem., 251, 916, 10.1046/j.1432-1327.1998.2510916.x

Cai, 2009, Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution, Genome Biol Evol., 1, 239, 10.1093/gbe/evp019

Calisti, 2008, Regulation of ferulic catabolic genes in Pseudomonas fluorescens BF13: involvement of a MarR family regulator, Appl Microbiol Biotechnol., 80, 475, 10.1007/s00253-008-1557-4

Chen, 2003, Comparative genome analysis of Vibrio vulnificus, a marine pathogen, Genome Res., 13, 2577, 10.1101/gr.1295503

Chen, 2010, Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome, BMC Microbiol., 10, 198, 10.1186/1471-2180-10-198

Choi, 2005, An improved method for rapid generation of unmarked Pseudomonas aeruginosa deletion mutants, BMC Microbiol., 5, 30, 10.1186/1471-2180-5-30

Civolani, 2000, Bioconversion of ferulic acid into vanillic acid by means of a vanillate-negative mutant of Pseudomonas fluorescens strain BF13, Appl Environ Microbiol., 66, 2311, 10.1128/AEM.66.6.2311-2317.2000

Cock, 2009, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, 25, 1422, 10.1093/bioinformatics/btp163

Cohan, 2002, Sexual isolation and speciation in bacteria, Genetica, 116, 359, 10.1023/A:1021232409545

Connor, 2010, Ecology of speciation in the genus Bacillus, Appl Environ Microbiol., 76, 1349, 10.1128/AEM.01988-09

Costechareyre, 2009, Homologous recombination in Agrobacterium: potential implications for the genomic species concept in bacteria, Mol Biol Evol., 26, 167, 10.1093/molbev/msn236

Costechareyre, 2010, Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity, Microb Ecol., 60, 862, 10.1007/s00248-010-9685-7

Datsenko, 2000, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci U S A., 97, 6640, 10.1073/pnas.120163297

Dufour, 2007, The ade4 package: implementing the duality diagram for ecologists, J Stat Softw. [Internet], 22

Felsenstein, 1993, PHYLIP (Phylogeny Inference Package) version 3.5c. Seattle (WA): Department of Genome Sciences, University of Washington

Fraser, 2009, The bacterial species challenge: making sense of genetic and ecological diversity, Science, 323, 741, 10.1126/science.1159388

Galibert, 2001, The composite genome of the legume symbiont Sinorhizobium meliloti, Science, 293, 668, 10.1126/science.1060966

Gevers, 2005, Re-evaluating prokaryotic species, Nat Rev Microbiol., 3, 733, 10.1038/nrmicro1236

Goodner, 2001, Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58, Science, 294, 2323, 10.1126/science.1066803

Guéguen, 2005, Sarment: Python modules for HMM analysis and partitioning of sequences, Bioinformatics, 21, 3427, 10.1093/bioinformatics/bti533

Hardin, 1960, The competitive exclusion principle, Science, 131, 1292, 10.1126/science.131.3409.1292

Hartmann, 2009, Plant-driven selection of microbes, Plant Soil, 321, 235, 10.1007/s11104-008-9814-y

Hosie, 2002, Rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (Bra/LIV) of the ABC family, J Bacteriol., 184, 4071, 10.1128/JB.184.15.4071-4080.2002

Humphreys, 1999, New routes for lignin biosynthesis defined by biochemical characterization of recombinant ferulate 5-hydroxylase, a multifunctional cytochrome P450-dependent monooxygenase, Proc Natl Acad Sci U S A., 96, 10045, 10.1073/pnas.96.18.10045

Johnson, 2006, Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients, Science, 311, 1737, 10.1126/science.1118052

Kneen, 1983, Congo red absorption by Rhizobium leguminosarum, Appl Environ Microbiol., 45, 340, 10.1128/AEM.45.1.340-342.1983

Krimi, 2002, Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils, Appl Environ Microbiol., 68, 3358, 10.1128/AEM.68.7.3358-3365.2002

