Publications

Ten most important publications with a brief annotation indicating their significance.

  1. Stalder, T., M.O. Press, S. Sullivan, I. Liachko, and M. Top. 2019. Linking the resistome and plasmidome to the microbiome. ISME J. Published Online
  2. Loftie-Eaton, W., K. Bashford, H. Quinn, K. Dong, J. Millstein, S. Hunter, M. Thomason, H. Merrikh, H., J.M. Ponciano, and M. Top. 2017. Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecol. Evol. 1: 1354–1363. DOI: s41559-017-0243-2
    This study led to two important conclusions that impact the way we tackle the spread of multi-drug-resistance (MDR) plasmids: (1) bacteria can greatly improve the persistence of MDR plasmids through chromosomal mutations that affect accessory helicases, which are proteins involved in DNA and RNA metabolism, such as DNA repair; and (2) adaptation to one plasmid can pre-adapt bacteria to other MDR plasmids that they acquire later in time, leading to their persistence. This is the first time that antibiotic exposure has been shown to select for bacterial mutants that can better retain multiple MDR plasmids.
  3. Yano, K. Wegrzyn, W. Loftie-Eaton, J. Johnson, G.E. Deckert, L.M. Rogers, I. Konieczny, and E.M. Top. 2016. Evolved plasmid-host interactions reduce plasmid interference cost. Mol. Microbiol. 101: 743-756.
    Thanks to a unique combination of experimental microbial evolution and biochemical analysis, her research group discovered a molecular mechanism by which a plasmid can adapt to a novel bacterial host. They determined that plasmid fitness cost decreased through mutations in the plasmid’s replication initiation protein. These mutations simultaneously increased plasmid copy number and decreased unfavorably high affinity to one of the host’s essential proteins, DNA helicase.
  4. Loftie-Eaton, H. Yano, S. Burleigh, R.S. Simmons, J.M. Hughes, L.M. Rogers, S.S. Hunter, M.L. Settles, L.J. Forney, J.M. Ponciano, and E.M. Top. 2016. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol. Biol. Evol. 33: 885–897.
    For the first time her research group was able to determine a novel mechanism behind the epistatic interactions between a bacterial host and its newly acquired antibiotic resistance plasmid that improved plasmid persistence. They showed that transposition of a putative toxin–antitoxin system from a native plasmid into the antibiotic resistance plasmid improved persistence of the latter in the co-evolved as well as naive hosts, thus expanding the plasmid’s host range. Inferring these underlying mechanisms was made possible through a unique combination of molecular genetics and their mechanistic mathematical model.
  5. Sen, D., C.J. Brown, M. Top and J. Sullivan. 2013. Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol. Biol. Evol. 30: 154-166.
    Over the past 15 years she has engaged in studies to better understand the vast genetic diversity of natural plasmids that are able to spread antibiotic resistance genes among a wide range of bacteria. This work has significantly increased the number of annotated whole plasmid genome sequences that are known. Here the first robust phylogeny of one of these plasmid families was built. It demonstrated that in spite of horizontal gene exchange both within and among IncP-1 plasmid subgroups, the plasmids retain a detectable vertical evolutionary history. Dr. Top’s unique contribution was to provide knowledge of plasmid biology to this interdisciplinary phylogenetic study.
  6. Suzuki, H., H. Yano, C.J. Brown and M. Top. 2010. Predicting plasmid promiscuity based on genomic signature. J. Bacteriol. 192: 6045-6055.
    Dr. Top’s group developed and optimized a method to predict the hosts and host-range of plasmids based on their genomic signature. As many plasmids move between bacteria in their natural ecosystem, being able to determine the natural long-term range of hosts in which plasmids reside is a valuable tool in our attempt to understand and control the spread of antibiotic resistance. This method has become a useful tool for the research community. It was developed by postdoctoral scientist Suzuki under Dr. Top’s mentorship.
