Biodegradation and Bioremediation: An Introduction
The scientific interest of the fate of environmental pollutants generated by industrial and urban activities is not only about the pursuit of ways to foster the mitigation or ideally the complete removal from the afflicted sites. It also provides insights on how environmental microorganisms evolve new molecular devices for first tolerating and then catabolizing many of such otherwise toxic molecules. Along with resistance to antibiotics, emergence of fresh biodegradative routes for new compounds is one of the most conspicuous cases of contemporary biological evolution in real time. Understanding the rules of such evolution thus provides new principles for predicting – and in case accelerating – biochemical adaptation to novel chemical structures. These phenomena occur in space and time and also at very different scales depending on the nature and dimension of the pollutants at stake. The impact of contaminants that received considerable attention decades ago is decreasing in many cases owing to better industrial procedures along with growing environmental awareness and legal regulations. Alas, the last decade has witnessed also the emergence of other types of contaminants (in particular greenhouse gases, plastics, and micropollutants) that threaten not just specific sites but also the functioning of the planet’s homeostasis at a global scale. This state of affairs calls for new bioremediation strategies that take into account the multiscale complexity involved in possible interventions much beyond the focus on specific biodegradative pathways. Fortunately, the environmental microbiome and the possibilities of engineering it with the tools of Systems and Synthetic Biology remains the best resource to tackle the phenomenal challenge of preserving the biosphere in good shape for the future generations.
This work was funded by the HELIOS Project of the Spanish Ministry of Economy and Competitiveness BIO 2015-66960-C3-2-R (MINECO/FEDER), ARISYS (ERC-2012-ADG-322797), EmPowerPutida (EU-H2020-BIOTEC-2014-2015-6335536), MADONNA (H2020-FET-OPEN-RIA-2017-1-766975), Contracts of the European Union, and InGEMICS-CM (B2017/BMD-3691) contract of the Comunidad de Madrid.
- Alexander M (1999) Biodegradation and bioremediation. Academic, San DiegoGoogle Scholar
- Aparicio T, de Lorenzo V, Martinez-Garcia E (2017) CRISPR/Cas9-based counterselection boosts recombineering efficiency in Pseudomonas putida. Biotechnol J. https://doi.org/10.1002/biot.201700161
- de Lorenzo V, Prather KLJ, Chen GQ, O’Day E, von Kameke C, Oyarzún DA et al (2018) The power of synthetic biology for bioproduction, remediation and pollution control. EMBO Rep 19(4): e45658Google Scholar
- Dejonghe W, Goris J, El Fantroussi S, Hofte M, De Vos P, Verstraete W, Top EM (2000) Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons. Appl Environ Microbiol 66:3297–3304CrossRefPubMedPubMedCentralGoogle Scholar
- Donnelly AE, Murphy GS, Digianantonio KM, Hecht MH (2018) A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol. https://doi.org/10.1038/nchembio.2550
- Latino DA, Wicker J, Gütlein M, Schmid E, Kramer S, Fenner K (2017) Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data. Environ Sci Process Impacts 19:449–464Google Scholar
- Pérez-Pantoja D, Donoso R, Junca H, Gonzalez B, Pieper D (2016) Phylogenomics of aerobic bacterial degradation of aromatics. In: Aerobic utilization of hydrocarbons, oils and lipids. Springer International Publishing AG. pp 1–48Google Scholar
- Ramos JL, Andersson P, Jensen LB, Ramos C, Ronchel MC, Diaz E et al (1995) Suicide microbes on the loose. Biotechnology (NY) 13:35–37Google Scholar
- Taleb NN (2007) The black swan: the impact of the highly improbable. Random House, New YorkGoogle Scholar
- von Wintersdorff CJH, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB et al (2016) Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol 7:173Google Scholar