A. Thibessard and P. Leblond, Subtelomere plasticity in the bacterium Streptomyces, Louis EJ, Becker MM, pp.243-258, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01478830

V. M. D'costa, K. M. Mcgrann, D. W. Hughes, and G. D. Wright, Sampling the antibiotic resistome, Science, vol.311, pp.374-377, 2006.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic Local alignment search tool, J Mol Biol, vol.215, issue.05, pp.80360-80362, 1990.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

T. Kieser, M. Bibb, M. Buttner, K. Chater, and D. Hopwood, Practical Streptomyces genetics, John Innes Foundation, 2000.

H. Rintala, A. Nevalainen, E. Rönkä, and M. Suutari, PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes, Mol Cell Probes, vol.15, pp.337-347, 2001.

E. A. Barka, P. Vatsa, L. Sanchez, N. Gaveau-vaillant, C. Jacquard et al., Taxonomy, physiology, and natural products of Actinobacteria, Microbiol Mol Biol Rev, vol.80, pp.1-43, 2016.

O. S. Olanrewaju and O. O. Babalola, Streptomyces: implications and interactions in plant growth promotion, Appl Microbiol Biotechnol, vol.103, pp.1179-1188, 2019.

B. Aigle, S. Lautru, D. Spiteller, J. S. Dickschat, G. L. Challis et al., Genome mining of Streptomyces ambofaciens, J Ind Microbiol Biotechnol, vol.41, pp.251-263, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01475037

R. H. Baltz, Gifted microbes for genome mining and natural product discovery, J Ind Microbiol Biotechnol, vol.44, pp.573-588, 2017.

F. Choulet, B. Aigle, A. Gallois, S. Mangenot, C. Gerbaud et al., 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

M. Redenbach, H. M. Kieser, D. Denapaite, A. Eichner, J. Cullum et al., A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb, 1996.

, Mol Microbiol, vol.21, pp.77-96

X. Tian, Z. Zhang, T. Yang, M. Chen, J. Li et al., 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.

J. Kim, Y. Kim, Y. Jeong, J. Roe, B. Kim et al., Comparative genomics reveals the core and accessory genomes of Streptomyces species, J Microbiol Biotechnol, vol.25, pp.1599-1605, 2015.

Z. Zhou, J. Gu, Y. Li, and Y. Wang, Genome plasticity and systems evolution in Streptomyces, BMC Bioinformatics, vol.13, 2012.

Y. S. Lin, H. M. Kieser, D. A. Hopwood, and C. W. Chen, The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993.

C. H. Huang, Y. S. Lin, Y. L. Yang, S. W. Huang, and C. W. Chen, The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998.

C. W. Chen, C. Huang, H. Lee, H. Tsai, and R. Kirby, Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes, Trends Genet, vol.18, issue.02, p.2752, 2002.

A. Thibessard and P. Leblond, Subtelomere plasticity in the bacterium Streptomyces, Louis EJ, Becker MM, pp.243-258, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01478830

J. R. Doroghazi and D. H. Buckley, Widespread homologous recombination within and between Streptomyces species, ISME J, vol.4, pp.1136-1143, 2010.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

S. Wielgoss, X. Didelot, R. R. Chaudhuri, X. Liu, G. D. Weedall et al., A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus, ISME J, vol.10, pp.2468-2477, 2016.

M. Vos, A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk, Micro-scale determinants of bacterial diversity in soil, FEMS Microbiol Rev, vol.37, pp.936-954, 2013.

A. B. Wolf, M. Vos, W. De-boer, and G. A. Kowalchuk, 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.

X. Raynaud and N. Nunan, Spatial ecology of bacteria at the microscale in soil, PLoS One, vol.9, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01252483

E. W. Sayers, R. Agarwala, E. E. Bolton, J. R. Brister, K. Canese et al., Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.47, pp.23-28, 2019.

T. Wenner, V. Roth, G. Fischer, C. Fourrier, B. Aigle et al., 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

G. Fischer, T. Wenner, B. Decaris, and P. Leblond, 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

T. Uchida, M. Miyawaki, and H. Kinashi, Chromosomal arm replacement in Streptomyces griseus, J Bacteriol, vol.185, pp.1120-1124, 2003.

S. Clerc and P. Simonet, 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

J. T. Sullivan and C. W. Ronson, 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.

K. Blin, T. Wolf, M. G. Chevrette, X. Lu, C. J. Schwalen et al., 0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res, vol.45, pp.36-41, 2017.

J. O. Mcinerney, A. Mcnally, and M. J. O'connell, Why prokaryotes have pangenomes, Nat Microbiol, vol.2, p.17040, 2017.

G. Hoff, C. Bertrand, E. Piotrowski, A. Thibessard, and P. Leblond, 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

S. Casjens, N. Palmer, R. Van-vugt, W. M. Huang, B. Stevenson et al., 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.

M. Ricchetti, B. Dujon, and C. Fairhead, 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.

E. V. Linardopoulou, E. M. Williams, Y. Fan, C. Friedman, J. M. Young et al., Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature, vol.437, pp.94-100, 2005.

S. D. Bentley, K. F. Chater, A. Cerdeño-tárraga, G. L. Challis, N. R. Thomson et al., , 2002.

Y. Colin, O. Nicolitch, M. Turpault, and S. Uroz, 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

A. S. Adams, M. S. Jordan, S. M. Adams, G. Suen, L. A. Goodwin et al.,

, Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio, ISME J, vol.5, pp.1323-1331

R. H. Baltz, Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities, J Ind Microbiol Biotechnol, vol.46, pp.281-299, 2019.

G. R. Lewin, C. Carlos, M. G. Chevrette, H. A. Horn, B. R. Mcdonald et al., Evolution and Ecology of Actinobacteria and Their Bioenergy Applications, Annu Rev Microbiol, vol.70, pp.235-254, 2016.

S. Casjens and W. M. Huang, Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent, Mol Microbiol, vol.8, pp.967-980, 1993.

D. W. Wood, J. C. Setubal, R. Kaul, D. E. Monks, J. P. Kitajima et al., The genome of the natural genetic engineer Agrobacterium tumefaciens C58, vol.294, pp.2317-2323, 2001.

M. P. Mcleod, R. L. Warren, W. Hsiao, N. Araki, M. Myhre et al., 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.

D. Weaver, N. Karoonuthaisiri, H. Tsai, C. Huang, M. Ho et al., Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome, Mol Microbiol, vol.51, pp.1535-1550, 2004.

T. Wenner, V. Roth, G. Fischer, C. Fourrier, B. Aigle et al., 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

D. A. Hopwood, Soil to genomics: the Streptomyces chromosome, Annu Rev Genet, vol.40, pp.1-23, 2006.

W. Chen, F. He, X. Zhang, Z. Chen, Y. Wen et al., Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome, BMC Microbiol, vol.10, 0198.

F. Choulet, A. Gallois, B. Aigle, S. Mangenot, C. Gerbaud et al., 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

C. Yang, S. Tseng, H. Pan, C. Huang, and C. W. Chen, Telomere associated primase Tap repairs truncated telomeres of Streptomyces, Nucleic Acids Res, vol.45, pp.5838-5849, 2017.

P. C. Chang and S. N. Cohen, Bidirectional replication from an internal origin in a linear Streptomyces plasmid, Science, vol.265, pp.952-954, 1994.

C. W. Chen, T. W. Yu, Y. S. Lin, H. M. Kieser, and D. A. Hopwood, The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule, Mol Microbiol, vol.7, pp.925-932, 1993.

Y. S. Lin, H. M. Kieser, D. A. Hopwood, and C. W. Chen, The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993.

C. H. Huang, Y. S. Lin, Y. L. Yang, S. W. Huang, and C. W. Chen, The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998.

Y. Ohnishi, J. Ishikawa, H. Hara, H. Suzuki, M. Ikenoya et al., Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350, J Bacteriol, vol.190, pp.4050-4060, 2008.

H. Suzuki, K. Marushima, Y. Ohnishi, and S. Horinouchi, 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.

C. Yang, C. Huang, C. Li, Y. Tsay, S. Lee et al., The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins, Mol Microbiol, vol.43, pp.297-305, 2002.

K. Bao and S. N. Cohen, Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces, Genes Dev, vol.15, pp.1518-1527, 2001.

K. Bao and S. N. Cohen, 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.

A. Tidjani, J. Lorenzi, M. Toussaint, E. Van-dijk, D. Naquin et al.,

, Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

A. Tidjani, J. Lorenzi, M. Toussaint, E. Van-dijk, D. Naquin et al.,

, Genome Sequences of 11 Conspecific Streptomyces sp, Strains. Microbiol Resour Announc, vol.8

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST Server: rapid annotations using subsystems technology, vol.9, p.75, 2008.

