Soil microbiome interventions for carbon sequestration and climate mitigation.

mSystems. 2024 Dec 18. 10.1128/msystems.01129-24

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes.

Nat Commun. 2024 Aug 31. 10.1038/s41467-024-51944-z

Bacttle: a microbiology educational board game for lay public and schools.

J Microbiol Biol Educ. 2024 Aug 29. 10.1128/jmbe.00097-24

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.

Nat Commun. 2024 Mar 22. 10.1038/s41467-024-46933-1

Inferring bacterial interspecific interactions from microcolony growth expansion.

Microlife. 2024. 10.1093/femsml/uqae020

From microbiome composition to functional engineering, one step at a time.

Microbiol Mol Biol Rev. 2023 Dec 20. 10.1128/mmbr.00063-23

Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.

mSphere. 2023 Dec 20. 10.1128/msphere.00517-23

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.

Microbiome. 2023 Sep 29. 10.1186/s40168-023-01660-5

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.

PLoS Comput Biol. 2023 Aug. 10.1371/journal.pcbi.1011402

Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2.

mSystems. 2023 Apr 27. 10.1128/msystems.01174-22

STrack: A Tool to Simply Track Bacterial Cells in Microscopy Time-Lapse Images.

mSphere. 2023 Apr 20. 10.1128/msphere.00658-22

Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.

Nucleic Acids Res. 2023 Mar 21. 10.1093/nar/gkad024

A bistable prokaryotic differentiation system underlying development of conjugative transfer competence.

PLoS Genet. 2022 Jun. 10.1371/journal.pgen.1010286

Recent advances in microbial community analysis from machine learning of multiparametric flow cytometry data.

Curr Opin Biotechnol. 2022 Jun. 10.1016/j.copbio.2022.102688

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation.

mSystems. 2022 Apr 26. 10.1128/msystems.00160-22

Subcellular Localization Defects Characterize Ribose-Binding Mutant Proteins with New Ligand Properties in Escherichia coli.

Appl Environ Microbiol. 2022 Jan 25. 10.1128/AEM.02117-21

Predicting spatial patterns of soil bacteria under current and future environmental conditions.

ISME J. 2021 Sep. 10.1038/s41396-021-00947-5

A Miniaturized Microbe-Silicon-Chip Based on Bioluminescent Engineered Escherichia coli for the Evaluation of Water Quality and Safety.

Int J Environ Res Public Health. 2021 Jul 16. 10.3390/ijerph18147580

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils.

Environ Microbiome. 2021 Apr 29. 10.1186/s40793-021-00378-x

Environmental connectivity controls diversity in soil microbial communities.

Commun Biol. 2021 Apr 22. 10.1038/s42003-021-02023-2

Miniaturized electrochemical biosensor based on whole-cell for heavy metal ions detection in water.

Biotechnol Bioeng. 2021 Apr. 10.1002/bit.27646

Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry.

mSystems. 2021 Feb 9. 10.1128/mSystems.01143-20

Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol.

Front Bioeng Biotechnol. 2021. 10.3389/fbioe.2021.705534

Greater topoclimatic control of above- versus below-ground communities.

Glob Chang Biol. 2020 Dec. 10.1111/gcb.15330

Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1.

Genes (Basel). 2020 Aug 12. 10.3390/genes11080930

An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element.

Elife. 2020 Jul 28. 10.7554/eLife.57915

Bioluminescence-Triggered Photoswitchable Bacterial Adhesions Enable Higher Sensitivity and Dual-Readout Bacterial Biosensors for Mercury.

ACS Sens. 2020 Jul 24. 10.1021/acssensors.0c00855

Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data.

Commun Biol. 2020 Jul 15. 10.1038/s42003-020-1106-y

Author Correction: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models.

NPJ Syst Biol Appl. 2020 Jan 30. 10.1038/s41540-020-0123-2

Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol.

Sci Rep. 2019 Nov 15. 10.1038/s41598-019-53507-5

Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element.

mBio. 2019 Jun 11. 10.1128/mBio.01133-19

The urgent need for microbiology literacy in society.

Environ Microbiol. 2019 May. 10.1111/1462-2920.14611

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.

Mol Ecol. 2019 May. 10.1111/mec.15075

Probing chemotaxis activity in Escherichia coli using fluorescent protein fusions.

