Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Design and regulation of engineered bacteria for environmental release

Nature Microbiology volume 10, pages 281–300 (2025)Cite this article

Subjects

A Publisher Correction to this article was published on 24 February 2025

This article has been updated

Abstract

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Applications of engineered bacteria that lead to environmental release.
Fig. 2: Paths to regulatory approval.
Fig. 3: Persistence of engineered bacteria in the field.
Fig. 4: Design principles to streamline regulatory approval.
Fig. 5: Advanced methods to improve genetic stability and biocontainment.
Fig. 6: Proposed regulatory structure for the release of engineered microbes.

Similar content being viewed by others

Change history

References

  1. Velkov, V. V. Environmental genetic engineering: hope or hazard? Curr. Sci. 70, 823–832 (1996).

    Google Scholar 

  2. Waltz, E. Small innovators advance microbes as alternatives to chemical crop sprays. Nat. Biotechnol. 41, 162–164 (2023).

    Article  CAS  PubMed  Google Scholar 

  3. Voigt, C. A. Synthetic biology 2020–2030: six commercially-available products that are changing our world. Nat. Commun. 11, 6379 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Gallup, O., Ming, H. & Ellis, T. Ten future challenges for synthetic biology. Eng. Biol. 5, 51–59 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Brooks, S. M. & Alper, H. S. Applications, challenges and needs for employing synthetic biology beyond the lab. Nat. Commun. 12, 1390 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Berg, P. & Singer, M. F. The recombinant DNA controversy: twenty years later. Proc. Natl Acad. Sci. USA 92, 9011–9013 (1995).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Goeddel, D. V. et al. Direct expression in Escherichia coli of a DNA sequence coding for human growth hormone. Nature 281, 544–548 (1979).

    Article  CAS  PubMed  Google Scholar 

  8. Mbanya, J. C., Sandow, J., Landgraf, W. & Owens, D. R. Recombinant human insulin in global diabetes management–focus on clinical efficacy. Eur. Endocrinol. 13, 21–25 (2017).

    PubMed  PubMed Central  Google Scholar 

  9. Chakrabarty, A. M. Microorganisms having multiple compatible degradative energy-generating plasmids and preparation thereof. US patent US4,259,444A (1972).

  10. Wrubel, R. P., Krimsky, S. & Anderson, M. D. Regulatory oversight of genetically engineered microorganisms: has regulation inhibited innovation? Environ. Manag. 21, 571–586 (1997).

    Article  CAS  Google Scholar 

  11. Carter, S. R., Rodemeyer, M., Garfinkel, M. S. & Friedman, R. M. Synthetic Biology and the US Biotechnology Regulatory System: Challenges and Options (J. Craig Venter Institute, 2014).

  12. National Academies of Sciences, Engineering & Medicine. in Preparing for Future Products of Biotechnology 72 (National Academies Press, 2017).

  13. Environmental Protection Agency—Office of Pollution Prevention and Toxics. Points to Consider in the Preparation of TSCA Biotechnology Submissions for Microorganisms (EPA, 1997); https://www.epa.gov/sites/default/files/2015-08/documents/biotech_points_to_consider.pdf

  14. Environmental Protection Agency. in Pesticide Registration Manual Ch. 3 (EPA, 2024); https://www.epa.gov/pesticide-registration/pesticide-registration-manual-chapter-3-additional-considerations

  15. US Government Biotechnology Working Group. Modernizing the Regulatory System for Biotechnology Products: Final Version of the 2017 Update to the Coordinated Framework for the Regulation of Biotechnology (EPA, 2017); https://www.epa.gov/sites/default/files/2017-01/documents/2017_coordinated_framework_update.pdf

  16. Coordinated Framework for Regulation of Biotechnology. Report No. FR 23302 (Office of Science and Technology Policy, 1986).

  17. Wozniak, C. A., McClung, G., Gagliardi, J., Segal, M. & Matthews, K. in Regulation of Agricultural Biotechnology: the United States and Canada (eds Wozniak, C. A. & McHughen, A.) Ch. 4, 57–94 (Springer, 2012); https://doi.org/10.1007/978-94-007-2156-2_4 (2012).

  18. Microbial Pesticides Data Requirements. Code of Federal Regulations (United States Government Publishing Office, 2020); https://www.govinfo.gov/app/details/CFR-2020-title40-vol26/CFR-2020-title40-vol26-sec158-2110

  19. US Department of Agriculture, Animal and Plant Health Inspection Service. Guide for Submitting Permit Applications for Microorganisms Developed Using Genetic Engineering Under 7 CFR part 340 (US Department of Agriculture, 2023); https://www.aphis.usda.gov/biotechnology/downloads/draft-brs-microbe-permit-guide.pdf

  20. US Department of Agriculture, Animal and Plant Inspection Service. Laws and Regulations (US Department of Agriculture, 2024); https://www.aphis.usda.gov/laws-regs

  21. Council on Environmental Quality Executive Office of the President. A Citizen’s Guide to the NEPA. Having Your Voice Heard (US Department of Envornment, 2007); https://ceq.doe.gov/docs/get-involved/Citizens_Guide_Dec07.pdf

  22. US Food and Drug Administration. What We Do (ES EPA, 2023); https://www.fda.gov/about-fda/what-we-do#:~:text=Information%20for%20Consumers-,FDA%20Mission,and%20products%20that%20emit%20radiation

  23. Hoffman, N. E. Revisions to USDA biotechnology regulations: the SECURE rule. Proc. Natl Acad. Sci. USA 118, e2004841118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Graham, A. E. & Ledesma-Amaro, R. The microbial food revolution. Nat. Commun. 14, 2231 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. US Food & Drug Administration. Center for Biologics Evaluation and Research (CBER) (US FDA, 2024); https://www.fda.gov/about-fda/fda-organization/center-biologics-evaluation-and-research-cber

  26. US Food & Drug Administration. Generally Recognized as Safe (GRAS) (US FDA, 2023); https://www.fda.gov/food/food-ingredients-packaging/generally-recognized-safe-gras

  27. McCold, L. N. & Saulsbury, J. W. Defining the no-action alternative for national environmental policy act analyses of continuing actions. Environ. Impact Assess. Rev. 18, 15–37 (1998).

