Ecological Firewalls for Synthetic Biology

Overview

Journal iScience

Publisher Cell Press

Date 2022 Jul 14

PMID 35832885

Authors

Blai Vidiella

Ricard Sole

Affiliations

Soon will be listed here.

Abstract

It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while-when required-preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined.

Citing Articles

Xenobiology for the Biocontainment of Synthetic Organisms: Opportunities and Challenges.

Gomez-Tatay L, Hernandez-Andreu J Life (Basel). 2024; 14(8).

PMID: 39202738 PMC: 11355180. DOI: 10.3390/life14080996.

The whack-a-mole governance challenge for AI-enabled synthetic biology: literature review and emerging frameworks.

Undheim T Front Bioeng Biotechnol. 2024; 12:1359768.

PMID: 38481570 PMC: 10933118. DOI: 10.3389/fbioe.2024.1359768.

Genetic Circuit Design in Rhizobacteria.

Dundas C, Dinneny J Biodes Res. 2023; 2022:9858049.

PMID: 37850138 PMC: 10521742. DOI: 10.34133/2022/9858049.

High stability in filtration apparatus of African shrimp.

Liao Y, Wang J, Lyu J, Jiang W, Wu Z, Wu J iScience. 2023; 26(8):107444.

PMID: 37599830 PMC: 10432203. DOI: 10.1016/j.isci.2023.107444.

Ecological complexity and the biosphere: the next 30 years.

Sole R, Levin S Philos Trans R Soc Lond B Biol Sci. 2022; 377(1857):20210376.

PMID: 35757877 PMC: 9234814. DOI: 10.1098/rstb.2021.0376.

References

de Lorenzo V, Marliere P, Sole R . Bioremediation at a global scale: from the test tube to planet Earth. Microb Biotechnol. 2016; 9(5):618-25. PMC: 4993180. DOI: 10.1111/1751-7915.12399. View

Benner S, Sismour A . Synthetic biology. Nat Rev Genet. 2005; 6(7):533-43. PMC: 7097405. DOI: 10.1038/nrg1637. View

de Lorenzo V . Seven microbial bio-processes to help the planet. Microb Biotechnol. 2017; 10(5):995-998. PMC: 5609242. DOI: 10.1111/1751-7915.12816. View

Levine J, Lin Y, Elowitz M . Functional roles of pulsing in genetic circuits. Science. 2013; 342(6163):1193-200. PMC: 4100686. DOI: 10.1126/science.1239999. View

Flemming H, Wingender J, Szewzyk U, Steinberg P, Rice S, Kjelleberg S . Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016; 14(9):563-75. DOI: 10.1038/nrmicro.2016.94. View

Tran P, Prindle A . Synthetic biology in biofilms: Tools, challenges, and opportunities. Biotechnol Prog. 2021; 37(5):e3123. DOI: 10.1002/btpr.3123. View

Vidiella B, Sardanyes J, Sole R . Synthetic soil crusts against green-desert transitions: a spatial model. R Soc Open Sci. 2020; 7(8):200161. PMC: 7481726. DOI: 10.1098/rsos.200161. View

Duran-Nebreda S, Pla J, Vidiella B, Pinero J, Conde-Pueyo N, Sole R . Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies. ACS Synth Biol. 2021; 10(2):277-285. PMC: 8486170. DOI: 10.1021/acssynbio.0c00318. View

Purnick P, Weiss R . The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol. 2009; 10(6):410-22. DOI: 10.1038/nrm2698. View

10.

Schmidt M, de Lorenzo V . Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms. Curr Opin Biotechnol. 2016; 38:90-6. DOI: 10.1016/j.copbio.2016.01.006. View

11.

Ruder W, Lu T, Collins J . Synthetic biology moving into the clinic. Science. 2011; 333(6047):1248-52. DOI: 10.1126/science.1206843. View

12.

Leggieri P, Liu Y, Hayes M, Connors B, Seppala S, OMalley M . Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng. 2021; 23:169-201. PMC: 8277735. DOI: 10.1146/annurev-bioeng-082120-022836. View

13.

Jaramillo A . Synthetic biology: Engineered stable ecosystems. Nat Microbiol. 2017; 2:17119. DOI: 10.1038/nmicrobiol.2017.119. View

14.

Schmidt M, de Lorenzo V . Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett. 2012; 586(15):2199-206. PMC: 3396840. DOI: 10.1016/j.febslet.2012.02.022. View

15.

Wu M, Jusiak B, Lu T . Engineering advanced cancer therapies with synthetic biology. Nat Rev Cancer. 2019; 19(4):187-195. DOI: 10.1038/s41568-019-0121-0. View

16.

de Lorenzo V . Systems biology approaches to bioremediation. Curr Opin Biotechnol. 2008; 19(6):579-89. DOI: 10.1016/j.copbio.2008.10.004. View

17.

Johns N, Blazejewski T, Gomes A, Wang H . Principles for designing synthetic microbial communities. Curr Opin Microbiol. 2016; 31:146-153. PMC: 4899134. DOI: 10.1016/j.mib.2016.03.010. View

18.

Maestre F, Sole R, Singh B . Microbial biotechnology as a tool to restore degraded drylands. Microb Biotechnol. 2017; 10(5):1250-1253. PMC: 5609258. DOI: 10.1111/1751-7915.12832. View

19.

Kassinger S, van Hoek M . Biofilm architecture: An emerging synthetic biology target. Synth Syst Biotechnol. 2020; 5(1):1-10. PMC: 6961760. DOI: 10.1016/j.synbio.2020.01.001. View

20.

Piaggio A, Segelbacher G, Seddon P, Alphey L, Bennett E, Carlson R . Is It Time for Synthetic Biodiversity Conservation?. Trends Ecol Evol. 2016; 32(2):97-107. DOI: 10.1016/j.tree.2016.10.016. View