Jan Roelof van der Meer

Publications | Mémoires et thèses

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221 publications

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | ...
2024
Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.
Čaušević S., Dubey M., Morales M., Salazar G., Sentchilo V., Carraro N., Ruscheweyh H.J., Sunagawa S., van der Meer J.R., 2024/03/22. Nature communications, 15 (1) p. 2557. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_E3381CFCB35A]
2023
Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.
Benigno V., Carraro N., Sarton-Lohéac G., Romano-Bertrand S., Blanc D.S., van der Meer J.R., 2023/12/20. mSphere, 8 (6) pp. e0051723. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C8BBFFC92257]
 
From microbiome composition to functional engineering, one step at a time.
Burz S.D., Causevic S., Dal Co A., Dmitrijeva M., Engel P., Garrido-Sanz D., Greub G., Hapfelmeier S., Hardt W-D, Hatzimanikatis V. et al., 2023/12/20. Microbiology and molecular biology reviews, 87 (4) pp. e0006323. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_422DE1C48246]
Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere.
Garrido-Sanz D., Čaušević S., Vacheron J., Heiman C.M., Sentchilo V., van der Meer J.R., Keel C., 2023/09/29. Microbiome, 11 (1) p. 214. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_46EF5F18A042]
 
Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.
Guex I., Mazza C., Dubey M., Batsch M., Li R., van der Meer J.R., 2023/08. PLoS computational biology, 19 (8) pp. e1011402. Peer-reviewed.
[DOI][Pmid][serval:BIB_1DE186CB16FB]
Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2.
Morales M., Sentchilo V., Carraro N., Causevic S., Vuarambon D., van der Meer J.R., 2023/04/27. mSystems, 8 (2) pp. e0117422. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E45105A859F9]
 
STrack: A Tool to Simply Track Bacterial Cells in Microscopy Time-Lapse Images.
Todorov H., Miguel Trabajo T., van der Meer J.R., 2023/04/20. mSphere, 8 (2) pp. e0065822. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CC63374B0997]
Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.
Daveri A., Benigno V., van der Meer J.R., 2023/03/21. Nucleic acids research, 51 (5) pp. 2345-2362. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B2A6E41DC556]
2022
A bistable prokaryotic differentiation system underlying development of conjugative transfer competence.
Sulser S., Vucicevic A., Bellini V., Moritz R., Delavat F., Sentchilo V., Carraro N., van der Meer J.R., 2022/06. PLoS genetics, 18 (6) pp. e1010286. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_4D561966E16C]
Recent advances in microbial community analysis from machine learning of multiparametric flow cytometry data.
Özel Duygan B.D., van der Meer J.R., 2022/06. Current opinion in biotechnology, 75 p. 102688. Peer-reviewed.
[DOI][Pmid][serval:BIB_A9FCFB45172D]
Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation.
Čaušević S., Tackmann J., Sentchilo V., von Mering C., van der Meer J.R., 2022/04/26. mSystems, 7 (2) pp. e0016022. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7CFDBD42F375]
 
Subcellular Localization Defects Characterize Ribose-Binding Mutant Proteins with New Ligand Properties in Escherichia coli.
Tavares D., van der Meer J.R., 2022/01/25. Applied and environmental microbiology, 88 (2) pp. e0211721. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B146B2AFB72E]
2021
 
Assessing Antibiotics Biodegradation and Effects at Sub-inhibitory Concentrations by Quantitative Microbial Community Deconvolution
Özel Duygan Birge D., Gaille Caroline, Fenner Kathrin, van der Meer Jan R., 2021/09/16. Frontiers in Environmental Science, 9 p. 737247.
[DOI][WoS][serval:BIB_4D5A579D7A32]
Predicting spatial patterns of soil bacteria under current and future environmental conditions.
Mod H.K., Buri A., Yashiro E., Guex N., Malard L., Pinto-Figueroa E., Pagni M., Niculita-Hirzel H., van der Meer J.R., Guisan A., 2021/09. The ISME journal, 15 (9) pp. 2547-2560. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_595C7D7FADB0]
 
A Miniaturized Microbe-Silicon-Chip Based on Bioluminescent Engineered Escherichia coli for the Evaluation of Water Quality and Safety.
Sciuto E.L., Corso D., Libertino S., van der Meer J.R., Faro G., Coniglio M.A., 2021/07/16. International journal of environmental research and public health, 18 (14) p. 7580. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DC12ED645274]
Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils.
Morales M., Sentchilo V., Hadadi N., van der Meer J.R., 2021/04/29. Environmental microbiome, 16 (1) p. 8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_48CD2F7B7CBA]
Environmental connectivity controls diversity in soil microbial communities.
Dubey M., Hadadi N., Pelet S., Carraro N., Johnson D.R., van der Meer J.R., 2021/04/22. Communications biology, 4 (1) p. 492. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D2457E5CE56F]
 
Miniaturized electrochemical biosensor based on whole-cell for heavy metal ions detection in water.
Sciuto E.L., Petralia S., van der Meer J.R., Conoci S., 2021/04. Biotechnology and bioengineering, 118 (4) pp. 1456-1465. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_99F692FA2472]
Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry.
Özel Duygan B.D., Rey S., Leocata S., Baroux L., Seyfried M., van der Meer J.R., 2021/02/09. mSystems, 6 (1) pp. e01143-20. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E4E8C7ED5B31]
Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol.
Tavares D., van der Meer J.R., 2021. Frontiers in bioengineering and biotechnology, 9 p. 705534. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7CA24711D1A5]
2020
Greater topoclimatic control of above- versus below-ground communities.
Mod H.K., Scherrer D., Di Cola V., Broennimann O., Blandenier Q., Breiner F.T., Buri A., Goudet J., Guex N., Lara E. et al., 2020/12. Global change biology, 26 (12) pp. 6715-6728. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_858D58CF6336]
Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1.
Carraro N., Sentchilo V., Polák L., Bertelli C., van der Meer J.R., 2020/08/12. Genes, 11 (8) p. 930. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_206C29759190]
An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element.
Carraro N., Richard X., Sulser S., Delavat F., Mazza C., van der Meer J.R., 2020/07/28. eLife, 9 pp. e57915. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AD5E010A817F]
 
Bioluminescence-Triggered Photoswitchable Bacterial Adhesions Enable Higher Sensitivity and Dual-Readout Bacterial Biosensors for Mercury.
Chen F., Warnock R.L., Van der Meer J.R., Wegner S.V., 2020/07/24. ACS sensors, 5 (7) pp. 2205-2210. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C359D80C3590]
Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data.
Özel Duygan B.D., Hadadi N., Babu A.F., Seyfried M., van der Meer J.R., 2020/07/15. Communications biology, 3 (1) p. 379. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2AAB8F56D9C5]
2019
Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol.
Tavares D., Reimer A., Roy S., Joublin A., Sentchilo V., van der Meer J.R., 2019/11/15. Scientific reports, 9 (1) p. 16940. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5A2ABAB8B9CC]
 