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, vol.31, pp.3406-3415, 2003.

J. D. Thompson, D. G. Higgins, and T. J. Gibson, 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.

S. Kumar, G. Stecher, M. Li, C. Knyaz, and K. Tamura, MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol Biol Evol, vol.35, pp.1547-1549, 2018.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990.

A. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-1403, 2004.

D. P. Martin, B. Murrell, A. Khoosal, B. Muhire, P. González-torres et al., Detecting and Analyzing Genetic Recombination Using RDP4, Methods Mol Biol Clifton NJ, vol.1525, pp.433-460, 2017.

O. Skovgaard, M. Bak, A. Løbner-olesen, and N. Tommerup, Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing, Genome Res, vol.21, pp.1388-1393, 2011.

G. Hoff, C. Bertrand, L. Zhang, E. Piotrowski, L. Chipot et al., 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

X. Pang, B. Aigle, J. Girardet, S. Mangenot, J. Pernodet et al., 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

H. Kinashi, M. Shimaji-murayama, and T. Hanafusa, Integration of SCP1, a giant linear plasmid, into the Streptomyces coelicolor chromosome, Gene, vol.115, pp.35-41, 1992.

M. Yamasaki and H. Kinashi, 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.

V. Barbe, M. Bouzon, S. Mangenot, B. Badet, J. Poulain et al., 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

W. M. Huang, M. Robertson, A. J. Casjens, and S. , Telomere exchange between linear replicons of Borrelia burgdorferi, J Bacteriol, vol.186, pp.4134-4141, 2004.

G. Chaconas and K. Kobryn, Structure, function, and evolution of linear replicons in Borrelia, Annu Rev Microbiol, vol.64, pp.185-202, 2010.

B. Li, DNA double-strand breaks and telomeres play important roles in trypanosoma brucei antigenic variation, REFERENCES BIBLIOGRAPHIQUES, vol.14, pp.196-205, 2015.

S. S. Abby, J. Cury, J. Guglielmini, B. Néron, M. Touchon et al., Identification of protein secretion systems in bacterial genomes, Scientific Reports, vol.6, p.23080, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01677379

M. Achtman, P. A. Manning, B. Kusecek, S. Schwuchow, and N. Willetts, A genetic analysis of F sex factor cistrons needed for surface exclusion in Escherichia coli, J Mol Biol, vol.138, pp.779-795, 1980.

M. Achtman and M. Wagner, Microbial diversity and the genetic nature of microbial species, Nat Rev Microbiol, vol.6, pp.431-440, 2008.

B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts et al., Site-Specific Recombination, Molecular Biology of the Cell, 2002.

J. Altenbuchner and J. Cullum, Structure of an amplifiable DNA sequence in Streptomyces lividans 66, Mol Gen Genet, vol.201, pp.192-197, 1985.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990.

C. E. Alvarez-martinez, C. , and P. J. , Biological diversity of prokaryotic type IV secretion systems, Microbiol Mol Biol Rev, vol.73, pp.775-808, 2009.

C. Ambroset, C. Coluzzi, G. Guédon, M. Devignes, V. Loux et al., 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

N. A. Andreani, E. Hesse, and M. Vos, Prokaryote genome fluidity is dependent on effective population size, The ISME Journal, 2017.

R. Angel, M. I. Soares, E. D. Ungar, and O. Gillor, Biogeography of soil archaea and bacteria along a steep precipitation gradient, ISME J, vol.4, pp.553-563, 2010.

M. A. Ansari and X. Didelot, Inference of the Properties of the Recombination Process from Whole Bacterial Genomes, Genetics, vol.196, pp.253-265, 2014.

S. Antony-babu, J. E. Stach, and M. Goodfellow, 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.

S. Antony-babu, D. Stien, V. Eparvier, D. Parrot, S. Tomasi et al., 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

K. Arakawa and M. Tomita, 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.

W. Arber, Genetic variation: molecular mechanisms and impact on microbial evolution, FEMS Microbiol Rev, vol.24, pp.1-7, 2000.

R. Ari, The SOS system, Biochimie, vol.67, pp.343-347, 1985.

P. Arya, R. Joseph, and D. T. Chou, Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age, Chem Biol, vol.9, pp.145-156, 2002.


E. Avni and S. Snir, Toxic genes present a unique phylogenetic signature, Mol Phylogenet Evol, vol.116, pp.141-148, 2017.

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, pp.75-75, 2008.

L. G. Baas-becking and E. Nicolai, On the ecology of a Sphagnum Bog, Evolution and Biogeography of Plants, vol.1, pp.10-45, 1934.

D. A. Baltrus, Exploring the costs of horizontal gene transfer, Trends Ecol Evol (Amst), vol.28, pp.489-495, 2013.

N. Bamas-jacques, S. Lorenzon, P. Lacroix, C. De-swetschin, and J. Crouzet, 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.

K. Bao and S. N. Cohen, Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces, Genes Dev, vol.15, pp.1518-1527, 2001.

K. Bao and S. N. Cohen, 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.

E. Bapteste, P. Lopez, F. Bouchard, F. Baquero, J. O. Mcinerney et al., 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

C. Baril, C. Richaud, G. Baranton, and I. S. Girons, Linear chromosome of Borrelia burgdorferi, Res Microbiol, vol.140, pp.507-516, 1989.

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval et al., CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, pp.1709-1712, 2007.

J. E. Barrick and R. E. Lenski, Genome dynamics during experimental evolution, Nat Rev Genet, vol.14, pp.827-839, 2013.

T. Bell, Experimental tests of the bacterial distance-decay relationship, The ISME Journal, vol.4, pp.1357-1365, 2010.

S. D. Bentley, K. F. Chater, A. Cerdeño-tárraga, G. L. Challis, N. R. Thomson et al., Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, vol.417, pp.141-147, 2002.

J. Bérdy, Bioactive microbial metabolites, J Antibiot, vol.58, pp.1-26, 2005.

G. Berg and K. Smalla, 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.

F. Bertolla and P. Simonet, 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

A. N. Bezbaruah and T. C. Zhang, An innovative electro-corrosion recess creation technique for improved microelectrode fabrication, Water Research, vol.36, pp.4428-4432, 2002.

S. K. Bhatnagar and M. J. Bessman, 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.

M. J. Bibb and D. A. Hopwood, Genetic Studies of the Fertility Plasmid SCP2 and its SCP2* Variants in Streptomyces coelicolor A3(2), Microbiology, vol.126, pp.427-442, 1981.

M. J. Bibb, J. M. Ward, T. Kieser, S. N. Cohen, and D. A. Hopwood, 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.

A. Birch, A. Häusler, C. Rüttener, and R. Hütter, Chromosomal deletion and rearrangement in Streptomyces glaucescens, J Bacteriol, vol.173, pp.3531-3538, 1991.

A. Birch, A. Häusler, M. Vögtli, W. Krek, and R. Hütter, 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.

E. H. Blackburn, Switching and Signaling at the, Telomere. Cell, vol.106, pp.661-673, 2001.

K. Blin, S. Shaw, K. Steinke, R. Villebro, N. Ziemert et al., ) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline, Nucleic Acids Res, vol.47, pp.81-87, 2019.

Z. D. Blount, C. Z. Borland, and R. E. Lenski, 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.

F. Boccard, T. Smokvina, J. Pernodet, A. Friedmann, and M. Guérineau, Structural analysis of loci involved in pSAM2 site-specific integration in Streptomyces, Plasmid, vol.21, pp.59-70, 1989.

C. Bontemps, M. Toussaint, P. Revol, L. Hotel, M. Jeanbille et al., 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

E. Bordeleau, M. G. Ghinet, and V. Burrus, Diversity of integrating conjugative elements in actinobacteria, Mob Genet Elements, vol.2, pp.119-124, 2012.

Y. Boucher, O. X. Cordero, A. Takemura, D. E. Hunt, K. Schliep et al., Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations, vol.2, pp.335-345, 2011.

S. Bourras, T. Rouxel, and M. Meyer, 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

T. Brautaset, O. N. Sekurova, H. Sletta, T. E. Ellingsen, A. R. Str?m et al., 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.

B. A. Bridges, Hypermutation in bacteria and other cellular systems, Philos Trans R Soc Lond, B, Biol Sci, vol.356, pp.29-39, 2001.

C. Brochier, H. Philippe, and D. Moreira, 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

D. F. Brolle, H. Pape, D. A. Hopwood, and T. Kieser, Analysis of the transfer region of the Streptomyces plasmid SCP2, Mol Microbiol, vol.10, pp.157-170, 1993.

D. P. Brown, J. S. Tuan, K. A. Boris, J. P. Dewitt, K. B. Idler et al., Plasmid-chromosome interactions in Saccharopolyspora erythraea and Streptomyces lividans, Dev Ind Microbiol, vol.29, pp.97-105, 1988.

