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Publications since 2000

Evolution of catabolic pathways | Regulation of gene expression | Development of whole-cell biosensors | Environmental Microbiology
 

Evolution of catabolic pathways

Pradervand, N., Delavat, F., Sulser, S., Miyazaki, R., and van der Meer, J.R. (2014). The TetR-type MfsR protein of the integrative and conjugative element ICEclc controls both a putative efflux system and initiation of ICE transfer. J Bacteriol. 10.1128/JB.02129-14

Pradervand, N., Sulser, S., Delavat, F., Miyazaki, R., Lamas, I., and J. R. van der Meer. 2014. An operon of three transcriptional regulators controls horizontal gene transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13. PLoS Genet. 10(6): e1004441.

Ryo Miyazaki, Claire Bertelli, Paola Benaglio, Jonas Canton, Nicoló De Coi, Walid H. Gharid, Bebeka Gjoksi, Alexander Goesmann, Gilbert Greub, Keith Harshman, Burkhard Linke, Josip Mikulic, Linda Mueller, Damien Nicolas, Marc Robinson-Rechavi, Carlo Rivolta, Clémence Roggo, Shantanu Roy, Vladimir Sentchilo, Alexandra Von Siebenthal, Laurent Falquet, and Jan Roelof van der Meer. 2014. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environm Microbiol. 10.1111/1462-2920.12498.

Reinhard F, van der Meer JR. 2014. Life history analysis of an integrative and conjugative element (ICE) in Pseudomonas. J. Bacteriol. 196 (7): 1425. DOI: 10.1128/JB.01333-13.

Reinhard F, van der Meer JR. 2013. Improved statistical analysis of low abundance phenomena in bimodal bacterial populations PLoS ONE 8(10):e78288

Miyazaki, R. and J. R. van der Meer. (2013) A new large-DNA-fragment delivery system based on integrase activity from an Integrative and Conjugative Element. Appl. Environ. Microbiol. 79(14):4440-4447.

Sentchilo, V., Mayer, A. P., Guy, L., Miyazaki, R., Green Tringe, S., Barry, K., Malfatti, S., Goessmann, A., Robinson-Rechavi, M., and J. R. van der Meer. (2013) Community-wide plasmid gene mobilization and selection. ISME J. 7(6):1173-1186

Reinhard F, Miyazaki R, Pradervand N, van der Meer JR. (2013). Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria. Curr Biol. 2013 Feb 4;23(3):255-9. doi: 10.1016/j.cub.2012.12.025. Epub 2013 Jan 17.

Miyazaki, R., Minoia, M., Pradervand, N., Reinhard, F., Sulser, S. and J. R. van der Meer. (2012) Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element. PLoS Genet. 8(7): e1002818.

Miyazaki, R., Minoia, M., Pradervand, N., Sentchilo, V., Sulser, S., Reinhard, F. and J. R. van der Meer. 2011. The clc element and related genomic islands in Proteobacteria. “Bacterial Integrative Mobile Genetic Elements” edited by (Adam Roberts and Peter Mullany, Eds). Landes Bioscience, Madame Curie Online Database.

Miyazaki, R., and J. R. van der Meer. 2011. How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element? Mobile Genetic Elements, in press.

Miyazaki, R. and J. R. van der Meer. 2011. The ICEclc element of Pseudomonas knackmussii B13 has two active origins of transfer. Mol. Microbiol. 79(3):743-758.

Gaillard, M., Pradervand, N. Minoia, M., Sentchilo, V., Johnson, D. R. and J. R. van der Meer. (2010). Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiology. 10:153

Sentchilo, V., Czechowska, K., Minoia, M., Pradervand, N., Miyazaki, R. and van der Meer, J. R. (2009) Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol. Microbiol. 72:1293-1306.

Juhas, M., van der Meer, J. R., Gaillard, M., Harding, R. M., Hood, D. W. and D. W. Crook. (2008) Genomic islands: tools of bacterial hoizontal gene transfer and evolution. FEMS Microbiol. Rev.33: 376-393.