    Article  Google Scholar 

  28. Wang, W. et al. Harnessing the hygroscopic and biofluorescent behaviors of genetically tractable microbial cells to design biohybrid wearables. Sci. Adv. 3, e1601984 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Manfredini, A. et al. Current methods, common practices, and perspectives in tracking and monitoring bioinoculants in soil. Front. Microbiol. 12, 698491 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  30. Van Elsas, J., Duarte, G., Rosado, A. & Smalla, K. Microbiological and molecular biological methods for monitoring microbial inoculants and their effects in the soil environment. J. Microbiol. Methods 32, 133–154 (1998).

    Article  Google Scholar 

  31. Corich, V. et al. Aspects of marker/reporter stability and selectivity in soil microbiology. Microb. Ecol. 41, 333–340 (2001).

    Article  CAS  PubMed  Google Scholar 

  32. Rastogi, G., Tech, J. J., Coaker, G. L. & Leveau, J. H. J. A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments. J. Microbiol. Methods 83, 127–132 (2010).

    Article  CAS  PubMed  Google Scholar 

  33. Techtmann, S. M. & Hazen, T. C. Metagenomic applications in environmental monitoring and bioremediation. J. Ind. Microbiol. Biotechnol. 43, 1345–1354 (2016).

    Article  CAS  PubMed  Google Scholar 

  34. Shen, J., McFarland, A. G., Young, V. B., Hayden, M. K. & Hartmann, E. M. Toward accurate and robust environmental surveillance using metagenomics. Front. Genet. 12, 600111 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Recorbet, G. et al. Conditional suicide system of Escherichia coli released into soil that uses the Bacillus subtilis sacB gene. Appl. Environ. Microbiol. 59, 1361–1366 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Scanferlato, V. S., Orvos, D. R., Cairns, J. & Lacy, G. H. Genetically engineered Erwinia carotovora in aquatic microcosms: survival and effects on functional groups of indigenous bacteria. Appl. Environ. Microbiol. 55, 1477–1482 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Franz, E. et al. Manure-amended soil characteristics affecting the survival of E. coli O157:H7 in 36 Dutch soils. Environ. Microbiol. 10, 313–327 (2008).

    Article  CAS  PubMed  Google Scholar 

  38. Matz, C. & Kjelleberg, S. Off the hook—how bacteria survive protozoan grazing. Trends Microbiol. 13, 302–307 (2005).

    Article  CAS  PubMed  Google Scholar 

  39. Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Dillewijn, P. V., Villadas, P. J. & Toro, N. Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa. Appl. Environ. Microbiol. 68, 4201–4208 (2002).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Iwasaki, K., Uchiyama, H. & Yagi, O. Survival and impact of genetically engineered Pseudomonas putida harboring mercury resistance gene in aquatic microcosms. Biosci. Biotechnol. Biochem. 57, 1264–1269 (1993).

    Article  CAS  PubMed  Google Scholar 

  42. Glandorf, D. C. M. et al. Effect of genetically modified Pseudomonas putida WCS358r on the fungal rhizosphere microflora of field-grown wheat. Appl. Environ. Microbiol. 67, 3371–3378 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Zhang, X., Nesme, J., Simonet, P. & Frostegård, Å. Fate of invading bacteria in soil and survival of transformants after simulated uptake of transgenes, as evaluated by a model system based on lindane degradation. Res. Microbiol. 163, 200–210 (2012).

    Article  CAS  PubMed  Google Scholar 

  44. Nuti, M. et al. in Ecological Impact of GMO Dissemination in Agro-Ecosystems (eds Lelley, T. et al.) 45–54 (Facultas Verlags-und Buchhandels, 2002).

  45. Ripp, S. et al. Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control. Environ. Sci. Technol. 34, 846–853 (2000).

    Article  CAS  Google Scholar 

  46. Hirsch, P. R. Population dynamics of indigenous and genetically modified rhizobia in the field. N. Phytol. 133, 159–171 (1996).

    Article  Google Scholar 

  47. Corich, V. et al. Long term evaluation of field-released genetically modified rhizobia. Environ. Biosaf. Res. 6, 167–181 (2007).

    Article  CAS  Google Scholar 

  48. McBee, R. M. et al. Engineering living and regenerative fungal–bacterial biocomposite structures. Nat. Mater. 21, 471–478 (2022).

    Article  CAS  PubMed  Google Scholar 

  49. De Leij, F. A. A. M., Sutton, E. J., Whipps, J. M., Fenlon, J. S. & Lynch, J. M. Field release of a genetically modified Pseudomonas fluorescens on wheat: establishment, survival and dissemination. Nat. Biotechnol. 13, 1488–1492 (1995).

    Article  Google Scholar 

  50. Wiehe, W. & Höflich, G. Survival of plant growth promoting rhizosphere bacteria in the rhizosphere of different crops and migration to non-inoculated plants under field conditions in north-east Germany. Microbiol. Res. 150, 201–206 (1995).

    Article  Google Scholar 

  51. Kluepfel, D., Kline, E., Skipper, H., Hughes, T. & Gooden, D. The release and tracking of genetically engineered bacteria in the environment. Phytopathology 81, 348–352 (1991).

    Google Scholar 

  52. Jäderlund, L., Hellman, M., Sundh, I., Bailey, M. J. & Jansson, J. K. Use of a novel nonantibiotic triple marker gene cassette to monitor high survival of Pseudomonas fluorescens SBW25 on winter wheat in the field. FEMS Microbiol. Ecol. 63, 156–168 (2008).

    Article  PubMed  Google Scholar 

  53. Shaw, J. J., Dane, F., Geiger, D. & Kloepper, J. W. Use of bioluminescence for detection of genetically engineered microorganisms released into the environment. Appl. Environ. Microbiol. 58, 267–273 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Brown, G. G., Doube, B. M. & Edwards, C. Functional interactions between earthworms, microorganisms, organic matter and plants. Earthworm Ecol. 2, 213–239 (2004).