J. R. Brown, Ancient horizontal gene transfer, Nat Rev Genet, vol.4, pp.121-132, 2003.

J. Burke, D. Schneider, and J. Westpheling, Generalized transduction in Streptomyces coelicolor, Proc Natl Acad Sci, vol.98, pp.6289-6294, 2001.

J. Cairns, The Chromosome of Escherichia coli, Cold Spring Harb Symp Quant Biol, vol.28, pp.43-46, 1963.

J. K. Carson, V. Gonzalez-quiñones, D. V. Murphy, C. Hinz, J. A. Shaw et al., Low pore connectivity increases bacterial diversity in soil, Appl Environ Microbiol, vol.76, pp.3936-3942, 2010.

T. J. Carver, K. M. Rutherford, M. Berriman, M. Rajandream, B. G. Barrell et al., ACT: the Artemis comparison tool, Bioinformatics, vol.21, pp.3422-3423, 2005.

S. Casjens, M. Murphy, M. Delange, L. Sampson, R. Vugt et al., 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.

S. R. Casjens, E. F. Mongodin, W. Qiu, B. J. Luft, S. E. Schutzer et al., , 2012.

, Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids, vol.7, 2019.

H. F. Castro, A. T. Classen, E. E. Austin, R. J. Norby, and C. W. Schadt, Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers, Appl Environ Microbiol, vol.76, pp.999-1007, 2010.

G. L. Challis and J. H. Naismith, Structural aspects of non-ribosomal peptide biosynthesis, Curr Opin Struct Biol, vol.14, pp.748-756, 2004.

W. Champness, Actinomycete Development, Antibiotic Production, and Phylogeny: Questions and Challenges, pp.11-31, 2000.

R. L. Charlebois, Organization of the prokaryotic genome, 1999.

Z. Charlop-powers, J. G. Owen, B. V. Reddy, M. A. Ternei, and S. F. Brady, Chemicalbiogeographic survey of secondary metabolism in soil, Proc Natl Acad Sci, vol.111, p.3757, 2014.

K. F. Chater, Genetics of differentiation in Streptomyces, Annu Rev Microbiol, vol.47, pp.685-713, 1993.

K. F. Chater, 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.

K. F. Chater and D. A. Hopwood, Streptornyces genetics, Biology of the Actinomycetes, pp.229-286, 1984.

J. F. Chau, A. C. Bagtzoglou, and M. R. Willig, The Effect of Soil Texture on Richness and Diversity of Bacterial Communities, Environmental Forensics, vol.12, pp.333-341, 2011.

C. W. Chen, Complications and implications of linear bacterial chromosomes, Trends in Genetics, vol.12, pp.192-196, 1996.

C. W. Chen, C. Huang, H. Lee, H. Tsai, and R. Kirby, Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes, Trends in Genetics, vol.18, pp.522-529, 2002.

C. W. Chen, T. Yu, Y. Lin, H. M. Kieser, and D. A. Hopwood, The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule, Molecular Microbiology, vol.7, pp.925-932, 1993.

I. Chen and D. Dubnau, DNA uptake during bacterial transformation, Nat Rev Microbiol, vol.2, pp.241-249, 2004.

Z. Chen, L. Zhong, M. Shen, P. Fang, and Z. Qin, Characterization of Streptomyces plasmidphage pFP4 and its evolutionary implications, Plasmid, vol.68, pp.170-178, 2012.

F. Choulet, B. Aigle, A. Gallois, S. Mangenot, C. Gerbaud et al., 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

F. Choulet, A. Gallois, B. Aigle, S. Mangenot, C. Gerbaud et al., 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

N. Chowdhury, P. Marschner, and R. Burns, Response of microbial activity and community structure to decreasing soil osmotic and matric potential, 2011.

B. Christen, E. Abeliuk, J. M. Collier, V. S. Kalogeraki, B. Passarelli et al., The essential genome of a bacterium, Mol Syst Biol, vol.7, p.528, 2011.

P. J. Christie, N. Whitaker, and C. González-rivera, Mechanism and structure of the bacterial type IV secretion systems, Biochim Biophys Acta, vol.1843, pp.1578-1591, 2014.

M. J. Claesson, Q. Wang, O. O'sullivan, R. Greene-diniz, J. R. Cole et al., 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.

M. F. Claridge, A. H. Dawah, and W. , Species: The units of biodiversity, 1997.

J. Claverys, B. Martin, and L. S. Håvarstein, Competence-induced fratricide in streptococci, Mol Microbiol, vol.64, pp.1423-1433, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00154610

F. Cohan, Chapter 5 Are Species Cohesive ? -A View from Bacteriology, 2011.

F. M. Cohan, What are Bacterial Species?, Annual Review of Microbiology, vol.56, pp.457-487, 2002.

F. M. Cohan, Sexual isolation and speciation in bacteria. In Genetics of Mate Choice: From Sexual Selection to Sexual Isolation, pp.359-370, 2002.

F. M. Cohan, Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla. Microbiol Spectr, vol.5, 2017.

F. M. Cohan and E. B. Perry, A systematics for discovering the fundamental units of bacterial diversity, Curr Biol, vol.17, pp.373-386, 2007.

O. X. Cordero and M. S. Datta, Microbial interactions and community assembly at microscales, Current Opinion in Microbiology, vol.31, pp.227-234, 2016.

O. X. Cordero and P. Hogeweg, The impact of long-distance horizontal gene transfer on prokaryotic genome size, PNAS, vol.106, pp.21748-21753, 2009.

O. X. Cordero and M. F. Polz, Explaining microbial genomic diversity in light of evolutionary ecology, Nature Reviews Microbiology, vol.12, pp.263-273, 2014.

O. X. Cordero, L. Ventouras, E. F. Delong, and M. F. Polz, Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations, Proc Natl Acad Sci, vol.109, 2012.

N. J. Croucher, P. G. Coupland, A. E. Stevenson, A. Callendrello, S. D. Bentley et al., Diversification of bacterial genome content through distinct mechanisms over different timescales, Nat Commun, vol.5, pp.1-12, 2014.

F. Cruz, L. S. Frost, R. J. Meyer, and E. L. Zechner, Conjugative DNA metabolism in Gramnegative bacteria, FEMS Microbiol Rev, vol.34, pp.18-40, 2010.

K. Cruz-martínez, K. B. Suttle, E. L. Brodie, M. E. Power, G. L. Andersen et al., 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.

R. Daniel, The metagenomics of soil, Nat Rev Microbiol, vol.3, pp.470-478, 2005.

;. C. Darwin, On the origin of the species by means of natural selection, pp.1809-1882, 1859.

J. Davies, Specialized microbial metabolites: functions and origins, J Antibiot, vol.66, pp.361-364, 2013.

R. Dawkins, Defence of Selfish Genes, vol.56, pp.556-573, 1981.

A. Dechesne, C. Pallud, D. Debouzie, J. P. Flandrois, T. M. Vogel et al., 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

G. E. Degnen and E. C. Cox, Conditional Mutator Gene in Escherichia coli: Isolation, Mapping, and Effector Studies, J Bacteriol, vol.117, pp.477-487, 1974.

T. O. Delmont, E. Prestat, K. P. Keegan, M. Faubladier, P. Robe et al., 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

P. Demuyter, P. Leblond, B. Decaris, and J. M. Simonet, 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

K. M. Derbyshire and T. A. Gray, Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria, Microbiol Spectr, vol.2, 2014.

T. Z. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie et al., Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl Environ Microbiol, vol.72, pp.5069-5072, 2006.

M. Di-giambattista, G. Chinali, and C. Cocito, 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.

D. Ditmarsch and J. B. Xavier, Seeing is believing: what experiments with microbes reveal about evolution, Trends in Microbiology, vol.22, pp.2-4, 2014.

U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker, Genomic islands in pathogenic and environmental microorganisms, Nat Rev Microbiol, vol.2, pp.414-424, 2004.

M. S. Donia, B. J. Hathaway, S. Sudek, M. G. Haygood, M. J. Rosovitz et al., Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians, Nat Chem Biol, vol.2, pp.729-735, 2006.

W. F. Doolittle and O. Zhaxybayeva, On the origin of prokaryotic species, Genome Res, vol.19, pp.744-756, 2009.

J. R. Doroghazi, J. C. Albright, A. W. Goering, K. Ju, R. R. Haines et al., A roadmap for natural product discovery based on large-scale genomics and metabolomics, Nature Chemical Biology, vol.10, pp.963-968, 2014.

J. R. Doroghazi and W. W. Metcalf, Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes, BMC Genomics, vol.14, p.611, 2013.