Biosensors in Monitoring Water Quality and Safety: An Example of a Miniaturizable Whole-Cell Based Sensor for Hg2+ Optical Detection in Water
Sciuto Emanuele Luigi, Coniglio Maria Anna, Corso Domenico, van der Meer Jan Roelof, Acerbi Fabio, Gola Alberto, Libertino Sebania, 2019/09/24. Water, 11 (10) p. 1986.
[DOI][WoS][serval:BIB_52F382C05F62]
Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element.
Delavat F., Moritz R., van der Meer J.R., 2019/06/11. mBio, 10 (3). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3E18AD31C59A]
 
Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.
Ellegaard K.M., Brochet S., Bonilla-Rosso G., Emery O., Glover N., Hadadi N., Jaron K.S., van der Meer J.R., Robinson-Rechavi M., Sentchilo V. et al., 2019/05. Molecular ecology, 28 (9) pp. 2224-2237. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_37C4AFA6D4D6]
 
The urgent need for microbiology literacy in society.
Timmis K., Cavicchioli R., Garcia J.L., Nogales B., Chavarría M., Stein L., McGenity T.J., Webster N., Singh B.K., Handelsman J. et al., 2019/05. Environmental microbiology, 21 (5) pp. 1513-1528. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5EE7480BEA52]
Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities.
Pinto-Figueroa E.A., Seddon E., Yashiro E., Buri A., Niculita-Hirzel H., van der Meer J.R., Guisan A., 2019. Frontiers in microbiology, 10 p. 656. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AA333B1F4320]
Bridging the Holistic-Reductionist Divide in Microbial Ecology.
Tecon R., Mitri S., Ciccarese D., Or D., van der Meer J.R., Johnson D.R., 2019. mSystems, 4 (1) pp. e00265-18. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2408248DE884]
Probing chemotaxis activity in Escherichia coli using fluorescent protein fusions.
Roggo C., Carraro N., van der Meer J.R., 2019. Scientific Reports, 9 (1) p. 3845. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_73F38E4B18B0]
2018
Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities.
Yashiro E., Pinto-Figueroa E., Buri A., Spangenberg J.E., Adatte T., Niculita-Hirzel H., Guisan A., van der Meer J.R., 2018/04/10. Scientific reports, 8 (1) p. 5758. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_ED0B5621943C]
Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element.
Miyazaki R., Yano H., Sentchilo V., van der Meer J.R., 2018/04/03. Scientific reports, 8 (1) p. 5550. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_73BE1A6DF8A9]
 
Bacterial bioreporter detection of arsenic associated with iron oxides.
van Genuchten C.M., Finger A., van der Meer J.R., Peña J., 2018. Environmental Science. Processes & Impacts, 20 (6) pp. 913-922. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E6394958E0C3]
Genomic Islands Confer Heavy Metal Resistance in <i>Mucilaginibacter kameinonensis</i> and <i>Mucilaginibacter rubeus</i> Isolated from a Gold/Copper Mine.
Li Y.P., Carraro N., Yang N., Liu B., Xia X., Feng R., Saquib Q., Al-Wathnani H.A., van der Meer J.R., Rensing C., 2018. Genes, 9 (12) p. 573. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3EFBB2B378E7]
 
Heterologous Expression of Pseudomonas putida Methyl-Accepting Chemotaxis Proteins Yields Escherichia coli Cells Chemotactic to Aromatic Compounds.
Roggo C., Clerc E.E., Hadadi N., Carraro N., Stocker R., van der Meer J.R., 2018. Applied and Environmental Microbiology, 84 (18) pp. UNSP e01362-18. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3E2FA14125EB]
Host diet mediates a negative relationship between abundance and diversity of <i>Drosophila</i> gut microbiota.
Erkosar B., Yashiro E., Zajitschek F., Friberg U., Maklakov A.A., van der Meer J.R., Kawecki T.J., 2018. Ecology and Evolution, 8 (18) pp. 9491-9502. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F58157E65CCA]
 
Prospects for harnessing biocide resistance for bioremediation and detoxification.
Atashgahi S., Sánchez-Andrea I., Heipieper H.J., van der Meer J.R., Stams AJM, Smidt H., 2018. Science, 360 (6390) pp. 743-746. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CE3E9B851FB6]
Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips.
Roggo C., Picioreanu C., Richard X., Mazza C., van Lintel H., van der Meer J.R., 2018/01. Environmental microbiology, 20 (1) pp. 241-258. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A44B85643995]
2017
Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in <i>Drosophila melanogaster</i>.
Erkosar B., Kolly S., van der Meer J.R., Kawecki T.J., 2017/10/24. mBio, 8 (5) pp. e01496-17. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_184BA4E039A0]
Complete alanine scanning of the Escherichia coli RbsB ribose binding protein reveals residues important for chemoreceptor signaling and periplasmic abundance.
Reimer A., Maffenbeier V., Dubey M., Sentchilo V., Tavares D., Gil M.H., Beggah S., van der Meer J.R., 2017/08/15. Scientific reports, 7 (1) p. 8245. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5AD53A0AA296]
 
Editorial overview: Environmental biotechnology.
van der Meer J.R., Gu M.B., 2017/06. Current opinion in biotechnology, 45 pp. ix-xi. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6A10872796B7]
 
Miniaturized and integrated whole cell living bacterial sensors in field applicable autonomous devices.
Roggo C., van der Meer J.R., 2017/06. Current opinion in biotechnology, 45 pp. 24-33. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B1D25502E729]
 
Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation.
Berset Y., Merulla D., Joublin A., Hatzimanikatis V., van der Meer J.R., 2017/05/19. ACS synthetic biology, 6 (5) pp. 862-874. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7DB8AF3E6328]
Draft Genome Sequence of Microbacterium foliorum Strain 122 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
Lumactud R., Fulthorpe R., Sentchilo V., van der Meer J.R., 2017. Genome Announcements, 5 (21) pp. e00434-17. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_63E505728E9E]
Draft Genome Sequence of Plantibacterflavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
Lumactud R., Fulthorpe R., Sentchilo V., van der Meer J.R., 2017. Genome announcements, 5 (17) p. 0. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7F75295C2E48]
The hidden life of integrative and conjugative elements.
Delavat F., Miyazaki R., Carraro N., Pradervand N., van der Meer J.R., 2017. FEMS Microbiology Reviews, 41 (4) pp. 512-537. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6E8C309F2480]
2016
Towards improved biomonitoring tools for an intensified sustainable multi-use environment.
van der Meer J.R., 2016/09. Microbial biotechnology, 9 (5) pp. 658-665. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_3556836E77FF]
An automated microreactor for semi-continuous biosensor measurements.
Buffi N., Beggah S., Truffer F., Geiser M., van Lintel H., Renaud P., van der Meer J.R., 2016/04/21. Lab on a chip, 16 (8) pp. 1383-1392. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7C142343503E]
 
Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties.
Moreno-Forero S.K., Rojas E., Beggah S., van der Meer J.R., 2016/02. Environmental microbiology reports, 8 (1) pp. 91-102.
[DOI][Pmid][serval:BIB_FF2CB4936A57]
Challenges in microbial ecology: building predictive understanding of community function and dynamics.
Widder S., Allen R.J., Pfeiffer T., Curtis T.P., Wiuf C., Sloan W.T., Cordero O.X., Brown S.P., Momeni B., Shou W. et al., 2016. The ISME Journal, 10 (11) pp. 2557-2568. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_248C690340DC]
 
Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.
Delavat F., Mitri S., Pelet S., van der Meer J.R., 2016. Proceedings of the National Academy of Sciences of the United States of America, 113 (24) pp. E3375-E3383. Peer-reviewed.
[DOI][Pmid][serval:BIB_803A374889D3]
Immediate ecotoxicological effects of short-lived oil spills on marine biota.
Brussaard C.P., Peperzak L., Beggah S., Wick L.Y., Wuerz B., Weber J., Samuel Arey J., van der Burg B., Jonas A., Huisman J. et al., 2016. Nature Communications, 7 p. 11206. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F95CE134EFB7]
 
Local environmental factors drive divergent grassland soil bacterial communities in the Western Swiss Alps
Yashiro E., Pinto-Figueroa E., Buri A., Spangenberg J.E., Adatte T., Niculita-Hirzel Hélène, Guisan A., van der Meer J.R., 2016. Applied and Environmental Microbiology, 82 (21) pp. 6303-6316. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D1CE0974236C]
 
Regulatable and modulable background expression control in prokaryotic synthetic circuits by auxiliary repressor binding sites.
Merulla D., van der Meer J.R., 2016. ACS Synthetic Biology, 5 (1) pp. 36-45.
[DOI][WoS][Pmid][serval:BIB_15016DFBBC79]
The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.
Morales M., Sentchilo V., Bertelli C., Komljenovic A., Kryuchkova-Mostacci N., Bourdilloud A., Linke B., Goesmann A., Harshman K., Segers F. et al., 2016. PloS one, 11 (11) pp. e0165850. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_14197457242A]
2015
Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.
Miyazaki R., Bertelli C., Benaglio P., Canton J., De Coi N., Gharib W.H., Gjoksi B., Goesmann A., Greub G., Harshman K. et al., 2015. Environmental Microbiology, 17 (1) pp. 91-104.
[URN][DOI][WoS][Pmid][serval:BIB_EBE76C19261B]
Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea.
Chronopoulou P.M., Sanni G.O., Silas-Olu D.I., van der Meer J.R., Timmis K.N., Brussaard C.P., McGenity T.J., 2015. Microbial Biotechnology, 8 (3) pp. 434-447.
[URN][DOI][WoS][Pmid][serval:BIB_CF21C7BD3304]
Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand.
Moreno-Forero S.K., van der Meer J.R., 2015. ISME Journal, 9 (1) pp. 150-165.
[URN][DOI][WoS][Pmid][serval:BIB_D49FBEEC9FA0]
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.
Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P. et al., 2015. Frontiers in Microbiology, 6 (101) p. 101. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5BB2A564D83D]
 
Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms.
Coronado E., Valtat A., van der Meer J.R., 2015. Environmental Microbiology Reports, 7 (3) pp. 480-488.
[DOI][WoS][Pmid][serval:BIB_A27088838400]
2014
An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13.
Pradervand N., Sulser S., Delavat F., Miyazaki R., Lamas I., van der Meer J.R., 2014. PLoS Genetics, 10 (6) pp. e1004441.
[URN][DOI][WoS][Pmid][serval:BIB_FBF01B4AAD20]
 
Compact portable biosensor for arsenic detection in aqueous samples with Escherichia coli bioreporter cells.
Truffer F., Buffi N., Merulla D., Beggah S., van Lintel H., Renaud P., van der Meer J.R., Geiser M., 2014. Review of Scientific Instruments, 85 (1) p. 015120.
[DOI][WoS][Pmid][serval:BIB_580F45009EC8]
Escherchia coli ribose binding protein based bioreporters revisited.
Reimer A., Yagur-Kroll S., Belkin S., Roy S., van der Meer J.R., 2014. Scientific Reports, 4 p. 5626.
[URN][DOI][WoS][Pmid][serval:BIB_81FA3F0E8394]
 
First day of an oil spill on the open sea: early mass transfers of hydrocarbons to air and water.
Gros J., Nabi D., Würz B., Wick L.Y., Brussaard C.P., Huisman J., van der Meer J.R., Reddy C.M., Arey J.S., 2014. Environmental Science and Technology, 48 (16) pp. 9400-9411.
[DOI][WoS][Pmid][serval:BIB_B037D8FC21CA]
Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery.
Coronado E., Roggo C., van der Meer J.R., 2014. Frontiers in Microbiology, 5 p. 585. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FB37DCA4633B]
 
Identification of opsA, a gene involved in solute stress mitigation and survival in soil, in the polycyclic aromatic hydrocarbon-degrading bacterium Novosphingobium sp. strain LH128.
Fida T.T., Breugelmans P., Lavigne R., van der Meer J.R., De Mot R., Vaysse P.J., Springael D., 2014. Applied and Environmental Microbiology, 80 (11) pp. 3350-3361.
[DOI][WoS][Pmid][serval:BIB_9B7DB2135E47]
 
Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.
Reinhard F., van der Meer J.R., 2014. Journal of Bacteriology, 196 (7) pp. 1425-1434. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_31B26B4E0819]
 
The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer.
Pradervand N., Delavat F., Sulser S., Miyazaki R., van der Meer J.R., 2014. Journal of Bacteriology, 196 (22) pp. 3971-3979.
[DOI][WoS][Pmid][serval:BIB_73DABBD0EAB1]
 
Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.
Scheublin T.R., Deusch S., Moreno-Forero S.K., Müller J.A., van der Meer J.R., Leveau J.H., 2014. Environmental Microbiology, 16 (7) pp. 2212-2225.
[DOI][WoS][Pmid][serval:BIB_72524887A306]
2013
 
A New Large-DNA-Fragment Delivery System Based on Integrase Activity from an Integrative and Conjugative Element.
Miyazaki R., van der Meer J.R., 2013. Applied and Environmental Microbiology, 79 (14) pp. 4440-4447. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_064586E230F3]
 
Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem.
Merulla D., Buffi N., Beggah S., Truffer F., Geiser M., Renaud P., van der Meer J.R., 2013. Current Opinion in Biotechnology, 24 (3) pp. 534-541.
[DOI][WoS][Pmid][serval:BIB_FAF803CA1333]
 
Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria.
Reinhard F., Miyazaki R., Pradervand N., van der Meer J.R., 2013. Current Biology, 23 (3) pp. 255-259.
[DOI][WoS][Pmid][serval:BIB_9AC49313302F]
Characterization of a MexAB-OprM efflux system necessary for productive metabolism of Pseudomonas azelaica HBP1 on 2-hydroxybiphenyl.
Czechowska K., Reimmann C., van der Meer J.R., 2013. Frontiers in Microbiology, 4 p. 203.
[URN][DOI][WoS][Pmid][serval:BIB_C10F602C3AD8]
Community-wide plasmid gene mobilization and selection.
Sentchilo V., Mayer A.P., Guy L., Miyazaki R., Green Tringe S., Barry K., Malfatti S., Goessmann A., Robinson-Rechavi M., van der Meer J.R., 2013. ISME Journal, 7 (6) pp. 1173-1186.
[URN][DOI][WoS][Pmid][serval:BIB_B5128FCC3FB5]
 