Sci Rep. 2019 Mar 7. 10.1038/s41598-019-40655-x

Bridging the Holistic-Reductionist Divide in Microbial Ecology.

mSystems. 2019 Jan-Feb. 10.1128/mSystems.00265-18

Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities.

Front Microbiol. 2019. 10.3389/fmicb.2019.00656

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine.

Genes (Basel). 2018 Nov 23. 10.3390/genes9120573

Heterologous Expression of Pseudomonas putida Methyl-Accepting Chemotaxis Proteins Yields Escherichia coli Cells Chemotactic to Aromatic Compounds.

Appl Environ Microbiol. 2018 Sep 15. 10.1128/AEM.01362-18

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota.

Ecol Evol. 2018 Sep. 10.1002/ece3.4444

Bacterial bioreporter detection of arsenic associated with iron oxides.

Environ Sci Process Impacts. 2018 Jun 20. 10.1039/c8em00071a

Prospects for harnessing biocide resistance for bioremediation and detoxification.

Science. 2018 May 18. 10.1126/science.aar3778

Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities.

Sci Rep. 2018 Apr 10. 10.1038/s41598-018-24253-x

Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element.

Sci Rep. 2018 Apr 3. 10.1038/s41598-018-23858-6

Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips.

Environ Microbiol. 2018 Jan. 10.1111/1462-2920.13982

Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster.

mBio. 2017 Oct 24. 10.1128/mBio.01496-17

Complete alanine scanning of the Escherichia coli RbsB ribose binding protein reveals residues important for chemoreceptor signaling and periplasmic abundance.

Sci Rep. 2017 Aug 15. 10.1038/s41598-017-08035-5

The hidden life of integrative and conjugative elements.

FEMS Microbiol Rev. 2017 Jul 1. 10.1093/femsre/fux008

Editorial overview: Environmental biotechnology.

Curr Opin Biotechnol. 2017 Jun. 10.1016/j.copbio.2017.05.001

Miniaturized and integrated whole cell living bacterial sensors in field applicable autonomous devices.

Curr Opin Biotechnol. 2017 Jun. 10.1016/j.copbio.2016.11.023

Draft Genome Sequence of Microbacterium foliorum Strain 122 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.

Genome Announc. 2017 May 25. 10.1128/genomeA.00434-17

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation.

ACS Synth Biol. 2017 May 19. 10.1021/acssynbio.6b00364

Draft Genome Sequence of Plantibacterflavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.

Genome Announc. 2017 Apr 27. 10.1128/genomeA.00276-17

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

Appl Environ Microbiol. 2016 Nov 1. 10.1128/AEM.01170-16

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

ISME J. 2016 Nov. 10.1038/ismej.2016.45

Towards improved biomonitoring tools for an intensified sustainable multi-use environment.

Microb Biotechnol. 2016 Sep. 10.1111/1751-7915.12395

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.

Proc Natl Acad Sci U S A. 2016 Jun 14. 10.1073/pnas.1604479113

An automated microreactor for semi-continuous biosensor measurements.

Lab Chip. 2016 Apr 21. 10.1039/c6lc00119j

Immediate ecotoxicological effects of short-lived oil spills on marine biota.

Nat Commun. 2016 Apr 4. 10.1038/ncomms11206

Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties.

Environ Microbiol Rep. 2016 Feb. 10.1111/1758-2229.12356

Regulatable and Modulable Background Expression Control in Prokaryotic Synthetic Circuits by Auxiliary Repressor Binding Sites.

ACS Synth Biol. 2016 Jan 15. 10.1021/acssynbio.5b00111

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

PLoS One. 2016. 10.1371/journal.pone.0165850

Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms.

Environ Microbiol Rep. 2015 Jun. 10.1111/1758-2229.12276

Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea.

Microb Biotechnol. 2015 May. 10.1111/1751-7915.12176

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Front Microbiol. 2015. 10.3389/fmicb.2015.00101

Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand.

ISME J. 2015 Jan. 10.1038/ismej.2014.101

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Environ Microbiol. 2015 Jan. 10.1111/1462-2920.12498

The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer.

J Bacteriol. 2014 Nov. 10.1128/JB.02129-14

First day of an oil spill on the open sea: early mass transfers of hydrocarbons to air and water.

Environ Sci Technol. 2014 Aug 19. 10.1021/es502437e

Escherichia [corrected] coli ribose binding protein based bioreporters revisited.

