selected publications
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academic article
- Long-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated Wastewater. Applied and Environmental Microbiology. 88. 2022
- Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nature Microbiology. 2022
- Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut. Applied and Environmental Microbiology. 87:e02735-20. 2021
- Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Frontiers in Microbiology. 12:606409. 2021
- Dairy Manure as a Potential Source of Crop Nutrients and Environmental Contaminants. Journal of environmental sciences (China). 100:117-130. 2021
- Evolving Populations in Biofilms Contain More Persistent Plasmids. Molecular Biology and Evolution. 37:1563-1576. 2020
- Coevolution of Host-plasmid Pairs Facilitates the Emergence of Novel Multidrug resistance. Nature Ecology and Evolution. 4:863-869. 2020
- Linking the resistome and plasmidome to the microbiome.. The ISME (International Society for Microbial Ecology) Journal. 13:2437-2446. 2019
- The Transferable Resistome of Produce. MBio. 9. 2018
- Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation. Environmental Microbiology. 20:4091-4111. 2018
- Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland. Frontiers in Microbiology. 8.0. 2017
- Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance. Scientific Reports. 7:4853. 2017
- Persistence of antibiotic resistance plasmids in bacterial biofilms. Evolutionary Applications. 10.0:640.0-647.0. 2017
- Annotation of plasmid genes. Plasmid. 91:61-67. 2017
- Evolved plasmid-host interactions reduce plasmid interference cost. Molecular Microbiology. 101:743-756. 2016
- High Diversity of CTX-M Extended-Spectrum beta-Lactamases in Municipal Wastewater and Urban Wetlands. Microbial Drug Resistance. 22:312-320. 2016
- Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation. Microbial Ecology. 71:974-989. 2016
- Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Molecular Biology and Evolution. 33:885-897. 2016
- Plasmid transfer in biofilms: a perspective on limitations and opportunities.. NPJ Biofilms and Microbiomes. 2. 2016
- The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family. Frontiers in Microbiology. 5. 2015
- Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes. FEMS Microbiology Ecology. 2015
- Draft Genome Sequence of Pseudomonas moraviensis R28-S. Genome Announcements. 2. 2014
- Invasion of E. coli biofilms by antibiotic resistance plasmids. Plasmid. 70:110-119. 2013
- Cointegrate-resolution of toluene-catabolic transposon Tn4651: Determination of crossover site and the segment required for full resolution activity. Plasmid. . 2013
- Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees.. Molecular Biology and Evolution. 30:154-166. 2013
- On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations. Journal of Theoretical Biology. 294:144-152. 2013
- Role of IncP-1? plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses.. Applied and Environmental Microbiology. 78:828-838. 2013
- Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids. Journal of Bacteriology. 194:1533-1543. 2013
- The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. MBio. 3:e00077. 2013
- The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid. 68:13-24. 2012
- Strain-Specific Transfer of Antibiotic Resistance from an Environmental Plasmid to Foodborne Pathogens. Journal of Biomedicine And Biotechnology. 834598. 2012
- Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Applied and Environmental Microbiology. 77:7975-7983. 2011
- Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface. Applied and Environmental Microbiology. 77. 2011
- Selection pressure required for long-term persistence of {blaCMY-2-positive} {IncA/C} plasmids. Applied and Environmental Microbiology. 77:4486-4493. 2011
- Sequencing and comparative analysis of {IncP-1a} antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Journal of Biotechnology. 155:95-103. 2011
- Accounting for mating pair formation in plasmid population dynamics. Journal of Theoretical Biology. 262:711-719. 2010
- Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone. Plasmid. 63:98-107. 2010
- Dual reporter system for in situ detection of plasmid transfer under aerobic and anaerobic conditions.. Applied and Environmental Microbiology. 76:4553-4556. 2010
- Predicting plasmid promiscuity based on genomic signature.. Journal of Bacteriology. 192:6045-6055. 2010
- Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. The ISME (International Society for Microbial Ecology) Journal. 4:1568-1580. 2010
- Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology. 96:193-204. 2009
- Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G plus C content. Environmental Microbiology. 11:937-949. 2009
- Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid. Genetics. 178:2179-2190. 2008
- Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Research: an International Journal for Rapid Publication of Reports on Genes and Genomes. 15:357-365. 2008
- Host-specific factors determine the persistence of IncP-1 plasmids. World Journal of Microbiology and Biotechnology. 24:1951-1954. 2008
- Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. The ISME (International Society for Microbial Ecology) Journal. 2:1024-1039. 2008
- Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.. Nucleic Acids Research. 36. 2008
- Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host. FEMS Microbiology Ecology. 59:738-748. 2007
- Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiology Reviews. 31:449-477. 2007
- Modelling the spatial dynamics of plasmid transfer and persistence.. Microbiology. 153:2803-2816. 2007
- Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. Journal of Bacteriology. 189:3091-3098. 2007
- Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology. 153:452-463. 2007
- The population biology of bacterial plasmids: A hidden Markov model approach. Genetics. 176:957-968. 2007
- Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. Journal of Microbiological Methods. 64:250-265. 2006
- Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. Journal of Bacteriology. 188:4057-4067. 2006
- PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbiology Ecology. 55:262-273. 2006
- Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1 beta plasmids without accessory mobile elements. Microbiology. 152:3477-3484. 2006
- Culture independent detection of Sphingomonas sp EPA 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Microbial Ecology. 49:443-450. 2005
- Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons. FEMS Microbiology Ecology. 51:375-388. 2005
- Combined effect of fertilizer and herbicide applications on the abundance, community structure and performance of the soil methanotrophic community. Soil Biology and Biochemistry. 37:187-193. 2005
- Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene toluene, ethylbenzene, and xylenes: an in situ mesocosm study. Applied and Environmental Microbiology. 71:3815-3825. 2005
- Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution.. Journal of Mathematical Biology. 50:645-662. 2005
- Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community. Applied and Environmental Microbiology. 71:5309-5317. 2005
- Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein. Plasmid. 54:135-148. 2005
- Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic-sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics. 168:1131-1144. 2004
- Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends in Microbiology. 12:53-58. 2004
- Impact of agricultural practices on the Zea mays L. endophytic community. Applied and Environmental Microbiology. 70:1475-1482. 2004
- Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Applied and Environmental Microbiology. 70:1944-1955. 2004
- The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1beta group without any accessory genes. Microbiology. 150:3591-3599. 2004
- Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. FEMS Microbiology Ecology. 46:139-146. 2003
- Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils. Environmental Microbiology. 5:867-877. 2003
- Replication functions of new broad host range plasmids isolated from polluted soils. Research In Microbiology. 154:499-509. 2003
- Linking floc structure and settling properties to activated sludge population dynamics in an SBR. Water Science and Technology. 47:9-18. 2003
- Erratum to "Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters".. FEMS Microbiology Ecology. 44. 2003
- Pollution induced community tolerance (PICT) and analysis of 16S rRNA genes to evaluate the long-term effects of herbicides on methanotrophic communities in soil. European Journal Of Soil Science. 54:679-684. 2003
- Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading Variovorax strain. Applied and Environmental Microbiology. 69:1532-1541. 2003
- The 64 508 bp IncP-1 beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1 beta group. Microbiology. 149:3139-3153. 2003
- The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Current Opinion in Biotechnology. 14:262-269. 2003
- Bioaugmenting bioreactors for the continuous removal of 3-chloroaniline by a slow release approach. Environmental Science and Technology. 36:4698-4704. 2002
- Biodegradation of linuron in a Phaseolus bioassay detected by chlorophyll fluorescence. New Phytologist. 154:821-829. 2002
- Assessment of the estrogenic activity of flue gases from burning processes by means of the yeast based human estrogen receptor (hER) bioassay. Environmental Technology. 23:287-291. 2002
- Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology. 39:101-112. 2002
- Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiology Ecology. 42:198-208. 2002
- Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp nov and Burkholderia terricola sp nov. Systematic and Applied Microbiology. 25:340-352. 2002
- Molecular Fingerprinting of Bacterial Populations in Groundwater and Bottled Mineral Water. Applied Microbiology and Biotechnology. 57:412-418. 2001
- Monitoring of the evolving diversity of the microbial community present in rotifer cultures. Aquaculture. 198:237-252. 2001
- Microbial sulfate reduction with acetate: process performance and composition of the bacterial communities in the reactor at different salinity levels. Applied Microbiology and Biotechnology. 55:787-793. 2001
- Bioaugmentation of soils by increasing microbial richness: missing links. Environmental Microbiology. 3:649-657. 2001
- Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae. Applied and Environmental Microbiology. 67:1107-1115. 2001
- Comparison of the spatial homogeneity of physico-chemical parameters and bacterial 16S rRNA genes in sediment samples from a dumping site for dredging sludge. Applied Microbiology and Biotechnology. 53:742-747. 2000
- Modification of the aggregation behaviour of the environmental Ralstonia eutropha-like strain AE815 is reflected by both surface hydrophobicity and amplified fragment length polymorphism (AFLP) patterns. Environmental Microbiology. 2:51-58. 2000
- Bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading Comamonas testosteroni strain, I2gfp. Applied and Environmental Microbiology. 66:2906-2913. 2000
- Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons. Applied and Environmental Microbiology. 66:3297-3304. 2000
- PCR-based detection of mobile genetic elements in total community DNA. Microbiology. 146:1256-1257. 2000
- Bioaugmentation of a soil bioreactor designed for pilot-scale anaerobic bioremediation studies. Environmental Science and Technology. 33:2992-3001. 1999
- Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Applied and Environmental Microbiology. 65:982-988. 1999
- Methane oxidation as a method to evaluate the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) from soil by plasmid-mediated bioaugmentation. FEMS Microbiology Ecology. 28:203-213. 1999
- Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil. FEMS Microbiology Letters. 176:105-110. 1999
- Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology. 145:3321-3329. 1999
- Soil clean-up: lessons to remember. International Biodeterioration and Biodegradation. 43:147-153. 1999
- Effect of mercury addition on plasmid incidence and gene mobilizing capacity in bulk soil. FEMS Microbiology Ecology. 27:381-394. 1998
- Gene transfer in soil systems using microcosms. FEMS Microbiology Ecology. 25:319-329. 1998
- Bioaugmentation in activated sludge: current features and future perspectives. Applied Microbiology and Biotechnology. 50:16-23. 1998
- Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology. 73:87-94. 1998
- Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid alpha-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. Applied and Environmental Microbiology. 62:2470-2476. 1996
- Retromobilization Of Heavy-metal Resistance Genes In Unpolluted And Heavy-metal Polluted Soil. FEMS Microbiology Ecology. 18:191-203. 1995
- Characterization Of Diverse 2,4-dichlorophenoxyacetic Acid-degradative Plasmids Isolated From Soil By Complementation. Applied and Environmental Microbiology. 61:1691-1698. 1995
- Transfer Of The Catabolic Plasmid Rp4tn4371 To Indigenous Soil Bacteria And Its Effect On Respiration And Biphenyl Breakdown. FEMS Microbiology Ecology. 15:71-77. 1994
- Evolution Of Heavy-metal Resistant Transconjugants In A Soil Environment With A Concomitant Selective Pressure. FEMS Microbiology Ecology. 14:263-273. 1994
- Exogenous Isolation Of Mobilizing Plasmids From Polluted Soils And Sludges. Applied and Environmental Microbiology. 60:831-839. 1994
- Use Of DNA Probes And Plasmid Capture In A Search For New Interesting Environmental Genes. Science of the Total Environment. 139-140:471-478. 1993
- Determination Of The Mechanism Of Retrotransfer By Mechanistic Mathematical-modeling. Journal of Bacteriology. 174:5953-5960. 1992
- How Can Biotechnology Solve The Environmental Problems Of Modern Society. Biotech Forum Europe. 8:496-498. 1991
- Gene Escape Model - Transfer Of Heavy-metal Resistance Genes From Escherichia-coli To Alcaligenes-eutrophus On Agar Plates And In Soil Samples. Applied and Environmental Microbiology. 56:2471-2479. 1990
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editorial article
- Editorial. Plasmid. 105:102437. 2019