  7. Krone, S.M., R. Lu, R. Fox, H. Suzuki, and M. Top. 2007. Modeling the spatial dynamics of plasmid transfer and persistence. Microbiology 153: 2803-2816.
    Most natural bacterial populations are not well mixed but grow in spatially distinct microcolonies or structured biofilms attached to surfaces. This was the first study to directly address the consequences of this common mode of growth on the spread of antibiotic resistance genes using a spatially explicit mathematical model. Top and mathematician Krone were co-PI’s on this project and jointly designed the experimental and modeling studies.
  8. De Gelder, L., J. M. Ponciano, P. Joyce, and M. Top. 2007. Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship. Microbiology 153: 452-463.
    For the first time it was convincingly demonstrated in a joint experimental-theoretical study that the ability of a multi-drug-resistance plasmid to persist in a bacterial population in the absence of antibiotics differs widely between species. Dr. Top was the major professor of first author De Gelder and oversaw the project.
  9. Top, E.M., and D. Springael. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr. Opin. Biotechnol. 14: 262-269.
    This review paper provided a timely summary of, and unique perspective on the role of mobile genetic elements in the in situ spread and de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics.
  10. Top, E.M.,E. Holben, and L.J. Forney. 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid- degradative plasmids isolated from soil by complementation. Appl. Environ. Microbiol. 61: 1691-1698.
    Through a method known as exogenous plasmid isolation we were able for the first time to capture catabolic plasmids straight from an environmental habitat.

Publications in peer-reviewed journals:

  1. Stalder, T., M.O. Press, S. Sullivan, I. Liachko, and M. Top. 2019. Linking the resistome and plasmidome to the microbiome. ISME J. In press.
  2. Blau, K., A. Bettermann, S. Jechalke, E. Fornefeld, Y. Vanrobaeys, T. Stalder, Top, and K. Smalla. 2018. The transferable resistome of produce. mBio 9 (6): e01300-18.
  3. Dunon, V., K. Bers, R. Lavigne, M. Top, and D. Springael. 2018. Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation. Environ. Microbiol. 20: 4091-4111 (https://doi.org/10.1111/1462-2920.14404)
  4. Botts, R.T., B.A. Apffel, C.J. Walters, K.E. Davidson, R.S. Echols, M.R. Geiger, V.L. Guzman, V.S. Haase, M.A. Montana, C.A. La Chat, J.A. Mielke, K.L. Mullen, C.C. Virtue, C.J. Brown, M. Top, and D.E. Cummings. 2017. Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland. Frontiers in Microbiology 8:1922, PMCID: PMC5641379.
  5. Loftie-Eaton, W., K. Bashford, H. Quinn, K. Dong, J. Millstein, S. Hunter, M. Thomason, H. Merrikh, H., J.M. Ponciano, and M. Top. 2017. Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecol. Evol. 1: 1354–1363. (PMC5649373).
  6. Stalder, T., M. Rogers, C. Renfrow, H. Yano, Z. Smith, and E.M. Top. 2017. Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance. Scientific Reports 7: 4853. (PMC5501780)
  7. Thomas, C.M., N. R. Thomson, A. M. Cerdeño-Tárraga, C. J. Brown, M. Top, and L. S. Frost. 2017. Annotation of Plasmid Genes. Plasmid 91:61-67.
  8. Ridenhour, B., G. Metzger, M. France, K. Gliniewicz, J. Millstein, L. Forney, M. Top. 2017. Persistence of antibiotic resistance plasmids in bacterial biofilms. Evol. Appl. 10:640-647.