E. Duchaud, C. Rusniok, L. Frangeul, C. Buchrieser, A. Givaudan et al., 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

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.430, pp.35-44, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00104411

G. M. Dunny, Genetic functions and cell-cell interactions in the pheromone-inducible plasmid transfer system of Enterococcus faecalis, Mol Microbiol, vol.4, pp.689-696, 1990.

S. Dutta, J. R. Whicher, D. A. Hansen, W. A. Hale, J. A. Chemler et al., Structure of a modular polyketide synthase, Nature, vol.510, pp.512-517, 2014.

N. &. Eldredge, . Schopf, . Freeman, &. Cooper, S. Co et al., Punctuated equilibria: an alternative to phyletic gradualism // (1972) pp 82-115 in "Models in paleobiology, 1972.

N. Eldredge, J. N. Thompson, P. M. Brakefield, S. Gavrilets, D. Jablonski et al., The dynamics of evolutionary stasis, Paleobiology, vol.31, pp.133-145, 2005.

M. A. Elliot, M. J. Buttner, and J. R. Nodwell, Multicellular Development in Streptomyces, pp.419-438, 2008.

R. J. Ellis, Artificial soil microcosms: a tool for studying microbial autecology under controlled conditions, J Microbiol Methods, vol.56, pp.287-290, 2004.

M. Faucher, L. Nouvel, E. Dordet-frisoni, E. Sagné, E. Baranowski et al., Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer, PLoS Genet, vol.15, p.1007910, 2019.

F. Fiegna and G. J. Velicer, Exploitative and Hierarchical Antagonism in a Cooperative Bacterium, PLOS Biology, vol.3, p.370, 2005.

N. Fierer, C. L. Lauber, K. S. Ramirez, J. Zaneveld, M. A. Bradford et al., Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients, ISME J, vol.6, pp.1007-1017, 2012.

R. Finking and M. A. Marahiel, Biosynthesis of nonribosomal peptides1, Annu Rev Microbiol, vol.58, pp.453-488, 2004.

M. A. Fischbach, C. T. Walsh, and J. Clardy, The evolution of gene collectives: How natural selection drives chemical innovation, Proc Natl Acad Sci, vol.105, pp.4601-4608, 2008.

G. Fischer, B. Decaris, and P. Leblond, 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.

G. Fischer, C. Neuvéglise, P. Durrens, C. Gaillardin, and B. Dujon, 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

G. Fischer, T. Wenner, B. Decaris, and P. Leblond, 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

R. A. Fisher, XVII.-The Distribution of Gene Ratios for Rare Mutations, Proceedings of the Royal Society of Edinburgh, vol.50, pp.204-219, 1931.

P. M. Flatt, M. , and T. , Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, Nat Prod Rep, vol.24, pp.358-392, 2007.

R. D. Fleischmann, M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness et al., Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, pp.496-512, 1995.

G. E. Fox, L. J. Magrum, W. E. Balch, R. S. Wolfe, and C. R. Woese, Classification of methanogenic bacteria by 16S ribosomal RNA characterization, Proc Natl Acad Sci, vol.74, pp.4537-4541, 1977.

C. Fraser, E. J. Alm, M. F. Polz, B. G. Spratt, and W. P. Hanage, The bacterial species challenge: making sense of genetic and ecological diversity, Science, vol.323, pp.741-746, 2009.

C. M. Fraser, J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton et al., The minimal gene complement of Mycoplasma genitalium, Science, vol.270, pp.397-403, 1995.

R. Fronzes, P. J. Christie, and G. Waksman, The structural biology of type IV secretion systems, Nat Rev Microbiol, vol.7, pp.703-714, 2009.

L. S. Frost, K. Ippen-ihler, and R. A. Skurray, Analysis of the sequence and gene products of the transfer region of the F sex factor, Microbiol Rev, vol.58, pp.162-210, 1994.

E. Y. Furuya and F. D. Lowy, Antimicrobial-resistant bacteria in the community setting, Nature Reviews Microbiology, vol.4, pp.36-45, 2006.

R. Garcia, K. Gemperlein, and R. Müller, 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.

S. L. Garcia, S. L. Stevens, B. Crary, M. Martinez-garcia, R. Stepanauskas et al., Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations, The ISME Journal, vol.12, pp.742-755, 2018.

M. J. Gardner, N. Hall, E. Fung, O. White, M. Berriman et al., Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, vol.419, pp.498-511, 2002.

D. Gevers, F. M. Cohan, J. G. Lawrence, B. G. Spratt, T. Coenye et al., Opinion: Reevaluating prokaryotic species, Nat Rev Microbiol, vol.3, pp.733-739, 2005.

M. G. Ghinet, E. Bordeleau, J. Beaudin, R. Brzezinski, S. Roy et al., Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria, PLOS ONE, vol.6, p.27846, 2011.

J. P. Gogarten, W. F. Doolittle, and J. G. Lawrence, Prokaryotic Evolution in Light of Gene Transfer, Mol Biol Evol, vol.19, pp.2226-2238, 2002.

P. Gómez and A. Buckling, Bacteria-Phage Antagonistic Coevolution in Soil, Science, vol.332, pp.106-109, 2011.

L. V. Gonod, F. Martin-laurent, and C. Chenu, 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

M. Goodfellow, R. Freeman, and P. R. Sisson, Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology, Zentralbl Bakteriol, vol.285, pp.133-156, 1997.

T. A. Gray and K. M. Derbyshire, Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT, Molecular Microbiology, vol.108, pp.601-613, 2018.

F. Griffith, The Significance of Pneumococcal Types, J Hyg (Lond), vol.27, pp.113-159, 1928.

R. I. Griffiths, B. C. Thomson, P. James, T. Bell, M. Bailey et al., The bacterial biogeography of British soils, Environ Microbiol, vol.13, pp.1642-1654, 2011.

I. Grissa, G. Vergnaud, and C. Pourcel, 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

G. L. Grundmann, Spatial scales of soil bacterial diversity--the size of a clone, FEMS Microbiol Ecol, vol.48, pp.119-127, 2004.

G. L. Grundmann, A. Dechesne, F. Bartoli, J. P. Flandrois, J. L. Chassé et al., 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

G. L. Grundmann, N. , and P. , 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.

B. Guenet, J. Leloup, C. Hartmann, S. Barot, A. et al., A new protocol for an artificial soil to analyse soil microbiological processes, Applied Soil Ecology, vol.48, pp.243-246, 2011.

J. Guglielmini, B. Néron, S. S. Abby, M. P. Garcillán-barcia, F. Cruz et al., 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

J. Hacker, G. Blum-oehler, I. Mühldorfer, and H. Tschäpe, Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution, Mol Microbiol, vol.23, pp.1089-1097, 1997.

J. Hacker and J. B. Kaper, Pathogenicity islands and the evolution of microbes, Annu Rev Microbiol, vol.54, pp.641-679, 2000.

D. H. Haft, J. Selengut, E. F. Mongodin, and K. E. Nelson, 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.

J. Hagège, F. Boccard, T. Smokvina, J. L. Pernodet, A. Friedmann et al., Identification of a gene encoding the replication initiator protein of the Streptomyces integrating element, pSAM2, Plasmid, vol.31, pp.166-183, 1994.

J. Hagège, J. L. Pernodet, A. Friedmann, and M. Guérineau, Mode and origin of replication of pSAM2, a conjugative integrating element of Streptomyces ambofaciens, Mol Microbiol, vol.10, pp.799-812, 1993.

J. Hagège, J. L. Pernodet, G. Sezonov, C. Gerbaud, A. Friedmann et al., 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.

C. A. Hanson, J. A. Fuhrman, M. C. Horner-devine, and J. B. Martiny, Beyond biogeographic patterns: processes shaping the microbial landscape, Nat Rev Microbiol, vol.10, pp.497-506, 2012.

J. R. Hanson, Natural products: the secondary metabolites. Natural products: the secondary metabolites, 2003.

T. Hattori and U. Tohoku, Soil aggregates as microhabitats of microorganisms, 1988.

, ?recordID=JP8903709. Accessed, 2019.

I. Haug, A. Weissenborn, D. Brolle, S. Bentley, T. Kieser et al., Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence, Microbiology (Reading, Engl), vol.149, pp.505-513, 2003.

R. J. Haynes and R. S. Swift, Stability of soil aggregates in relation to organic constituents and soil water content, Journal of Soil Science, vol.41, pp.73-83, 1990.

K. Heister, C. Höschen, G. J. Pronk, C. W. Mueller, and I. Knabner, NanoSIMS as a tool for characterizing soil model compounds and organomineral associations in artificial soils, J Soils Sediments, vol.12, pp.35-47, 2012.

U. Herbig, W. A. Jobling, B. P. Chen, D. J. Chen, and J. M. Sedivy, 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

P. Hieter, C. Mann, M. Snyder, and R. W. Davis, Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss, Cell, vol.40, pp.381-392, 1985.