Sci Rep. 2014 Jul 9. 10.1038/srep05626

Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

Environ Microbiol. 2014 Jul. 10.1111/1462-2920.12375

An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13.

PLoS Genet. 2014 Jun. 10.1371/journal.pgen.1004441

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.

Appl Environ Microbiol. 2014 Jun. 10.1128/AEM.00306-14

Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.

J Bacteriol. 2014 Apr. 10.1128/JB.01333-13

Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery.

Front Microbiol. 2014. 10.3389/fmicb.2014.00585

Compact portable biosensor for arsenic detection in aqueous samples with Escherichia coli bioreporter cells.

Rev Sci Instrum. 2014 Jan. 10.1063/1.4863333

Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1.

Environ Microbiol. 2013 Oct. 10.1111/1462-2920.12125

Electrochemical As(III) whole-cell based biochip sensor.

Biosens Bioelectron. 2013 Sep 15. 10.1016/j.bios.2013.03.011

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters.

Microb Biotechnol. 2013 Sep. 10.1111/1751-7915.12031

Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria.

Environ Sci Technol. 2013 Jul 2. 10.1021/es304378d

A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element.

Appl Environ Microbiol. 2013 Jul. 10.1128/AEM.00711-13

Community-wide plasmid gene mobilization and selection.

ISME J. 2013 Jun. 10.1038/ismej.2013.13

Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem.

Curr Opin Biotechnol. 2013 Jun. 10.1016/j.copbio.2012.09.002

Examining chemical compound biodegradation at low concentrations through bacterial cell proliferation.

Environ Sci Technol. 2013 Feb 19. 10.1021/es303592c

Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria.

Curr Biol. 2013 Feb 4. 10.1016/j.cub.2012.12.025

Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.

PLoS One. 2013. 10.1371/journal.pone.0078288

Characterization of a MexAB-OprM efflux system necessary for productive metabolism of Pseudomonas azelaica HBP1 on 2-hydroxybiphenyl.

Front Microbiol. 2013. 10.3389/fmicb.2013.00203

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 Dec. 10.1128/AEM.02516-12

Field testing of arsenic in groundwater samples of Bangladesh using a test kit based on lyophilized bioreporter bacteria.

Environ Sci Technol. 2012 Mar 20. 10.1021/es203511k

Reversible and irreversible pollutant-induced bacterial cellular stress effects measured by ethidium bromide uptake and efflux.

Environ Sci Technol. 2012 Jan 17. 10.1021/es203352y

Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1.

Front Microbiol. 2012. 10.3389/fmicb.2012.00300

Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element.

PLoS Genet. 2012. 10.1371/journal.pgen.1002818

Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.

BMC Microbiol. 2011 Nov 14. 10.1186/1471-2180-11-250

Miniaturized bacterial biosensor system for arsenic detection holds great promise for making integrated measurement device.

Bioeng Bugs. 2011 Sep-Oct. 10.4161/bbug.2.5.17236

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. 10.1111/j.1462-2920.2011.02552.x

Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples.

Lab Chip. 2011 Jul 21. 10.1039/c1lc20274j

A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury.

Environ Sci Technol. 2011 Jul 1. 10.1021/es200591v

How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element?

Mob Genet Elements. 2011 May. 10.4161/mge.1.1.15744

Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis.

PLoS One. 2011 Feb 17. 10.1371/journal.pone.0016539

A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13.

Mol Microbiol. 2011 Feb. 10.1111/j.1365-2958.2010.07484.x

Transcriptomic analysis of phenanthrene degrading Sphingomonas biofilms exposed to environmentally relevant solute and matric stresses.

Commun Agric Appl Biol Sci. 2011.

Where microbiology meets microengineering: design and applications of reporter bacteria.

Nat Rev Microbiol. 2010 Jul. 10.1038/nrmicro2392

Let the sun shine.

Curr Opin Biotechnol. 2010 Jun. 10.1016/j.copbio.2010.04.003

Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi.

ISME J. 2010 Jun. 10.1038/ismej.2010.5

Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13.

BMC Microbiol. 2010 May 26. 10.1186/1471-2180-10-153

Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments.

Environ Sci Technol. 2010 Feb 1. 10.1021/es902849w

Effect of two types of biosurfactants on phenanthrene availability to the bacterial bioreporter Burkholderia sartisoli strain RP037.

Appl Microbiol Biotechnol. 2010 Jan. 10.1007/s00253-009-2216-0

Double-tagged fluorescent bacterial bioreporter for the study of polycyclic aromatic hydrocarbon diffusion and bioavailability.

