1. Head, I. M., Jones, D. M. & Röling, W. F. M. Marine microorganisms make a meal of oil. Nat. Rev. Microbiol. 4, 173–182 (2006).

2. Keller, L. & Surette, M. G. Communication in bacteria: an ecological and evolutionary perspective. Nat. Rev. Microbiol. 4, 249–258 (2006).

3. Clardy, J., Fischbach, M. A. & Walsh, C. T. New antibiotics from bacterial natural products. Nat. Biotechnol. 24, 1541–1550 (2006).

4. Adams, B. L. The next generation of synthetic biology chassis: moving synthetic biology from the laboratory to the field. ACS Synth. Biol. 5, 1328–1330 (2016).

5. Dubnau, D. DNA uptake in bacteria. Annu. Rev. Microbiol. 53, 217–244 (1999).

6. Aune, T. E. V. & Aachmann, F. L. Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Appl. Microbiol. Biotechnol. 85, 1301–1313 (2010).

7. Johnston, C., Martin, B., Fichant, G., Polard, P. & Claverys, J.-P. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat. Rev. Microbiol. 12, 181–196 (2014).

8. Norman, A., Hansen, L. H. & Sørensen, S. J. Conjugative plasmids: vessels of the communal gene pool. Phil. Trans. R. Soc. B 364, 2275–2289 (2009).

9. Mazodier, P. & Davies, J. Gene transfer between distantly related bacteria. Annu. Rev. Genet. 25, 147–171 (1991).

10. Huddleston, J. R. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect. Drug Resist. 7, 167–176 (2014).

11. Shoeb, E. et al. Horizontal gene transfer of stress resistance genes through plasmid transport. World J. Microbiol. Biotechnol. 28, 1021–1025 (2012).

12. Frost, L. S., Leplae, R., Summers, A. O. & Toussaint, A. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3, 722–732 (2005).

13. Hoekema, A., Hirsch, P. R., Hooykaas, P. J. J. & Schilperoort, R. A. A binary plant vector strategy based on separation of vir- and T-region of the Agrobacterium tumefaciens Ti-plasmid. Nature 303, 179–180 (1983).

14. Simon, R., Priefer, U. & Pühler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Bio/Technology 1, 784–791 (1983).

15. Cuív, P. Ó. et al. Isolation of genetically tractable most-wanted bacteria by metaparental mating. Sci. Rep. 5, 13282 (2015).

16. Henschke, R. B. & Schmidt, F. R. J. Plasmid mobilization from genetically engineered bacteria to members of the indigenous soil microflora in situ. Curr. Microbiol. 20, 105–110 (1990).

17. Babic, A., Guérout, A.-M. & Mazel, D. Construction of an improved RP4 (RK2)-based conjugative system. Res. Microbiol. 159, 545–549 (2008).

18. Ferrières, L. et al. Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J. Bacteriol. 192, 6418–6427 (2010).

19. Strand, T. A., Lale, R., Degnes, K. F., Lando, M. & Valla, S. A new and improved host-independent plasmid system for RK2-based conjugal transfer. PLOS ONE 9, e90372 (2014).

20. Bañuelos-Vazquez, L. A., Tejerizo, G. T. & Brom, S. Regulation of conjugative transfer of plasmids and integrative conjugative elements. Plasmid 91, 82–89 (2017).

21. Roberts, A. P. & Mullany, P. A modular master on the move: the Tn916 family of mobile genetic elements. Trends Microbiol. 17, 251–258 (2009).

22. Lee, C. A., Auchtung, J. M., Monson, R. E. & Grossman, A. D. Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis. Mol. Microbiol. 66, 1356–1369 (2007).

23. Auchtung, J. M., Lee, C. A., Monson, R. E., Lehman, A. P. & Grossman, A. D. Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc. Natl Acad. Sci. USA 102, 12554–12559 (2005).

24. Auchtung, J. M., Lee, C. A., Garrison, K. L. & Grossman, A. D. Identification and characterization of the immunity repressor (ImmR) that controls the mobile genetic element ICEBs1 of Bacillus subtilis. Mol. Microbiol. 64, 1515–1528 (2007).

25. Auchtung, J. M., Lee, C. A. & Grossman, A. D. Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. J. Bacteriol. 188, 5273–5285 (2006).

