Subtelomere plasticity in the bacterium Streptomyces, Louis EJ, Becker MM, pp.243-258, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01478830
Sampling the antibiotic resistome, Science, vol.311, pp.374-377, 2006. ,
Basic Local alignment search tool, J Mol Biol, vol.215, issue.05, pp.80360-80362, 1990. ,
MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016. ,
Practical Streptomyces genetics, John Innes Foundation, 2000. ,
PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes, Mol Cell Probes, vol.15, pp.337-347, 2001. ,
Taxonomy, physiology, and natural products of Actinobacteria, Microbiol Mol Biol Rev, vol.80, pp.1-43, 2016. ,
Streptomyces: implications and interactions in plant growth promotion, Appl Microbiol Biotechnol, vol.103, pp.1179-1188, 2019. ,
Genome mining of Streptomyces ambofaciens, J Ind Microbiol Biotechnol, vol.41, pp.251-263, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01475037
Gifted microbes for genome mining and natural product discovery, J Ind Microbiol Biotechnol, vol.44, pp.573-588, 2017. ,
Evolution of the terminal regions of the Streptomyces linear chromosome, Mol Biol Evol, vol.23, pp.2361-2369, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-02661267
A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb, 1996. ,
, Mol Microbiol, vol.21, pp.77-96
Comparative genomics analysis of Streptomyces species reveals their adaptation to the marine environment and their diversity at the genomic level, Front Microbiol, vol.7, 2016. ,
Comparative genomics reveals the core and accessory genomes of Streptomyces species, J Microbiol Biotechnol, vol.25, pp.1599-1605, 2015. ,
Genome plasticity and systems evolution in Streptomyces, BMC Bioinformatics, vol.13, 2012. ,
The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993. ,
The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998. ,
Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes, Trends Genet, vol.18, issue.02, p.2752, 2002. ,
Subtelomere plasticity in the bacterium Streptomyces, Louis EJ, Becker MM, pp.243-258, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01478830
Widespread homologous recombination within and between Streptomyces species, ISME J, vol.4, pp.1136-1143, 2010. ,
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000. ,
A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus, ISME J, vol.10, pp.2468-2477, 2016. ,
Micro-scale determinants of bacterial diversity in soil, FEMS Microbiol Rev, vol.37, pp.936-954, 2013. ,
Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria, PLoS One, vol.8, p.83661, 2013. ,
Spatial ecology of bacteria at the microscale in soil, PLoS One, vol.9, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01252483
Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.47, pp.23-28, 2019. ,
End-to-end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens, Mol Microbiol, vol.50, pp.411-425, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02678526
Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens, Proc Natl Acad Sci U S A, vol.95, pp.14296-14301, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-01625341
Chromosomal arm replacement in Streptomyces griseus, J Bacteriol, vol.185, pp.1120-1124, 2003. ,
Efficiency of the transfer of a pSAM2-derivative plasmid between two strains of Streptomyces lividans in conditions ranging from agar slants to non-sterile soil microcosms, FEMS Microbiol Ecol, vol.21, pp.157-165, 1996. ,
URL : https://hal.archives-ouvertes.fr/hal-02874486
Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene, Proc Natl Acad Sci U S A, vol.95, p.5145, 1998. ,
0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res, vol.45, pp.36-41, 2017. ,
Why prokaryotes have pangenomes, Nat Microbiol, vol.2, p.17040, 2017. ,
Genome plasticity is governed by double strand break DNA repair in Streptomyces, Sci Rep, vol.8, p.5272, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01757262
A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi, Mol Microbiol, vol.35, pp.490-516, 2002. ,
Distance from the chromosome end determines the efficiency of double strand break repair in subtelomeres of haploid yeast, J Mol Biol, vol.328, issue.03, pp.315-317, 2003. ,
Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature, vol.437, pp.94-100, 2005. ,
, , 2002.
Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities, Appl Environ Microbiol, vol.83, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01548673
,
, Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio, ISME J, vol.5, pp.1323-1331
Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities, J Ind Microbiol Biotechnol, vol.46, pp.281-299, 2019. ,
Evolution and Ecology of Actinobacteria and Their Bioenergy Applications, Annu Rev Microbiol, vol.70, pp.235-254, 2016. ,
Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent, Mol Microbiol, vol.8, pp.967-980, 1993. ,
, The genome of the natural genetic engineer Agrobacterium tumefaciens C58, vol.294, pp.2317-2323, 2001.
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse, Proc Natl Acad Sci U S A, vol.103, pp.15582-15587, 2006. ,
Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome, Mol Microbiol, vol.51, pp.1535-1550, 2004. ,
End-to-end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens, Mol Microbiol, vol.50, pp.411-425, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02678526
Soil to genomics: the Streptomyces chromosome, Annu Rev Genet, vol.40, pp.1-23, 2006. ,
Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome, BMC Microbiol, vol.10, 0198. ,
Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens, J Bacteriol, vol.188, pp.6599-6610, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-01659064
Telomere associated primase Tap repairs truncated telomeres of Streptomyces, Nucleic Acids Res, vol.45, pp.5838-5849, 2017. ,
Bidirectional replication from an internal origin in a linear Streptomyces plasmid, Science, vol.265, pp.952-954, 1994. ,
The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule, Mol Microbiol, vol.7, pp.925-932, 1993. ,
The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993. ,
The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998. ,
Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350, J Bacteriol, vol.190, pp.4050-4060, 2008. ,
A novel pair of terminal protein and telomere-associated protein for replication of the linear chromosome of Streptomyces griseus IFO13350, Biosci Biotechnol Biochem, vol.72, pp.2973-2980, 2008. ,
The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins, Mol Microbiol, vol.43, pp.297-305, 2002. ,
Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces, Genes Dev, vol.15, pp.1518-1527, 2001. ,
Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication, Genes Dev, vol.17, pp.774-785, 2003. ,
,
, Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics
,
, Genome Sequences of 11 Conspecific Streptomyces sp, Strains. Microbiol Resour Announc, vol.8
, The RAST Server: rapid annotations using subsystems technology, vol.9, p.75, 2008.
Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, vol.31, pp.3406-3415, 2003. ,
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, pp.4673-4680, 1994. ,
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol Biol Evol, vol.35, pp.1547-1549, 2018. ,
Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990. ,
Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-1403, 2004. ,
Detecting and Analyzing Genetic Recombination Using RDP4, Methods Mol Biol Clifton NJ, vol.1525, pp.433-460, 2017. ,
Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing, Genome Res, vol.21, pp.1388-1393, 2011. ,
Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens, Front Microbiol, vol.7, 1901. ,
URL : https://hal.archives-ouvertes.fr/hal-01521993
Functional angucycline-like antibiotic gene cluster in the terminal inverted repeats of the Streptomyces ambofaciens linear chromosome, Antimicrob Agents Chemother, vol.48, pp.575-588, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-02675577
Integration of SCP1, a giant linear plasmid, into the Streptomyces coelicolor chromosome, Gene, vol.115, pp.35-41, 1992. ,
Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wild-type chromosome and linear plasmid scp1, J Bacteriol, vol.186, pp.6553-6559, 2004. ,
Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites, J Bacteriol, vol.193, pp.5055-5056, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00628567
Telomere exchange between linear replicons of Borrelia burgdorferi, J Bacteriol, vol.186, pp.4134-4141, 2004. ,
Structure, function, and evolution of linear replicons in Borrelia, Annu Rev Microbiol, vol.64, pp.185-202, 2010. ,
DNA double-strand breaks and telomeres play important roles in trypanosoma brucei antigenic variation, REFERENCES BIBLIOGRAPHIQUES, vol.14, pp.196-205, 2015. ,
Identification of protein secretion systems in bacterial genomes, Scientific Reports, vol.6, p.23080, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01677379
A genetic analysis of F sex factor cistrons needed for surface exclusion in Escherichia coli, J Mol Biol, vol.138, pp.779-795, 1980. ,
Microbial diversity and the genetic nature of microbial species, Nat Rev Microbiol, vol.6, pp.431-440, 2008. ,
Site-Specific Recombination, Molecular Biology of the Cell, 2002. ,
Structure of an amplifiable DNA sequence in Streptomyces lividans 66, Mol Gen Genet, vol.201, pp.192-197, 1985. ,
Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990. ,
Biological diversity of prokaryotic type IV secretion systems, Microbiol Mol Biol Rev, vol.73, pp.775-808, 2009. ,
New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through, Extensive Genome Exploration. Front Microbiol, vol.6, p.1483, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01262284
Prokaryote genome fluidity is dependent on effective population size, The ISME Journal, 2017. ,
Biogeography of soil archaea and bacteria along a steep precipitation gradient, ISME J, vol.4, pp.553-563, 2010. ,
Inference of the Properties of the Recombination Process from Whole Bacterial Genomes, Genetics, vol.196, pp.253-265, 2014. ,
Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system, Antonie Van Leeuwenhoek, vol.94, pp.63-74, 2008. ,
Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences, Scientific Reports, vol.7, p.11089, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01590493
Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes, Evol Bioinform Online, vol.3, pp.279-286, 2007. ,
Genetic variation: molecular mechanisms and impact on microbial evolution, FEMS Microbiol Rev, vol.24, pp.1-7, 2000. ,
The SOS system, Biochimie, vol.67, pp.343-347, 1985. ,
Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age, Chem Biol, vol.9, pp.145-156, 2002. ,
STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES, J Exp Med, vol.79, pp.137-158, 1944. ,
Toxic genes present a unique phylogenetic signature, Mol Phylogenet Evol, vol.116, pp.141-148, 2017. ,
The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, pp.75-75, 2008. ,
On the ecology of a Sphagnum Bog, Evolution and Biogeography of Plants, vol.1, pp.10-45, 1934. ,
Exploring the costs of horizontal gene transfer, Trends Ecol Evol (Amst), vol.28, pp.489-495, 2013. ,
Cluster organization of the genes of Streptomyces pristinaespiralis involved in pristinamycin biosynthesis and resistance elucidated by pulsed-field gel electrophoresis, Journal of Applied Microbiology, 1999. ,
Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces, Genes Dev, vol.15, pp.1518-1527, 2001. ,
Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication, Genes Dev, vol.17, pp.774-785, 2003. ,
Evolutionary analyses of non-genealogical bonds produced by introgressive descent, PNAS, vol.109, pp.18266-18272, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01544803
Linear chromosome of Borrelia burgdorferi, Res Microbiol, vol.140, pp.507-516, 1989. ,
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, pp.1709-1712, 2007. ,
Genome dynamics during experimental evolution, Nat Rev Genet, vol.14, pp.827-839, 2013. ,
Experimental tests of the bacterial distance-decay relationship, The ISME Journal, vol.4, pp.1357-1365, 2010. ,
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, vol.417, pp.141-147, 2002. ,
Bioactive microbial metabolites, J Antibiot, vol.58, pp.1-26, 2005. ,
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiol Ecol, vol.68, pp.1-13, 2009. ,
Horizontal gene transfers in the environment: natural transformation as a putative process for gene transfers between transgenic plants and microorganisms, Res Microbiol, vol.150, pp.375-384, 1999. ,
URL : https://hal.archives-ouvertes.fr/hal-02868636
An innovative electro-corrosion recess creation technique for improved microelectrode fabrication, Water Research, vol.36, pp.4428-4432, 2002. ,
Studies on the mutator gene, mutT of Escherichia coli. Molecular cloning of the gene, purification of the gene product, and identification of a novel nucleoside triphosphatase, J Biol Chem, vol.263, pp.8953-8957, 1988. ,
Genetic Studies of the Fertility Plasmid SCP2 and its SCP2* Variants in Streptomyces coelicolor A3(2), Microbiology, vol.126, pp.427-442, 1981. ,
Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans, Mol Gen Genet, vol.184, pp.230-240, 1981. ,
Chromosomal deletion and rearrangement in Streptomyces glaucescens, J Bacteriol, vol.173, pp.3531-3538, 1991. ,
Extremely large chromosomal deletions are intimately involved in genetic instability and genomic rearrangements in Streptomyces glaucescens, Mol Gen Genet, vol.217, pp.447-458, 1989. ,
Switching and Signaling at the, Telomere. Cell, vol.106, pp.661-673, 2001. ,
) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline, Nucleic Acids Res, vol.47, pp.81-87, 2019. ,
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, Proc Natl Acad Sci, vol.105, pp.7899-7906, 2008. ,
Structural analysis of loci involved in pSAM2 site-specific integration in Streptomyces, Plasmid, vol.21, pp.59-70, 1989. ,
Taxonomic and functional diversity of Streptomyces in a forest soil, FEMS Microbiol Lett, vol.342, pp.157-167, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01655681
Diversity of integrating conjugative elements in actinobacteria, Mob Genet Elements, vol.2, pp.119-124, 2012. ,
Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations, vol.2, pp.335-345, 2011. ,
Agrobacterium tumefaciens Gene Transfer: How a Plant Pathogen Hacks the Nuclei of Plant and Nonplant Organisms, Phytopathology, vol.105, pp.1288-1301, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01535270
Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway, Chem Biol, vol.7, pp.395-403, 2000. ,
Hypermutation in bacteria and other cellular systems, Philos Trans R Soc Lond, B, Biol Sci, vol.356, pp.29-39, 2001. ,
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome, Trends Genet, vol.16, pp.529-533, 2000. ,
URL : https://hal.archives-ouvertes.fr/hal-02335661
Analysis of the transfer region of the Streptomyces plasmid SCP2, Mol Microbiol, vol.10, pp.157-170, 1993. ,
Plasmid-chromosome interactions in Saccharopolyspora erythraea and Streptomyces lividans, Dev Ind Microbiol, vol.29, pp.97-105, 1988. ,
Ancient horizontal gene transfer, Nat Rev Genet, vol.4, pp.121-132, 2003. ,
Generalized transduction in Streptomyces coelicolor, Proc Natl Acad Sci, vol.98, pp.6289-6294, 2001. ,
The Chromosome of Escherichia coli, Cold Spring Harb Symp Quant Biol, vol.28, pp.43-46, 1963. ,
Low pore connectivity increases bacterial diversity in soil, Appl Environ Microbiol, vol.76, pp.3936-3942, 2010. ,
ACT: the Artemis comparison tool, Bioinformatics, vol.21, pp.3422-3423, 2005. ,
Telomeres of the linear chromosomes of Lyme disease spirochaetes: nucleotide sequence and possible exchange with linear plasmid telomeres, Mol Microbiol, vol.26, pp.581-596, 1997. ,
, , 2012.
, Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids, vol.7, 2019.
Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers, Appl Environ Microbiol, vol.76, pp.999-1007, 2010. ,
Structural aspects of non-ribosomal peptide biosynthesis, Curr Opin Struct Biol, vol.14, pp.748-756, 2004. ,
Actinomycete Development, Antibiotic Production, and Phylogeny: Questions and Challenges, pp.11-31, 2000. ,
Organization of the prokaryotic genome, 1999. ,
Chemicalbiogeographic survey of secondary metabolism in soil, Proc Natl Acad Sci, vol.111, p.3757, 2014. ,
Genetics of differentiation in Streptomyces, Annu Rev Microbiol, vol.47, pp.685-713, 1993. ,
Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.361, p.761, 2006. ,
Streptornyces genetics, Biology of the Actinomycetes, pp.229-286, 1984. ,
The Effect of Soil Texture on Richness and Diversity of Bacterial Communities, Environmental Forensics, vol.12, pp.333-341, 2011. ,
Complications and implications of linear bacterial chromosomes, Trends in Genetics, vol.12, pp.192-196, 1996. ,
Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes, Trends in Genetics, vol.18, pp.522-529, 2002. ,
The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule, Molecular Microbiology, vol.7, pp.925-932, 1993. ,
DNA uptake during bacterial transformation, Nat Rev Microbiol, vol.2, pp.241-249, 2004. ,
Characterization of Streptomyces plasmidphage pFP4 and its evolutionary implications, Plasmid, vol.68, pp.170-178, 2012. ,
Evolution of the Terminal Regions of the Streptomyces Linear Chromosome, Mol Biol Evol, vol.23, pp.2361-2369, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-02661267
Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of Streptomyces ambofaciens, J Bacteriol, vol.188, pp.6599-6610, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-01659064
Response of microbial activity and community structure to decreasing soil osmotic and matric potential, 2011. ,
The essential genome of a bacterium, Mol Syst Biol, vol.7, p.528, 2011. ,
Mechanism and structure of the bacterial type IV secretion systems, Biochim Biophys Acta, vol.1843, pp.1578-1591, 2014. ,
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions, Nucleic Acids Res, vol.38, p.200, 2010. ,
Species: The units of biodiversity, 1997. ,
Competence-induced fratricide in streptococci, Mol Microbiol, vol.64, pp.1423-1433, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00154610
Chapter 5 Are Species Cohesive ? -A View from Bacteriology, 2011. ,
What are Bacterial Species?, Annual Review of Microbiology, vol.56, pp.457-487, 2002. ,
Sexual isolation and speciation in bacteria. In Genetics of Mate Choice: From Sexual Selection to Sexual Isolation, pp.359-370, 2002. ,
Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla. Microbiol Spectr, vol.5, 2017. ,
A systematics for discovering the fundamental units of bacterial diversity, Curr Biol, vol.17, pp.373-386, 2007. ,
Microbial interactions and community assembly at microscales, Current Opinion in Microbiology, vol.31, pp.227-234, 2016. ,
The impact of long-distance horizontal gene transfer on prokaryotic genome size, PNAS, vol.106, pp.21748-21753, 2009. ,
Explaining microbial genomic diversity in light of evolutionary ecology, Nature Reviews Microbiology, vol.12, pp.263-273, 2014. ,
Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations, Proc Natl Acad Sci, vol.109, 2012. ,
Diversification of bacterial genome content through distinct mechanisms over different timescales, Nat Commun, vol.5, pp.1-12, 2014. ,
Conjugative DNA metabolism in Gramnegative bacteria, FEMS Microbiol Rev, vol.34, pp.18-40, 2010. ,
Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland, ISME J, vol.3, pp.738-744, 2009. ,
The metagenomics of soil, Nat Rev Microbiol, vol.3, pp.470-478, 2005. ,
On the origin of the species by means of natural selection, pp.1809-1882, 1859. ,
Specialized microbial metabolites: functions and origins, J Antibiot, vol.66, pp.361-364, 2013. ,
, Defence of Selfish Genes, vol.56, pp.556-573, 1981.
