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Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

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.

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Notes

  1. 1.

    The metaphor developed by Nassim Taleb to argue that the non-occurrence of a certain event thus far is not an evidence that it cannot happen.

References

  • Alexander M (1999) Biodegradation and bioremediation. Academic, San Diego

    Google Scholar 

  • Andrady AL (2011) Microplastics in the marine environment. Mar Pollut Bull 62:1596–1605

    Article  CAS  PubMed  Google Scholar 

  • Antonovsky N, Gleizer S, Milo R (2017) Engineering carbon fixation in E. coli: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle. Curr Opin Biotechnol 47:83–91

    Article  CAS  PubMed  Google Scholar 

  • Aparicio T, Jensen SI, Nielsen AT, de Lorenzo V, Martinez-Garcia E (2016) The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 11:1309–1319

    Article  CAS  PubMed  Google 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

  • Arnold FH (2017) Directed evolution: bringing new chemistry to life. Angew Chem Int Ed Engl 57:4143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cases I, de Lorenzo V (2005) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8:213–222

    PubMed  CAS  Google Scholar 

  • Celiker H, Gore J (2014) Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment. Nat Commun 5:4643

    Article  CAS  PubMed  Google Scholar 

  • Ceroni F, Algar R, Stan GB, Ellis T (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods 12:415–418

    Article  CAS  PubMed  Google Scholar 

  • Chae TU, Choi SY, Kim JW, Ko YS, Lee SY (2017) Recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol 47:67–82

    Article  CAS  PubMed  Google Scholar 

  • Champer J, Buchman A, Akbari OS (2016) Cheating evolution: engineering gene drives to manipulate the fate of wild populations. Nat Rev Genet 17:146

    Article  CAS  PubMed  Google Scholar 

  • Choi KR, Lee SY (2016) CRISPR technologies for bacterial systems: current achievements and future directions. Biotechnol Adv 34:1180–1209

    Article  CAS  PubMed  Google Scholar 

  • Conrad HE, Hedegaard J, Gunsalus IC (1965) Lactone intermediates in the microbial oxidation of (+)-camphor. Tetrahedron Lett 10:561–565

    Article  CAS  PubMed  Google Scholar 

  • de las Heras A, de Lorenzo V (2011) In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal Bioanal Chem 400:1093–1104

    Article  CAS  PubMed  Google Scholar 

  • de Lorenzo V (2017) Seven microbial bio-processes to help the planet. Microb Biotechnol 10:995–998

    Article  PubMed  PubMed Central  Google Scholar 

  • de Lorenzo V, Schmidt M (2018) Biological standards for the Knowledge-Based BioEconomy: what is at stake. N Biotechnol 40:170–180

    Article  CAS  PubMed  Google Scholar 

  • de Lorenzo V, Fraile S, Jiménez J (2010) Emerging systems and synthetic biology approaches to hydrocarbon biotechnology. In: Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1411–1435

    Chapter  Google Scholar 

  • 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): e45658

    Google 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 66:3297–3304

    Article  CAS  PubMed  PubMed Central  Google 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

  • Dvorak P, Nikel PI, Damborsky J, de Lorenzo V (2017) Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 35:845–866

    Article  CAS  PubMed  Google Scholar 

  • Ellis LB, Roe D, Wackett LP (2006) The University of Minnesota biocatalysis/biodegradation database: the first decade. Nucleic Acids Res 34:D517–D521

    Article  CAS  PubMed  Google Scholar 

  • Eriksen M, Lebreton LC, Carson HS, Thiel M, Moore CJ, Borerro JC et al (2014) Plastic pollution in the world’s oceans: more than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLoS One 9:e111913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • French HK, Kastner M, van der Zee SE (2014) New approaches for low-invasive contaminated site characterization, monitoring and modelling. Environ Sci Pollut Res Int 21:8893–8896

    Article  PubMed  Google Scholar 

  • Gomez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A (2007) The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol 3:114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gunsalus IC, Gunsalus CF, Stanier RY (1953) The enzymatic conversion of mandelic acid to benzoic acid. I. Gross fractionation of the system into soluble and particulate components. J Bacteriol 66:538–542

    PubMed  PubMed Central  CAS  Google Scholar 

  • Gyorgy A, Del Vecchio D (2014) Modular composition of gene transcription networks. PLoS Comput Biol 10:e1003486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V (2016) ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synth Biol 5:1155–1166

    Article  CAS  PubMed  Google Scholar 

  • Harms H, Wells MC, van der Meer JR (2006) Whole-cell living biosensors-are they ready for environmental application? Appl Microbiol Biotechnol 70:273–280

    Article  CAS  PubMed  Google Scholar 

  • Jordan A, Gathergood N (2015) Biodegradation of ionic liquids–a critical review. Chem Soc Rev 44:8200–8237

    Article  CAS  PubMed  Google Scholar 

  • Kan SB, Lewis RD, Chen K, Arnold FH (2016) Directed evolution of cytochrome c for carbon-silicon bond formation: bringing silicon to life. Science 354:1048–1051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karig DK (2017) Cell-free synthetic biology for environmental sensing and remediation. Curr Opin Biotechnol 45:69–75