  9. Stalder, T., and M. Top. 2016. Plasmid transfer in biofilms: A perspective on limitations and opportunities. NPJ Biofilms and Microbiomes 16022: 1-5. PMC5416938
  10. Yano, K. Wegrzyn, W. Loftie-Eaton, J. Johnson, G.E. Deckert, L.M. Rogers, I. Konieczny, and E.M. Top. 2016. Evolved plasmid-host interactions reduce plasmid interference cost. Mol. Microbiol. 101: 743-756. (PMCID: PMC5024541)
  11. Li, H., Z. Xu, S. Yang, X. Li, M. Top, R. Wang, Y. Zhang, J. Cai, F. Yao, X. Han, and Y. Jiang. 2016. Responses of soil bacterial communities to nitrogen deposition and precipitation increment are closely linked with aboveground community variation. Microb. Ecol. 71:974-989 (doi: 10.1007/s00248-016-0730-z).
  12. Loftie-Eaton, H. Yano, S. Burleigh, R.S. Simmons, J.M. Hughes, L.M. Rogers, S.S. Hunter, M.L. Settles, L.J. Forney, J.M. Ponciano, and E.M. Top. 2016. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol. Biol. Evol. 33: 885–897. (doi:10.1093/molbev/msv339). PMC4840908
  13. Li, X., Y. Wang, C. Brown, F. Yao, Y. Jiang, M. Top, and H. Li. 2016. Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes. FEMS Microbiol. Ecol. 92: fiv151 (doi: http://dx.doi.org/10.1093/femsec/fiv151).
  14. Borgogna,T. R., J-L. Borgogna, J.A. Mielke, C.J. Brown, M. Top, R.T. Botts, and D.E. Cummings. 2016. High diversity of CTX-M extended-spectrum β-lactamases in municipal wastewater and urban wetlands. Microbial Drug Resistance 22: 312-320.
  15. Li, X., M. Top, Y. Wang, C. J. Brown, Y. Jiang, and H. Li. 2015. The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family. Frontiers in Microbiology 5: 777 (1-12).
  16. Loftie-Eaton, W., A. Tucker, A. Norton, and M. Top. 2014. Flow cytometry and Real-Time qPCR as tools for assessing plasmid persistence. Appl Environ Microbiol. 80: 5439-5446 (PMCID: PMC4136099).
  17. Brown, C. J., D. Sen, H. Yano, M. L. Bauer, L. M. Rogers, G. A. Van der Auwera, and M. Top. 2013. Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl. Environ. Microbiol. 79: 7684-7695. (PMCID: PMC3837812)
  18. Yano, H., L.M. Rogers, M.G. Knox, H. Heuer, K. Smalla, C.J. Brown, and E.M. Top. 2013. Host range diversification within the IncP-1 plasmid group. Microbiology 159: 2303-2315. (PMCID: PMC3836486)
  19. Oliveira, C.S., A. Moura, I. Henriques, C.J. Brown, L.M. Rogers, M. Top, and A. Correia. 2013. Comparative genomics of IncP-1ε plasmids from water environments reveals diverse and unique accessory genetic elements. Plasmid 70: 412-149.
  20. Król, J. E., J. Wojtowicz, L. M. Rogers, H. Heuer, K. Smalla, S. M. Krone, and E.M. Top. 2013. Invasion of E. coli biofilms by multidrug resistance plasmids. Plasmid 70: 110–119. (PMCID: PMC3687034)
  21. Sen, D., C.J. Brown, M. Top and J. Sullivan. 2013. Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol. Biol. Evol. 30: 154-166. (PMCID: PMC3525142)
  22. Yano H, Genka H, Ohtsubo Y, Nagata Y, Top E.M., Tsuda M. 2013. Cointegrate-resolution of toluene-catabolic transposon Tn4651: Determination of crossover site and the segment required for full resolution activity. Plasmid 69: 24–35.
  23. Van Meervenne, E., E. Van Coillie, F. Devlieghere, L. Herman, L.S.P. De Gelder,M. Top, and N. Boon. 2012. Strain specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens. J. Biomed. Biotechnol. 2012: ID 834598.