    Google Scholar 

  55. Singer, A. C., Jury, W., Luepromchai, E., Yahng, C. S. & Crowley, D. E. Contribution of earthworms to PCB bioremediation. Soil Biol. Biochem. 33, 765–776 (2001).

    Article  CAS  Google Scholar 

  56. Abu-Ashour, J. & Lee, H. Transport of bacteria on sloping soil surfaces by runoff. Environ. Toxicol. 15, 149–153 (2000).

    Article  CAS  Google Scholar 

  57. Meola, M., Lazzaro, A. & Zeyer, J. Bacterial composition and survival on Sahara dust particles transported to the European Alps. Front. Microbiol. 6, 1454 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Gorbushina, A. A. et al. Life in Darwin’s dust: intercontinental transport and survival of microbes in the nineteenth century. Environ. Microbiol. 9, 2911–2922 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Kolmer, J. A. Tracking wheat rust on a continental scale. Curr. Opin. Plant Biol. 8, 441–449 (2005).

    Article  PubMed  Google Scholar 

  60. Ford, C. Z., Sayler, G. S. & Burlage, R. S. Containment of a genetically engineered microorganism during a field bioremediation application. Appl. Microbiol. Biotechnol. 51, 397–400 (1999).

    Article  CAS  PubMed  Google Scholar 

  61. Mancinelli, R. L. & Shulls, W. A. Airborne bacteria in an urban environment. Appl. Environ. Microbiol. 35, 1095–1101 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Tong, X., Leung, M. H., Wilkins, D. & Lee, P. K. City-scale distribution and dispersal routes of mycobiome in residences. Microbiome 5, 131 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Gattinger, D., Schlenz, V., Weil, T. & Sattler, B. From remote to urbanized: dispersal of antibiotic-resistant bacteria under the aspect of anthropogenic influence. Sci. Total Environ. 924, 171532 (2024).

    Article  CAS  PubMed  Google Scholar 

  64. Mhuireach, G. et al. Urban greenness influences airborne bacterial community composition. Sci. Total Environ. 571, 680–687 (2016).

    Article  CAS  PubMed  Google Scholar 

  65. Zurek, L. & Ghosh, A. Insects represent a link between food animal farms and the urban environment for antibiotic resistance traits. Appl. Environ. Microbiol. 80, 3562–3567 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Arnold, K. E., Williams, N. J. & Bennett, M. ‘Disperse abroad in the land’: the role of wildlife in the dissemination of antimicrobial resistance. Biol. Lett. 12, 20160137 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Bankhead, S. B., Landa, B. B., Lutton, E., Weller, D. M. & Gardener, B. B. M. Minimal changes in rhizobacterial population structure following root colonization by wild type and transgenic biocontrol strains. FEMS Microbiol. Ecol. 49, 307–318 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Lindow, S. E. Competitive exclusion of epiphytic bacteria by Ice−Pseudomonas syringae mutants. Appl. Environ. Microbiol. 53, 2520–2527 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Schwieger, F. & Tebbe, C. C. Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant Medicago sativa and a non-target plant Chenopodium album—linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl. Environ. Microbiol. 66, 3556–3565 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Xiong, M., Hu, Z., Zhang, Y., Cheng, X. & Li, C. Survival of GFP-tagged Rhodococcus sp. D310-1 in chlorimuron-ethyl-contaminated soil and its effects on the indigenous microbial community. J. Hazard. Mater. 252-253, 347–354 (2013).

    Article  CAS  PubMed  Google Scholar 

  71. Mawarda, P. C., Le Roux, X., Dirk van Elsas, J. & Salles, J. F. Deliberate introduction of invisible invaders: a critical appraisal of the impact of microbial inoculants on soil microbial communities. Soil Biol. Biochem. 148, 107874 (2020).

    Article  CAS  Google Scholar 

  72. Philippot, L., Griffiths, B. S. & Langenheder, S. Microbial community resilience across ecosystems and multiple disturbances. Microbiol. Mol. Biol. Rev. https://doi.org/10.1128/mmbr.00026-20 (2021).

  73. Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 417 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Lawson, C. E. et al. Common principles and best practices for engineering microbiomes. Nat. Rev. Microbiol. 17, 725–741 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Gómez Expósito, R., de Bruijn, I., Postma, J. & Raaijmakers, J. M. Current insights into the role of rhizosphere bacteria in disease suppressive soils. Front. Microbiol. 8, 2529 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  76. van Elsas, J. D. et al. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc. Natl Acad. Sci. USA 109, 1159–1164 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Rizzo, L. et al. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. Sci. Total Environ. 447, 345–360 (2013).

    Article  CAS  PubMed  Google Scholar 

  79. Andersen, J. T., Schäfer, T., Jørgensen, P. L. & Møller, S. Using inactivated microbial biomass as fertilizer: the fate of antibiotic resistance genes in the environment. Res. Microbiol. 152, 823–833 (2001).

    Article  CAS  PubMed  Google Scholar 

  80. Peters, M. et al. Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl. Environ. Microbiol. 63, 4899–4906 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. National Research Council; Division on Earth and Life Studies; Commission on Life Sciences; Committee on Scientific Evaluation of the Introduction of Genetically Modified Microorganisms and Plants into the Environment. Field Testing Genetically Modified Organisms: Framework for Decisions (The National Academies Press, 1989).

  82. Lilley, A. K. & Bailey, M. J. The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl. Environ. Microbiol. 63, 1577–1583 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Munck, C., Sheth, R. U., Freedberg, D. E. & Wang, H. H. Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform. Nat. Commun. 11, 95 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Allgeier, S., Friedrich, A. & Brühl, C. A. Mosquito control based on Bacillus thuringiensis israelensis (Bti) interrupts artificial wetland food chains. Sci. Total Environ. 686, 1173–1184 (2019).

    Article  CAS  PubMed  Google Scholar 

  85. Hernández-Rodríguez, C. S., de Escudero, I. R., Asensio, A. C., Ferré, J. & Caballero, P. Encapsulation of the Bacillus thuringiensis secretable toxins Vip3Aa and Cry1Ia in Pseudomonas fluorescens. Biol. Control 66, 159–165 (2013).