Environ Microbiol. 2009 Sep. 10.1111/j.1462-2920.2009.01952.x

Unlike PAHs from Exxon Valdez crude oil, PAHs from Gulf of Alaska coals are not readily bioavailable.

Environ Sci Technol. 2009 Aug 1. 10.1021/es900734k

Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry.

Environ Microbiol. 2009 Jul. 10.1111/j.1462-2920.2009.01893.x

Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13.

Mol Microbiol. 2009 Jun. 10.1111/j.1365-2958.2009.06726.x

Development of bacteria-based bioassays for arsenic detection in natural waters.

Anal Bioanal Chem. 2009 Jun. 10.1007/s00216-009-2785-x

Bioremediation, a broad perspective.

Microb Biotechnol. 2009 Mar. 10.1111/j.1751-7915.2009.00091.x

Optimization of preservation conditions of As (III) bioreporter bacteria.

Appl Microbiol Biotechnol. 2009 Mar. 10.1007/s00253-009-1888-9

Genomic islands: tools of bacterial horizontal gene transfer and evolution.

FEMS Microbiol Rev. 2009 Mar. 10.1111/j.1574-6976.2008.00136.x

Novel use of a whole cell E. coli bioreporter as a urinary exposure biomarker.

Environ Sci Technol. 2009 Jan 15. 10.1021/es801325u

Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas.

Proc Natl Acad Sci U S A. 2008 Dec 30. 10.1073/pnas.0806164106

Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax.

Environ Pollut. 2008 Dec. 10.1016/j.envpol.2008.06.001

Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.

Microb Ecol. 2008 Aug. 10.1007/s00248-007-9337-8

Bacterial Biosensors for Measuring Availability of Environmental Pollutants.

Sensors (Basel). 2008 Jul 10. 10.3390/s8074062

Use of flow cytometric methods for single-cell analysis in environmental microbiology.

Curr Opin Microbiol. 2008 Jun. 10.1016/j.mib.2008.04.006

Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1.

Proc Natl Acad Sci U S A. 2008 May 13. 10.1073/pnas.0801269105

Internal arsenite bioassay calibration using multiple bioreporter cell lines.

Microb Biotechnol. 2008 Mar. 10.1111/j.1751-7915.2007.00011.x

Burkholderia sartisoli sp. nov., isolated from a polycyclic aromatic hydrocarbon-contaminated soil.

Int J Syst Evol Microbiol. 2008 Feb. 10.1099/ijs.0.65451-0

Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A.

Biodegradation. 2008 Feb. 10.1007/s10532-007-9112-z

Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting.

Microb Biotechnol. 2008 Jan. 10.1111/j.1751-7915.2007.00008.x

Analysis of bioavailable arsenic in rice with whole cell living bioreporter bacteria.

J Agric Food Chem. 2007 Mar 21. 10.1021/jf0631676

Bioreporters: gfp versus lux revisited and single-cell response.

Biosens Bioelectron. 2007 Mar 15. 10.1016/j.bios.2006.07.005

Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH.

Appl Environ Microbiol. 2006 Jul. 10.1128/AEM.02758-05

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

FEMS Microbiol Ecol. 2006 Jul. 10.1111/j.1574-6941.2006.00103.x

A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes.

Environ Microbiol. 2006 Apr. 10.1111/j.1462-2920.2005.00948.x

Whole-cell living biosensors--are they ready for environmental application?

Appl Microbiol Biotechnol. 2006 Apr. 10.1007/s00253-006-0319-4

The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties.

J Bacteriol. 2006 Mar. 10.1128/JB.188.5.1999-2013.2006

Analytics with engineered bacterial bioreporter strains and systems.

Curr Opin Biotechnol. 2006 Feb. 10.1016/j.copbio.2006.01.005

Information from single-cell bacterial biosensors: what is it good for?

Curr Opin Biotechnol. 2006 Feb. 10.1016/j.copbio.2005.11.001

Enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A.

Appl Environ Microbiol. 2005 Dec. 10.1128/AEM.71.12.8514-8518.2005

Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples.

Environ Sci Technol. 2005 Oct 1. 10.1021/es050992e

Ultrasensitive reporter protein detection in genetically engineered bacteria.

Anal Chem. 2005 May 1. 10.1021/ac048127k

Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain.