  24. Hughes, J.M., B.K. Lohman, G.E. Deckert, E.P. Nichols, M. Settles, Z. Abdo, and M. Top. 2012. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. mBio 3(4): e00077-12. (PMCID: PMC3398533)
  25. Stolze, Y., F. Eikmeyer1, D. Wibberg, G. Brandis, C. Karsten, I. Krahn, S. Schneiker-Bekel, P. Viehöver, A. Barsch, M. Keck, Top, K. Niehaus, and A. Schlüter. 2012. IncP-1b plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet. Microbiology 158: 2060-2072.
  26. Yano, H., G. E. Deckert, L. M. Rogers, and M. Top. 2012. Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids. J. Bacteriol. 194: 1533–1543. (PMCID: PMC3294859)
  27. Eikmeyer, F.G., R. Szczepanowski, D.Wibberg, A. Hadiati, S. Schneiker-Bekel, L. M. Rogers, C.J. Brown, M. Top, A. Pühler, A. Schlüter. 2012. 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.
  28. Heuer, H., C.T.T. Binh, S. Jechalke, C. Kopmann, U. Zimmerling, E. Krögerrecklenfort, T. Ledger, B. Gonzalez, M. Top, K. Smalla. 2012. IncP-1e plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes. Frontiers in Microbiology 3: 2.
  29. Król, J.E., J.T. Penrod, H. McCaslin, L.M. Rogers, H. Yano, W. Dejonghe, C.J. Brown, R.E. Parales, S. Wuertz, M. Top. 2012. Genomic and functional analysis of the IncP-1b plasmids pNB8c and pWDL7::rfpexplains their role in 3-chloroaniline catabolism. Appl. Environ. Microbiol. 78: 828-838.
  30. Zhong, X., J. Droesch, R. Fox, M. Top, and S M. Krone. 2012. On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations. J. Theor. Biol. 294: 144–152. (PMCID: PMC3346278)
  31. Sen, D., G. Van Der Auwera, L. Rogers, C.M. Thomas, C.J. Brown, and M. Top. 2011. Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl. Environ. Microbiol. 77: 7975-7983. (PMCID: PMC3209000)
  32. Król, J.E., H. D. Nguyen, L. M. Rogers, H. Beyenal, S. M. Krone, M. Top. 2011. Increased plasmid transfer in E. coli K12 biofilms at the liquid-air interface. Appl. Environ. Microbiol. 77: 5079-5088. (PMCID: PMC3147451)
  33. Subbiah, M., D. Shah, M. Top, and D. Call. 2011. The long-term persistence of blaCMY-2 positive, IncA/C plasmids requires selection pressure. Appl. Environ. Microbiol. 77: 4486-4493. (PMCID: PMC3127679)
  34. Szczepanowski R, F. Eikmeyer, J. Harfmann, J. Blom, L.M. Rogers,M. Top, and A. Schlüter. 2011. Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. J. Biotechnol. 155(1): 95-103.
  35. Sota, M., H. Yano, J. Hughes, G.W. Daughdrill, Z. Abdo, L.J. Forney, andM. Top. 2010. Shifts in host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. The ISME J. 4: 1568–1580. (doi:10.1038/ismej.2010.72) (PMCID: PMC3042886)
  36. Suzuki, H., H. Yano, C.J. Brown and M. Top. 2010. Predicting plasmid promiscuity based on genomic signature. J. Bacteriol. 192: 6045-6055. (doi:10.1128/JB.00277-10) (PMCID: PMC2976448)
  37. Król, J.E, L.M. Rogers, S.M. Krone, and M. Top. 2010. A dual reporter system for in situ detection of plasmid transfer in aerobic and anaerobic conditions. Appl. Environ. Microbiol. 76: 4553 – 4556 (doi:10.1128/AEM.00226-10) (PMCID: PMC2897451)
  38. Sen, D., H. Yano, H. Suzuki, J.E. Król, L. Rogers, C.J. Brown, and M. Top. 2010. Comparative genomics of pAKD4, the prototype IncP-1d plasmid with a complete backbone. Plasmid 63: 98-107 (PMCID: PMC2819548).
