Publications

Czechowska, K. and J. R. van der Meer. A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury. 

Environ Sci Technol. 2012 Mar 6;46(5):3038

De las Heras A. and de Lorenzo, V.  Engineering a whole-cell biosensor with no antibiotic markers for monitoring aromatic compounds in the environment.

Methods Mol Biol. 2012; 834:261-81.
 

Fernández M, Conde S, de la Torre J, Ramos JL, Duque E. Mechanisms of resistance to chloramphenicol by Pseudomonas putida KT2440.

Antimicrob Agents Chemother. 2012 Feb;56(2):1001-9.
 

Schoug Bergenholtz Å, Wessman P, Wuttke A, Håkansson S. A case study on stress preconditioning of a Lactobacillus strain prior to freeze drying.

Cryobiology (in press). 2012 Jan 15. 

Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser V-S, Kralova M, Junca H and H. Pieper D. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system.

Environmental Microbiology (in press).

Gertler, C.; Näther, D.; Cappello, S.; Gerdts, G.; Quilliam, R.; Yakimov, M.; Golyshin, P.  Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study.

FEMS Microbiology Ecology (in press).

Arce-Rodríguez, A., Durante-Rodríguez, G., Platero, R., Krell, T., Calles, B. and de Lorenzo V. (2011). The Crp regulator of Pseudomonas putida: evidence of an unusually high affinity for its physiological effector, cAMP.

Env Microbiol. 14:3 (702-13).

Chavarría, M., Santiago, C., Platero, R., Krell, T., Casasnovas, J.M. and de Lorenzo, V. (2011) Fructose 1-Phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida.

J. Biol. Chem. 286: 9351-9359.

Chrzanowski L., Owsianiak M., Szulc A., Marecik R., Piotrowska-Cyplik A., Olejnik-Schmidt A.K., Staniewski J., Lisiecki P., Ciesielczyk F., Jesionowski T., Heipieper H.J. Interactions between rhamnolipid biosurfactants and toxic chlorinated phenols enhance biodegradation of a model hydrocarbon-rich effluent.

Int. Biodeter. Biodegr. 2011.  65:605-611.

Cialfi S., Uccelletti D., Carducci A., Wesolowski-Louvel M., Mancini P., Heipieper H.J., Saliola M. KlHsl1 is a component of glycerol response pathways in the milk yeast Kluyveromyces lactis.

Microbiology SGM. 2011.  157:1509-1518.
 

Cyplik P., Schmidt M., Szulc A., Marecik R., Lisiecki P., Heipieper H.J., Owsianiak M., Vainshtein M., Chrzanowski L. Relative quantitative PCR to assess bacterial community dynamics during degradation of diesel and biodiesel fuels under various aeration conditions.

Bioresour. Technol. 2011. 102:4347-4352.
 

de las Heras, A. and de Lorenzo, V. Cooperative amino acid changes shift the response of the s54-dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene.

Mol Microbiol. 2011.  79: 1248-1259.

de las Heras, A. and de Lorenzo, V. In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules.

Analyt. Bioanalyt. Chem. 2011. 400:1093-1104
 

de Lorenzo, V. Beware of metaphors: chasses and orthogonality in Synthetic Biology.

BioEngineered Bugs. 2011. 2: 1-5

de Lorenzo, V. Genes that move the window of viability of life: lessons from bacteria thriving at the cold extreme.

BioEssays. 2011. 33: 38-42.

Koutinas, M., Kiparissides, A., Lam, M.C., Silva-Rocha, R., Godinho, M. de Lorenzo, V., Martins dos Santos, M.V., Pistikopoulos, E.N., Mantalaris, A. (2011) Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid.

Biochemical Engineering Journal 55 (2011)2. - ISSN 1369-703X - p. 108 - 118.
 

Kralova M., Jurak J., Machackova J., Proksova S., Stavelova M. „Biodegradation of Jet Fuel Contaminated Soil Enhanced by Chemical Oxidation“. Battelle Bioremediation & Sustainable Environmental Technologies Conference. Reno, Nevada, June 27- 30, 2011
 

Kumari, R., Tecon, R., Beggah, S., Rutler, R., Samuel Arey, J., and J. R. van der Meer. Development of Bioreporter Assays for the Detection of Bioavailability of Long Chain Alkanes Based on the Marine Bacterium Alcanivorax borkumensis strain SK2.

Environ. Microbiol. 2011 Oct;13(10):2808-19.
 

Lacal, J., F. Muñoz-Martínez, J.A. Reyes-Darías, E. Duque, M. Matilla, A. Segura, J.J. Ortega-Calvo, C. Jiménez-Sánchez, T. Krell, and J.L. Ramos Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas.

Environ. Micrbiol 2011. 13:1733-1744.  

Martínez-García, E., Calles, B., Arévalo-Rodríguez, M. and de Lorenzo, V. pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes.