    Article  Google Scholar 

  86. Code of Federal Regulations, CFR § 158.2150—Microbial Pesticides Nontarget Organisms and Environmental Fate Data Requirements Table (National Archives, 2015); https://www.ecfr.gov/current/title-40/chapter-I/subchapter-E/part-158/subpart-V/section-158.2150 (2015).

  87. US Environmental Protection Agency. OCSPP Harmonized Test Guidelines—Master List (US EPA, 2019); https://www.epa.gov/sites/default/files/2019-10/documents/ocspp-testguidelines_masterlist-2019-09-24.pdf

  88. Rathinam, M., Singh, S., Pattanayak, D. & Sreevathsa, R. Comprehensive in silico allergenicity assessment of novel protein engineered chimeric Cry proteins for safe deployment in crops. BMC Biotechnol. 17, 64 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Wozniak, C. & Kough, J. Regulation of transgenic forage grasses under the proposed plant-pesticide rule. In Proc. Thirty Sixth Grass Breeders’ Work Planning Conference 18–24 (The Noble Foundation, 2000).

  90. Environmental Protection Agency. Status Report: TSCA Biotechnology Submissions for Fiscal Years 87–98 (US EPA, 1999); https://www.epa.gov/sites/default/files/2016-05/documents/bistat98.pdf

  91. Miller, T. A. in Regulation of Agricultural Biotechnology: The United States and Canada (eds Wozniak, C. A. & McHughen, A.) 103–122 (Springer, 2012).

  92. Kerr, A. & Bullard, G. Biocontrol of crown gall by Rhizobium rhizogenes: challenges in biopesticide commercialisation. Agronomy 10, 1126 (2020).

    Article  CAS  Google Scholar 

  93. Arana, I. et al. Effect of temperature and starvation upon survival strategies of Pseudomonas fluorescens CHA0: comparison with Escherichia coli. FEMS Microbiol. Ecol. 74, 500–509 (2010).

    Article  CAS  PubMed  Google Scholar 

  94. Winnenburg, R. et al. PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 34, D459–D464 (2006).

    Article  CAS  PubMed  Google Scholar 

  95. Bartoszewicz, J. M., Seidel, A., Rentzsch, R. & Renard, B. Y. DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. Bioinformatics 36, 81–89 (2020).

    Article  CAS  PubMed  Google Scholar 

  96. Cosentino, S., Voldby Larsen, M., Møller Aarestrup, F. & Lund, O. PathogenFinder—distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE 8, e77302 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Sperschneider, J. Machine learning in plant-pathogen interactions: empowering biological predictions from field scale to genome scale. N. Phytol. 228, 35–41 (2020).

    Article  Google Scholar 

  98. Hays, S. G., Patrick, W. G., Ziesack, M., Oxman, N. & Silver, P. A. Better together: engineering and application of microbial symbioses. Curr. Opin. Biotechnol. 36, 40–49 (2015).

    Article  CAS  PubMed  Google Scholar 

  99. McCarty, N. S. & Ledesma-Amaro, R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol. 37, 181–197 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Pivot Bio. PROVEN40 Safety Data Sheet (Pivot Bio, 2023); https://www.pivotbio.com/hubfs/Safety%20Data%20Sheets/2022%20SDS-Pivot%20Bio%20PROVEN40%20LIF.pdf

  101. Baghapour, M. A., Nasseri, S. & Derakhshan, Z. Atrazine removal from aqueous solutions using submerged biological aerated filter. J. Environ. Health Sci. Eng. 11, 6 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  102. Mnif, I. et al. Biodegradation of diesel oil by a novel microbial consortium: comparison between co-inoculation with biosurfactant-producing strain and exogenously added biosurfactants. Environ. Sci. Pollut. Res. 22, 14852–14861 (2015).

    Article  CAS  Google Scholar 

  103. Rawlings, D. E. & Johnson, D. B. The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153, 315–324 (2007).

    Article  CAS  PubMed  Google Scholar 

  104. Cheng, A. G. et al. Design, construction and in vivo augmentation of a complex gut microbiome. Cell https://doi.org/10.1016/j.cell.2022.08.003 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  105. Bhagwat, A. A. & Keister, D. L. Improved inoculant strains of Bradyrhizobium japonicum. PCT patent WO2001038492A1 (2000).

  106. Halperin, S. O. et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560, 248–252 (2018).

    Article  CAS  PubMed  Google Scholar 

  107. Zhang, Y.-X. et al. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415, 644–646 (2002).

    Article  CAS  PubMed  Google Scholar 

  108. Gong, J., Zheng, H., Wu, Z., Chen, T. & Zhao, X. Genome shuffling: progress and applications for phenotype improvement. Biotechnol. Adv. 27, 996–1005 (2009).

    Article  PubMed  Google Scholar 

  109. Bloch, S. E. et al. Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph. J. Exp. Bot. 71, 4591–4603 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Jones, D. A., Ryder, M. H., Clare, B. G., Farrand, S. K. & Kerr, A. Construction of a Tra− deletion mutant of pAgK84 to safeguard the biological control of crown gall. Mol. Gen. Genet. MGG 212, 207–214 (1988).

    Article  CAS  Google Scholar 

  111. 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).

    Article  CAS  PubMed  Google Scholar 

  112. US Environmental Protection Agency. TSCA Biotechnology Notifications Status for Cases Reviewed Prior to June 22, 2016 (US EPA, 2024); https://www.epa.gov/regulation-biotechnology-under-tsca-and-fifra/tsca-biotechnology-notifications-status-cases

  113. Wen, A. et al. Enabling biological nitrogen fixation for cereal crops in fertilized fields. ACS Synth. Biol. 10, 3264–3277 (2021).

    Article  CAS  PubMed  Google Scholar 

  114. Hmelo, L. R. et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange. Nat. Protoc. 10, 1820–1841 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z. & Hwa, T. Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099–1102 (2010).