  39. Zhong, X., J. Król, E.M. Top and S.M. Krone. 2010. Accounting for mating pair formation in plasmid population dynamics. J. Theor. Biol. 262: 711–719. (PMCID: PMC2821984)
  40. Van der Auwera, G.A., J.E. Król, H. Suzuki, B. Foster, R. Van Houdt, C.J. Brown, M. Mergeay, and M. Top. 2009. Plasmids captured in C. metallidurans: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 96:193-204.
  41. Heuer , H., C. Kopmann, C.T.T. Binh, M. Top, and K. Smalla. 2009. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environ. Microbiol. 11: 937-949.
  42. Suzuki, H., C.J. Brown, L. J. Forney, and M. Top. 2008. Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Res. 15: 357-365. (PMCID: PMC2608848)
  43. Suzuki, H., M. Sota, C.J. Brown, and M. Top. 2008. Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. Nucl. Acids Res. 36: e147. (PMCID: PMC2602791).
  44. Fox, R., X. Zhong, S.M. Krone, and M. Top. 2008. Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. The ISME J. 2: 1024-1039. (PMCID: PMC2605096)
  45. De Gelder, L., J. J. Williams, J. Ponciano, M. Sota, and M. Top. 2008. Adaptive plasmid evolution results in host range expansion of a broad-host-range plasmid. Genetics 178: 2179-2190. (PMCID: PMC2323807)
  46. Sota, M, and M. Top. 2008. Host-specific factors determine the persistence of IncP-1 plasmids. World J. Microbiol. Biotechnol. 24: 1951-1954.
  47. Krone, S.M., R. Lu, R. Fox, H. Suzuki, and M. Top. 2007. Modeling the spatial dynamics of plasmid transfer and persistence. Microbiology 153: 2803-2816 (PMCID: PMC2613009).
  48. Schlüter, A., R. Szczepanowski, A. Pühler, and M. Top. 2007. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol. Rev. 31: 449-477.
  49. Sota, M., M. Tsuda, H. Yano, H. Suzuki, L.J. Forney, and M. Top. 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. J. Bacteriol. 189: 3091-3098. (PMCID: PMC1855856)
  50. Ponciano, J., L. De Gelder, M. Top, and P. Joyce. 2007. The population biology of bacterial plasmids: a Hidden-Markov model approach. Genetics 176: 957-968. (PMCID: PMC1894622)
  51. De Gelder, L., J. M. Ponciano, P. Joyce, and M. Top. 2007. Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship. Microbiology 153: 452-463.
  52. Heuer, H., Fox, and E.M. Top. 2007. Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavourable Pseudomonas putida host. FEMS Microbiol. Ecol. 59: 738-748.
  53. Kamachi, K., M. Sota, Y. Tamai, N. Nagata, T. Konda, T. Inoue, M. Top, and Y. Arakawa. 2006. Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1b plasmids without accessory mobile elements. Microbiology 152:3477-3484.
  54. Sota, M., H. Yano, A. Ono, R. Miyazaki, H. Ishii, H. Genka, M. Top, and M. Tsuda. 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. J. Bacteriol. 188: 4057-4067.
  55. Hendrickx, B., W. Dejonghe, F. Fabert, W. Boënne, L. Bastiaens, W. Verstraete, M. Top, and D. Springael. 2006. PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbiol. Ecol. 55: 262-273.
  56. Leys, N., A. Ryngaert, L. Bastiaens, M. Top, W. Verstraete, and D. Springael. 2005. Culture independent detection of Sphingomonas sp. EPA 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Microbial Ecology 49: 443-450.
  57. Hendrickx, B., H. Junca, J. Vosahlova, A. Lindner, I. Rüegg, M. Bucheli-Witschel, F. Faber, T. Egli, M. Mau, M. Schlömann, M. Brennerova, V. Brenner, D.H. Pieper, M. Top, W. Dejonghe, L. Bastiaens, and D. Springael. 2005. 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. J. Microb. Methods. 64: 250-265.