BMC Microbiology 2011. 11: 38
 

Martínez-García, E. and de Lorenzo, V. Transposon- based and plasmid-based genetic tools for editing genomes of Gram-negative bacteria.

Methods Mol Biol. 2012;813:267-83.
 

Martínez-Rodriguez, E., De Lorenzo, V.  Engineering multiple genomic deletions in Gram-negative bacteria: Analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440.

Environ Microbiol. 2011 Oct;13(10):2702-16.

Matilla MA, Pizarro-Tobias P, Roca A, Fernández M, Duque E, Molina L, Wu X, van der Lelie D, Gómez MJ, Segura A, Ramos JL. Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1.

J. Bacteriol.2011. 193(5):1290.

 

Molina, L., E. Duque, M.J. Gómez, T. Krell, J. Lacal, A. García-Puente, V. García, M.A. Matilla, J.L. Ramos, and A. Segura. The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditons in the environment.

Environ Microbiol. 2011 Aug;13(8):2315-27.

Pérez-Pantoja D, Donoso R, Agulló L, Córdova M, Seeger M, Pieper DH, González B. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales.

Environ Microbiol. 2011 Oct 26. doi: 10.1111/j.1462-2920.2011.02613.x.

Per Wessman, Denny Mahlin, Sultan Akhtar, Stefano Rubino, Klaus Leifer, Vadim Kessler and Sebastian Håkansson. Impact of matrix properties on survival of freeze-dried bacteria.

Journal of the Science of Food and Agriculture 2011. DOI: 10.1002/jsfa.4343

PflÜger-Grau, K, Chavarría, M. and de Lorenzo, V. The interplay of the EIIANtr component of the nitrogen-related phosphotransferase system (PTSNtr) of Pseudomonas putida with pyruvate dehydrogenase. 

Biochim Biophys Acta. 2011 Oct; 1810(10) :995-1005.

Porcar, M., Danchin, A., de Lorenzo, V., Martins dos Santos, V., Krasnogor, N., Rasmussen, S, and Moya A. The ten grand challenges of synthetic life.

Syst Synth Biol. 2011 June; 5(1-2): 1–9.
 

Ramos JL, Marqués S, van Dillewijn P, Espinosa-Urgel M, Segura A, Duque E, Krell T, Ramos-González MI, Bursakov S, Roca A, Solano J, Fernández M, Niqui JL, Pizarro P, and Wittich RM. Laboratory research aimed at closing the gaps in microbial bioremediation.

Trends in Biotechnology 2011, Volume 29, Issue 12, 641-647
 

Silva-Rocha, R., de Jong, H., Tamames, J. and de Lorenzo, V. (2011) The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene BMC

Systems Biology 5: 191. 

Silva-Rocha, R., De Lorenzo, V. Implementing an OR-NOT (ORN) logic gate with components the SOS regulatory network of Escherichia coli.

Mol Biosyst. 2011 Aug;7(8):2389-96.  

Silva-Rocha R., Tamames J., and de Lorenzo V. (2011) The logic of decision-making in environmental bacteria. In E. Katz (Ed.) Molecular and Biomolecular Information Processing: From Logic Systems to Sensors and Actuators. Wiley-VCH.

BMC Syst Biolo. 5:191  

Silva-Rocha R, Tamames J, dos Santos VM and de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.

Environ Microbiol. 2011 Sep;13(9):2389-402.  

Valls, M., Silva-Rocha, R., Cases, I., Muñoz, A., and de Lorenzo, V. (2011) Functional analysis of the integration host factor site of the s54 Pu promoter of Pseudomonas putida by in vivo UV imprinting.

Mol Microbiol 82:3 (591-601). 

Van der Meer, J. R. Bacterial Sensors: Synthetic design and Application Principles.

(Editor: Martyn Amos, Manchester Metropolitan University). Synthesis Lectures on Synthetic Biology, Morgan & Claypool Publishers. 2011.
 

Wessman P, Mahlin D, Rubino S, Leifer K, Kessler V, Håkansson S. Impact of matrix properties on survival of freeze-dried bacteria.

J. Sci Food Agri 2011. 91(14):2518-2528

Zafra, O., Fraile, S, Gutiérrez, C., Haro, A., Páez-Espino, D., Jiménez, J.I. and de Lorenzo, V. Monitoring
biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins.

Environ Microbiol. 2011.  13:960-974

Duldhardt I., Gaebel J., Chrzanowski L., Nijenhuis I., Hartig C., Schauer F., Heipieper H.J. Adaptation of anaerobically grown Thauera aromatica, Geobacter sulfurreducens, and Desulfococcus multivorans to organic solvents on the level of membrane fatty acid composition.

Microbial Biotechnol. 2010. 3:201-209.

Fischer J., Schauer F., Heipieper H.J. The trans/cis ratio of unsaturated fatty acids is not applicable as biomarker for environmental stress in case of long-term contaminated habitats.

Appl. Microbiol. Biotechnol. 2010. 87:365-371.