A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil, Soil Biology and Biochemistry, vol.35, pp.1537-1546, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02573523
Conditional Mutator Gene in Escherichia coli: Isolation, Mapping, and Effector Studies, J Bacteriol, vol.117, pp.477-487, 1974. ,
Structure, fluctuation and magnitude of a natural grassland soil metagenome, ISME J, vol.6, pp.1677-1687, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00747243
Characterization of two families of spontaneously amplifiable units of DNA in Streptomyces ambofaciens, J Gen Microbiol, vol.134, 1988. ,
URL : https://hal.archives-ouvertes.fr/hal-01658578
Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria, Microbiol Spectr, vol.2, 2014. ,
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl Environ Microbiol, vol.72, pp.5069-5072, 2006. ,
The molecular basis of the inhibitory activities of type A and type B synergimycins and related antibiotics on ribosomes, J Antimicrob Chemother, vol.24, pp.485-507, 1989. ,
Seeing is believing: what experiments with microbes reveal about evolution, Trends in Microbiology, vol.22, pp.2-4, 2014. ,
Genomic islands in pathogenic and environmental microorganisms, Nat Rev Microbiol, vol.2, pp.414-424, 2004. ,
Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians, Nat Chem Biol, vol.2, pp.729-735, 2006. ,
On the origin of prokaryotic species, Genome Res, vol.19, pp.744-756, 2009. ,
A roadmap for natural product discovery based on large-scale genomics and metabolomics, Nature Chemical Biology, vol.10, pp.963-968, 2014. ,
Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes, BMC Genomics, vol.14, p.611, 2013. ,
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens, Nat Biotechnol, vol.21, pp.1307-1313, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02681540
Genome evolution in yeasts, Nature, vol.430, pp.35-44, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00104411
Genetic functions and cell-cell interactions in the pheromone-inducible plasmid transfer system of Enterococcus faecalis, Mol Microbiol, vol.4, pp.689-696, 1990. ,
Structure of a modular polyketide synthase, Nature, vol.510, pp.512-517, 2014. ,
Punctuated equilibria: an alternative to phyletic gradualism // (1972) pp 82-115 in "Models in paleobiology, 1972. ,
The dynamics of evolutionary stasis, Paleobiology, vol.31, pp.133-145, 2005. ,
Multicellular Development in Streptomyces, pp.419-438, 2008. ,
Artificial soil microcosms: a tool for studying microbial autecology under controlled conditions, J Microbiol Methods, vol.56, pp.287-290, 2004. ,
Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer, PLoS Genet, vol.15, p.1007910, 2019. ,
Exploitative and Hierarchical Antagonism in a Cooperative Bacterium, PLOS Biology, vol.3, p.370, 2005. ,
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients, ISME J, vol.6, pp.1007-1017, 2012. ,
Biosynthesis of nonribosomal peptides1, Annu Rev Microbiol, vol.58, pp.453-488, 2004. ,
The evolution of gene collectives: How natural selection drives chemical innovation, Proc Natl Acad Sci, vol.105, pp.4601-4608, 2008. ,
Occurrence of deletions, associated with genetic instability in Streptomyces ambofaciens, is independent of the linearity of the chromosomal DNA, J Bacteriol, vol.179, pp.4553-4558, 1997. ,
Evolution of gene order in the genomes of two related yeast species, Genome Res, vol.11, pp.2009-2019, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-00306595
Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens, PNAS, vol.95, pp.14296-14301, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-01625341
XVII.-The Distribution of Gene Ratios for Rare Mutations, Proceedings of the Royal Society of Edinburgh, vol.50, pp.204-219, 1931. ,
Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, Nat Prod Rep, vol.24, pp.358-392, 2007. ,
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, pp.496-512, 1995. ,
Classification of methanogenic bacteria by 16S ribosomal RNA characterization, Proc Natl Acad Sci, vol.74, pp.4537-4541, 1977. ,
The bacterial species challenge: making sense of genetic and ecological diversity, Science, vol.323, pp.741-746, 2009. ,
The minimal gene complement of Mycoplasma genitalium, Science, vol.270, pp.397-403, 1995. ,
The structural biology of type IV secretion systems, Nat Rev Microbiol, vol.7, pp.703-714, 2009. ,
Analysis of the sequence and gene products of the transfer region of the F sex factor, Microbiol Rev, vol.58, pp.162-210, 1994. ,
Antimicrobial-resistant bacteria in the community setting, Nature Reviews Microbiology, vol.4, pp.36-45, 2006. ,
Minicystis rosea gen. nov., sp. nov., a polyunsaturated fatty acid-rich and steroid-producing soil myxobacterium, International Journal of Systematic and Evolutionary Microbiology, vol.64, pp.3733-3742, 2014. ,
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations, The ISME Journal, vol.12, pp.742-755, 2018. ,
Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, vol.419, pp.498-511, 2002. ,
Opinion: Reevaluating prokaryotic species, Nat Rev Microbiol, vol.3, pp.733-739, 2005. ,
Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria, PLOS ONE, vol.6, p.27846, 2011. ,
Prokaryotic Evolution in Light of Gene Transfer, Mol Biol Evol, vol.19, pp.2226-2238, 2002. ,
Bacteria-Phage Antagonistic Coevolution in Soil, Science, vol.332, pp.106-109, 2011. ,
4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil, FEMS Microbiology Ecology, vol.2, pp.529-537, 2006. ,
URL : https://hal.archives-ouvertes.fr/bioemco-00176213
Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology, Zentralbl Bakteriol, vol.285, pp.133-156, 1997. ,
Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT, Molecular Microbiology, vol.108, pp.601-613, 2018. ,
The Significance of Pneumococcal Types, J Hyg (Lond), vol.27, pp.113-159, 1928. ,
The bacterial biogeography of British soils, Environ Microbiol, vol.13, pp.1642-1654, 2011. ,
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats, BMC Bioinformatics, vol.8, p.172, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194456
Spatial scales of soil bacterial diversity--the size of a clone, FEMS Microbiol Ecol, vol.48, pp.119-127, 2004. ,
Spatial Modeling of Nitrifier Microhabitats in Soil, Soil Science Society of America Journal, vol.65, pp.1709-1716, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-02332596
Microscale Diversity of the Genus Nitrobacter in Soil on the Basis of Analysis of Genes Encoding rRNA, Appl Environ Microbiol, vol.66, pp.4543-4546, 2000. ,
A new protocol for an artificial soil to analyse soil microbiological processes, Applied Soil Ecology, vol.48, pp.243-246, 2011. ,
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res, vol.42, pp.5715-5727, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374962
Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution, Mol Microbiol, vol.23, pp.1089-1097, 1997. ,
Pathogenicity islands and the evolution of microbes, Annu Rev Microbiol, vol.54, pp.641-679, 2000. ,
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes, PLoS Comput Biol, vol.1, p.60, 2005. ,
Identification of a gene encoding the replication initiator protein of the Streptomyces integrating element, pSAM2, Plasmid, vol.31, pp.166-183, 1994. ,
Mode and origin of replication of pSAM2, a conjugative integrating element of Streptomyces ambofaciens, Mol Microbiol, vol.10, pp.799-812, 1993. ,
Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer, J Bacteriol, vol.175, pp.5529-5538, 1993. ,
Beyond biogeographic patterns: processes shaping the microbial landscape, Nat Rev Microbiol, vol.10, pp.497-506, 2012. ,
Natural products: the secondary metabolites. Natural products: the secondary metabolites, 2003. ,
Soil aggregates as microhabitats of microorganisms, 1988. ,
, ?recordID=JP8903709. Accessed, 2019.
Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence, Microbiology (Reading, Engl), vol.149, pp.505-513, 2003. ,
Stability of soil aggregates in relation to organic constituents and soil water content, Journal of Soil Science, vol.41, pp.73-83, 1990. ,
NanoSIMS as a tool for characterizing soil model compounds and organomineral associations in artificial soils, J Soils Sediments, vol.12, pp.35-47, 2012. ,
Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not, p.16, 2004. ,
, Mol Cell, vol.14, pp.501-513
Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss, Cell, vol.40, pp.381-392, 1985. ,
Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection, PLoS Pathog, vol.6, p.1001108, 2010. ,
Genome plasticity is governed by double strand break DNA repair in Streptomyces, Scientific Reports, vol.8, p.5272, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01757262
Linear Plasmid SLP2 Is Maintained by Partitioning, Intrahyphal Spread, and Conjugal Transfer in Streptomyces, Journal of Bacteriology, vol.192, pp.307-315, 2010. ,
Linear plasmid SLP2 of Streptomyces lividans is a composite replicon, Mol Microbiol, vol.47, pp.1563-1576, 2003. ,
The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998. ,
Exploring prokaryotic diversity in the genomic era, Genome Biol, vol.3, pp.3-4, 2002. ,
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing, PLOS Genetics, vol.4, p.1000255, 2008. ,
Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis, Nat Biotechnol, vol.21, pp.526-531, 2003. ,
Chromosomal circularization in Streptomyces griseus by nonhomologous recombination of deletion ends, Biosci Biotechnol Biochem, vol.67, pp.1101-1108, 2003. ,
Mechanisms of cellular senescence in human and mouse cells, Biogerontology, vol.5, pp.1-10, 2004. ,
Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis, PLoS Computational Biology, vol.2, pp.1210-1218, 2006. ,
Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora, Appl Environ Microbiol, vol.73, pp.1146-1152, 2007. ,
Natural genetic transformation: prevalence, mechanisms and function, Res Microbiol, vol.158, pp.767-778, 2007. ,
Genomic islands: tools of bacterial horizontal gene transfer and evolution, FEMS Microbiol Rev, vol.33, pp.376-393, 2009. ,
Control of Pore Geometry in Soil Microcosms and Its Effect on the Growth and Spread of Pseudomonas and Bacillus sp, Front Environ Sci, vol.6, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01824177
Analysis of Fusion Junctions of Circularized Chromosomes in Streptomyces griseus, J Bacteriol, vol.181, pp.5711-5717, 1999. ,
Five genes involved in self-transmission of pSN22, a Streptomyces plasmid, J Bacteriol, vol.173, pp.4220-4228, 1991. ,
Site-specific recombination inEscherichia coli between theatt sites of plasmid pSE211 fromSaccharopolyspora erythraea, Molec Gen Genet, vol.227, pp.155-159, 1991. ,
Experimental evolution, Trends Ecol Evol (Amst), vol.27, pp.547-560, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00162893
Aggregate Stability and Size Distribution 1. Methods of Soil Analysis: Part 1-Physical and Mineralogical Methods sssabookseries, pp.425-442, 1986. ,
Plasmid transfer in Streptomyces lividans: identification of a kil-kor system associated with the transfer region of pIJ101, J Bacteriol, vol.169, pp.4177-4183, 1987. ,
Bacterial metapopulations in nanofabricated landscapes, PNAS, vol.103, pp.17290-17295, 2006. ,
) pIJ101, a multi-copy broad hostrange Streptomyces plasmid: functional analysis and development of DNA cloning vectors, Mol Gen Genet, vol.185, pp.223-228, 1982. ,
DNA and the neutral theory, Philos Trans R Soc Lond, B, Biol Sci, vol.312, pp.343-354, 1986. ,
On Some Principles Governing Molecular Evolution*, Proc Natl Acad Sci U S A, vol.71, pp.2848-2852, 1974. ,
Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes, Nature, vol.328, pp.454-456, 1987. ,
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics, Proc Natl Acad Sci U S A, vol.105, pp.2504-2509, 2008. ,
The bacterial species definition in the genomic era, Philos Trans R Soc Lond B Biol Sci, vol.361, pp.1929-1940, 2006. ,
Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions, 2016. ,
Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils, Front Microbiol, vol.5, p.516, 2014. ,
Natural variation in developmental life-history traits of the bacterium Myxococcus xanthus, FEMS Microbiol Ecol, vol.73, pp.226-233, 2010. ,
Discovering the Hidden Secondary Metabolome of Myxococcus xanthus: a Study of Intraspecific Diversity, Appl Environ Microbiol, vol.74, pp.3058-3068, 2008. ,
Circos: An information aesthetic for comparative genomics, Genome Res, 2009. ,
Soil characteristics more strongly influence soil bacterial communities than land-use type, FEMS Microbiol Ecol, vol.79, pp.12-24, 2012. ,
Microbial hotspots and hot moments in soil: Concept & review, Soil Biology and Biochemistry, vol.83, pp.184-199, 2015. ,
Insights from 20 years of bacterial genome sequencing, Funct Integr Genomics, vol.15, pp.141-161, 2015. ,
Detecting genomic islands using bioinformatics approaches, Nat Rev Microbiol, vol.8, pp.373-382, 2010. ,
Estimating the size of the bacterial pan-genome, Trends Genet, vol.25, pp.107-110, 2009. ,
Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis, Research in Microbiology, vol.166, pp.729-741, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02487319
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale, Appl Environ Microbiol, vol.75, pp.5111-5120, 2009. ,
Where are the pseudogenes in bacterial genomes?, Trends Microbiol, vol.9, pp.535-540, 2001. ,
Molecular archaeology of the Escherichia coli genome, Proc Natl Acad Sci, vol.95, pp.9413-9417, 1998. ,
Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides, Nat Microbiol, vol.3, pp.718-731, 2018. ,
Hypervariability, a new phenomenon of genetic instability, related to DNA amplification in Streptomyces ambofaciens, Journal of Bacteriology, vol.171, pp.419-423, 1989. ,
URL : https://hal.archives-ouvertes.fr/hal-01658652
Genetic instability and hypervariability in Streptomyces ambofaciens: towards an understanding of a mechanism of genome plasticity, Molecular Microbiology, vol.4, pp.707-714, 1990. ,
URL : https://hal.archives-ouvertes.fr/hal-01658674
The unstable region of Streptomyces ambofaciens includes 210 kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA, Mol Microbiol, vol.19, pp.261-271, 1996. ,
URL : https://hal.archives-ouvertes.fr/hal-01658762
Recombination analysis of bacterial heredity, Cold Spring Harb Symp Quant Biol, vol.16, pp.413-443, 1951. ,
Gene Recombination in Escherichia Coli, Nature, vol.158, p.558, 1946. ,
Linear plasmids mobilize linear but not circular chromosomes in Streptomyces: support for the 'end first' model of conjugal transfer, Microbiology, vol.157, pp.2556-2568, 2011. ,
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe, PNAS, vol.112, pp.10967-10972, 2015. ,
Genome mining for ribosomally synthesized and posttranslationally modified peptides (RiPPs) in anaerobic bacteria, BMC Genomics, vol.15, p.983, 2014. ,
Vibrio cholerae genomic diversity within and between patients, Microb Genom, vol.3, 2017. ,
Reverse Ecology: from systems to environments and back, Adv Exp Med Biol, vol.751, pp.329-345, 2012. ,
, REVERSE ECOLOGY" AND THE POWER OF POPULATION GENOMICS. Evolution, vol.62, pp.2984-2994, 2008.