Electrochemical As(III) whole-cell based biochip sensor.
Cortés-Salazar F., Beggah S., van der Meer J.R., Girault H.H., 2013. Biosensors and Bioelectronics, 47 pp. 237-242.
[DOI][WoS][Pmid][serval:BIB_A2F5B964F7BC]
 
Examining chemical compound biodegradation at low concentrations through bacterial cell proliferation.
Czechowska K., Sentchilo V., Beggah S., Rey S., Seyfried M., van der Meer J.R., 2013. Environmental Science and Technology, 47 (4) pp. 1913-1921.
[DOI][WoS][Pmid][serval:BIB_904323C94D10]
 
Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1.
Roggo C., Coronado E., Moreno-Forero S.K., Harshman K., Weber J., van der Meer J.R., 2013. Environmental Microbiology, 15 (10) pp. 2681-2695.
[DOI][WoS][Pmid][serval:BIB_98FA785B3C61]
 
Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria.
Schamfuß S., Neu T.R., van der Meer J.R., Tecon R., Harms H., Wick L.Y., 2013. Environmental Science and Technology, 47 (13) pp. 6908-6915.
[DOI][WoS][Pmid][serval:BIB_DE4D9C95B242]
Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.
Reinhard F., van der Meer J.R., 2013. PLoS One, 8 (10) pp. e78288.
[URN][DOI][WoS][Pmid][serval:BIB_816AAE447B04]
 
The clc element and related genomic islands in Proteobacteria
Miyazaki R., Minoia M., Pradervand N., Sentchilo V., Sulser S., Reinhard F., van der Meer J. R., 2013/01. p. 336 dans Roberts A.P., Mullany P. (eds.) Bacterial integrative mobile genetic elements, Landes Bioscience.
[serval:BIB_E4924A2BDD7E]
Tunable reporter signal production in feedback-uncoupled arsenic bioreporters.
Merulla D., Hatzimanikatis V., van der Meer J.R., 2013. Microbial Biotechnology, 6 (5) pp. 503-514. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5B9F1130187F]
2012
Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element.
Miyazaki R., Minoia M., Pradervand N., Sulser S., Reinhard F., van der Meer J.R., 2012. PLoS Genetics, 8 (7) pp. e1002818. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_24349ACB7339]
 
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms.
Fida T.T., Breugelmans P., Lavigne R., Coronado E., Johnson D.R., van der Meer J.R., Mayer A.P., Heipieper H.J., Hofkens J., Springael D., 2012. Applied and Environmental Microbiology, 78 (23) pp. 8311-8320.
[DOI][WoS][Pmid][serval:BIB_A6551D5DB05A]
 
Field testing of arsenic in groundwater samples of Bangladesh using a test kit based on lyophilized bioreporter bacteria.
Siegfried K., Endes C., Bhuiyan A.F., Kuppardt A., Mattusch J., van der Meer J.R., Chatzinotas A., Harms H., 2012. Environmental Science and Technology, 46 (6) pp. 3281-3287.
[DOI][WoS][Pmid][serval:BIB_470EFE2AD81B]
Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1.
Coronado E., Roggo C., Johnson D.R., van der Meer J.R., 2012. Frontiers in Microbiology, 3 p. 300.
[URN][DOI][WoS][Pmid][serval:BIB_45EC0FCE50E2]
 
Reversible and irreversible pollutant-induced bacterial cellular stress effects measured by ethidium bromide uptake and efflux.
Czechowska K., van der Meer J.R., 2012. Environmental Science and Technology, 46 (2) pp. 1201-1208.
[DOI][WoS][Pmid][serval:BIB_A2708E1774B4]
2011
 
A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13.
Miyazaki R., van der Meer J.R., 2011. Molecular Microbiology, 79 (3) pp. 743-758.
[DOI][WoS][Pmid][serval:BIB_BB1C7BF33938]
 
A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury.
Czechowska K., van der Meer J.R., 2011. Environmental Science and Technology, 45 (13) pp. 5820-5827.
[DOI][WoS][Pmid][serval:BIB_33320468370A]
Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis.
Vogne C., Bisht H., Arias S., Fraile S., Lal R., van der Meer J.R., 2011. PLoS One, 6 (2) pp. e16539.
[URN][DOI][WoS][Pmid][serval:BIB_EB607C562CAB]
 
Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples.
Buffi N., Merulla D., Beutier J., Barbaud F., Beggah S., van Lintel H., Renaud P., van der Meer J.R., 2011. Lab On A Chip, 11 (14) pp. 2369-2377.
[DOI][WoS][Pmid][serval:BIB_97E35BF48444]
 
Development of bioreporter assays for the detection of bioavailability of long-chain alkanes based on the marine bacterium Alcanivorax borkumensis strain SK2.
Kumari R., Tecon R., Beggah S., Rutler R., Arey J.S., van der Meer J.R., 2011. Environmental Microbiology, 13 (10) pp. 2808-2819.
[DOI][WoS][Pmid][serval:BIB_8B3CADD159D3]
 
How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element?
Miyazaki R., van der Meer J.R., 2011. Mobile Genetic Elements, 1 (1) pp. 82-84.
[DOI][Pmid][serval:BIB_BEC5C28504DD]
 
Miniaturized bacterial biosensor system for arsenic detection holds great promise for making integrated measurement device.
Buffi N., Merulla D., Beutier J., Barbaud F., Beggah S., van Lintel H., Renaud P., van der Meer J.R., 2011. Bioengineered Bugs, 2 (5) pp. 296-298.
[DOI][Pmid][serval:BIB_FC72B353364A]
Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.
Johnson D.R., Coronado E., Moreno-Forero S.K., Heipieper H.J., van der Meer J.R., 2011. BMC Microbiology, 11 (1) p. 250.
[URN][DOI][WoS][Pmid][serval:BIB_7D06CCB4205A]
 
Transcriptomic analysis of phenanthrene degrading Sphingomonas biofilms exposed to environmentally relevant solute and matric stresses.
Fida T.T., Breugelmans P., Lavigne R., Coronado E., Johnson D., Van Der Meer J.R., Mayer A., Hofkens J., Springael D., 2011. Communications in Agricultural and Applied Biological Sciences, 76 (1) pp. 69-72.
[Pmid][serval:BIB_AEA8E9CEE052]
2010
 
Bacterial bioreporter assays to measure hydrocarbons
Tecon R., Beggah S., van der Meer J. R., 2010. pp. 3642-3652 dans Timmis K. N. (eds.) Handbook of hydrocarbon and lipid microbiology chap. 24, Springer.
[DOI][serval:BIB_700D794058C7]
 
Bacterial sensors: synthetic design and application principles
van der Meer J.R., 2010. Synthesis Lectures on Synthetic Biology 167, Morgan & Claypool Publ..
[DOI][serval:BIB_B2F2FE9B85C9]
 
Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi.
Scheublin T.R., Sanders I.R., Keel C., van der Meer J.R., 2010. ISME Journal, 4 (6) pp. 752-763.
[DOI][WoS][Pmid][serval:BIB_0DF7E6CB4E97]
 
Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments.
Tecon R., Beggah S., Czechowska K., Sentchilo V., Chronopoulou P.M., McGenity T.J., van der Meer J.R., 2010. Environmental science and technology, 44 (3) pp. 1049-1055. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4DFCA9B14DB6]
Effect of two types of biosurfactants on phenanthrene availability to the bacterial bioreporter Burkholderia sartisoli strain RP037.
Tecon R., van der Meer J.R., 2010. Applied microbiology and biotechnology, 85 (4) pp. 1131-1139. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B7567FDB5CBA]
 
Let the sun shine.
van der Meer J.R., 2010. Current Opinion in Biotechnology, 21 (3) pp. 235-237.
[DOI][WoS][Pmid][serval:BIB_2F5A7BB67DF9]
 
Microcolony growth assays
Reinhard F., van der Meer J. R., 2010. pp. 3562-3570 dans Timmis K. N. (eds.) Handbook of hydrocarbon and lipid microbiology chap. 16, Springer.
[DOI][serval:BIB_EC257933284F]
 
Random and site-directed mutagenesis of transcriptional regulator proteins implicated in hydrocarbon degradation pathways
Vogne C., Beggah S., van der Meer J. R., 2010. pp. 4430-4444 dans Timmis K. N. (eds.) Handbook of hydrocarbon and lipid microbiology chap. 83, Springer.
[DOI][serval:BIB_005831520FFD]
 
Response to Comment on "Unlike PAHs from Exxon Valdez Crude Oil, PAHs from Gulf of Alaska Coals are not Readily Bioavailable".
Deepthike H.U., Tecon R., Kooten G.K., Meer J.R., Harms H., Wells M., Short J., 2010. Environmental Science and Technology, 44 (6) pp. 2212-2213.
[DOI][WoS][Pmid][serval:BIB_5B194F33F0E7]
Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13.
Gaillard M., Pradervand N., Minoia M., Sentchilo V., Johnson D.R., van der Meer J.R., 2010. BMC Microbiology, 10 p. 153.
[URN][DOI][WoS][Pmid][serval:BIB_4301FC5CF60A]
 
Where microbiology meets microengineering: design and applications of reporter bacteria.
van der Meer J.R., Belkin S., 2010. Nature Reviews. Microbiology, 8 (7) pp. 511-522.
[DOI][WoS][Pmid][serval:BIB_44099BB15053]
2009
Development of bacteria-based bioassays for arsenic detection in natural waters.
Diesel E., Schreiber M., van der Meer J.R., 2009. Analytical and Bioanalytical Chemistry, 394 (3) pp. 687-693. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_52FEEDE4E201]
 
Double-tagged fluorescent bacterial bioreporter for the study of polycyclic aromatic hydrocarbon diffusion and bioavailability.
Tecon R., Binggeli O., van der Meer J.R., 2009. Environmental Microbiology, 11 (9) pp. 2271-2283.
[DOI][WoS][Pmid][serval:BIB_9835D80F2A1F]
 
Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13.
Sentchilo V., Czechowska K., Pradervand N., Minoia M., Miyazaki R., van der Meer J.R., 2009. Molecular microbiology, 72 (5) pp. 1293-1306. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_42A460EF5F13]
 
Novel use of a whole cell E. coli bioreporter as a urinary exposure biomarker.
Ewis C.L., Beggah S., Pook C., Guitart C., Redshaw C., van der Meer J.R., Readman J.W., Galloway T., 2009. Environmental Science and Technology, 43 (2) pp. 423-428. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F6C5CA5221DE]
 
Optimization of preservation conditions of As (III) bioreporter bacteria.
Kuppardt A., Chatzinotas A., Breuer U., van der Meer J.R., Harms H., 2009. Applied microbiology and biotechnology, 82 (4) pp. 785-792. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A61913A483DC]
 
Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry.
Johnson D.R., Czechowska K., Chèvre N., van der Meer J.R., 2009. Environmental Microbiology, 11 pp. 1682-1691. Peer-reviewed.
[DOI][WoS][serval:BIB_F3E7DD936B0A]
 
Unlike PAHs from Exxon Valdez crude oil, PAHs from Gulf of Alaska coals are not readily bioavailable.
Deepthike H.U., Tecon R., Van Kooten G., Van der Meer J.R., Harms H., Wells M., Short J., 2009. Environmental Science and Technology, 43 (15) pp. 5864-5870. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E391322CF69A]
2008
 
Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.
Meier C., Wehrli B., van der Meer J.R., 2008/08. Microbial ecology, 56 (2) pp. 210-222. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_44B11AA49069]
Bacterial biosensors for measuring availability of environmental pollutants
Tecon R., van der Meer J. R., 2008. Sensors, 8 (7) pp. 4062-4080. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_3926B9861EA9]
 
Burkholderia sartisoli sp. nov., isolated from a polycyclic aromatic hydrocarbon-contaminated soil.
Vanlaere E., van der Meer J.R., Falsen E., Salles J.F., de Brandt E., Vandamme P., 2008. International Journal of Systematic and Evolutionary Microbiology, 58 (Pt 2) pp. 420-423.
[DOI][WoS][Pmid][serval:BIB_0F4DE4659FCC]
Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax
Kohlmeier S., Mancuso M., Deepthike U., Tecon R., van der Meer J.R., Harms H., Wells M., 2008. Environmental Pollution, 156 (3) pp. 803-808. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EFB2D1AC4E95]
 
Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A.
Raina V., Suar M., Singh A., Prakash O., Dadhwal M., Gupta S.K., Dogra C., Lawlor K., Lal S., van der Meer J.R. et al., 2008. Biodegradation, 19 (1) pp. 27-40.
[DOI][WoS][Pmid][serval:BIB_BF67FF08B7E7]
Genomic islands: tools of bacterial horizontal gene transfer and evolution.
Juhas M., van der Meer J.R., Gaillard M., Harding R.M., Hood D.W., Crook D.W., 2008. FEMS Microbiology Reviews, 33 (2) pp. 376-393. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E141F168AF54]
 
Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1
Gaillard M., Pernet N., Vogne C., Hagenbuchle O., van der Meer J. R., 2008. Proceedings of the National Academy of Sciences of the United States of America, 105 (19) pp. 7058-7063. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_341690BB4E4B]
Internal arsenite bioassay calibration using multiple reporter cell lines
Wackwitz A., Harms H., Chatzinotas A., Breuer U., Vogne C., van der Meer J. R., 2008. Microbial Biotechnology, 1 (2) pp. 149-157. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_D3D7C035CF00]
Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting.
Beggah S., Vogne C., Zenaro E., Van Der Meer J.R., 2008. Microbial Biotechnology, 1 (1) pp. 68-78.
[URN][DOI][WoS][Pmid][serval:BIB_808BE6B1F75F]
Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas.
Minoia M., Gaillard M., Reinhard F., Stojanov M., Sentchilo V., van der Meer J.R., 2008. Proceedings of the National Academy of Sciences of the United States of America, 105 (52) pp. 20792-20797. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FA49C421D122]
 
Use of flow cytometric methods for single-cell analysis in environmental microbiology
Czechowska K., Johnson D. R., van der Meer J. R., 2008. Current Opinion in Microbiology, 11 (3) pp. 205-212. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6FF19A356C09]
2007
 