Minoia, M., Gaillard, M., Reinhard, F., Stojanov, M., Sentchilo, V., and J. R. van der Meer. (i2008) Random or not: bistable control of genomic island transfer in Pseudomonas. Proc. Natl. Acad. Sci. USA. 105: 20792-20797

Gaillard, M., Pernet, N., Vogne, C. Hagenbüchle, O., and J. R. van der Meer. (2008) Host and invader impact of the clc genomic island into Pseudomonas aeruginosa PAO1. Proc. Natl. Acad. Sci. USA. 105:7058-7063.

Raina, V., Suar, M., Dogra, C., Prakash, O., Pal, R., Lawlor, K., Lal, S., van der Meer, J. R., Holliger, C., and Rup Lal.  (2008) Enhanced biodegradation of hexychlorocyclohexane (HCH9 in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation 19: 27-40.

Van der Meer, J. R. (2007) A genomic view on the evolution of catabolic pathways and bacterial adaptation to toxic compounds. In: Microbial biodegradation. Genomics and Molecular Biology (E. Diaz, Ed.). Caister Academic Press, Norfolk UK. Pp. 219-269

Müller, T. A., Fleischmann, T., J. R. van der Meer and H.-P. E. Kohler. (2006) Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH. Appl. Environ. Microbiol. 72(7): 4853-4861.

Van der Meer, J. R. (2006) Evolution of catabolic pathways in Pseudomonas through gene transfer. In: J. L. Ramos and R. Levesque (Ed.). Pseudomonas vol. IV. Springer. Pp. 189-236

Van der Meer, J. R. (2006) Environmental pollution promotes selection of microbial degradation pathways. Frontiers Ecol Environ 4: 35-42.

Gaillard, M., Vallaeys, T., Minoia, M., Vorhoelter, F., Werlen, C., Sentchilo, V., Pühler, A. and J. R. van der Meer. (2006) The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties. J. Bacteriol. 188: 1999-2013

Lacour, S., Gaillard, M. and J. R. van der Meer. (2006). Genomic islands and the evolution of catabolic pathways. In: prokaryotic diversity: mechanisms and significance (Logan, N. A., Lappin-Scott, H. M. and P.C.F. Oyston, Ed.). Cambridge University Press. Pp. 255-274

Dogra, C., Raina, V., Pal, R., Suar, M., Lal, S., Gartemann, K.-H., Holliger, C., van der Meer, J. R., and R. Lal. (2004) Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane - degrading Sphingomonas paucimobilis: Evidence for horizontal gene transfer. J. Bacteriol. 186: 2225-2235.

Laemmli, C., Werlen, C., and J. R. van der Meer. Mutational analysis of the two tfd clusters for chloroaromatic degradation in Ralstonia eutropha JMP134. (2004) Arch. Microbiol. 181: 112 -121.

Müller, T. A., Byrde, S. M., Werlen, C., van der Meer, J. R., and H.-P. Kohler. (2004) Genetic Analysis of Phenoxyalkanoic Acid Degradation in Sphingomonas herbicidovorans MH. Appl. Environ. Microbiol. 70: 6066-6075.

Suar, M., van der Meer, J. R., Lawlor, K., Holliger, C., and R. Lal. (2004) Dynamics of multi lin gene expression in Sphingomonas paucimobilis B90A in response to different HCH isomers. Appl. Environ. Microbiol. 70: 6650-6656.

Müller, T. A., Werlen, C., Spain, J. C., and J. R. van der Meer. (2003) Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia. Environ. Microbiol. 5: 163-173.

van der Meer, J. R., and V. Sentchilo. (2003) Genomic islands and evolution of catabolic pathways in bacteria. Curr. Opin. Biotechnol. 14: 248-254.

Sentchilo, V., Zehnder, A. J. B., and J. R. van der Meer. (2003) Characterization of two alternative promoters and a transcription regulator for integrase expression in the clc catabolic genomic island of Pseudomonas sp. strain B13. Mol. Microbiol. 49: 93-104.