26. Thomas, J., Lee, C. A. & Grossman, A. D. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element. PLoS Genet. 9, e1003198 (2013).

27. Wright, L. D., Johnson, C. M. & Grossman, A. D. Identification of a single strand origin of replication in the integrative and conjugative element ICEBs1 of Bacillus subtilis. PLoS Genet. 11, e1005556 (2015).

28. Leonetti, C. T. et al. Critical components of the conjugation machinery of the integrative and conjugative element ICEBs1 of Bacillus subtilis. J. Bacteriol. 197, 2558–2567 (2015).

29. DeWitt, T. & Grossman, A. D. The bifunctional cell wall hydrolase CwlT is needed for conjugation of the integrative and conjugative element ICEBs1 in Bacillus subtilis and B. anthracis. J. Bacteriol. 196, 1588–1596 (2014).

30. Lee, C. A., Thomas, J. & Grossman, A. D. The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J. Bacteriol. 194, 3165–3172 (2012).

31. Lee, C. A. & Grossman, A. D. Identification of the origin of transfer (oriT) and DNA relaxase required for conjugation of the integrative and conjugative element ICEBs1 of Bacillus subtilis. J. Bacteriol. 189, 7254–7261 (2007).

32. Chopra, I. & Roberts, M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev. 65, 232–260 (2001).

33. Horinouchi, S. & Weisblum, B. Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance. J. Bacteriol. 150, 815–825 (1982).

34. Bhavsar, A. P., Zhao, X. & Brown, E. D. Development and characterization of a xylose-dependent system for expression of cloned genes in Bacillus subtilis: conditional complementation of a teichoic acid mutant. Appl. Environ. Microbiol. 67, 403–410 (2001).

35. Wecke, J., Madela, K. & Fischer, W. The absence of d-alanine from lipoteichoic acid and wall teichoic acid alters surface charge, enhances autolysis and increases susceptibility to methicillin in Bacillus subtilis. Microbiology 143, 2953–2960 (1997).

36. Chung, Y. S. & Dubnau, D. ComC is required for the processing and translocation of comGC, a pilin-like competence protein of Bacillus subtilis. Mol. Microbiol. 15, 543–551 (1995).

37. Menard, K. L. & Grossman, A. D. Selective pressures to maintain attachment site specificity of integrative and conjugative elements. PLoS Genet. 9, e1003623 (2013).

38. Lee, C. A., Babic, A. & Grossman, A. D. Autonomous plasmid-like replication of a conjugative transposon. Mol. Microbiol. 75, 268–279 (2010).

39. Zhu, B. & Stülke, J. SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. Nucleic Acids Res. 46, D743–D748 (2018).

40. Leonhardt, H. & Alonso, J. C. Parameters affecting plasmid stability in Bacillus subtilis. Gene 103, 107–111 (1991).

41. Cardinale, S., Joachimiak, M. P. & Arkin, A. P. Effects of genetic variation on the E. coli host–circuit interface. Cell Rep. 4, 231–237 (2013).

42. Smanski, M. J. et al. Functional optimization of gene clusters by combinatorial design and assembly. Nat. Biotechnol. 32, 1241–1249 (2014).

43. Wang, L. et al. A minimal nitrogen fixation gene cluster from Paenibacillus sp. WLY78 enables expression of active nitrogenase in Escherichia coli. PLoS Genet. 9, e1003865 (2013).

44. Kushwaha, M. & Salis, H. M. A portable expression resource for engineering cross-species genetic circuits and pathways. Nat. Commun. 6, 7832 (2015).

45. Vieira, F. C. S. & Nahas, E. Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiol. Res. 160, 197–202 (2005).

46. Nielsen, A. A. & Voigt, C. A. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol. Syst. Biol. 10, 763 (2014).

47. Wang, K., Neumann, H., Peak-Chew, S. Y. & Chin, J. W. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25, 770–777 (2007).

48. Liu, C.C. et al. Toward an orthogonal central dogma. Nat. Chem. Bio. 14, 103–106 (2018).

49. Dereeper, A. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465–W469 (2008).

50. Das, S., Noe, J. C., Paik, S. & Kitten, T. An improved arbitrary primed PCR method for rapid characterization of transposon insertion sites. J. Microbiol. Methods 63, 89–94 (2005).