N. L. Hiller, A. Ahmed, E. Powell, D. P. Martin, R. Eutsey et al., 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.

G. Hoff, C. Bertrand, E. Piotrowski, A. Thibessard, and P. Leblond, 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

C. Hsu, C. , and C. W. , Linear Plasmid SLP2 Is Maintained by Partitioning, Intrahyphal Spread, and Conjugal Transfer in Streptomyces, Journal of Bacteriology, vol.192, pp.307-315, 2010.

C. Huang, C. Chen, H. Tsai, C. Chen, Y. Lin et al., Linear plasmid SLP2 of Streptomyces lividans is a composite replicon, Mol Microbiol, vol.47, pp.1563-1576, 2003.

C. H. Huang, Y. S. Lin, Y. L. Yang, S. W. Huang, C. et al., The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998.

P. Hugenholtz, Exploring prokaryotic diversity in the genomic era, Genome Biol, vol.3, pp.3-4, 2002.

S. M. Huse, L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman et al., Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing, PLOS Genetics, vol.4, p.1000255, 2008.

H. Ikeda, J. Ishikawa, A. Hanamoto, M. Shinose, H. Kikuchi et al., Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis, Nat Biotechnol, vol.21, pp.526-531, 2003.

S. Inoue, K. Higashiyama, T. Uchida, K. Hiratsu, and H. Kinashi, Chromosomal circularization in Streptomyces griseus by nonhomologous recombination of deletion ends, Biosci Biotechnol Biochem, vol.67, pp.1101-1108, 2003.

K. Itahana, J. Campisi, and G. P. Dimri, Mechanisms of cellular senescence in human and mouse cells, Biogerontology, vol.5, pp.1-10, 2004.

H. Jenke-kodama, T. Börner, and E. Dittmann, Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis, PLoS Computational Biology, vol.2, pp.1210-1218, 2006.

P. R. Jensen, P. G. Williams, D. Oh, L. Zeigler, and W. Fenical, Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora, Appl Environ Microbiol, vol.73, pp.1146-1152, 2007.

O. Johnsborg, V. Eldholm, and L. S. Håvarstein, Natural genetic transformation: prevalence, mechanisms and function, Res Microbiol, vol.158, pp.767-778, 2007.

M. Juhas, J. R. Meer, . Van-der, M. Gaillard, R. M. Harding et al., Genomic islands: tools of bacterial horizontal gene transfer and evolution, FEMS Microbiol Rev, vol.33, pp.376-393, 2009.

A. Juyal, T. Eickhorst, R. Falconer, P. C. Baveye, A. Spiers et al., 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

D. Kameoka, A. Lezhava, H. Zenitani, K. Hiratsu, M. Kawamoto et al., Analysis of Fusion Junctions of Circularized Chromosomes in Streptomyces griseus, J Bacteriol, vol.181, pp.5711-5717, 1999.

M. Kataoka, T. Seki, Y. , and T. , Five genes involved in self-transmission of pSN22, a Streptomyces plasmid, J Bacteriol, vol.173, pp.4220-4228, 1991.

L. Katz, D. P. Brown, and S. Donadio, Site-specific recombination inEscherichia coli between theatt sites of plasmid pSE211 fromSaccharopolyspora erythraea, Molec Gen Genet, vol.227, pp.155-159, 1991.

T. J. Kawecki, R. E. Lenski, D. Ebert, B. Hollis, I. Olivieri et al., Experimental evolution, Trends Ecol Evol (Amst), vol.27, pp.547-560, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00162893

W. D. Kemper and R. C. Rosenau, Aggregate Stability and Size Distribution 1. Methods of Soil Analysis: Part 1-Physical and Mineralogical Methods sssabookseries, pp.425-442, 1986.

K. J. Kendall and S. N. Cohen, 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.

J. E. Keymer, P. Galajda, C. Muldoon, S. Park, A. et al., Bacterial metapopulations in nanofabricated landscapes, PNAS, vol.103, pp.17290-17295, 2006.

T. Kieser, D. A. Hopwood, H. M. Wright, and C. J. Thompson, ) 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.

M. Kimura, DNA and the neutral theory, Philos Trans R Soc Lond, B, Biol Sci, vol.312, pp.343-354, 1986.

M. Kimura and T. Ohta, On Some Principles Governing Molecular Evolution*, Proc Natl Acad Sci U S A, vol.71, pp.2848-2852, 1974.

H. Kinashi, M. Shimaji, and A. Sakai, Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes, Nature, vol.328, pp.454-456, 1987.

A. Koeppel, E. B. Perry, J. Sikorski, D. Krizanc, A. Warner et al., 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.

K. T. Konstantinidis, A. Ramette, and J. M. Tiedje, The bacterial species definition in the genomic era, Philos Trans R Soc Lond B Biol Sci, vol.361, pp.1929-1940, 2006.

E. V. Koonin, Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions, 2016.

A. Koyama, M. D. Wallenstein, R. T. Simpson, and J. C. Moore, Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils, Front Microbiol, vol.5, p.516, 2014.

S. A. Kraemer, M. A. Toups, and G. J. Velicer, Natural variation in developmental life-history traits of the bacterium Myxococcus xanthus, FEMS Microbiol Ecol, vol.73, pp.226-233, 2010.

D. Krug, G. Zurek, O. Revermann, M. Vos, G. J. Velicer et al., Discovering the Hidden Secondary Metabolome of Myxococcus xanthus: a Study of Intraspecific Diversity, Appl Environ Microbiol, vol.74, pp.3058-3068, 2008.

M. I. Krzywinski, J. E. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: An information aesthetic for comparative genomics, Genome Res, 2009.

E. E. Kuramae, E. Yergeau, L. C. Wong, A. S. Pijl, J. A. Veen et al., Soil characteristics more strongly influence soil bacterial communities than land-use type, FEMS Microbiol Ecol, vol.79, pp.12-24, 2012.

Y. Kuzyakov and E. Blagodatskaya, Microbial hotspots and hot moments in soil: Concept & review, Soil Biology and Biochemistry, vol.83, pp.184-199, 2015.

M. Land, L. Hauser, S. Jun, I. Nookaew, M. R. Leuze et al., Insights from 20 years of bacterial genome sequencing, Funct Integr Genomics, vol.15, pp.141-161, 2015.

M. G. Langille, W. W. Hsiao, and F. S. Brinkman, Detecting genomic islands using bioinformatics approaches, Nat Rev Microbiol, vol.8, pp.373-382, 2010.

P. Lapierre and J. P. Gogarten, Estimating the size of the bacterial pan-genome, Trends Genet, vol.25, pp.107-110, 2009.

F. Lassalle, D. Muller, and X. Nesme, 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

C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, 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.

J. G. Lawrence, R. W. Hendrix, and S. Casjens, Where are the pseudogenes in bacterial genomes?, Trends Microbiol, vol.9, pp.535-540, 2001.

J. G. Lawrence and H. Ochman, Molecular archaeology of the Escherichia coli genome, Proc Natl Acad Sci, vol.95, pp.9413-9417, 1998.

V. Lázár, A. Martins, R. Spohn, L. Daruka, G. Grézal et al., Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides, Nat Microbiol, vol.3, pp.718-731, 2018.

P. Leblond, P. Demuyter, L. Moutier, M. Laakel, B. Decaris et al., 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

P. Leblond, P. Demuyter, J. M. Simonet, and B. Decaris, 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

P. Leblond, G. Fischer, F. X. Francou, F. Berger, M. Guérineau et al., 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

J. Lederberg, E. M. Lederberg, N. D. Zinder, and E. R. Lively, Recombination analysis of bacterial heredity, Cold Spring Harb Symp Quant Biol, vol.16, pp.413-443, 1951.

J. Lederberg and E. L. Tatum, Gene Recombination in Escherichia Coli, Nature, vol.158, p.558, 1946.

H. Lee, C. Hsu, Y. Lin, C. , and C. W. , 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.

J. W. Leff, S. E. Jones, S. M. Prober, A. Barberán, E. T. Borer et al., Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe, PNAS, vol.112, pp.10967-10972, 2015.

A. Letzel, S. J. Pidot, and C. Hertweck, Genome mining for ribosomally synthesized and posttranslationally modified peptides (RiPPs) in anaerobic bacteria, BMC Genomics, vol.15, p.983, 2014.

I. Levade, Y. Terrat, J. Leducq, A. A. Weil, L. M. Mayo-smith et al., Vibrio cholerae genomic diversity within and between patients, Microb Genom, vol.3, 2017.

R. Levy and E. Borenstein, Reverse Ecology: from systems to environments and back, Adv Exp Med Biol, vol.751, pp.329-345, 2012.