The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993. ,
An African origin for the intimate association between humans and Helicobacter pylori, Nature, vol.445, pp.915-918, 2007. ,
Hybrid nonribosomal peptide-polyketide interfaces in epothilone biosynthesis: minimal requirements at N and C termini of EpoB for elongation, Chem Biol, vol.11, pp.1533-1542, 2004. ,
Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since, Lancet, vol.379, pp.2151-2161, 2000. ,
Conjugational recombination in Escherichia coli: genetic analysis of recombinant formation in Hfr x F-crosses, Genetics, vol.139, pp.1123-1148, 1995. ,
Bacterial gene transfer by natural genetic transformation in the environment, Microbiol Rev, vol.58, pp.563-602, 1994. ,
Conjugation, Encyclopedia of Genetics, pp.449-453, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-01081881
Mutations of Bacteria from Virus Sensitivity to Virus Resistance, Genetics, vol.28, pp.491-511, 1943. ,
Organic chemistry with biological applications, Secondary Metabolites: An Introduction to Natural Products Chemistry, pp.1016-1046, 2015. ,
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc Natl Acad Sci, vol.95, pp.3140-3145, 1998. ,
Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation, Journal of Bacteriology, vol.182, pp.1016-1023, 2000. ,
Bacterial growth and motility in sub-micron constrictions, PNAS, vol.106, pp.14861-14866, 2009. ,
Proliferation of mutators in A cell population, J Bacteriol, vol.179, pp.417-422, 1997. ,
CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, vol.322, pp.1843-1845, 2008. ,
Site-specific integration of the Streptomyces plasmid pSAM2 in Mycobacterium smegmatis, Molecular Microbiology, vol.5, pp.2499-2502, 1991. ,
Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights, Nat Prod Rep, vol.34, pp.712-783, 2017. ,
Systematics and the Origin of Species, from the Viewpoint of a Zoologist, 1999. ,
Why prokaryotes have pangenomes, Nat Microbiol, vol.2, p.17040, 2017. ,
MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III, Nucleic Acids Res, vol.18, pp.3841-3845, 1990. ,
Yersiniabactin synthetase: a fourprotein assembly line producing the nonribosomal peptide/polyketide hybrid siderophore of Yersinia pestis, Chem Biol, vol.9, pp.333-344, 2002. ,
Microorganisms and Biotic Interactions, Environmental Microbiology: Fundamentals and Applications: Microbial Ecology, 2015. ,
, , pp.395-444, 2019.
Comparative Analysis of Myxococcus Predation on Soil Bacteria, Appl Environ Microbiol, vol.76, pp.6920-6927, 2010. ,
The Black Queen Hypothesis: Evolution of Dependencies through, Adaptive Gene Loss. mBio, vol.3, pp.36-48, 2012. ,
Cell envelope components contributing to biofilm growth and survival of Pseudomonas putida in low-water-content habitats, Mol Microbiol, vol.52, pp.735-750, 2004. ,
Streptomyces ghanaensis plasmid pSG5: nucleotide sequence analysis of the self-transmissible minimal replicon and characterization of the replication mode, Plasmid, vol.33, pp.113-126, 1995. ,
The minimal replicon of the Streptomyces ghanaensis plasmid pSG5 identified by subcloning and Tn5 mutagenesis, Molec Gen Genet, vol.211, pp.424-429, 1988. ,
Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation, Appl Microbiol Biotechnol, vol.98, pp.795-806, 2014. ,
Estrogen and ovariectomy regulate mRNA and protein of glutamic acid decarboxylases and cation-chloride cotransporters in the adult rat hippocampus, Neuroendocrinology, vol.80, pp.308-323, 2004. ,
Migration and horizontal gene transfer divide microbial genomes into multiple niches, Nat Commun, vol.6, p.8924, 2015. ,
Horizontal gene transfer from transgenic plants to terrestrial bacteria--a rare event?, FEMS Microbiol Rev, vol.22, pp.79-103, 1998. ,
Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil, FEMS Microbiol Ecol, vol.44, pp.203-215, 2003. ,
Calibrating bacterial evolution, PNAS, vol.96, pp.12638-12643, 1999. ,
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000. ,
Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, pp.1096-1099, 2001. ,
Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350, J Bacteriol, vol.190, pp.4050-4060, 2008. ,
, Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes, vol.65, pp.3182-3191, 1999.
Structural and Enzymatic Characterization of ABgp46, a Novel Phage Endolysin with Broad Anti-Gram-Negative Bacterial Activity, Front Microbiol, vol.7, 2016. ,
, , 2019.
High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection, Science, vol.288, pp.1251-1254, 2000. ,
The viable but nonculturable state in bacteria, Journal of microbiology, vol.43, pp.93-100, 2005. ,
New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products, Cell Chem Biol, vol.23, pp.31-44, 2016. ,
On the track of natural transformation in soil, FEMS Microbiol Ecol, vol.15, pp.109-117, 1994. ,
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer, Nature Genetics, vol.37, p.1372, 2005. ,
Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends, Mol Microbiol, vol.28, pp.1165-1176, 1998. ,
Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus, Front Microbiol, vol.10, 2019. ,
New developments in lantibiotic biosynthesis and mode of action, Curr Opin Microbiol, vol.8, pp.543-551, 2005. ,
Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus, Microbiology (Reading, Engl), vol.150, pp.759-774, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-01659488
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria, ISME J, vol.3, pp.1193-1203, 2009. ,
Plasmids in different strains of Streptomyces ambofaciens: free and integrated form of plasmid pSAM2, Mol Gen Genet, vol.198, pp.35-41, 1984. ,
Transfer of the plJ101 plasmid in Streptomyces lividans requires a cis-acting function dispensable for chromosomal gene transfer, Molecular Microbiology, vol.13, pp.955-964, 1994. ,
Actinomycete integrative and conjugative elements, Antonie Van Leeuwenhoek, vol.94, pp.127-143, 2008. ,
Horizontal gene transfer and the evolution of bacterial and archaeal population structure, Trends in Genetics, vol.29, pp.170-175, 2013. ,
Cell Size Distributions of Soil Bacterial and Archaeal Taxa, Appl Environ Microbiol, vol.79, pp.7610-7617, 2013. ,
Conjugal immunity of Streptomyces strains carrying the integrative element pSAM2 is due to the pif gene (pSAM2 immunity factor), Molecular Microbiology, vol.47, pp.1385-1393, 2003. ,
The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer, Mol Microbiol, vol.42, pp.159-166, 2001. ,
Microbial life on a sand grain: from bulk sediment to single grains, ISME J, vol.12, pp.623-633, 2018. ,
The General Lineage Concept of Species, Species Criteria, and the Process of Speciation, Endless Forms: Species and, pp.57-75, 1998. ,
The rational exploration of microbial diversity, ISME J, vol.2, pp.997-1006, 2008. ,
SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis, Basic Life Sci, vol.5, pp.355-367, 1975. ,
Enzymes of evolutionary change, Nature, vol.401, pp.866-867, 1999. ,
Anaerobic Growth, a Property Horizontally Transferred by an Hfr-Like Mechanism among Extreme Thermophiles, J Bacteriol, vol.180, pp.3137-3143, 1998. ,
Quantitative and qualitative microscale distribution of bacteria in soil, Research in Microbiology, vol.152, pp.707-716, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-02681726
Structure of the chromosomal insertion site for pSAM2: functional analysis in Escherichia coli, Molecular Microbiology, vol.28, pp.333-342, 1998. ,
Spatial Ecology of Bacteria at the Microscale in Soil, PLoS One, vol.9, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01252483
Experimental evolution and the dynamics of genomic mutation rate modifiers, Heredity (Edinb), vol.113, pp.375-380, 2014. ,
