Molecular Environmental Microbiology Laboratory



Victor de Lorenzo

Group Leader



Research summary

Our laboratory is committed to understanding how bacteria that inhabit natural niches sense and process multiple environmental signals into distinct responses –both at the level of single cells and as a community. Unlike laboratory settings, in which growth conditions can be controlled and changed one at a time, bacteria in the environment must perpetually make decisions between activating metabolic genes for available, frequently mixed C-sources and those for escaping or adapting to physicochemical stress.



Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv. 2017 Nov 15;35(7):845-866

Chavarría M, Goñi-Moreno A, de Lorenzo V, Nikel PI. A metabolic widget adjusts the phosphoenolpyruvate-dependent fructose influx in Pseudomonas putida KT2440. mSystems 2016; 1: e00154-16

Goñi-Moreno A, Carcajona M, Kim J, Martínez-García E, Amos M, de Lorenzo V. An implementation-focussed bio/algorithmic workflow for synthetic biology. ACS Synth Biol 2016; 5: 1127-1135

Guantes R, Benedetti I, Silva-Rocha R, de Lorenzo V. Transcription factor levels enable metabolic diversification of single cells of environmental bacteria. ISME J 2016; 10: 1122-1133

Nikel PI, Romero-Campero J, Zeidman JA, Goñi-Moreno A, de Lorenzo V. The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor. mBio 2015; 6: e00340-1


logo ministerio eco com FEDER




Convocatoria Retos-Colaboración 2014, RTC-2014-1777-3: Desarrollo de herramientas metagenómicas para producción de biocombustibles (CAMBIOS).




The longstanding aim of our team is to produce biological agents for biosensing, remediation and (wherever possible) transformation of urban and industrial chemical waste that is otherwise dumped into the environment. To this end, we explore and capitalize on the interface between environmental microbiology and synthetic biology. Our workhorse is the soil bacterium Pseudomonas putida, which combines the ease of genetic programming typical of Escherichia coli with the safety, robustness and metabolic abilities required of whole-cell catalysts for applications in harsh biotechnological settings. Specific activities include [i] development of P. putida as a reliable chassis for implantation of genetic and metabolic circuits. This involves editing the extant genome of this microorganism to enhance desirable properties and reduce drawbacks. We also use surface-display systems to design complex catalytic properties completely separate from the cell metabolism, as well as artificial communities by expression of ectopic adhesins. [ii] Use of camel antibodies as tools for metabolic and regulatory engineering of P. putida. Various expression systems allow the targeting of camelid VHH fragments to the intracellular compartment, the periplasm or the external medium of the cells. This allows selective perturbations of chosen metabolic routes to enhance desired metabolic and regulatory qualities of cells. [iii] Genetic tools for deep refactoring of P. putida metabolic properties. The new assets we are developing include a large collection of standardised plasmid and transposon vectors, as well as dedicated reporter systems for parameterisation of the gene expression flow and for switching entire metabolic regimes. [iv] The TOL system borne by plasmid pWW0 as a reference for metabolic circuit implantation. The two operons for toluene and m xylene biodegradation encoded in pWW0 offer a natural case of expansion of the metabolic repertoire of environmental bacteria through acquisition of new genes. [v] Deep metabolic engineering of P. putida. Current efforts attempt to develop strains programmed to adopt an entirely anoxic metabolism and/or a genuine glycolytic mode of utilizing glucose. This involves the re-engineering of dozens of genes and metabolic modules.




Víctor de Lorenzo Principal investigator
Yamal Al-Ramahí Postdoctoral scientist
Ilaria Benedetti Postdoctoral scientist
Belén Calles Postdoctoral scientist
Angel Goñi Postdoctoral scientist
Esteban Martínez Postdoctoral scientist
Pablo I. Nikel Postdoctoral scientist
Mª de los Angeles Hueso Predoctoral scientist
Alberto Sánchez-Pascuala Predoctoral scientist
Sofia Fraile Technicians
Tomás Aparicio Technicians
Inés Merino Administrative assistant

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