  58. De Gelder, L., F. P.J. Vandecasteele, C. J. Brown, L. J. Forney, and M. Top. 2005. Plasmid donor affects host range of the promiscuous IncP-1ß plasmid pB10 in an activated sludge microbial community. Appl. Environ. Microbiol. 71:5309-5317.
  59. Schlüter, A., H. Heuer, R. Szczepanowski, S.M. Poler, S. Schneiker, A. Pühler, and M. Top. 2005. Plasmid pB8 is closely related to the prototype IncP-1b plasmid R751 but transfers poorly to E. coli and carries a new transposon encoding a small multidrug resistance (SMR) efflux protein. Plasmid 54:135-148.
  60. Hendrickx, B., W. Dejonghe, W. Boënne, M. Brennerova, M. Cernik, T. Lederer, M. Bucheli-Witschel, L. Bastiaens, W. Verstraete, M. Top, L. Diels, and D. Springael. 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. Appl. Environ. Microbiol. 71: 3815-3825.
  61. Joyce, P., Z. Abdo, J. Ponciano, L. De Gelder, L.J. Forney, and M. Top. 2005. Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution. J. Math. Biol. 50: 645-662.
  62. Leys, N., A. Ryngaert, L. Bastiaens, P. Wattiau, Top, W. Verstraete, and D. Springael. 2005. Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons. FEMS Microbiol. Ecol. 51: 375-388.
  63. Seghers, D., S.D. Siciliano, M. Top, and W. Verstraete. 2005. Combined effect of fertilizer and herbicide applications on the abundance, community structure and performance of the soil methanotrophic community. Soil Biol. Biochem. 37: 187-193.
  64. De Gelder, L., J. Ponciano, Z. Abdo, P. Joyce, L.J. Forney, and M. Top. 2004. 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.
  65. Heuer, H., R. Szczepanowski, S. Schneiker, A. Pühler, M. Top, and A. Schlüter. 2004. The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1ß group without any accessory genes. Microbiology 150: 3591-3599.
  66. Leys, N.M.E.J., A. Ryngaert, L. Bastiaens, W. Verstraete, M. Top, and D. Springael. 2004. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 70: 1944-1955.
  67. Seghers, D., L. Wittebolle, M. Top, W. Verstraete, and S.D. Siciliano. 2004. Impact of agricultural practices on the Zea mays L. endophytic community. Appl. Environ. Microbiol. 70:1475-1482.
  68. Springael, D. and M. Top. 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.
  69. Schlüter A., H. Heuer, R. Szczepanowski, L. J. Forney, C. M. Thomas, A. Pühler, and M. Top. 2003. The 64,508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1β group. Microbiology 149: 3139-3153.
  70. Seghers, D., K. Verthé, D. Reheul, R. Bulcke, S.D. Siciliano, W. Verstraete, and M. Top. 2003. Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. FEMS Microbiol. Ecol. 46: 139-146.
  71. Seghers, D., M. Top, D. Reheul, R. Bulcke, P. Boeckx, W. Verstraete, and S. D. Siciliano. 2003. Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils. Environ. Microbiol. 5: 867-877.
  72. Seghers, D., R. Bulcke, D. Reheul, S.D. Siciliano, M. Top, and W. Verstraete. 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. Eur. J. Soil Sci. 54: 679-684.
  73. Gstalder, M-E., M. Faelen, N. Mine, M. Top, M. Mergeay, and M. Couturier. 2003. Replication functions of new broad host range plasmids isolated from polluted soils. Research in Microbiology 154:499-509.
  74. Top, E.M., and D. Springael. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr. Opin. Biotechnol. 14: 262-269.
  75. Dejonghe, W., E. Berteloot, J. Goris, N. Boon, K. Crul, S. Maertens, M. Höfte, P. De Vos, W. Verstraete, and M. Top. 2003. Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron degrading Variovorax sp. strain. Appl. Environ. Microbiol. 69: 1532-1541.