Y. F. Li, J. C. Costello, A. K. Holloway, and M. W. Hahn, REVERSE ECOLOGY" AND THE POWER OF POPULATION GENOMICS. Evolution, vol.62, pp.2984-2994, 2008.

Y. S. Lin, H. M. Kieser, D. A. Hopwood, C. , and C. W. , The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993.

B. Linz, F. Balloux, Y. Moodley, A. Manica, H. Liu et al., An African origin for the intimate association between humans and Helicobacter pylori, Nature, vol.445, pp.915-918, 2007.

F. Liu, S. Garneau, and C. T. Walsh, 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.

L. Liu, H. L. Johnson, S. Cousens, J. Perin, S. Scott et al., 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.

R. G. Lloyd and C. Buckman, Conjugational recombination in Escherichia coli: genetic analysis of recombinant formation in Hfr x F-crosses, Genetics, vol.139, pp.1123-1148, 1995.

M. G. Lorenz and W. Wackernagel, Bacterial gene transfer by natural genetic transformation in the environment, Microbiol Rev, vol.58, pp.563-602, 1994.

K. B. Low, Conjugation, Encyclopedia of Genetics, pp.449-453, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01081881

S. E. Luria and M. Delbrück, Mutations of Bacteria from Virus Sensitivity to Virus Resistance, Genetics, vol.28, pp.491-511, 1943.

J. E. Mcmurry, Organic chemistry with biological applications, Secondary Metabolites: An Introduction to Natural Products Chemistry, pp.1016-1046, 2015.

M. C. Maiden, J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell et al., 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.

J. Majewski, P. Zawadzki, P. Pickerill, F. M. Cohan, and C. G. Dowson, Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation, Journal of Bacteriology, vol.182, pp.1016-1023, 2000.

J. Männik, R. Driessen, P. Galajda, J. E. Keymer, and C. Dekker, Bacterial growth and motility in sub-micron constrictions, PNAS, vol.106, pp.14861-14866, 2009.

E. F. Mao, L. Lane, J. Lee, and J. H. Miller, Proliferation of mutators in A cell population, J Bacteriol, vol.179, pp.417-422, 1997.

L. A. Marraffini and E. J. Sontheimer, CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, vol.322, pp.1843-1845, 2008.

C. Martin, P. Mazodier, M. V. Mediola, B. Gicquel, T. Smokvina et al., Site-specific integration of the Streptomyces plasmid pSAM2 in Mycobacterium smegmatis, Molecular Microbiology, vol.5, pp.2499-2502, 1991.

J. Masschelein, M. Jenner, and G. L. Challis, Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights, Nat Prod Rep, vol.34, pp.712-783, 2017.

E. Mayr, Systematics and the Origin of Species, from the Viewpoint of a Zoologist, 1999.

J. O. Mcinerney, A. Mcnally, and M. J. Connell, Why prokaryotes have pangenomes, Nat Microbiol, vol.2, p.17040, 2017.

M. L. Michaels, L. Pham, Y. Nghiem, C. Cruz, and J. H. Miller, MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III, Nucleic Acids Res, vol.18, pp.3841-3845, 1990.

D. A. Miller, L. Luo, N. Hillson, T. A. Keating, and C. T. Walsh, Yersiniabactin synthetase: a fourprotein assembly line producing the nonribosomal peptide/polyketide hybrid siderophore of Yersinia pestis, Chem Biol, vol.9, pp.333-344, 2002.

Y. Moënne-loccoz, P. Mavingui, C. Combes, P. Normand, C. Steinberg et al., Microorganisms and Biotic Interactions, Environmental Microbiology: Fundamentals and Applications: Microbial Ecology, 2015.

, , pp.395-444, 2019.

A. D. Morgan, R. C. Maclean, K. L. Hillesland, and G. J. Velicer, Comparative Analysis of Myxococcus Predation on Soil Bacteria, Appl Environ Microbiol, vol.76, pp.6920-6927, 2010.

J. J. Morris, R. E. Lenski, and E. R. Zinser, The Black Queen Hypothesis: Evolution of Dependencies through, Adaptive Gene Loss. mBio, vol.3, pp.36-48, 2012.

M. Mortel, . Van-de, and L. J. Halverson, 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.

G. Muth, M. Farr, V. Hartmann, and W. Wohlleben, 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.

G. Muth, W. Wohlleben, and A. Pühler, The minimal replicon of the Streptomyces ghanaensis plasmid pSG5 identified by subcloning and Tn5 mutagenesis, Molec Gen Genet, vol.211, pp.424-429, 1988.

M. Myronovskyi, B. Tokovenko, E. Brötz, C. Rückert, J. Kalinowski et al., Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation, Appl Microbiol Biotechnol, vol.98, pp.795-806, 2014.

N. H. Nakamura, D. R. Rosell, K. T. Akama, and B. S. Mcewen, 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.

R. Niehus, S. Mitri, A. G. Fletcher, and K. R. Foster, Migration and horizontal gene transfer divide microbial genomes into multiple niches, Nat Commun, vol.6, p.8924, 2015.

K. M. Nielsen, A. M. Bones, K. Smalla, J. D. Elsas, and . Van, Horizontal gene transfer from transgenic plants to terrestrial bacteria--a rare event?, FEMS Microbiol Rev, vol.22, pp.79-103, 1998.

N. Nunan, K. Wu, I. M. Young, J. W. Crawford, and K. Ritz, Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil, FEMS Microbiol Ecol, vol.44, pp.203-215, 2003.

H. Ochman, S. Elwyn, and N. A. Moran, Calibrating bacterial evolution, PNAS, vol.96, pp.12638-12643, 1999.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

H. Ochman and N. A. Moran, Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, pp.1096-1099, 2001.

Y. Ohnishi, J. Ishikawa, H. Hara, H. Suzuki, M. Ikenoya et al., Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350, J Bacteriol, vol.190, pp.4050-4060, 2008.

S. Okabe, H. Satoh, and Y. Watanabe, Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes, vol.65, pp.3182-3191, 1999.

H. Oliveira, D. Vilas-boas, S. Mesnage, L. D. Kluskens, R. Lavigne et al., Structural and Enzymatic Characterization of ABgp46, a Novel Phage Endolysin with Broad Anti-Gram-Negative Bacterial Activity, Front Microbiol, vol.7, 2016.

. Accessed, , 2019.

A. Oliver, R. Cantón, P. Campo, F. Baquero, and J. Blázquez, High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection, Science, vol.288, pp.1251-1254, 2000.

J. D. Oliver, The viable but nonculturable state in bacteria, Journal of microbiology, vol.43, pp.93-100, 2005.

M. A. Ortega, W. A. Donk, and . Van-der, 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.

E. Paget and P. Simonet, On the track of natural transformation in soil, FEMS Microbiol Ecol, vol.15, pp.109-117, 1994.

C. Pál, B. Papp, and M. J. Lercher, Adaptive evolution of bacterial metabolic networks by horizontal gene transfer, Nature Genetics, vol.37, p.1372, 2005.

S. Pandza, G. Biukovi?, A. Paravi?, A. Dadbin, J. Cullum et al., 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.

C. J. Park and C. P. Andam, Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus, Front Microbiol, vol.10, 2019.

G. C. Patton, W. A. Donk, and . Van-der, New developments in lantibiotic biosynthesis and mode of action, Curr Opin Microbiol, vol.8, pp.543-551, 2005.

G. Pavlovic, V. Burrus, B. Gintz, B. Decaris, and G. Guédon, 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

K. Penn, C. Jenkins, M. Nett, D. W. Udwary, E. A. Gontang et al., Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria, ISME J, vol.3, pp.1193-1203, 2009.

J. L. Pernodet, J. M. Simonet, and M. Guérineau, Plasmids in different strains of Streptomyces ambofaciens: free and integrated form of plasmid pSAM2, Mol Gen Genet, vol.198, pp.35-41, 1984.

G. S. Pettis and S. N. Cohen, 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.

E. M. Poele, H. Bolhuis, and L. Dijkhuizen, Actinomycete integrative and conjugative elements, Antonie Van Leeuwenhoek, vol.94, pp.127-143, 2008.

M. F. Polz, E. J. Alm, and W. P. Hanage, Horizontal gene transfer and the evolution of bacterial and archaeal population structure, Trends in Genetics, vol.29, pp.170-175, 2013.

M. C. Portillo, J. W. Leff, C. L. Lauber, and N. Fierer, Cell Size Distributions of Soil Bacterial and Archaeal Taxa, Appl Environ Microbiol, vol.79, pp.7610-7617, 2013.

C. Possoz, J. Gagnat, G. Sezonov, M. Guérineau, and J. Pernodet, 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.

C. Possoz, C. Ribard, J. Gagnat, J. L. Pernodet, and M. Guérineau, The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer, Mol Microbiol, vol.42, pp.159-166, 2001.