Sentchilo, V., Ravatn, R., Werlen, C., Zehnder, A. J. B., and J. R. van der Meer. (2003) Unusual expression of the integrase gene in the clc genomic island of Pseudomonas sp. strain B13. J. Bacteriol. 185: 4530-4538.

van der Meer, J. R. (2002) Evolution of metabolic pathways for degradation of environmental pollutants. In: Encyclopedia of environmental microbiology (G. Bitton, Ed.) 1194-1207. John Wiley & Sons, N. Y.

Springael, D., Peys, K., Ryngaert, A., van Roy, S., Hooyberghs, L., Ravatn, R., Heyndrickx, M., van der Meer, J. R., Vandecasteele, C., Mergeay, M., and L. Diels. (2002) Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: Indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Env. Microbiol. 4: 70-80.

Laemmli, C. M., Schönenberger, R., Suter, M. J.-F., Zehnder, A. J. B., and J. R. van der Meer. (2002) TfdDII, one of the two chloromuconate cycloisomerases of Ralstonia eutropha JMP134 (pJP4), cannot efficiently convert 2-chloro-cis,cis-muconate to trans-dienelactone to allow growth on 3-chlorobenzoate. Arch. Microbiol. 178: 13-25.

Kumari, R., Subudhi, S., Suar, M., Dhingra, G., Raina, V., Dogra, C., Lal, S., Holliger, C., van der Meer, J. R., and R. Lal (2002) Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers in Sphingomonas paucimobilis strain B90. Appl. Environ. Microbiol. 68: 6021-6028.

van der Meer, J. R., Ravatn, R., and V. Sentchilo. (2001) The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases. Arch. Microbiol. 175: 79-85.

Sentchilo, V. S., Perebituk, A. N., Zehnder, A. J. B., and J. R. van der Meer. (2000) Molecular diversity of plasmids encoding toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus. Appl. Env. Microbiol. 66: 2842-2852.

Laemmli, C. M., Leveau, J. H. J., Zehnder, A. J. B., and J. R. van der Meer. (2000) Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134 (pJP4). J. Bacteriol. 182: 4165-4172.

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Regulation of gene expression

Merulla D, Hatzimanikatis V, van der Meer JR. (2013). Tunable reporter signal production in feedback-uncoupled arsenic bioreporters. Microb Biotechnol. 2013 Jan 15. doi: 10.1111/1751-7915.12031. [Epub ahead of print] PMID: 23316865

Vogne, C., Kumari, H., Arias, S., Lal, R. and J. R. van der Meer. 2011. Characterisation of the putative effector binding site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis. PloS ONE. 2011 Feb 17;6(2):e16539.

Vogne, C., Beggah, S. and J. R. van der Meer. 2010. Random and site-directed mutagenesis of transcriptional regulator proteins implicated in hydrocarbon degradation pathways. Handbook of Hydrocarbon and Lipid Microbiology. Vol. 5. (Timmis, K.N., de Lorenzo, V., McGenity, T. and J.R. van der Meer, Eds). Springer Verlag. P.4430-4444.

Beggah, S., Vogne, C., Zenaro, E. and J. R. van der Meer. (2008) Mutant transcription activator isolation via green fluorescent protein based flow cytometry and cell sorting. Microb. Biotechnol. 1: 68-78. 

Tropel, D. and J. R. van der Meer. (2005) Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain. FEBS Journal 272: 1756-1766.

Tropel, D., Bähler, A., Globig, K., and J. R. van der Meer. (2004) Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR. Environ. Microbiol. 6: 1186-1196.

Tropel, D. and J. R. van der Meer. (2004) Bacterial transcriptional regulators for aromatic degradation pathways. Microbiol. Mol. Biol. Rev. 68: 474-500.

Tropel, D. and J. R. van der Meer. (2002) Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters. J. Bacteriol. 184: 2914-2924.

Jaspers, M. C., Schmid, A., Sturme, M. H., Goslings, D. A., Kohler, H.-P., and J. R. van der Meer. (2001) Transcriptional organization and dynamic expression of the hbpCAD genes, which encode the first three enzymes for 2-hydroxybiphenyl degradation in Pseudomonas azelaica HBP1 J. Bacteriol. 183: 270-279.

M. C. Jaspers, M. Sturme, and J. R. van der Meer. (2001) Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of 'Pseudomonas azelaica' HBP1. Microbiology 147: 2183-2194.