FEBS J. 2005 Apr. 10.1111/j.1742-4658.2005.04607.x

Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers.

Appl Environ Microbiol. 2004 Nov. 10.1128/AEM.70.11.6650-6656.2004

Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR.

Environ Microbiol. 2004 Nov. 10.1111/j.1462-2920.2004.00645.x

Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas herbicidovorans MH.

Appl Environ Microbiol. 2004 Oct. 10.1128/AEM.70.10.6066-6075.2004

Illuminating the detection chain of bacterial bioreporters.

Environ Microbiol. 2004 Oct. 10.1111/j.1462-2920.2004.00655.x

Bacterial transcriptional regulators for degradation pathways of aromatic compounds.

Microbiol Mol Biol Rev. 2004 Sep. 10.1128/MMBR.68.3.474-500.2004

Development of a Set of Simple Bacterial Biosensors for Quantitative and Rapid Measurements of Arsenite and Arsenate in Potable Water.

Environ Sci Technol. 2004 May 15. 10.1021/es040385b

Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer.

J Bacteriol. 2004 Apr. 10.1128/JB.186.8.2225-2235.2004

Mutation analysis of the different tfd genes for degradation of chloroaromatic compounds in Ralstonia eutropha JMP134.

Arch Microbiol. 2004 Feb. 10.1007/s00203-003-0634-4

Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor.

Appl Environ Microbiol. 2004 Jan. 10.1128/AEM.70.1.43-51.2004

Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable water.

Environ Sci Technol. 2003 Oct 15. 10.1021/es034258b

Effect of integration of a GFP reporter gene on fitness of Ralstonia eutropha during growth with 2,4-dichlorophenoxyacetic acid.

Environ Microbiol. 2003 Oct. 10.1046/j.1462-2920.2003.00479.x

Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13.

J Bacteriol. 2003 Aug. 10.1128/JB.185.15.4530-4538.2003

Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13.

Mol Microbiol. 2003 Jul. 10.1046/j.1365-2958.2003.03548.x

Genomic islands and the evolution of catabolic pathways in bacteria.

Curr Opin Biotechnol. 2003 Jun. 10.1016/s0958-1669(03)00058-2

Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors.

Appl Environ Microbiol. 2003 Jun. 10.1128/AEM.69.6.3213-3222.2003

Microbial composition and structure of a rotating biological contactor biofilm treating ammonium-rich wastewater without organic carbon.

Microb Ecol. 2003 May. 10.1007/s00248-002-2037-5

Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia.

Environ Microbiol. 2003 Mar. 10.1046/j.1462-2920.2003.00400.x

Cloning and characterization of lin genes responsible for the degradation of Hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90.

Appl Environ Microbiol. 2002 Dec. 10.1128/AEM.68.12.6021-6028.2002

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.

Arch Microbiol. 2002 Jul. 10.1007/s00203-002-0417-3

Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters.

J Bacteriol. 2002 Jun. 10.1128/JB.184.11.2914-2924.2002

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.

Environ Microbiol. 2002 Feb. 10.1046/j.1462-2920.2002.00267.x

Measuring mass transfer processes of octane with the help of an alkSalkB::gfp-tagged Escherichia coli.

Environ Microbiol. 2001 Aug. 10.1046/j.1462-2920.2001.00218.x

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 (Reading). 2001 Aug. 10.1099/00221287-147-8-2183

Biotransformation of various substituted aromatic compounds to chiral dihydrodihydroxy derivatives.

Appl Environ Microbiol. 2001 Aug. 10.1128/AEM.67.8.3333-3339.2001

Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate.

Arch Microbiol. 2001 Mar. 10.1007/s002030100255

The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases.

Arch Microbiol. 2001 Feb. 10.1007/s002030000244

Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134(pJP4).

J Bacteriol. 2000 Aug. 10.1128/JB.182.15.4165-4172.2000

Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus.

Appl Environ Microbiol. 2000 Jul. 10.1128/AEM.66.7.2842-2852.2000

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.

J Bacteriol. 2000 Jan. 10.1128/JB.182.2.405-417.2000

cis-chlorobenzene dihydrodiol dehydrogenase (TcbB) from Pseudomonas sp. strain P51, expressed in Escherichia coli DH5alpha(pTCB149), catalyzes enantioselective dehydrogenase reactions.

Appl Environ Microbiol. 1999 Dec. 10.1128/AEM.65.12.5242-5246.1999

Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge.