A genomic view on the evolution of catabolic pathways and bacterial adaptation to toxic compounds
Van Der Meer J. R., 2007. pp. 219-269 dans Diaz E. (eds.) Microbial biodegradation : genomics and molecular biology chap. 8, Caister Academic Press.
[serval:BIB_8C4BDA0BC7CC]
 
Analysis of bioavailable arsenic in rice with whole cell living bioreporter bacteria.
Baumann B., van der Meer J.R., 2007. Journal of Agricultural and Food Chemistry, 55 (6) pp. 2115-2120.
[DOI][WoS][Pmid][serval:BIB_B1F89D158CEE]
 
Artificial neural network study of whole-cell bacterial bioreporter response determined using fluorescence flow cytometry.
Busam S., McNabb M., Wackwitz A., Senevirathna W., Beggah S., Meer J.R., Wells M., Breuer U., Harms H., 2007. Analytical Chemistry, 79 (23) pp. 9107-9114.
[DOI][WoS][Pmid][serval:BIB_37B3BDC1EC23]
 
Bioreporters: gfp versus lux revisited and single-cell response.
Kohlmeier S., Mancuso M., Tecon R., Harms H., van der Meer J.R., Wells M., 2007. Biosensors and Bioelectronics, 22 (8) pp. 1578-1585.
[DOI][WoS][Pmid][serval:BIB_5FD7B1735A6E]
2006
 
A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes.
Tecon R., Wells M., van der Meer J.R., 2006. Environmental Microbiology, 8 (4) pp. 697-708.
[DOI][WoS][Pmid][serval:BIB_D451BC2BE0DA]
 
Analytics with engineered bacterial bioreporter strains and systems.
van der Meer J.R., 2006. Current Opinion in Biotechnology, 17 (1) pp. 1-3.
[DOI][WoS][Pmid][serval:BIB_1BB0FFCBF4BB]
Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.
Paul D., Pandey G., Meier C., van der Meer J.R., Jain R.K., 2006. Fems Microbiology Ecology, 57 (1) pp. 116-127.
[URN][DOI][WoS][Pmid][serval:BIB_0A14F850ECDE]
 
Environmental pollution promotes selection of microbial degradation pathways
van der Meer J. R., 2006. Frontiers in Ecology and the Environment, 4 (1) pp. 35-42. Peer-reviewed.
[DOI][WoS][serval:BIB_BCEF0A861551]
 
Evolution of catabolic pathways in Pseudomonas through gene transfer
van der Meer J. R., 2006. pp. 189-236 dans Ramos J. L., Levesque R. C. (eds.) Pseudomonas : Molecular Biology of Emerging Issues, Springer.
[DOI][serval:BIB_8A0F87714F7F]
 
Genomic islands and the evolution of catabolic pathways
Lacour S., Gaillard M., Van Der Meer J. R., 2006. pp. 255-274 dans Logan N. A., Lappin-Scott H. M., Oyston P. C. F. (eds.) Prokaryotic diversity : mechanisms and significance, Cambridge University Press.
[serval:BIB_D69651CF1E98]
 
Information from single-cell bacterial biosensors: what is it good for?
Tecon R., van der Meer J.R., 2006. Current Opinion in Biotechnology, 17 (1) pp. 4-10.
[DOI][WoS][Pmid][serval:BIB_F08162BC7181]
 
Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH.
Müller T.A., Fleischmann T., van der Meer J.R., Kohler H.P., 2006. Applied and Environmental Microbiology, 72 (7) pp. 4853-4861.
[DOI][WoS][Pmid][serval:BIB_4D7377327DE3]
 
The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties.
Gaillard M., Vallaeys T., Vorhölter F.J., Minoia M., Werlen C., Sentchilo V., Pühler A., van der Meer J.R., 2006. Journal of Bacteriology, 188 (5) pp. 1999-2013.
[DOI][WoS][Pmid][serval:BIB_D5BE93CEBFEA]
 
Whole-cell living biosensors--are they ready for environmental application?
Harms H., Wells M.C., van der Meer J.R., 2006. Applied Microbiology and Biotechnology, 70 (3) pp. 273-280.
[DOI][WoS][Pmid][serval:BIB_C07260FF8F30]
2005
 
Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples.
Trang P.T., Berg M., Viet P.H., Van Mui N., Van Der Meer J.R., 2005. Environmental Science and Technology, 39 (19) pp. 7625-7630.
[DOI][WoS][Pmid][serval:BIB_A5BDB7442000]
 
Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain.
Tropel D., van der Meer J.R., 2005. FEBS Journal, 272 (7) pp. 1756-1766.
[DOI][WoS][Pmid][serval:BIB_D3E453C01AFA]
 
Effect of groundwater composition on arsenic detection by bacterial biosensors.
Harms H., Rime J., Hug S.J., van der Meer J.R., 2005. Microchimica Acta, 151 (3-4) pp. 217-222. Peer-reviewed.
[DOI][WoS][serval:BIB_37367]
 
Enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A.
Suar M., Hauser A., Poiger T., Buser H.R., Müller M.D., Dogra C., Raina V., Holliger C., van der Meer J.R., Lal R. et al., 2005. Applied and Environmental Microbiology, 71 (12) pp. 8514-8518.
[DOI][WoS][Pmid][serval:BIB_BBFEEF092872]
 
Response characteristics of arsenic-sensitive bioreporters expressing the gfp reporter gene
Wells M., Gösch M., Harms H., Van Der Meer J. R., 2005. Microchimica Acta, 151 (3-4) pp. 209-216. Peer-reviewed.
[DOI][WoS][serval:BIB_26268783A915]
 
Ultrasensitive reporter protein detection in genetically engineered bacteria.
Wells M., Gösch M., Rigler R., Harms H., Lasser T., van der Meer J.R., 2005. Analytical Chemistry, 77 (9) pp. 2683-2689.
[DOI][WoS][Pmid][serval:BIB_1771FB324C30]
2004
 
Bacterial transcriptional regulators for degradation pathways of aromatic compounds.
Tropel D., van der Meer J.R., 2004. Microbiology and Molecular Biology Reviews, 68 (3) pp. 474-500.
[DOI][WoS][Pmid][serval:BIB_78BF55226F75]
 
Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR.
Tropel D., Bähler A., Globig K., van der Meer J.R., 2004. Environmental Microbiology, 6 (11) pp. 1186-1196.
[DOI][WoS][Pmid][serval:BIB_8519E4BFC615]
 
Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers.
Suar M., van der Meer J.R., Lawlor K., Holliger C., Lal R., 2004. Applied and Environmental Microbiology, 70 (11) pp. 6650-6656.
[DOI][WoS][Pmid][serval:BIB_F279651A4881]
 
Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas herbicidovorans MH.
Müller T.A., Byrde S.M., Werlen C., van der Meer J.R., Kohler H.P., 2004. Applied and Environmental Microbiology, 70 (10) pp. 6066-6075.
[DOI][WoS][Pmid][serval:BIB_2B24F71A659B]
 