Jaspers, M. C., Schmid, S., Goslings, D. A., Suske, W. A., Kohler, H.-P., and J. R. van der Meer. (2000) Hbpr, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators regulates the expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1. J. Bacteriol. 182: 405-417.

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Development of whole-cell biosensors

Artur Reimer, Sharon Yagur-Kroll, Shimshon Belkin, Shantanu Roy and Jan Roelof van der Meer. (2014) Escherichia coli ribose binding protein based bioreporters revisited. Sci Rep 4: 5626

Truffer, F., Buffi, N., Merulla, D., Beggah, S., van Lintel, H., Renaud, P., van der Meer, J. R., and Martial Geiser (2014). Compact portable biosensor for arsenic detection in aqueous samples with Escherichia coli bioreporter cells. Rev Sci Instrum 85(1) DOI: 10.1063/1.4863333

Cortés-Salazar, F., Beggah, S., van der Meer, J. R. and Hubert H. Girault. (2013) Electrochemical As(III) whole-cell based biochip sensor. Biosensors Bioactuators 47:237-242.

Merulla, D., Buffi, N., Beggah, S., Truffer, F., Geiser, M., Renaud, P. and J. R. van der Meer. (2013) Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem. Curr. Opin. Biotechnol. 24(3):534-541

Siegfried, K., Endes, C., Bhuiyan, A.F., Kuppardt, A., Mattusch, J., van der Meer, J.R., et al. (2012) Field testing of arsenic in groundwater samples of bangladesh using a test kit based on lyophilized bioreporter bacteria. Environ. Sci. Technol. 46: 3281-3287.

Buffi N, Merulla D, Beutier J, Barbaud F, Beggah S, van Lintel H, Renaud, P., and J. R. van der Meer (2011). Miniaturized bacterial biosensor system for arsenic detection holds great promise for making integrated measurement device. Bioeng Bugs 2: 296-298.

Kumari, R., Tecon, R., Beggah, S., Rutler, R., Samuel Arey, J., and J. R. van der Meer. (2011) Development of Bioreporter Assays for the Detection of Bioavailability of Long Chain Alkanes Based on the Marine Bacterium Alcanivorax borkumensis strain SK2. Accepted in Environ Microbiol.

Van der Meer, J. R. (2011) Microbes watching over us. Microb. Biotechnol. 4:124-125.

Buffi, N., Merulla, D., Beutier, J. Barbaud, F., Beggah, S., van Lintel, H., Renaud, P. and J. R. van der Meer. (2011) Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples. Lab Chip, DOI: 10.1039/C1LC20274J.

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

Van der Meer, J. R. and S. Belkin. (2010). Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Microbiol. 8, 511-522

Tecon, R., Beggah, S., Czechowska, K.., Sentchilo, V., Chronopoulou, P.-M., McGenity, T. J., and Jan Roelof van der Meer. (2010) Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments. Environ. Sci. Technol. 44, 1049–1055

Tecon, R. and J. R. van der Meer. (2010) Effect of two types of biosurfactants on phenanthrene availability to the bacterial bioreporter Burkholderia sartisoli strain RP037. Appl. Microbiol. Biotechnol. 85: 1131-1139.

Diesel, B., Schreiber, M., and van der Meer, J. R., (2009) Development of bacteria-based bioassays for arsenic detection in natural waters. Anal. Bioanal. Chem. 394: 687-693.

Tecon, R. , Binggeli, O. and J. R. van der Meer. (2009) Double-tagged fluorescent bacterial bioreporter for the study of polycyclic aromatic hydrocarbon diffusion and bioavailability. Environ. Microbiol. 11: 2271-2283.

Deepthike, H. U., Tecon, R., van Kooten, G., van der Meer, J. R., Harms, H., Welss, M. and J. Short. (2009) Unlike PAHs from Exxon Valdez Crude oil, PAHs from Gulf of Alaska coals are not readily bioavailable. Environ. Sci. Technol. 43: 5864-5870.