    Article  CAS  PubMed  Google Scholar 

  116. Sleight, S. C., Bartley, B. A., Lieviant, J. A. & Sauro, H. M. Designing and engineering evolutionary robust genetic circuits. J. Biol. Eng. 4, 12 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  117. Shen, P. & Huang, H. V. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112, 441–457 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Menuhin-Gruman, I. et al. Evolutionary Stability Optimizer (ESO): a novel approach to identify and avoid mutational hotspots in DNA sequences while maintaining high expression levels. ACS Synth. Biol. 11, 1142–1151 (2022).

    Article  CAS  PubMed  Google Scholar 

  119. Jack, B. R. et al. Predicting the genetic stability of engineered DNA sequences with the EFM calculator. ACS Synth. Biol. 4, 939–943 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Blazejewski, T., Ho, H.-I. & Wang, H. H. Synthetic sequence entanglement augments stability and containment of genetic information in cells. Science 365, 595–598 (2019).

    Article  CAS  PubMed  Google Scholar 

  121. Posfai, G. et al. Emergent properties of reduced-genome Escherichia coli. Science 312, 1044–1046 (2006).

    Article  PubMed  Google Scholar 

  122. Csörgő, B., Fehér, T., Tímár, E., Blattner, F. R. & Pósfai, G. Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs. Microb. Cell Factories 11, 11 (2012).

    Article  Google Scholar 

  123. Unthan, S. et al. Chassis organism from Corynebacterium glutamicum–a top‐down approach to identify and delete irrelevant gene clusters. Biotechnol. J. 10, 290–301 (2015).

    Article  CAS  PubMed  Google Scholar 

  124. Komatsu, M., Uchiyama, T., Ōmura, S., Cane, D. E. & Ikeda, H. Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc. Natl Acad. Sci. USA 107, 2646–2651 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Shen, X. et al. Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites. BMC Genomics 18, 715 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Reuß, D. R., Commichau, F. M., Gundlach, J., Zhu, B. & Stülke, J. The blueprint of a minimal cell: MiniBacillus. Microbiol. Mol. Biol. Rev. 80, 955–987 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  127. Sturino, J. M. & Klaenhammer, T. R. Engineered bacteriophage-defence systems in bioprocessing. Nat. Rev. Microbiol. 4, 395–404 (2006).

    Article  CAS  PubMed  Google Scholar 

  128. Suttle, C. A. Marine viruses–major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007).

    Article  CAS  PubMed  Google Scholar 

  129. Ashelford, K. E., Day, M. J. & Fry, J. C. Elevated abundance of bacteriophage infecting bacteria in soil. Appl. Environ. Microbiol. 69, 285–289 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Ofir, G. et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat. Microbiol. 3, 90–98 (2018).

    Article  CAS  PubMed  Google Scholar 

  131. Lopatina, A., Tal, N. & Sorek, R. Abortive infection: bacterial suicide as an antiviral immune strategy. Annu. Rev. Virol. 7, 371–384 (2020).

    Article  CAS  PubMed  Google Scholar 

  132. Shen, Q., Zhou, X.-T., Guo, Q., Xue, Y.-P. & Zheng, Y.-G. Engineering laboratory/factory-specific phage-resistant strains of Escherichia coli by mutagenesis and screening. World J. Microbiol. Biotechnol. 38, 51 (2022).

    Article  CAS  PubMed  Google Scholar 

  133. Mutalik, V. K. et al. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol. 18, e3000877 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Tan, D. et al. A frameshift mutation in wcaJ associated with phage resistance in Klebsiella pneumoniae. Microorganisms 8, 378 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Cai, R. et al. A smooth-type, phage-resistant Klebsiella pneumoniae mutant strain reveals that OmpC is indispensable for infection by phage GH-K3. Appl. Environ. Microbiol. 84, e01585–01518 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Zheng, K. et al. Highly efficient base editing in bacteria using a Cas9-cytidine deaminase fusion. Commun. Biol. 1, 32 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  137. Hutton, P. O., Schneider, W. R. & Rispin, A. S. US EPA, Office of Pesticide Programs Memorandum: Classification of Killed Microbial Pesticides (US EPA, 1989).

  138. Strong, L. C., McTavish, H., Sadowsky, M. J. & Wackett, L. P. Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environ. Microbiol. 2, 91–98 (2000).

    Article  CAS  PubMed  Google Scholar 

  139. Fan, C. et al. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc. Natl Acad. Sci. USA 117, 6752–6761 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Qian, J. et al. Barcoded microbial system for high-resolution object provenance. Science 368, 1135–1140 (2020).

    Article  CAS  PubMed  Google Scholar 

  141. Silverman, A. D., Akova, U., Alam, K. K., Jewett, M. C. & Lucks, J. B. Design and optimization of a cell-free atrazine biosensor. ACS Synth. Biol. 9, 671–677 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Chemla, Y., Ozer, E., Schlesinger, O., Noireaux, V. & Alfonta, L. Genetically expanded cell-free protein synthesis using endogenous pyrrolysyl orthogonal translation system. Biotechnol. Bioeng. 112, 1663–1672 (2015).

    Article  CAS  PubMed  Google Scholar 

  143. Pardee, K. et al. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165, 1255–1266 (2016).

    Article  CAS  PubMed  Google Scholar 

  144. Tang, T.-C. et al. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nat. Chem. Biol. 17, 724–731 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Lin, G.-M. & Voigt, C. A. Design of a redox-proficient Escherichia coli for screening terpenoids and modifying cytochrome P450s. Nat. Catal. 6, 1016–1029 (2023).

    Article  CAS  Google Scholar 

  146. Sayler, G. S. et al. Field Application of a Genetically Engineered Microorganism for Polycyclic Aromatic Hydrocarbon Bioremediation Process Monitoring and Control (Springer, 1999).

  147. Belkin, S. et al. Remote detection of buried landmines using a bacterial sensor. Nat. Biotechnol. 35, 308–310 (2017).

    Article  CAS  PubMed  Google Scholar 

  148. Gallagher, R. R., Patel, J. R., Interiano, A. L., Rovner, A. J. & Isaacs, F. J. Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res. 43, 1945–1954 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Steidler, L. et al. Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10. Nat. Biotechnol. 21, 785–789 (2003).