Syst Appl Microbiol. 1999 Sep. 10.1016/S0723-2020(99)80055-1

Dynamics of multigene expression during catabolic adaptation of Ralstonia eutropha JMP134 (pJP4) to the herbicide 2, 4-dichlorophenoxyacetate.

Mol Microbiol. 1999 Jul. 10.1046/j.1365-2958.1999.01483.x

Population dynamics of an introduced bacterium degrading chlorinated benzenes in a soil column and in sewage sludge.

Biodegradation. 1999 Apr. 10.1023/a:1008368006917

Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater.

Appl Environ Microbiol. 1998 Nov. 10.1128/AEM.64.11.4185-4193.1998

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.

J Bacteriol. 1998 Nov. 10.1128/JB.180.21.5505-5514.1998

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).

FEMS Microbiol Lett. 1998 Oct 15. 10.1111/j.1574-6968.1998.tb13217.x

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.

J Bacteriol. 1998 Sep. 10.1128/JB.180.17.4360-4369.1998

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.

Appl Environ Microbiol. 1998 Jun. 10.1128/AEM.64.6.2126-2132.1998

The tfdK gene product facilitates uptake of 2,4-dichlorophenoxyacetate by Ralstonia eutropha JMP134(pJP4).

J Bacteriol. 1998 Apr. 10.1128/JB.180.8.2237-2243.1998

Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134.

Gene. 1997 Nov 20. 10.1016/s0378-1119(97)00460-5

Inhibition of denitrification activity but not of mRNA induction in Paracoccus denitrificans by nitrite at a suboptimal pH.

Antonie Van Leeuwenhoek. 1997 Oct. 10.1023/a:1000342125891

Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples.

Appl Environ Microbiol. 1997 Oct. 10.1128/aem.63.10.4053-4060.1997

Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds.

Antonie Van Leeuwenhoek. 1997 Feb. 10.1023/a:1000166400935

The tfdR gene product can successfully take over the role of the insertion element-inactivated TfdT protein as a transcriptional activator of the tfdCDEF gene cluster, which encodes chlorocatechol degradation in Ralstonia eutropha JMP134(pJP4).

J Bacteriol. 1996 Dec. 10.1128/jb.178.23.6824-6832.1996

Cloning and characterization of the genes encoding nitrilotriacetate monooxygenase of Chelatobacter heintzii ATCC 29600.

J Bacteriol. 1996 Nov. 10.1128/jb.178.21.6123-6132.1996

Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes.

J Bacteriol. 1996 Aug. 10.1128/jb.178.15.4367-4374.1996

The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation.

J Biol Chem. 1996 Feb 23. 10.1074/jbc.271.8.4009

Maturation pathway of nisin and other lantibiotics: post-translationally modified antimicrobial peptides exported by gram-positive bacteria.

Mol Microbiol. 1995 Aug. 10.1111/j.1365-2958.1995.mmi_17030427.x

Genetic adaptation of bacteria to chlorinated aromatic compounds.

FEMS Microbiol Rev. 1994 Oct. 10.1111/j.1574-6976.1994.tb00137.x

Analysis of the binding site of the LysR-type transcriptional activator TcbR on the tcbR and tcbC divergent promoter sequences.

J Bacteriol. 1994 Apr. 10.1128/jb.176.7.1850-1856.1994

Influence of amino acid substitutions in the nisin leader peptide on biosynthesis and secretion of nisin by Lactococcus lactis.

J Biol Chem. 1994 Feb 4.

Characterization of the Lactococcus lactis nisin A operon genes nisP, encoding a subtilisin-like serine protease involved in precursor processing, and nisR, encoding a regulatory protein involved in nisin biosynthesis.

J Bacteriol. 1993 May. 10.1128/jb.175.9.2578-2588.1993

Molecular mechanisms of genetic adaptation to xenobiotic compounds.

Microbiol Rev. 1992 Dec. 10.1128/mr.56.4.677-694.1992

Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51.

J Bacteriol. 1991 Nov. 10.1128/jb.173.22.7077-7083.1991

Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tcbCDEF chlorocatechol oxidative operon, and analysis of the regulatory region.

J Bacteriol. 1991 Jun. 10.1128/jb.173.12.3700-3708.1991

Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates.

J Bacteriol. 1991 Apr. 10.1128/jb.173.8.2425-2434.1991

Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51.

J Bacteriol. 1991 Jan. 10.1128/jb.173.1.6-15.1991