Tecon, R., Beggah, S. and J. R. van der Meer. 2010. Bacterial bioreporter assays to measure hydrocarbon concentrations, availabilities and fluxes. Handbook of Hydrocarbon and Lipid Microbiology. Vol. 5. (Timmis, K.N., de Lorenzo, V., McGenity, T. and J.R. van der Meer, Eds). Springer Verlag. P.3642-3652.

Kuppardt, A., Chatzinotas, A., Breuer, U., van der Meer, J. R. and H. Harms. 2009. Optimization of preservation conditions of As(III) bioreporter bacteria. Appl. Microbiol. Biotechnol. 82:785-792.

Lewis, C., Beggah, S., Pook, C., Guitart, C., Redshaw, C., van der Meer, J. R., Readman, J., and T. Galloway. Novel use of a whole cell E. coli bioreporter as a urinary exposure biomarker. 2009. Environ. Sci. Technol. 43:423-428.

Kohlmeier, S., Mancuso, M., Deepthike, U., Tecon, R., van der Meer, J. R., Harms, H., and M. Wells. 2008. Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax. Environ. Poll. 156: 803-808.

Tecon, R. and van der Meer, J. R. 2008. Bacterial biosensors for measuring availability of environmental pollutants. Sensors. 8: 99-05

Wackwitz, A., Harms, H., Chatzinotas, A., Breuer, U., Vogne, C. and J. R. van der Meer. (2008) Internal arsenite bioassay calibration using multiple reporter cell lines. Microb Biotechnol. 1:149-157

Busam, S. McNabb, M., Wackwitz, A., Senevirathna, W., Beggah, S., van der Meer, J. R., Wells, M., Breuer, U. and H. Harms. (2007) Artificial neural network study of whole-cell bacterial biosensor response determined using fluorescence flow cytometry. Anal. Chem. 79:9107-9114

Baumann, B. and J. R. van der Meer. (2007) Analysis of bioavailable arsenic in rice with whole cell living bioreporter bacteria. J. Agric. Food. Chem. 55, 2115-2120.

Kohlmeier, S., Mancuso, M., Tecon, R., Harms, H., van der Meer, J. R. and M. Wells. (2007) Bioreporters: gfp versus luxrevisited and single-cell response. Biosens. Bioelectr. 22: 1578-1585.

Tecon, R., Wells, M. and J. R. van der Meer. (2006) A new gfp-based bacterial biosensor for measuring phenanthrene fluxes. Environ. Microbiol. 8: 697-708.

Tecon, R. and J. R. van der Meer. (2006) Information from single cell biosensors: what is it good for? Curr. Opin. Biotechnol. 17: 4-10

Harms, H., Wells, M. C. and J. R. van der Meer. (2006) Whole-cell living biosensors - are they ready for environmental application? Appl. Microbiol. Biotechnol. 70: 273-280. DOI 10.1007/s00253-006-0319-4

Harms, H., Rime, J., Hug, S. J., and J. R. van der Meer. (2005) Effect of groundwater composition on arsenic detection by bacterial biosensors. Microchimica Acta. DOI 10.1007/s00604-005-0402-z

Wells, M., Gösch, M., Harms, H., and J. R. van der Meer. (2005) Response characteristics of arsenic-sensitive bioreporters expressing the gfp reporter gene. Microchimica Acta. DOI 10.1007/s00604-005-0401-0

Wells, M., Gösch, M., Rigler, R., Harms, H., Lasser, T., and J. R. van der Meer. (2005) Ultrasensitive reporter protein detection in genetically engineered bacteria. Anal. Chem. 77: 2683-2689

Pham Thi Kim Trang, M. Berg, Pham Hung Viet, Nguyen Van Mui, and J. R. van der Meer. (2005) Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples. Environ. Sci. Technol. 39: 7625-7630

Werlen, C., Jaspers, M. C., and J. R. van der Meer. (2004) Gas-phase end point measurements of bioavialable naphthalene using a Pseudomonas putida biosensor. Appl. Environ. Microbiol. 70:43-51.

Van der Meer, J. R., Tropel D., and M. Jaspers. (2004) Illuminating the detection chain of bacterial bioreporters. Environ. Microbiol. 6: 1005-1020.