    Article  CAS  PubMed  Google Scholar 

  150. Adolfsen, K. J. et al. Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering. Nat. Commun. 12, 6215 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Lubkowicz, D. et al. An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria. Mol. Syst. Biol. 18, e10539 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Arnaouteli, S., Bamford, N. C., Stanley-Wall, N. R. & Kovács, Á. T. Bacillus subtilis biofilm formation and social interactions. Nat. Rev. Microbiol. 19, 600–614 (2021).

    Article  CAS  PubMed  Google Scholar 

  153. US Environmental Protection Agency Office of Inspector General. Science to Support Rulemaking Report 2003-P-00003 (addendum) (US EPA, 2002); https://www.epa.gov/sites/default/files/2015-12/documents/ssrulemakingaddendum.pdf

  154. US Environmental Protection Agency Office of Pollution Prevention and Toxics. TSCA Experimental Release Application Approved for Pseudomonas putida Strains fact sheet (US EPA); https://www.epa.gov/regulation-biotechnology-under-tsca-and-fifra/tsca-experimental-release-application-approved-0

  155. Sikorski, J., Graupner, S., Lorenz, M. G. & Wackernagel, W. Natural genetic transformation of Pseudomonas stutzeri in a non-sterile soil. Microbiology 144, 569–576 (1998).

    Article  CAS  PubMed  Google Scholar 

  156. Asin-Garcia, E. et al. Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida. Microb. Cell Fact. 21, 156 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Gay, P., Le Coq, D., Steinmetz, M., Berkelman, T. & Kado, C. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164, 918–921 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Hayashi, N., Lai, Y., Fuerte-Stone, J., Mimee, M. & Lu, T. K. Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements. Nat. Commun. 15, 2096 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Lee, J. W., Chan, C. T. Y., Slomovic, S. & Collins, J. J. Next-generation biocontainment systems for engineered organisms. Nat. Chem. Biol. 14, 530–537 (2018).

    Article  CAS  PubMed  Google Scholar 

  160. Kim, D. & Lee, J. W. Genetic biocontainment systems for the safe use of engineered microorganisms. Biotechnol. Bioprocess Eng. 25, 974–984 (2020).

    Article  CAS  Google Scholar 

  161. Ishikawa, M., Kojima, T. & Hori, K. Development of a biocontained toluene-degrading bacterium for environmental protection. Microbiol. Spectrum 9, 10.1128/spectrum.00259-00221 (2021).

  162. Molin, S. et al. Conditional suicide system for containment of bacteria and plasmids. Nat. Biotechnol. 5, 1315–1318 (1987).

    Article  CAS  Google Scholar 

  163. Contreras, A., Molin, S. & Ramos, J.-L. Conditional-suicide containment system for bacteria which mineralize aromatics. Appl. Environ. Microbiol. 57, 1504–1508 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Bej, A. K., Perlin, M. H. & Atlas, R. M. Model suicide vector for containment of genetically engineered microorganisms. Appl. Environ. Microbiol. 54, 2472–2477 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Rottinghaus, A. G., Ferreiro, A., Fishbein, S. R. S., Dantas, G. & Moon, T. S. Genetically stable CRISPR-based kill switches for engineered microbes. Nat. Commun. 13, 672 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Caliando, B. J. & Voigt, C. A. Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nat. Commun. 6, 6989 (2015).

    Article  CAS  PubMed  Google Scholar 

  167. Chan, C. T. Y., Lee, J. W., Cameron, D. E., Bashor, C. J. & Collins, J. J. ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nat. Chem. Biol. 12, 82–86 (2016).

    Article  CAS  PubMed  Google Scholar 

  168. Halvorsen, T. M., Ricci, D. P., Park, D. M., Jiao, Y. & Yung, M. C. Comparison of kill switch toxins in plant-beneficial Pseudomonas fluorescens reveals drivers of lethality, stability and escape. ACS Synth. Biol. 11, 3785–3796 (2022).

    Article  CAS  PubMed  Google Scholar 

  169. Yaung, S. J. et al. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Mol. Syst. Biol. 11, 788 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  170. Kong, W. et al. Regulated programmed lysis of recombinant Salmonella in host tissues to release protective antigens and confer biological containment. Proc. Natl Acad. Sci. USA 105, 9361–9366 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Garson, J. et al. Detection of hepatitis C viral sequences in blood donations by ‘nested’ polymerase chain reaction and prediction of infectivity. Lancet 335, 1419–1422 (1990).

    Article  CAS  PubMed  Google Scholar 

  172. Jasinska, W. et al. Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution. Nat. Ecol. Evol. 4, 437–452 (2020).

    Article  PubMed  Google Scholar 

  173. Ahrenholtz, I., Lorenz, M. G. & Wackernagel, W. A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA. Appl. Environ. Microbiol. 60, 3746–3751 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Zürcher, J. F. et al. Refactored genetic codes enable bidirectional genetic isolation. Science 378, 516–523 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  175. Liu, C. C., Jewett, M. C., Chin, J. W. & Voigt, C. A. Toward an orthogonal central dogma. Nat. Chem. Biol. 14, 103–106 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  176. Rackham, O. & Chin, J. W. A network of orthogonal ribosome·mRNA pairs. Nat. Chem. Biol. 1, 159–166 (2005).

    Article  CAS  PubMed  Google Scholar 

  177. Schmidt, M. & de Lorenzo, V. Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett. 586, 2199–2206 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Zhang, Y. et al. A semi-synthetic organism that stores and retrieves increased genetic information. Nature 551, 644–647 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Fan, C., Deng, Q. & Zhu, T. F. Bioorthogonal information storage in l-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-00969-6 (2021).

    Article  PubMed  Google Scholar 

  180. Xu, Y. & Zhu, T. F. Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Science 378, 405–412 (2022).

    Article  CAS  PubMed  Google Scholar 

  181. Schmidt, M. & de Lorenzo, V. Synthetic bugs on the loose: containment options for deeply engineered (micro) organisms. Curr. Opin. Biotechnol. 38, 90–96 (2016).