Seasonal controls on grassland microbial biogeography: Are they governed by plants, abiotic properties or both?, Soil Biology and Biochemistry, vol.71, pp.21-30, 2014. ,
Mobilization of Chromosomes and Nonconjugative Plasmids by Cointegrative Mechanisms, pp.137-188, 1993. ,
Modular architecture of the conjugative plasmid pSVH1 from Streptomyces venezuelae, Plasmid, vol.55, pp.201-209, 2006. ,
Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata), Science, vol.275, pp.1934-1937, 1997. ,
Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) / CRISPR Associated (Cas) Systems, Viruses, vol.4, pp.2291-2311, 2012. ,
Population Genomics and the Bacterial Species Concept, Methods Mol Biol, vol.532, pp.367-377, 2009. ,
Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res, vol.31, pp.6570-6577, 2003. ,
Comparing microarrays and nextgeneration sequencing technologies for microbial ecology research, Trends Biotechnol, vol.28, pp.291-299, 2010. ,
Multivariate calibration of hyperspectral ?-ray energy spectra for proximal soil sensing, European Journal of Soil Science, vol.58, pp.343-353, 2007. ,
The species concept for prokaryotes, FEMS Microbiol Rev, vol.25, pp.39-67, 2001. ,
, , p.37
The mutT Defect Does Not Elevate Chromosomal Fragmentation in Escherichia coli Because of the Surprisingly Low Levels of MutM/MutY-Recognized DNA Modifications, J Bacteriol, vol.189, pp.6976-6988, 2007. ,
Microbial biogeography at the soil pore scale, Soil Biology and Biochemistry, vol.43, pp.280-286, 2011. ,
URL : https://hal.archives-ouvertes.fr/bioemco-00542769
Revenge of the phages: defeating bacterial defences, Nat Rev Microbiol, vol.11, pp.675-687, 2013. ,
Ecological Character Displacement in Adaptive Radiation, The American Naturalist, vol.156, pp.4-16, 2000. ,
Persistence of soil organic matter as an ecosystem property, Nature, vol.478, pp.49-56, 2011. ,
Strain-Level Diversity of Secondary Metabolism in Streptomyces albus, PLOS ONE, vol.10, p.116457, 2015. ,
Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13, Mol Microbiol, vol.72, pp.1293-1306, 2009. ,
Identification and properties of a novel clt locus in the Streptomyces phaeochromogenes plasmid pJV1, Journal of Bacteriology, vol.178, pp.4323-4326, 1996. ,
Sequence and functional analysis of the Streptomyces phaeochromogenes plasmid pJV1 reveals a modular organization of Streptomyces plasmids that replicate by rolling circle, Microbiology (Reading, Engl), pp.2499-2510, 1995. ,
Replicase, excisionase, and integrase genes of the Streptomyces element pSAM2 constitute an operon positively regulated by the pra gene, J Bacteriol, vol.180, pp.3056-3061, 1998. ,
Characterization of pra, a gene for replication control in pSAM2, the integrating element of Streptomyces ambofaciens, Molecular microbiology, 1995. ,
How clonal are bacteria over time?, Curr Opin Microbiol, vol.31, pp.116-123, 2016. ,
The population genetics of pangenomes, Nat Microbiol, vol.2, pp.1574-1574, 2017. ,
Population genomics of early events in the ecological differentiation of bacteria, Science, vol.336, pp.48-51, 2012. ,
Ordering microbial diversity into ecologically and genetically cohesive units, Trends in Microbiology, vol.22, pp.235-247, 2014. ,
Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms, Curr Opin Chem Biol, vol.7, pp.285-295, 2003. ,
Homologous recombination in Escherichia coli: dependence on substrate length and homology, Genetics, vol.112, pp.441-457, 1986. ,
Convergence of Campylobacter species: implications for bacterial evolution, Science, vol.320, pp.237-239, 2008. ,
A hybrid polyketide-nonribosomal peptide in nematodes that promotes larval survival, Nat Chem Biol, vol.12, pp.770-772, 2016. ,
, Mobility of plasmids. Microbiol Mol Biol Rev, vol.74, pp.434-452, 2010.
Functional analysis of the Streptomyces ambofaciens element pSAM2, Plasmid, vol.25, pp.40-52, 1991. ,
Evolution of high mutation rates in experimental populations of E. coli, Nature, vol.387, pp.703-705, 1997. ,
The Biological Species Concept: A Critical Evaluation, The American Naturalist, vol.104, pp.127-153, 1970. ,
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea, Nat Rev Microbiol, vol.6, pp.181-186, 2008. ,
Organization of the teicoplanin gene cluster in Actinoplanes teichomyceticus, Microbiology (Reading, Engl), vol.150, pp.95-102, 2004. ,
Characterization of the Streptomyces violaceoruber SANK95570 plasmids pSV1 and pSV2, FEMS Microbiology Letters, vol.213, pp.87-92, 2002. ,
Increased missegregation and chromosome loss with decreasing chromosome size in vertebrate cells, Chromosoma, vol.115, pp.60-74, 2006. ,
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int J Syst Evol Microbiol, vol.52, pp.1043-1047, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-02573548
Social Interactions and Distribution of Bacillus subtilis Pherotypes at Microscale, Journal of Bacteriology, vol.191, pp.1756-1764, 2009. ,
Quantifying community assembly processes and identifying features that impose them, ISME J, vol.7, pp.2069-2079, 2013. ,
A novel family of potentially mobile DNA elements encoding sitespecific gene-integration functions: integrons, Mol Microbiol, vol.3, pp.1669-1683, 1989. ,
A novel pair of terminal protein and telomere-associated protein for replication of the linear chromosome of Streptomyces griseus IFO13350, Biosci Biotechnol Biochem, vol.72, pp.2973-2980, 2008. ,
Principles and applications of soil microbiology, 2005. ,
Evolutionary implications of horizontal gene transfer, Annu Rev Genet, vol.46, pp.341-358, 2012. ,
The 120 592 bp IncF plasmid pRSB107 isolated from a sewage-treatment plant encodes nine different antibiotic-resistance determinants, two iron-acquisition systems and other putative virulenceassociated functions, Microbiology (Reading, Engl), vol.151, pp.1095-1111, 2005. ,
Role of mutator alleles in adaptive evolution, Nature, vol.387, pp.700-702, 1997. ,
URL : https://hal.archives-ouvertes.fr/hal-02122731
million years of genomic stasis in endosymbiotic bacteria, Science, vol.296, pp.2376-2379, 2002. ,
Cloning and Heterologous Expression of the Epothilone Gene Cluster, Science, vol.287, pp.640-642, 2000. ,
Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies, Genome Announc, vol.4, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01521992
Conjugative DNA transfer in Streptomyces by TraB: is one protein enough?, FEMS Microbiol Lett, vol.337, pp.81-88, 2012. ,
The conjugative DNA-transfer apparatus of Streptomyces, International Journal of Medical Microbiology, vol.305, pp.224-229, 2015. ,
Mechanisms of, and barriers to, horizontal gene transfer between bacteria, Nat Rev Microbiol, vol.3, pp.711-721, 2005. ,
Biologie évolutive, 2016. ,
Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics, MBio, vol.10, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02278804
Genome Sequences of 11 Conspecific Streptomyces sp, Strains. Microbiol Resour Announc, vol.8, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02292599
Chromosomal Arm Replacement in Streptomyces griseus, J Bacteriol, vol.185, pp.1120-1124, 2003. ,
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica, Proc Natl Acad Sci, vol.104, pp.10376-10381, 2007. ,
Distinct Ectomycorrhizospheres Share Similar Bacterial Communities as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes, Appl Environ Microbiol, vol.78, pp.3020-3024, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01268355
Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol Rev, vol.60, pp.407-438, 1996. ,
Ten years of pan-genome analyses, Curr Opin Microbiol, vol.23, pp.148-154, 2015. ,
Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico, PLOS Biology, vol.9, p.1001184, 2011. ,
, Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity. Antibiotics, p.7, 2018.
Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil, Appl Environ Microbiol, vol.69, pp.1482-1487, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427492
Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE, EMBO J, vol.30, pp.2246-2254, 2011. ,
A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution, FEMS Microbiol Lett, vol.186, pp.143-150, 2000. ,
A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity, PLOS ONE, vol.7, p.30600, 2012. ,
Isolation by Distance in the Spore-Forming Soil Bacterium Myxococcus xanthus, Current Biology, vol.18, pp.386-391, 2008. ,
Social Conflict in Centimeter-and Global-Scale Populations of the Bacterium Myxococcus xanthus, Current Biology, vol.19, pp.1763-1767, 2009. ,
Micro-scale determinants of bacterial diversity in soil, FEMS Microbiology Reviews, vol.37, pp.936-954, 2013. ,
Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination, Proc Natl Acad Sci, vol.99, pp.2094-2099, 2002. ,
Isolation of Streptomycin-producing Strains of Streptomyces griseus12, J Bacteriol, vol.52, pp.393-397, 1946. ,
Contributions to the Theory of Natural Selection: A Series of Essays, 1870. ,
Combinatorial biosynthesis of antibiotics: challenges and opportunities, Chembiochem, vol.3, pp.125-134, 2002. ,
Development of a Phosphate Ion-selective Microelectrode and Its Use in Studies of the Enhanced Biological Phosphorus Removal (ebpr) Process, Environmental Technology, vol.26, pp.381-388, 2005. ,
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics, International Journal of Systematic and Evolutionary Microbiology, vol.37, pp.463-464, 1987. ,
Sex pheromone plasmid pAD1-encoded surface exclusion protein of Enterococcus faecalis, Mol Gen Genet, vol.233, pp.161-168, 1992. ,
End-to-end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens, Molecular Microbiology, vol.50, pp.411-425, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02678526
Increased sample point density in farm soil mapping by local calibration of visible and near infrared prediction models, Geoderma, vol.156, pp.152-160, 2010. ,
Geographic barriers isolate endemic populations of hyperthermophilic archaea, Science, vol.301, pp.976-978, 2003. ,
Prokaryotes: The unseen majority, PNAS, vol.95, pp.6578-6583, 1998. ,
Streptomyces coelicolor Undergoes Spontaneous Chromosomal End Replacement, J Bacteriol, vol.189, pp.9117-9121, 2007. ,
Spontaneous Amplification of the Actinorhodin Gene Cluster in Streptomyces coelicolor Involving Native Insertion Sequence IS466, J Bacteriol, vol.190, pp.4754-4758, 2008. ,
Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches, FEMS Microbiology Reviews, vol.35, pp.957-976, 2011. ,
Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli, G3 (Bethesda), vol.1, pp.183-186, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00800695
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load, PNAS, vol.110, pp.222-227, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00800700
Kin discrimination and outer membrane exchange in Myxococcus xanthus: A comparative analysis among natural isolates, Molecular Ecology, vol.27, pp.3146-3158, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02613111
Antagonistic interactions mediated by marine bacteria: the role of small molecules, J Chem Ecol, vol.39, pp.879-891, 2013. ,
Bacterial evolution, Microbiol Rev, vol.51, pp.221-271, 1987. ,
Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nat Rev Microbiol, vol.8, pp.552-563, 2010. ,
Role of Pore Size Location in Determining Bacterial Activity during Predation by Protozoa in Soil, Appl Environ Microbiol, vol.61, pp.3537-3543, 1995. ,
The roles of mutation, inbreeding, crossbreeding and selection in evolution, Proceedings of the sixth international congress of Genetics, vol.1, pp.356-366, 1932. ,
The FK520 gene cluster of Streptomyces hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units, Gene, vol.251, pp.81-90, 2000. ,
Two Chimeric Chromosomes of Streptomyces coelicolor A3(2) Generated by Single Crossover of the Wild-Type Chromosome and Linear Plasmid SCP1, J Bacteriol, vol.186, pp.6553-6559, 2004. ,
Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus, Proc Natl Acad Sci, vol.103, pp.9661-9666, 2006. ,
The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins: Terminal proteins of Streptomyces, Molecular Microbiology, vol.43, pp.297-305, 2002. ,
A plausible mechanism for large-scale chromosomal DNA amplification in streptomycetes, FEBS Lett, vol.212, pp.10-14, 1987. ,
Two distinct conjugal transfer systems on Streptomyces plasmid pZL1, Acta Biochim Biophys Sin (Shanghai), vol.46, pp.1084-1086, 2014. ,
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales, Proc Natl Acad Sci, vol.106, pp.5865-5870, 2009. ,
Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage, Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages, PLoS One, vol.9, 2014. ,
Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora, PNAS, vol.111, pp.1130-1139, 2014. ,
Genomics-Based Insights into the Evolution of Secondary Metabolite Biosynthesis in Actinomycete Bacteria, 2014. ,