Füchslin, H. P., Rüegg, I., van der Meer, J. R., and T. Egli. (2003) Effect of integration of a GFP reporter gene in Ralstonia eutropha on growth kinetics with 2,4-dichlorophenoxyacetic acid . Environ. Microbiol. 5:878-887.

Stocker, J., Balluch, D., Gsell, M., Harms, H., Feliciano, J., Daunert, S., Malik, K. A., and J. R. van der Meer. (2003) Development of a set of simple bacterial biosensors for quantitative and rapid field measurements of arsenite and arsenate in potable water. Environ. Sci. Technol. 37: 4743-4750.

Jaspers, M. C., Meier, C., Zehnder, A. J., Harms, H., and J. R. van der Meer. (2001) Measuring mass transfer processes of octane with the help of an alkS-alkB::gfp-tagged Escherichia coli. Env. Microbiol. 3: 512-524.
 

 

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Environmental Microbiology

Moreno, S., and J. R. van der Meer. 2014. Genome-Wide Analysis of Sphingomonas wittichii RW1 Behaviour During Inoculation and Growth in Contaminated Sand. ISME J. 10.1038/ismej.2014.101

Fida, T. T., Philip Breugelmans, Rob Lavigne, Jan van der Meer, René De Mot, Pierre-Joseph Vaysse, and Dirk Springael. (2014). Identification of opsA, a gene involved in solute stress mitigation and survival in soil in the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128. Appl Environ Microbiol. 80 (11): 3350-3361

Scheublin, T. R., Deusch, S., Moreno-Forero, S. K., Müller, J. A., van der Meer, J. R. and Johan H.J. Leveau. (2014) Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds. Environ Microbiol. doi:10.1111/1462-2920.12375

Czechowska K, Reimmann C, van der Meer JR. 2013. Characterization of a MexAB-OprM efflux system necessary for productive metabolism of Pseudomonas azelaica HBP1 on 2-hydroxybiphenyl. Front Microbiol 4:203. doi:10.3389/fmicb.2013.00203

Roggo, C., Coronado, E., Moreno-Forero, S. K., Harshman, K., Weber, J., and van der Meer, JR. (2013) Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1. Environ Microbiol 15(10):2681-2695

Schamfuss, S., Neu, T. R., van der Meer, J. R., Tecon, R., Harms, H., and L. Y. Wick. (2013) Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria. Environ Sci Technol 47(13):6908-6915

Czechowska K, Sentchilo V, Beggah S, Rey S, Seyfried M, van der Meer JR. (2013). Examining Chemical Compound Biodegradation at Low Concentrations through Bacterial Cell Proliferation. Environ Sci Technol. 2013 Jan 31. [Epub ahead of print] PMID: 23339277

Fida TT, Breugelmans P, Lavigne R, Coronado E, Johnson DR, van der Meer JR, Mayer AP, Heipieper HJ, Hofkens J, Springael D. Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms. Appl Environ Microbiol. 2012 78(23):8311-8320.

Coronado, E., Roggo, C., Johnson, D. R., and J. R. van der Meer. (2012) Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas wittichii RW1. Front. Microbiology 3:300, doi: 10.3389/fmicb.2012.00300).

Czechowska, K. and J. R. van der Meer. (2012) Reversible and Irreversible Pollutant-Induced Bacterial Cellular Stress Effects Measured by Ethidium Bromide Uptake and Efflux. Environ. Sci. Technol. 46:1201-1208.

David R Johnson, Edith Coronado , Silvia K Moreno-Forero, Hermann J Heipieper and Jan Roelof van der Meer. (2011) Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii. BMC Microbiol 11: 250. 

Czechowska, K. and J. R. van der Meer. (2011) A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury. Environ. Sci. Technol. DOI: 10.1021/es200591v

Van der Meer, J. R. 2010. Let the sun shine. Curr. Opin. Biotechnol. 21:235-237

Reinhard, F. and J. R. van der Meer. Microcolony growth assays. Microbiology of Hydrocarbons, Oils, Lipids. (accepted)

Johnson, D., Czechowska, K., Chèvre, N., and J. R. van der Meer. Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry. 2009. Environ. Microbiol. 11: 1682-1691.