Illuminating the detection chain of bacterial bioreporters.
van der Meer J.R., Tropel D., Jaspers M., 2004. Environmental Microbiology, 6 (10) pp. 1005-1020.
[DOI][WoS][Pmid][serval:BIB_4FDEB1A60D64]
 
Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor.
Werlen C., Jaspers M.C., van der Meer J.R., 2004. Applied and Environmental Microbiology, 70 (1) pp. 43-51.
[DOI][WoS][Pmid][serval:BIB_B45D4D4D073E]
Mutation analysis of the different tfd genes for degradation of chloroaromatic compounds in Ralstonia eutropha JMP134.
Laemmli C., Werlen C., van der Meer J.R., 2004. Archives of Microbiology, 181 (2) pp. 112-121.
[DOI][WoS][Pmid][serval:BIB_13E7A2859831]
 
Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer.
Dogra C., Raina V., Pal R., Suar M., Lal S., Gartemann K.H., Holliger C., van der Meer J.R., Lal R., 2004. Journal of Bacteriology, 186 (8) pp. 2225-2235.
[DOI][Pmid][serval:BIB_500B9F8D12E8]
 
Relationship between sediment organic matter, bacteria composition, and the ecosystem metabolism of alpine streams
Brendan Logue J., Robinson C.T., Meier C., Van Der Meer J.R., 2004. Limnology and Oceanography, 49 (6) pp. 2001-2010. Peer-reviewed.
[WoS][serval:BIB_22093D9F64D2]
2003
 
Bakterielle biosensoren zur Bestimmung von arsen im Trinkwasser.
Stocker J, van der Meer JR, 2003. EAWAG News, 56 pp. 12-15.
[serval:BIB_27978]
 
Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13.
Sentchilo V., Zehnder A.J., van der Meer J.R., 2003. Molecular Microbiology, 49 (1) pp. 93-104.
[DOI][WoS][Pmid][serval:BIB_F79CFAABA4F8]
 
Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors.
Egli K., Langer C., Siegrist H.R., Zehnder A.J., Wagner M., van der Meer J.R., 2003. Applied and Environmental Microbiology, 69 (6) pp. 3213-3222.
[DOI][WoS][Pmid][serval:BIB_7DBB9E1CBB4E]
 
Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable water.
Stocker J., Balluch D., Gsell M., Harms H., Feliciano J., Daunert S., Malik K.A., van der Meer J.R., 2003. Environmental Science and Technology, 37 (20) pp. 4743-4750.
[DOI][WoS][Pmid][serval:BIB_4D9CF0E4323C]
 
Effect of integration of a GFP reporter gene on fitness of Ralstonia eutropha during growth with 2,4-dichlorophenoxyacetic acid.
Füchslin H.P., Rüegg I., Van Der Meer J.R., Egli T., 2003. Environmental Microbiology, 5 (10) pp. 878-887.
[DOI][WoS][Pmid][serval:BIB_D3856319C06E]
 
Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia.
Müller T.A., Werlen C., Spain J., Van Der Meer J.R., 2003. Environmental Microbiology, 5 (3) pp. 163-173.
[DOI][WoS][Pmid][serval:BIB_D8476292474E]
 
Genomic islands and the evolution of catabolic pathways in bacteria.
van der Meer J.R., Sentchilo V., 2003. Current Opinion in Biotechnology, 14 (3) pp. 248-254.
[DOI][WoS][Pmid][serval:BIB_032E4BAFD3C5]
 
Ilots génomiques et transfert horizontal de gènes entre bactéries
Van der Meer J.R., Gaillard M., Sentchilo V., 2003. EAWAG News, 56 pp. 6-9.
[serval:BIB_27981]
 
Le procédé Anammox pour l'élimination de l'azote dans les stations d'épuration
Fux C., Egli K., van der Meer J.R., Siegrist H.R., 2003. EAWAG News, 56 pp. 20-21.
[serval:BIB_27961]
 
Microbial composition and structure of a rotating biological contactor biofilm treating ammonium-rich wastewater without organic carbon.
Egli K., Bosshard F., Werlen C., Lais P., Siegrist H., Zehnder A.J., Van der Meer J.R., 2003. Microbial Ecology, 45 (4) pp. 419-432.
[DOI][WoS][Pmid][serval:BIB_1BFC261A1409]
 
Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13.
Sentchilo V., Ravatn R., Werlen C., Zehnder A.J., van der Meer J.R., 2003. Journal of Bacteriology, 185 (15) pp. 4530-4538.
[DOI][WoS][Pmid][serval:BIB_A4832C2709FB]
2002
 
Cloning and characterization of lin genes responsible for the degradation of Hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90.
Kumari R., Subudhi S., Suar M., Dhingra G., Raina V., Dogra C., Lal S., van der Meer J.R., Holliger C., Lal R., 2002. Applied and Environmental Microbiology, 68 (12) pp. 6021-6028.
[DOI][WoS][Pmid][serval:BIB_10F2BDE88A84]
 
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.
Springael D., Peys K., Ryngaert A., Van Roy S., Hooyberghs L., Ravatn R., Heyndrickx M., van der Meer J.R., Vandecasteele C., Mergeay M. et al., 2002. Environmental Microbiology, 4 (2) pp. 70-80. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_63617E067031]
 
Evolution of metabolic pathways for degradation of environmental pollutants
van der Meer J.R., 2002. pp. 1194-1207 dans Bitton G. (eds.) Encyclopedia of environmental microbiology, Wiley.
[DOI][serval:BIB_3EF7902B69EA]
 
Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters.
Tropel D., van der Meer J.R., 2002. Journal of Bacteriology, 184 (11) pp. 2914-2924. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_27E0209B2A53]
 
TfdD(II), 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.
Laemmli C.M., Schönenberger R., Suter M., Zehnder A.J., van der Meer J.R., 2002. Archives of Microbiology, 178 (1) pp. 13-25. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B825F86DE72C]
2001
 
Biotransformation of various substituted aromatic compounds to chiral dihydrodihydroxy derivatives.
Raschke H., Meier M., Burken J.G., Hany R., Müller M.D., Van Der Meer J.R., Kohler H.P., 2001. Applied and Environmental Microbiology, 67 (8) pp. 3333-3339. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EB35B2AD2317]
 
Colonization of aerobic biofilms by sulfate-reducing bacteria.
Power M., van der Meer J.R., Harms H., Wanner O., 2001. Biofouling, 17 (4) pp. 275-288.
[WoS][serval:BIB_CA0E0D0BB118]
 
Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate.
Egli K., Fanger U., Alvarez P.J., Siegrist H., van der Meer J.R., Zehnder A.J., 2001. Archives of Microbiology, 175 (3) pp. 198-207. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3143BCC95088]
 
Measuring mass transfer processes of octane with the help of an alkSalkB::gfp-tagged Escherichia coli.
Jaspers M.C., Meier C., Zehnder A.J., Harms H., van der Meer J.R., 2001. Environmental Microbiology, 3 (8) pp. 512-524. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_465AE7E59D09]
 
The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases.
van der Meer J.R., Ravatn R., Sentchilo V., 2001. Archives of Microbiology, 175 (2) pp. 79-85. Peer-reviewed.
[WoS][Pmid][serval:BIB_E6ACA67CDEA4]
 