    Article  CAS  PubMed  Google Scholar 

  182. Sanders, M. E. & Klaenhammer, T. R. Characterization of phage-sensitive mutants from a phage-insensitive strain of Streptococcus lactis: evidence for a plasmid determinant that prevents phage adsorption. Appl. Environ. Microbiol. 46, 1125–1133 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Zou, X. et al. Systematic strategies for developing phage resistant Escherichia coli strains. Nat. Commun. 13, 4491 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Vassallo, C. N., Doering, C. R., Littlehale, M. L., Teodoro, G. I. C. & Laub, M. T. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat. Microbiol. https://doi.org/10.1038/s41564-022-01219-4 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  185. Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Robertson, W. E. et al. Sense codon reassignment enables viral resistance and encoded polymer synthesis. Science 372, 1057–1062 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Nyerges, A. et al. A swapped genetic code prevents viral infections and gene transfer. Nature 615, 720–727 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Johns, N. I., Blazejewski, T., Gomes, A. L. C. & Wang, H. H. Principles for designing synthetic microbial communities. Curr. Opin. Microbiol. 31, 146–153 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  190. Kylilis, N., Tuza, Z. A., Stan, G.-B. & Polizzi, K. M. Tools for engineering coordinated system behaviour in synthetic microbial consortia. Nat. Commun. 9, 2677 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  191. Gupta, S. et al. Investigating the dynamics of microbial consortia in spatially structured environments. Nat. Commun. 11, 2418 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Qian, Y., Lan, F. & Venturelli, O. S. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr. Opin. Microbiol. 62, 84–92 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Ren, X. & Murray, R. M. Cooperation enhances robustness of coexistence in spatially structured consortia. In Proc. 2019 18th European Control Conference (ECC) (eds Garofalo, F. et al.) 2651–2656 (IEEE, 2019).

  194. Kiers, E. T., Hutton, M. G. & Denison, R. F. Human selection and the relaxation of legume defences against ineffective rhizobia. Proc. R. Soc. B Biol. Sci. 274, 3119–3126 (2007).

    Article  CAS  Google Scholar 

  195. Bulgarelli, D., Schlaeppi, K., Spaepen, S., Themaat, E. V. L. V. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).

    Article  CAS  PubMed  Google Scholar 

  196. Haskett, T. L. et al. Engineered plant control of associative nitrogen fixation. Proc. Natl Acad. Sci. USA 119, e2117465119 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Sayler, G. S. & Ripp, S. Field applications of genetically engineered microorganisms for bioremediation processes. Curr. Opin. Biotechnol. 11, 286–289 (2000).

    Article  CAS  PubMed  Google Scholar 

  198. Wilson, M. & Lindow, S. Release of recombinant microorganisms. Annu. Rev. Microbiol. 47, 913–944 (1993).

    Article  CAS  PubMed  Google Scholar 

  199. Sheahan, T. & Wieden, H.-J. Emerging regulatory challenges of next-generation synthetic biology. Biochem. Cell Biol. 99, 766–771 (2021).

    Article  CAS  PubMed  Google Scholar 

  200. US Office of Science and Technology Policy. Coordinated framework for regulation of biotechnology. Fed. Regist. 51, 23302-50 (1986).

    Google Scholar 

  201. Marken, J. P., Maxon, M. E. & Murray, R. M. Policy Recommendations for the Regulation of Engineered Microbes for Environmental Release (Linde Center for Science, Society and Policy, Caltech, 2024); https://doi.org/10.57959/bgny-v542

  202. Marchant, G. E. The Growing Gap between Emerging Technologies and the Law (Springer, 2011).

  203. French, K. E., Zhou, Z. & Terry, N. Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation. Sci. Rep. 10, 15091 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Mutalik, V. K. et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 10, 354–360 (2013).

    Article  CAS  PubMed  Google Scholar 

  205. Reichman, J. R. et al. Research Needs for Novel Engineered Microbes & Biopesticides Intended for Open Release into the Environment. Report EPA/600/R-22/163 (US EPA, 2022).

  206. Warner, C. M. et al. in Synthetic Biology 2020: Frontiers in Risk Analysis and Governance (eds Trump, B. D. et al.) 19–50 (Springer, 2020).

  207. US Department of Agriculture—Animal and Plant Health Inspection Service. APHIS eFile: New SOP Template for Modified Microbe Movement Permits (US Department of Agriculture, 2024); https://www.aphis.usda.gov/news/program-update/aphis-efile-new-sop-template-modified-microbe-movement-permits

  208. US Department of Agriculture—Animal and Plant Health Inspection Service. Draft: Guide for Submitting Permit Applications for Microorganisms Developed Using Genetic Engineering Under 7 CFR Part 340 (US Department of Agriculture, 2023); https://www.aphis.usda.gov/biotechnology/downloads/draft-brs-microbe-permit-guide.pdf

  209. US Congress National Security Commission on Emerging Biotechnology. Interim Report—December 2023 (National Security Commission on Emerging Biotechnology, 2023); https://www.biotech.senate.gov/wp-content/uploads/2024/01/Biotech-Commission-Dec2023-Report.pdf

  210. Defense Advanced Reseach Projects Agency. A Scent-Based Strategy for Preventing Mosquito Transmission of Disease (DARPA, 2019); https://www.darpa.mil/news-events/2019-05-03a#:~:text=ReVector%2C%20a%20new%20program%20from,to%20temporarily%20alter%20chemical%20production

  211. Rosewitz, J. A., Wang, S., Scarlata, S. F. & Rahbar, N. An enzymatic self-healing cementitious material. Appl. Mater. Today 23, 101035 (2021).

    Article  Google Scholar 

  212. Xu, Y. & Lu, M. Microbially enhanced oil recovery at simulated reservoir conditions by use of engineered bacteria. J. Pet. Sci. Eng. 78, 233–238 (2011).

    Article  CAS  Google Scholar 

  213. Chen, Y. E. et al. Engineered skin bacteria induce antitumor T cell responses against melanoma. Science 380, 203–210 (2023).