Fischer J., Kappelmeyer U., Kastner M., Schauer F., Heipieper H.J. The degradation of bisphenol A by the newly isolated bacterium Cupriavidus basilensis JF1 can be enhanced by biostimulation with phenol.

Int. Biodeter. Biodegr. 2010. 64:324-330.
 

Löffler C., Eberlein C., Mäusezahl I., Kappelmeyer U., Heipieper H.J. Physiological evidence for the presence of a cis-trans isomerase of unsaturated fatty acids in Methylococcus capsulatus Bath to adapt to the presence of toxic organic compounds.

FEMS Microbiol. Lett. 2010. 308:68-75.

Maphosa, F., Smidt, H., de Vos, W.M. and Röling, W.F.M.: Microbial community and metabolite dynamics of an anoxic dechlorinating bioreactor.

Environmental Science and Technology 48, 4884-4890 (2010)

Martínez-Lavanchy P.M., Müller C., Nijenhuis I., Kappelmeyer U., Buffing M., McPherson K., Heipieper H.J.  High stability and fast recovery of the expression of the toluene catabolic TOL genes of Pseudomonas putida mt-2 when grown under oxygen limiting and oscillating conditions.

Appl. Environ. Microbiol. 2010.  76:6715-6723.

Röling, W.F.M., Ferrer M. and Golyshin, P.N.: Systems approaches to microbial communities and their functioning.

Current Opinion in Biotechnology 21: 532-538 (2010).

Röling, W.F.M.: Flux-related metabolic network descriptions.

In Timmis, K.N. (ed.), 2010 Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds. Springer-Verlag Berlin Heidelberg.. pp. 4339-4347.
 

Van der Meer, J. R. and S. Belkin. Where microbiology meets microengineering: design and applications
of reporter bacteria.

Nat. Rev. Microbiol. 8, 2010. 511-522
 

van der Meer J.R., Springael D., de Lorenzo V., Ramos J.L., Smid H., Heipieper H.J.  BACSIN(s): A European
project focused on targeted applications of bacterial strains for pollutant bioremediation.

J. Biotechnol. 2010. 150:S44-S45.

Vila J., Nieto J.M., Mertens J., Springael D., and Grifoll M. Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization.

FEMS Microbiol. Ecol., in press. DOI: 10.1111/j.1574-6941.2010.00902.x  

Vilchez-Vargas R, Junca H, Pieper DH. Metabolic networks, microbial ecology and ‘omics’ technologies:
towards understanding in situ biodegradation processes.

Environ. Microbiol. 12: 3089-3104. 2010

Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H.  Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.

Environ Microbiol. 2009 Sep;11(9):2216-27. Epub 2009 Feb 19. 

Chrzanowski L., Meulenkamp R., Kastner M., Wick L.Y., Heipieper H.J. Rhamnolipid biosurfactants decrease the toxicity of chlorinated phenols to Pseudomonas putida DOT-T1E. 

Lett Appl Microbiol. 2009 Jun;48(6):756-62. Epub 2009 Apr 1.

Fernández M., Duque E., Pizarro-Tobías P., van Dillewijn P., Wittich R-M., Ramos J. L. Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene.

Microb. Biotechnol. 2009 Feb;2(2): 287-294 

Heipieper H.J., Cornelissen S., Pepi M. Surface properties and cellular energetics of bacteria in response to the presence of hydrocarbons.

In: Timmis K.N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin. 2009 Vol. 2, Part 9, pp. 1615-1624.
 

Heipieper H.J., Fischer J. Bacterial solvent responses and tolerance: cis-trans isomerization.

In: Timmis K.N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin. 2009 Vol. 5, Part 4, pp. 4203-4211.

Heipieper H.J., Fischer J., Meinhardt F. Cis-trans isomerase of unsaturated fatty acids: an immediate bacterial adaptive mechanism to cope with emerging membrane perturbation caused by toxic hydrocarbons.

In: Timmis K.N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin. 2009 Vol. 2, Part 9, pp. 1605-1614.

Heipieper H.J. Isolation and analysis of lipids, biomarkers.

In: Timmis K.N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin. 2009 Vol. 5, Part 2, pp. 3743-3750.

Heipieper H.J., Martínez P. Toxicity of hydrocarbons to microorganisms.

In: Timmis K.N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin. 2009 Vol. 2, Part 9, pp. 1565-1573.

Pepi M., Lobianco A., Renzi M., Perra G., Bernardini E., Marvasi M., Gasperini S., Volterrani M., Franchi E., Heipieper H.J., Focardi S.E. Two naphthalene degrading bacteria belonging to the genera Paenibacillus and Pseudomonas isolated form a highly polluted lagoon perform different sensitivities to the organic and heavy metal contaminants. 

Extremophiles. 2009 Sep;13(5):839-48. 

Roca A., Rodríguez-Herva J. J., Duque E., Ramos J. L. Physiological responses of Pseudomonas putida to formaldehyde during detoxification.

Microb. Biotechnol. 2009 March 1(2),  Pages: 158-169