Transcriptional organization and dynamic expression of the hbpCAD genes, which encode the first three enzymes for 2-hydroxybiphenyl degradation in Pseudomonas azelaica HBP1.
Jaspers M.C., Schmid A., Sturme M.H., Goslings D.A., Kohler H.P., Roelof Van Der Meer J., 2001/01. Journal of bacteriology, 183 (1) pp. 270-279. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EA95DD5C1BCF]
 
Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of &quot;Pseudomonas azelaica&quot; HBP1.
Jaspers M.C., Sturme M., van der Meer J.R., 2001. Microbiology, 147 (Pt 8) pp. 2183-2194. Peer-reviewed.
[WoS][Pmid][serval:BIB_9F2185224841]
2000
 
Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134(pJP4).
Laemmli C.M., Leveau J.H., Zehnder A.J., van der Meer J.R., 2000. Journal of Bacteriology, 182 (15) pp. 4165-4172. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_17578297E6D1]
 
HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1.
Jaspers M.C., Suske W.A., Schmid A., Goslings D.A., Kohler H.P., van der Meer J.R., 2000. Journal of Bacteriology, 182 (2) pp. 405-417. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5E2DABF119B8]
 
Mathematical modeling of autotrophic denitrification in a nitrifying biofilm of a rotating biological contactor.
Koch G., Egli K., van der Meer J.R., Siegrist H., 2000. Water Science and Technology, 41 (4-5) pp. 191-198. Peer-reviewed.
[WoS][serval:BIB_05EF3F175D1C]
 
Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus.
Sentchilo V.S., Perebituk A.N., Zehnder A.J., van der Meer J.R., 2000. Applied and Environmental Microbiology, 66 (7) pp. 2842-2852. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0011C492494B]
1999
 
cis-chlorobenzene dihydrodiol dehydrogenase (TcbB) from Pseudomonas sp. strain P51, expressed in Escherichia coli DH5alpha(pTCB149), catalyzes enantioselective dehydrogenase reactions.
Raschke H., Fleischmann T., Van Der Meer J.R., Kohler H.P., 1999. Applied and Environmental Microbiology, 65 (12) pp. 5242-5246. Peer-reviewed.
[WoS][Pmid][serval:BIB_942A7A8EFA29]
 
Dynamics of multigene expression during catabolic adaptation of Ralstonia eutropha JMP134 (pJP4) to the herbicide 2, 4-dichlorophenoxyacetate.
Leveau J.H., König F., Füchslin H., Werlen C., Van Der Meer J.R., 1999. Molecular Microbiology, 33 (2) pp. 396-406. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3BD16674DCDA]
 
Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge.
Hesselmann R.P., Werlen C., Hahn D., van der Meer J.R., Zehnder A.J., 1999. Systematic and Applied Microbiology, 22 (3) pp. 454-465. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8AAF2F209A2B]
 
Monitoring sulfate-reducing bacteria in heterotrophic biofilms.
Power M., Araujo J.C., van der Meer J.R., Harms H., Wanner O., 1999. Water Science and Technology, 39 (7) pp. 49-56.
[DOI][serval:BIB_0ECE0AE5A194]
 
Population dynamics of an introduced bacterium degrading chlorinated benzenes in a soil column and in sewage sludge.
Tchelet R., Meckenstock R., Steinle P., van der Meer J.R., 1999. Biodegradation, 10 (2) pp. 113-125. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A008E29A5B60]
 
The use of whole-cell living biosensors to determine the bioavailability of pollutants to microorganisms
Jaspers M.C.M., Totevova S., Demnerova K., Harms H., van der Meer J.R., 1999. pp. 153-158 dans Baveye P., Block J.-C., Goncharuk V.V. (eds.) Bioavailability of organic xenobiotics in the environment : practical consequences for the environment, Kluwer Academic Publishers.
[serval:BIB_95452198B210]
1998
 
Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. Strain B13.
Ravatn R., Studer S., Springael D., Zehnder A.J., van der Meer J.R., 1998. Journal of Bacteriology, 180 (17) pp. 4360-4369. Peer-reviewed.
[WoS][Pmid][serval:BIB_F4740901DD86]
 
Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater
van der Meer J.R., Werlen C., Nishino S.F., Spain J.C., 1998. Applied and Environmental Microbiology, 64 (11) pp. 4185-4193. Peer-reviewed.
[WoS][Pmid][serval:BIB_EEED089C66E9]
 
Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. Strain B13.
Ravatn R., Studer S., Zehnder A.J., van der Meer J.R., 1998. Journal of Bacteriology, 180 (21) pp. 5505-5514. Peer-reviewed.
[WoS][Pmid][serval:BIB_DA6D79C006F5]
 
Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms.
Ravatn R., Zehnder A.J., van der Meer J.R., 1998. Applied and Environmental Microbiology, 64 (6) pp. 2126-2132. Peer-reviewed.
[WoS][Pmid][serval:BIB_3EF162A54B8F]
 
Molecular-based methods can contribute to assessments of toxicological risks and bioremediation strategies.
Power M., van der Meer J.R., Tchelet R., Egli T., Eggen R.I., 1998. Journal of Microbiological Methods, 32 (2) pp. 107-119.
[DOI][WoS][serval:BIB_22EEC8CA4377]
 
Prokaryotic whole-cell living bioreporters expressing bioluminescence upon the presence of bioavailable concentrations of specific pollutants: an overview.
Jaspers M.C.M., Harms H., van der Meer J.R., 1998. pp. 137-149 dans Fass R., Flashner Y., Reuveny S. (eds.) Novel approaches for bioremediation of organic pollution chap. 14, Kluwer Academic.
[serval:BIB_2BF8434DA524]
 
Quantification of bacterial mRNA involved in degradation of 1,2,4-trichlorobenzene by Pseudomonas sp. strain P51 from liquid culture and from river sediment by reverse transcriptase PCR (RT/PCR).
Meckenstock R., Steinle P., van der Meer J.R., Snozzi M., 1998. FEMS Microbiology Letters, 167 (2) pp. 123-129. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_76C6B47E50D6]
 
The tfdK gene product facilitates uptake of 2,4-dichlorophenoxyacetate by Ralstonia eutropha JMP134(pJP4).
Leveau J.H., Zehnder A.J., van der Meer J.R., 1998. Journal of Bacteriology, 180 (8) pp. 2237-2243. Peer-reviewed.
[WoS][Pmid][serval:BIB_1DAB906DE0B1]
1997
 
Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples.
Sticher P., Jaspers M.C., Stemmler K., Harms H., Zehnder A.J., van der Meer J.R., 1997. Applied and Environmental Microbiology, 63 (10) pp. 4053-4060. Peer-reviewed.
[WoS][Pmid][serval:BIB_FD9644D5BD89]
 
Development of stable denitrifying cultures during repeated aerobic-anaerobic transient periods.
Baumann B., Snozzi M., van der Meer J.R., Zehnder A.J.B., 1997. Water Research, 31 (8) pp. 1947-1954.
[DOI][serval:BIB_7F8FA61A32E6]
 
Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds.
van der Meer J.R., 1997. Antonie van Leeuwenhoek, 71 (1-2) pp. 159-178. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_95E7F218FB1A]
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