D. Probandt, T. Eickhorst, A. Ellrott, R. Amann, and K. Knittel, Microbial life on a sand grain: from bulk sediment to single grains, ISME J, vol.12, pp.623-633, 2018.

K. Queiroz and . De, The General Lineage Concept of Species, Species Criteria, and the Process of Speciation, Endless Forms: Species and, pp.57-75, 1998.

C. Quince, T. P. Curtis, and W. T. Sloan, The rational exploration of microbial diversity, ISME J, vol.2, pp.997-1006, 2008.

M. Radman, SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis, Basic Life Sci, vol.5, pp.355-367, 1975.

M. Radman, Enzymes of evolutionary change, Nature, vol.401, pp.866-867, 1999.

S. Ramírez-arcos, L. A. Fernández-herrero, I. Marín, and J. Berenguer, Anaerobic Growth, a Property Horizontally Transferred by an Hfr-Like Mechanism among Extreme Thermophiles, J Bacteriol, vol.180, pp.3137-3143, 1998.

L. Ranjard, R. , and A. , 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

A. Raynal, K. Tuphile, C. Gerbaud, T. Luther, M. Guérineau et al., Structure of the chromosomal insertion site for pSAM2: functional analysis in Escherichia coli, Molecular Microbiology, vol.28, pp.333-342, 1998.

X. Raynaud and N. Nunan, Spatial Ecology of Bacteria at the Microscale in Soil, PLoS One, vol.9, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01252483

Y. Raynes and P. D. Sniegowski, Experimental evolution and the dynamics of genomic mutation rate modifiers, Heredity (Edinb), vol.113, pp.375-380, 2014.

K. M. Regan, N. Nunan, R. S. Boeddinghaus, V. Baumgartner, D. Berner et al., 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.

C. Reimmann and D. Haas, Mobilization of Chromosomes and Nonconjugative Plasmids by Cointegrative Mechanisms, pp.137-188, 1993.

J. Reuther, W. Wohlleben, and G. Muth, Modular architecture of the conjugative plasmid pSVH1 from Streptomyces venezuelae, Plasmid, vol.55, pp.201-209, 2006.

D. N. Reznick, F. H. Shaw, F. H. Rodd, and R. G. Shaw, Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata), Science, vol.275, pp.1934-1937, 1997.

C. Richter, J. T. Chang, and P. C. Fineran, Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) / CRISPR Associated (Cas) Systems, Viruses, vol.4, pp.2291-2311, 2012.

M. A. Riley and M. Lizotte-waniewski, Population Genomics and the Bacterial Species Concept, Methods Mol Biol, vol.532, pp.367-377, 2009.

E. P. Rocha and A. Danchin, Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res, vol.31, pp.6570-6577, 2003.

S. W. Roh, G. C. Abell, K. Kim, Y. Nam, and J. Bae, Comparing microarrays and nextgeneration sequencing technologies for microbial ecology research, Trends Biotechnol, vol.28, pp.291-299, 2010.

R. A. Rossel, H. J. Taylor, and A. B. Mcbratney, Multivariate calibration of hyperspectral ?-ray energy spectra for proximal soil sensing, European Journal of Soil Science, vol.58, pp.343-353, 2007.

R. Rosselló-mora, A. , and R. , The species concept for prokaryotes, FEMS Microbiol Rev, vol.25, pp.39-67, 2001.

J. R. Roth, N. Benson, T. Galitski, K. Haack, J. G. Lawrence et al., , p.37

E. Rotman and A. Kuzminov, 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.

L. S. Ruamps, N. Nunan, and C. Chenu, 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

J. E. Samson, A. H. Magadán, M. Sabri, and S. Moineau, Revenge of the phages: defeating bacterial defences, Nat Rev Microbiol, vol.11, pp.675-687, 2013.

D. Schluter, Ecological Character Displacement in Adaptive Radiation, The American Naturalist, vol.156, pp.4-16, 2000.

M. W. Schmidt, M. S. Torn, S. Abiven, T. Dittmar, G. Guggenberger et al., Persistence of soil organic matter as an ecosystem property, Nature, vol.478, pp.49-56, 2011.

R. F. Seipke, Strain-Level Diversity of Secondary Metabolism in Streptomyces albus, PLOS ONE, vol.10, p.116457, 2015.

V. Sentchilo, K. Czechowska, N. Pradervand, M. Minoia, R. Miyazaki et al., Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13, Mol Microbiol, vol.72, pp.1293-1306, 2009.

L. Servín-gonzález, Identification and properties of a novel clt locus in the Streptomyces phaeochromogenes plasmid pJV1, Journal of Bacteriology, vol.178, pp.4323-4326, 1996.

L. Servín-gonzález, A. I. Sampieri, J. Cabello, L. Galván, V. Juárez et al., 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.

G. Sezonov, A. M. Duchêne, A. Friedmann, M. Guérineau, and J. L. Pernodet, 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.

G. Sezonov, J. Hagege, J. L. Pernodet, A. Friedmann, and M. Guerineau, Characterization of pra, a gene for replication control in pSAM2, the integrating element of Streptomyces ambofaciens, Molecular microbiology, 1995.

B. J. Shapiro, How clonal are bacteria over time?, Curr Opin Microbiol, vol.31, pp.116-123, 2016.

B. J. Shapiro, The population genetics of pangenomes, Nat Microbiol, vol.2, pp.1574-1574, 2017.

B. J. Shapiro, J. Friedman, O. X. Cordero, S. P. Preheim, S. C. Timberlake et al., Population genomics of early events in the ecological differentiation of bacteria, Science, vol.336, pp.48-51, 2012.

B. J. Shapiro and M. F. Polz, Ordering microbial diversity into ecologically and genetically cohesive units, Trends in Microbiology, vol.22, pp.235-247, 2014.

B. Shen, Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms, Curr Opin Chem Biol, vol.7, pp.285-295, 2003.

P. Shen and H. V. Huang, Homologous recombination in Escherichia coli: dependence on substrate length and homology, Genetics, vol.112, pp.441-457, 1986.

S. K. Sheppard, N. D. Mccarthy, D. Falush, and M. C. Maiden, Convergence of Campylobacter species: implications for bacterial evolution, Science, vol.320, pp.237-239, 2008.

Q. Shou, L. Feng, Y. Long, J. Han, J. K. Nunnery et al., A hybrid polyketide-nonribosomal peptide in nematodes that promotes larval survival, Nat Chem Biol, vol.12, pp.770-772, 2016.

C. Smillie, M. P. Garcillán-barcia, M. V. Francia, E. P. Rocha, F. Cruz et al., Mobility of plasmids. Microbiol Mol Biol Rev, vol.74, pp.434-452, 2010.

T. Smokvina, F. Boccard, J. Pernodet, A. Friedmann, and M. Guérineau, Functional analysis of the Streptomyces ambofaciens element pSAM2, Plasmid, vol.25, pp.40-52, 1991.

P. D. Sniegowski, P. J. Gerrish, and R. E. Lenski, Evolution of high mutation rates in experimental populations of E. coli, Nature, vol.387, pp.703-705, 1997.

R. R. Sokal and T. J. Crovello, The Biological Species Concept: A Critical Evaluation, The American Naturalist, vol.104, pp.127-153, 1970.

R. Sorek, V. Kunin, and P. Hugenholtz, CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea, Nat Rev Microbiol, vol.6, pp.181-186, 2008.

M. Sosio, H. Kloosterman, A. Bianchi, P. Vreugd, . De et al., Organization of the teicoplanin gene cluster in Actinoplanes teichomyceticus, Microbiology (Reading, Engl), vol.150, pp.95-102, 2004.

K. Spatz, H. Köhn, and M. Redenbach, Characterization of the Streptomyces violaceoruber SANK95570 plasmids pSV1 and pSV2, FEMS Microbiology Letters, vol.213, pp.87-92, 2002.

J. M. Spence, W. Mills, K. Mann, C. Huxley, and C. J. Farr, Increased missegregation and chromosome loss with decreasing chromosome size in vertebrate cells, Chromosoma, vol.115, pp.60-74, 2006.

E. Stackebrandt, W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kämpfer et al., 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

P. Stefanic and I. Mandic-mulec, Social Interactions and Distribution of Bacillus subtilis Pherotypes at Microscale, Journal of Bacteriology, vol.191, pp.1756-1764, 2009.

J. C. Stegen, X. Lin, J. K. Fredrickson, X. Chen, D. W. Kennedy et al., Quantifying community assembly processes and identifying features that impose them, ISME J, vol.7, pp.2069-2079, 2013.

H. W. Stokes and R. M. Hall, A novel family of potentially mobile DNA elements encoding sitespecific gene-integration functions: integrons, Mol Microbiol, vol.3, pp.1669-1683, 1989.