Czechowska, K., Johnson, D. R. and J. R. van der Meer. 2008. Use of Flow Cytometric Methods for Single-Cell Analysis in Environmental Microbiology. Curr Opin Microbiol. 11:205-212

Vanlaere, E., van der Meer, J. R., Falsen, E., Salles, J. F., De Brandt, E. and P. Vandamme. (2008) Burkholderia sartisoli s. nov., isolated from a polycyclic aromatic hydrcarbon contaminated soil. Intern. J. System. Appl. Microbiol. 58, 420-423.

Meier, C., Wehrli, B, and J. R. van der Meer. (2007) Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments. Microb. Ecol. (electronic first).

Paul, D., Pandey, G., Meier, C., van der Meer, J. R., and R. K. Jain. (2006) Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation. FEMS Microb. Ecol. 57(1): 116-127.

Koch, G., Egli, K., van der Meer, J. R., and H, Siegrist. (2000) Mathematical modeling of autotrophic denitrification in a nitrifying biofilm of a rotating biological contactor. Wat. Sci. Technol. 41: 191-198.

Egli, K., Fanger, U., Alvarez, P., Siegrist, H., van der Meer, J. R., and A. J. B. Zehnder. (2001) Enrichment and characterization of a new anammox bacterium from a rotating biological contactor treating an ammonium-rich leachate. Arch. Microbiol. 175: 198-207.

Raschke, H., Meier, M., Burken, J. G., Hany, R., Müller, M. D., van der Meer, J. R. and H.-P. Kohler. (2001) Biotransformation of various substituted aromatic compounds to chrial dihydrodihydroxy derivatives. Appl. Environ. Microbiol. 67: 3333-3339.

Power, M., van der Meer, J. R., Harms, H, and O. Wanner. (2001) Colonization of aerobic biofilms by sulfate-reducing bacteria. Biofouling 17: 275-288.

Egli, K., Bosshard, F., Werlen, C., Lais, P., Siegrist, H., Zehnder, A. J. B., and J. R. van der Meer. (2003) Microbial composition and structure of a rotating biological contactor biofilm treating ammonium rich wastewater without organic carbon. Microb. Ecol. 45: 419-432.

Egli, K., Langer, C., Siegrist, H.-R., Zehnder, A.J.B., Wagner, M., and J. R. van der Meer. (2003) Population analysis during start-up of nitritation reactors. Appl. Environ. Microbiol. 69: 3213-3222.

Logue, J. B., Robinson, C. T., Meier, C., and J. R. van der Meer. (2004) Relationship between bacteria genetic diversity, sediment organic matter, and the ecosystem metabolism of alpine streams. Limnology and Oceanography 49: 2001-2010.

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New publications

The evolutionary event that led to the massive increase of ICEclc transfer rates?

Pradervand, N., Delavat, F., Sulser, S., Miyazaki, R., and van der Meer, J.R. (2014). The TetR-type MfsR protein of the integrative and conjugative element ICEclc controls both a putative efflux system and initiation of ICE transfer. J Bacteriol. 10.1128/JB.02129-14

A set of master regulators controlling ICEclc transfer.

Pradervand, N., Sandra Sulser, François Delavat, Ryo Miyazaki, Iker Lamas, Jan Roelof van der Meer. An operon of three transcriptional regulators controls horizontal gene transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13. PLoS Genet. 10(6): e1004441.

Measuring the genome-wide reactions of bacteria inoculated for bioremediation.

Moreno, S., and J. R. van der Meer. 2014. Genome-Wide Analysis of Sphingomonas wittichii RW1 Behaviour During Inoculation and Growth in Contaminated Sand. ISME J. 10.1038/ismej.2014.101

After 40 years: the genome of Pseudomonas knackmussii B13 revealed.

Ryo Miyazaki et al. (2014). Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environm Microbiol. 10.1111/1462-2920.12498.

Model-based protein design is not so successful as it seemed:

Artur Reimer, Sharon Yagur-Kroll, Shimshon Belkin, Shantanu Roy and Jan Roelof van der Meer. (2014) Escherichia coli ribose binding protein based bioreporters revisited. Sci Rep 4: 5626

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