    Article  CAS  PubMed  Google Scholar 

  • Kellogg ST, Chatterjee DK, Chakrabarty AM (1981) Plasmid-assisted molecular breeding: new technique for enhanced biodegradation of persistent toxic chemicals. Science 214:1133–1135

    Article  CAS  PubMed  Google Scholar 

  • 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 19:449–464

    CAS  Google Scholar 

  • Lindow SE, Panopoulos NJ, McFarland BL (1989) Genetic engineering of bacteria from managed and natural habitats. Science 244:1300–1307

    Article  CAS  PubMed  Google Scholar 

  • Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM et al (2015) Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol Biol Evol 33:885–897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mayr A, Klambauer G, Unterthiner T, Hochreiter S (2016) DeepTox: toxicity prediction using deep learning. Front Environ Sci 3:80

    Article  Google Scholar 

  • Mena E, Villaseñor J, Cañizares P, Rodrigo M (2016) Effect of electric field on the performance of soil electro-bioremediation with a periodic polarity reversal strategy. Chemosphere 146:300–307

    Article  CAS  PubMed  Google Scholar 

  • Mertens B, Boon N, Verstraete W (2006) Slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane. Appl Environ Microbiol 72:622–627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nikel PI, Martinez-Garcia E, de Lorenzo V (2014) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12:368–379

    Article  CAS  PubMed  Google Scholar 

  • Nikel PI, Chavarria M, Danchin A, de Lorenzo V (2016) From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 34:20–29

    Article  CAS  PubMed  Google Scholar 

  • Oye KA, Esvelt K, Appleton E, Catteruccia F, Church G, Kuiken T et al (2014) Regulating gene drives. Science 345:626–628

    Article  CAS  PubMed  Google Scholar 

  • Pazos F, Guijas D, Valencia A, de Lorenzo V (2005) MetaRouter: bioinformatics for bioremediation. Nucleic Acids Res 33:D588–D592

    Article  CAS  PubMed  Google Scholar 

  • Perez-Pantoja D, Nikel PI, Chavarria M, de Lorenzo V (2013) Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria. PLoS Genet 9:e1003764

    Article  CAS  PubMed  PubMed Central  Google 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 1–48

    Google Scholar 

  • Ponomarova O, Gabrielli N, Sevin DC, Mulleder M, Zirngibl K, Bulyha K et al (2017) Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow. Cell Syst 5:345–357.e346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raina V, Suar M, Singh A, Prakash O, Dadhwal M, Gupta SK et al (2008) Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation 19:27–40

    Article  CAS  PubMed  Google Scholar 

  • Ramos JL, Andersson P, Jensen LB, Ramos C, Ronchel MC, Diaz E et al (1995) Suicide microbes on the loose. Biotechnology (NY) 13:35–37

    CAS  Google Scholar 

  • Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP et al (2017) Development of SimCells as a novel chassis for functional biosensors. Sci Rep 7:7261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ricaurte DE, Martinez-Garcia E, Nyerges A, Pal C, de Lorenzo V, Aparicio T (2018) A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. Microb Biotechnol 11:176–188

    Article  CAS  PubMed  Google Scholar 

  • Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM et al (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature 518:89–93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Schwarzenbach RP, Escher BI, Fenner K, Hofstetter TB, Johnson CA, Von Gunten U, Wehrli B (2006) The challenge of micropollutants in aquatic systems. Science 313:1072–1077

    Article  CAS  PubMed  Google Scholar 

  • Taleb NN (2007) The black swan: the impact of the highly improbable. Random House, New York

    Google Scholar 

  • Teuben A, Verhoef H (1992) Relevance of micro-and mesocosm experiments for studying soil ecosystem processes. Soil Biol Biochem 24:1179–1183

    Article  Google Scholar 

  • Top EM, Van Daele P, De Saeyer N, Forney LJ (1998) Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids. Antonie Van Leeuwenhoek 73:87–94

    Article  CAS  PubMed  Google Scholar 

  • van der Meer JR, Belkin S (2010) Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Microbiol 8:511–522

    Article  CAS  Google 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 7:173

    Google Scholar 

  • Waltz E (2016) Gene-edited CRISPR mushroom escapes US regulation. Nature 532:293

    Article  CAS  PubMed  Google Scholar 

  • Wicker J, Lorsbach T, Gutlein M, Schmid E, Latino D, Kramer S, Fenner K (2016) enviPath – the environmental contaminant biotransformation pathway resource. Nucleic Acids Res 44:D502–D508

    Article  CAS  PubMed  Google Scholar 

  • Zhou K, Qiao K, Edgar S, Stephanopoulos G (2015) Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol 33:377–383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

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.

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de Lorenzo, V. (2018). Biodegradation and Bioremediation: An Introduction. In: Steffan, R. (eds) Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-44535-9_1-1

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  • DOI: https://doi.org/10.1007/978-3-319-44535-9_1-1

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