Lake, 1994, Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances, Proc Natl Acad Sci U S A., 91, 1455, 10.1073/pnas.91.4.1455

Lang, 2008, The genistein stimulon of Bradyrhizobium japonicum, Mol Genet Genomics., 279, 203, 10.1007/s00438-007-0280-7

Lau, 1997, A bacterial basic region leucine zipper histidine kinase regulating toluene degradation, Proc Natl Acad Sci U S A., 94, 1453, 10.1073/pnas.94.4.1453

Lefébure, 2010, Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept, Genome Biol Evol., 2, 646, 10.1093/gbe/evq048

Luo, 1999, Cloning and characterization of a tetracycline resistance determinant present in Agrobacterium tumefaciens C58, J Bacteriol., 181, 618, 10.1128/JB.181.2.618-626.1999

Maddocks, 2008, Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins, Microbiology, 154, 3609, 10.1099/mic.0.2008/022772-0

Martens, 2007, Multilocus sequence analysis of Ensifer and related taxa, Int J Syst Evol Microbiol., 57, 489, 10.1099/ijs.0.64344-0

Matthysse, 1998, Root colonization by Agrobacterium tumefaciens is reduced in cel, attB, attD, and attR mutants, Appl Environ Microbiol., 64, 2341, 10.1128/AEM.64.7.2341-2345.1998

Mayr, 1942, Systematics and the origin of species, from the viewpoint of a zoologist

Moriyama, 2008, Multidrug and toxic compound extrusion (MATE)-type proteins as anchor transporters for the excretion of metabolic waste products and xenobiotics, Xenobiotica, 38, 1107, 10.1080/00498250701883753

Mougel, 2002, A mathematical method for determining genome divergence and species delineation using AFLP, Int J Syst Evol Microbiol., 52, 573, 10.1099/00207713-52-2-573

Nelder, 1965, A simplex method for function minimization, Comput J., 7, 308, 10.1093/comjnl/7.4.308

Nishikawa, 1998, Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate, Appl Environ Microbiol., 64, 836, 10.1128/AEM.64.3.836-842.1998

Olivera, 2001, Two different pathways are involved in the beta-oxidation of n-alkanoic and n-phenylalkanoic acids in Pseudomonas putida U: genetic studies and biotechnological applications, Mol Microbiol., 39, 863, 10.1046/j.1365-2958.2001.02296.x

Ophel, 1990, Agrobacterium vitis sp. nov. for strains of Agrobacterium biovar 3 from grapevines, Int J Syst Bacteriol., 40, 236, 10.1099/00207713-40-3-236

Overhage, 1999, Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199, Appl Environ Microbiol., 65, 4837, 10.1128/AEM.65.11.4837-4847.1999

Palumbo, 1998, An isoflavonoid-inducible efflux pump in Agrobacterium tumefaciens is involved in competitive colonization of roots, J Bacteriol., 180, 3107, 10.1128/JB.180.12.3107-3113.1998

Panke, 1998, Towards a biocatalyst for (S)-styrene oxide production: characterization of the styrene degradation pathway of Pseudomonas sp. strain VLB120, Appl Environ Microbiol., 64, 2032, 10.1128/AEM.64.6.2032-2043.1998

Parke, 1995, Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens, J Bacteriol., 177, 3808, 10.1128/jb.177.13.3808-3817.1995

Pelletier, 1998, 2-Ketocyclohexanecarboxyl coenzyme A hydrolase, the ring cleavage enzyme required for anaerobic benzoate degradation by Rhodopseudomonas palustris, J Bacteriol., 180, 2330, 10.1128/JB.180.9.2330-2336.1998

Penyalver, 2001, Iron-binding compounds from Agrobacterium spp.: biological control strain Agrobacterium rhizogenes K84 produces a hydroxamate siderophore, Appl Environ Microbiol., 67, 654, 10.1128/AEM.67.2.654-664.2001

Petit, 1978, Substrate induction of conjugative activity of Agrobacterium tumefaciens Ti plasmids, Nature, 271, 570, 10.1038/271570a0