    Article  CAS  PubMed  Google Scholar 

  214. Becker, M. H. et al. Towards a better understanding of the use of probiotics for preventing chytridiomycosis in Panamanian golden frogs. Ecohealth 8, 501–506 (2011).

    Article  PubMed  Google Scholar 

  215. Forkus, B., Ritter, S., Vlysidis, M., Geldart, K. & Kaznessis, Y. N. Antimicrobial probiotics reduce Salmonella enterica in Turkey gastrointestinal tracts. Sci. Rep. 7, 40695 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. US Department of Agriculture—Animal and Plant Health Inspection Service. Importation, Interstate Movement and Environmental Release of Certain Genetically Engineered Organisms (US Department of Agriculture, 2017); https://www.govinfo.gov/content/pkg/FR-2017-01-19/pdf/2017-00858.pdf

  217. US Food & Drug Administration. FDA Organization Charts (US FDA, 2019); https://www.fda.gov/about-fda/fda-organization/fda-organization-charts

  218. Environmental Protection Agency—Office of Pollution Prevention and Toxics. Overview of Biotechnology Under TSCA (US EPA, 2023); https://www.epa.gov/regulation-biotechnology-under-tsca-and-fifra/overview-biotechnology-under-tsca

  219. Lindow, S. E. & Panopoulos, N. Field tests of recombinant Ice− Pseudomonas syringae for biological frost control in potato. In Proc. First International Conference on the Release of Genetically-engineered Micro-organisms (eds Sussman, M. et al.) 121–138 (Academic, 1988).

  220. Dillewijn, P. V., Soto, M. A. J., Villadas, P. J. & Toro, N. Construction and environmental release of a Sinorhizobium meliloti strain genetically modified to be more competitive for alfalfa nodulation. Appl. Environ. Microbiol. 67, 3860–3865 (2001).

    Article  PubMed  PubMed Central  Google Scholar 

  221. Viebahn, M. et al. Repeated introduction of genetically modified Pseudomonas putida WCS358r without intensified effects on the indigenous microflora of field-grown wheat. Appl. Environ. Microbiol. 69, 3110–3118 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. O’flaherty, S. et al. Greenhouse and field evaluations of an autoselective system based on an essential thymidylate synthase gene for improved maintenance of plasmid vectors in modified Rhizobium meliloti. Appl. Environ. Microbiol. 61, 4051–4056 (1995).

    Article  PubMed  PubMed Central  Google Scholar 

  223. Vicedo, B., Peñalver, R., Asins, M. J. & López, M. M. Biological control of Agrobacterium tumefaciens, colonization and pAgK84 transfer with Agrobacterium radiobacter K84 and the Tra− mutant strain K1026. Appl. Environ. Microbiol. 59, 309–315 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Parakhonsky, E. ОСОБЕННОСТИ РАЗВИТИЯ, ТУШЕНИЯ И ЛИКВИДАЦИИ ПОСЛЕДСТВИЙ ПОДЗЕМНЫХ ПОЖАРОВ НА СЛАНЦЕВЫХ ШАХТАХ. Oil Shale 12, 63–77 (1995).

    Article  Google Scholar 

  225. Das, J. & Dangar, T. in Microbial Biotechnology: Methods and Applications (eds Mishra, B. B. & Thatoi, H.) 68–95 (Narosa Publishing House, 2011).

  226. Charnley, A. Microbial pathogens and insect pest control. Lett. Appl. Microbiol. 12, 149–157 (1991).

    Article  Google Scholar 

  227. Menegat, S., Ledo, A. & Tirado, R. Greenhouse gas emissions from global production and use of nitrogen synthetic fertilisers in agriculture. Sci. Rep. 12, 14490 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Pivot Bio. 2022 Impact Report (Pivot Bio, 2023); https://www.pivotbio.com/hubfs/1604%20-%20US%20Website%20-%20Impact%20Report%20LP/Pivot%20Bio%202022%20Impact%20Report.pdf

  229. Hillman, J. D. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek 82, 361–366 (2002).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank L. Canfora, B. Adams, N. Hubbard and I. Varkovitzsky for their insightful discussions. C. Voigt is supported as a Schmidt Futures Fellow. The work was also supported by the MIT Climate Grand Challenge program, the Ministry of Defense of Israel (MIT 4441024394) and by the Army Research Office and was accomplished under Cooperative Agreement no. W911NF-22-2-0210 (CHARMME). The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the US Government. The US Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein.

Author information

Authors and Affiliations

  1. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Yonatan Chemla, Connor J. Sweeney & Christopher A. Voigt

  2. Wozniak Biopesticide Consulting, LLC, Alexandria, VA, USA

    Christopher A. Wozniak

Authors
  1. Yonatan Chemla
    View author publications

    Search author on:PubMed Google Scholar

  2. Connor J. Sweeney
    View author publications

    Search author on:PubMed Google Scholar

  3. Christopher A. Wozniak
    View author publications

    Search author on:PubMed Google Scholar

  4. Christopher A. Voigt
    View author publications

    Search author on:PubMed Google Scholar

Contributions

Y.C., C.J.S., C.A.W. and C.A.V. wrote the manuscript.

Corresponding author

Correspondence to Christopher A. Voigt.

Ethics declarations

Competing interests

Y.C. declares no competing interests. C.A.V. is a founder of Pivot Bio. C.J.S. is a founder of Robigo, Inc., and C.A.V. serves on their Scientific Advisory Board. C.A.V. is a founder and Scientific Advisory Board member of Fieldstone Bio. C.A.W. used to work at the US Environmental Protection Agency but is now retired.

Peer review

Peer review information

Nature Microbiology thanks Matthew Sorbara, Yasuo Yoshikuni and Robert Egbert for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary notes 1–4 and Tables 1–5.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chemla, Y., Sweeney, C.J., Wozniak, C.A. et al. Design and regulation of engineered bacteria for environmental release. Nat Microbiol 10, 281–300 (2025). https://doi.org/10.1038/s41564-024-01918-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41564-024-01918-0

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research