H. Suzuki, K. Marushima, Y. Ohnishi, and S. Horinouchi, 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.

D. M. Sylvia, Principles and applications of soil microbiology, 2005.

M. Syvanen, Evolutionary implications of horizontal gene transfer, Annu Rev Genet, vol.46, pp.341-358, 2012.

R. Szczepanowski, S. Braun, V. Riedel, S. Schneiker, I. Krahn et al., 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.

F. Taddei, M. Radman, J. Maynard-smith, B. Toupance, P. H. Gouyon et al., Role of mutator alleles in adaptive evolution, Nature, vol.387, pp.700-702, 1997.
URL : https://hal.archives-ouvertes.fr/hal-02122731

I. Tamas, L. Klasson, B. Canbäck, A. K. Näslund, A. Eriksson et al., million years of genomic stasis in endosymbiotic bacteria, Science, vol.296, pp.2376-2379, 2002.

L. Tang, S. Shah, L. Chung, J. Carney, L. Katz et al., Cloning and Heterologous Expression of the Epothilone Gene Cluster, Science, vol.287, pp.640-642, 2000.

A. Thibessard and P. Leblond, 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

L. Thoma and G. Muth, Conjugative DNA transfer in Streptomyces by TraB: is one protein enough?, FEMS Microbiol Lett, vol.337, pp.81-88, 2012.

L. Thoma and G. Muth, The conjugative DNA-transfer apparatus of Streptomyces, International Journal of Medical Microbiology, vol.305, pp.224-229, 2015.

C. M. Thomas and K. M. Nielsen, Mechanisms of, and barriers to, horizontal gene transfer between bacteria, Nat Rev Microbiol, vol.3, pp.711-721, 2005.

F. Thomas, T. Lefèvre, R. , and M. , Biologie évolutive, 2016.

A. Tidjani, J. Lorenzi, M. Toussaint, E. Dijk, . Van et al., Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics, MBio, vol.10, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02278804

A. Tidjani, J. Lorenzi, M. Toussaint, E. Dijk, . Van et al., Genome Sequences of 11 Conspecific Streptomyces sp, Strains. Microbiol Resour Announc, vol.8, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02292599

T. Uchida, M. Miyawaki, and H. Kinashi, Chromosomal Arm Replacement in Streptomyces griseus, J Bacteriol, vol.185, pp.1120-1124, 2003.

D. W. Udwary, L. Zeigler, R. N. Asolkar, V. Singan, A. Lapidus et al., Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica, Proc Natl Acad Sci, vol.104, pp.10376-10381, 2007.

S. Uroz, P. Oger, E. Morin, and P. Frey-klett, 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

P. Vandamme, B. Pot, M. Gillis, P. Vos, . De et al., Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol Rev, vol.60, pp.407-438, 1996.

G. Vernikos, D. Medini, D. R. Riley, and H. Tettelin, Ten years of pan-genome analyses, Curr Opin Microbiol, vol.23, pp.148-154, 2015.

K. Vetsigian, R. Jajoo, and R. Kishony, Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico, PLOS Biology, vol.9, p.1001184, 2011.

C. M. Vicente, A. Thibessard, J. Lorenzi, M. Benhadj, L. Hôtel et al., Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity. Antibiotics, p.7, 2018.

J. Vogel, P. Normand, J. Thioulouse, X. Nesme, and G. L. Grundmann, 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

J. Vogelmann, M. Ammelburg, C. Finger, J. Guezguez, D. Linke et al., Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE, EMBO J, vol.30, pp.2246-2254, 2011.

J. N. Volff, A. , and J. , A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution, FEMS Microbiol Lett, vol.186, pp.143-150, 2000.

M. Vos, C. Quince, A. S. Pijl, M. Hollander, and G. A. Kowalchuk, A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity, PLOS ONE, vol.7, p.30600, 2012.

M. Vos and G. J. Velicer, Isolation by Distance in the Spore-Forming Soil Bacterium Myxococcus xanthus, Current Biology, vol.18, pp.386-391, 2008.

M. Vos and G. J. Velicer, Social Conflict in Centimeter-and Global-Scale Populations of the Bacterium Myxococcus xanthus, Current Biology, vol.19, pp.1763-1767, 2009.

M. Vos, A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk, Micro-scale determinants of bacterial diversity in soil, FEMS Microbiology Reviews, vol.37, pp.936-954, 2013.

J. Vries and W. Wackernagel, 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.

S. A. Waksman, H. C. Reilly, and D. B. Johnstone, Isolation of Streptomycin-producing Strains of Streptomyces griseus12, J Bacteriol, vol.52, pp.393-397, 1946.

A. R. Wallace, Contributions to the Theory of Natural Selection: A Series of Essays, 1870.

C. T. Walsh, Combinatorial biosynthesis of antibiotics: challenges and opportunities, Chembiochem, vol.3, pp.125-134, 2002.

J. J. Wang and P. Bishop, 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.

L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. Grimont, O. Kandler et al., 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.

G. Weidlich, R. Wirth, and D. Galli, Sex pheromone plasmid pAD1-encoded surface exclusion protein of Enterococcus faecalis, Mol Gen Genet, vol.233, pp.161-168, 1992.

T. Wenner, V. Roth, G. Fischer, C. Fourrier, B. Aigle et al., 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

J. Wetterlind, B. Stenberg, and M. Söderström, 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.

R. J. Whitaker, D. W. Grogan, and J. W. Taylor, Geographic barriers isolate endemic populations of hyperthermophilic archaea, Science, vol.301, pp.976-978, 2003.

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes: The unseen majority, PNAS, vol.95, pp.6578-6583, 1998.

E. M. Widenbrant, H. Tsai, C. W. Chen, and C. M. Kao, Streptomyces coelicolor Undergoes Spontaneous Chromosomal End Replacement, J Bacteriol, vol.189, pp.9117-9121, 2007.

E. M. Widenbrant, H. Tsai, C. W. Chen, and C. M. Kao, Spontaneous Amplification of the Actinorhodin Gene Cluster in Streptomyces coelicolor Involving Native Insertion Sequence IS466, J Bacteriol, vol.190, pp.4754-4758, 2008.

J. Wiedenbeck and F. M. Cohan, Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches, FEMS Microbiology Reviews, vol.35, pp.957-976, 2011.

S. Wielgoss, J. E. Barrick, O. Tenaillon, S. Cruveiller, B. Chane-woon-ming et al., 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

S. Wielgoss, J. E. Barrick, O. Tenaillon, M. J. Wiser, W. J. Dittmar et al., 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

S. Wielgoss, F. Fiegna, O. Rendueles, Y. N. Yu, and G. J. Velicer, 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

M. Wietz, K. Duncan, N. V. Patin, and P. R. Jensen, Antagonistic interactions mediated by marine bacteria: the role of small molecules, J Chem Ecol, vol.39, pp.879-891, 2013.

C. R. Woese, Bacterial evolution, Microbiol Rev, vol.51, pp.221-271, 1987.

R. A. Wozniak and M. K. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nat Rev Microbiol, vol.8, pp.552-563, 2010.

D. A. Wright, K. Killham, L. A. Glover, and J. I. Prosser, Role of Pore Size Location in Determining Bacterial Activity during Predation by Protozoa in Soil, Appl Environ Microbiol, vol.61, pp.3537-3543, 1995.

S. Wright, The roles of mutation, inbreeding, crossbreeding and selection in evolution, Proceedings of the sixth international congress of Genetics, vol.1, pp.356-366, 1932.

K. Wu, L. Chung, W. P. Revill, L. Katz, and C. D. Reeves, 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.

M. Yamasaki and H. Kinashi, 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.

K. Yanai, T. Murakami, and M. Bibb, 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.

C. Yang, C. Huang, C. Li, Y. Tsay, S. Lee et al., 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.

M. Young and J. Cullum, A plausible mechanism for large-scale chromosomal DNA amplification in streptomycetes, FEBS Lett, vol.212, pp.10-14, 1987.

L. Zhao, L. Zhong, and Z. Qin, Two distinct conjugal transfer systems on Streptomyces plasmid pZL1, Acta Biochim Biophys Sin (Shanghai), vol.46, pp.1084-1086, 2014.

O. Zhaxybayeva, K. S. Swithers, P. Lapierre, G. P. Fournier, D. M. Bickhart et al., On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales, Proc Natl Acad Sci, vol.106, pp.5865-5870, 2009.

H. Zhou, L. Ning, H. Zhang, and F. Guo, 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.

N. Ziemert, A. Lechner, M. Wietz, N. Millán-aguiñaga, K. L. Chavarria et al., Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora, PNAS, vol.111, pp.1130-1139, 2014.

S. B. Zotchev, Genomics-Based Insights into the Evolution of Secondary Metabolite Biosynthesis in Actinomycete Bacteria, 2014.