Philippot, 2010, The ecological coherence of high bacterial taxonomic ranks, Nat Rev Microbiol., 8, 523, 10.1038/nrmicro2367

Plaggenborg, 2003, Functional analyses of genes involved in the metabolism of ferulic acid in Pseudomonas putida KT2440, Appl Microbiol Biotechnol., 61, 528, 10.1007/s00253-003-1260-4

Portier, 2006, Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers, Appl Environ Microbiol., 72, 7123, 10.1128/AEM.00018-06

Portilho, 2006, Production of insoluble exopolysaccharide of Agrobacterium sp. (ATCC 31749 and IFO 13140), Appl Biochem Biotechnol., 131, 864, 10.1385/ABAB:131:1:864

Porwollik, 2002, Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis, Proc Natl Acad Sci U S A., 99, 8956, 10.1073/pnas.122153699

Quandt, 1993, Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria, Gene, 127, 15, 10.1016/0378-1119(93)90611-6

R Development Core Team, 2009, R: a language and environment for statistical computing

Rodríguez-Navarro, 2007, Attachment of bacteria to the roots of higher plants, FEMS Microbiol Lett., 272, 127, 10.1111/j.1574-6968.2007.00761.x

Rondon, 2004, Identification and analysis of a siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58, Microbiology, 150, 3857, 10.1099/mic.0.27319-0

Sambrook, 2001, Molecular cloning: a laboratory manual

Sanjay, 2008, Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system, Antonie Van Leeuwenhoekss, 94, 63, 10.1007/s10482-008-9246-y

Savka, 2002, Engineering bacterial competitiveness and persistence in the phytosphere, Mol Plant Microbe Interact., 15, 866, 10.1094/MPMI.2002.15.9.866

Schleheck, 2004, Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate, Int J Syst Evol Microbiol., 54, 1489, 10.1099/ijs.0.03020-0

Siddiqui, 2006, PGPR: biocontrol and biofertilization, 10.1007/1-4020-4152-7

Sikorski, 2005, Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel, Proc Natl Acad Sci U S A., 102, 15924, 10.1073/pnas.0507944102

Slater, 2009, Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria, J Bacteriol., 191, 2501, 10.1128/JB.01779-08

Sneath, 1973, Numerical taxonomy

Stackebrandt, 2002, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int J Syst Evol Microbiol., 52, 1043

Staley, 2004, Speciation and bacterial phylospecies, Microbial diversity and bioprospecting, 40, 10.1128/9781555817770.ch4

Touchon, 2009, Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet., 5, e1000344, 10.1371/journal.pgen.1000344

Vallenet, 2009, MicroScope: a platform for microbial genome annotation and comparative genomics, Database, 2009, bap021, 10.1093/database/bap021

Vaudequin-Dransart, 1995, Novel Ti plasmids in Agrobacterium strains isolated from fig tree and chrysanthemum tumors and their opine-like molecules, Mol Plant Microbe Interact., 8, 311, 10.1094/MPMI-8-0311

Velázquez, 2010, Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes, Syst Appl Microbiol., 33, 247, 10.1016/j.syapm.2010.04.004

Vesth, 2010, On the origins of a Vibrio species, Microb Ecol., 59, 1, 10.1007/s00248-009-9596-7

Vogel, 2003, Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil, Appl Environ Microbiol., 69, 1482, 10.1128/AEM.69.3.1482-1487.2003

Volff, 2000, A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution, FEMS Microbiol Lett., 186, 143, 10.1111/j.1574-6968.2000.tb09095.x

Wayne, 1987, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int J Syst Bacteriol., 37, 463, 10.1099/00207713-37-4-463

Wibberg, 2011, Complete genome sequencing of Agrobacterium sp. H13–3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid, J Biotechnol., 10.1016/j.jbiotec.2011.01.010

Wood, 2001, The genome of the natural genetic engineer Agrobacterium tumefaciens C58, Science, 294, 2317, 10.1126/science.1066804

Zhao, 2010, Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation, PLoS One, 5, e9109, 10.1371/journal.pone.0009109