  76. Boon, N., M. Top, W. Verstraete, and S.D. Siciliano. 2003. Bioaugmentation as a tool to protect the structure and function of an activated sludge microbial community against a 3-chloroaniline shock load. Appl. Environ. Microbiol. 69:1511-1520.
  77. Govoreanu, R., D. Seghers, I. Nopens, B. De Clercq, H. Saveyn, C. Capalozza1, P. Van der Meeren, W. Verstraete, Top and P. A. Vanrolleghem. 2003. Linking floc structure and settling properties to activated sludge population dynamics in an SBR. Wat. Sci. Technol. 47:9-18.
  78. Top, E.M., Springael, D., and N. Boon. 2002. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol. Ecol. 42: 199-208.
  79. Dejonghe, W., J. Goris, A. Dierickx, V. De Dobbeleer, K. Crul, P. De Vos, W. Verstraete, and M. Top. 2002. Diversity of 3-chloroaniline and 3,4-dichloroaniline degrading bacteria isolated from three different soils and involvement of their plasmids in chloroaniline degradation. FEMS Microbiol. Ecol. 42: 315-325.
  80. Boon, N., L. De Gelder, H. Lievens, S. D. Siciliano, M. Top, and W. Verstraete. 2002. Bioaugmenting bioreactors for the continuous removal of 3-chloroaniline by a slow release approach. Environ. Sci. Technol. 36:4698-4704.
  81. Goris, J., W. Dejonghe, E. Falsen, E. De Clerck, B. Geeraerts, B., A. Willems, M. Top, P. Vandamme, and P. De Vos. 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. Syst. Appl. Microbiol. 25: 340-352.
  82. Muthumbi, W., P. De Boever, I. D’Haese, W. D’Hooge, M. Top, J.G. Pieters, F. Comhaire, and W. Verstraete. 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.
  83. Hulsen, K., M. Top, and M. Höfte. 2002. Chlorophyll fluorescence to monitor microbial degradation of linuron applied in low concentrations to bean plants. New Phytologist 154:821-829.
  84. Boon, N., W. De Windt, W. Verstraete, and M. Top. 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 Microbiol. Ecol. 39, 101-112.
  85. Dejonghe, W., N. Boon, D. Seghers,M. Top, and W. Verstraete. 2001. Bioaugmentation of soils by increasing microbial richness: missing links. Environ. Microbiol. 3:649-657
  86. Dewettinck, T., W. Hulsbosch, K. Van Hege, M. Top, and W. Verstraete. 2001. Molecular fingerprinting of bacterial populations in groundwater and bottled mineral water.  Appl. Microbiol. Biotechnol. 57: 412-418
  87. Rombaut, G., G. Suantika, N. Boon, S. Maertens, P.H. Dhert, M. Top, P. Sorgeloos and W. Verstraete. 2001. Monitoring the evolving diversity of the microbial community present in rotifer cultures. Aquaculture 198:237-252.
  88. Boon, N., J. Goris, P. De Vos, W. Verstraete, and M. Top. 2001. Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae. Appl. Environ. Microbiol. 67: 1107-1115.
  89. Muthumbi, W., N. Boon, R. Boterdaele, I. De Vreese, M. Top, and W. Verstraete. 2001. Microbial sulfate reduction with acetate: process performance and composition of the bacterial communities in the reactor at different salinity levels. Appl. Microbiol. Biotechnol. 55:787–793
  90. El-Fantroussi, S., W. Verstraete, and E.M. Top. 2000. Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives. Appl. Environ. Microbiol. 66: 5110-51150.
  91. Dejonghe, W., J. Goris, S. El Fantroussi, M. Höfte, P. De Vos, W. Verstraete, andM. Top. 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. Appl. Environ. Microbiol. 66:3297-3304.
  92. Boon, N., J. Goris, P. De Vos, W. Verstraete, and M. Top. 2000. Bioaugmentation of activated sludge by an indigenous 3-chloroaniline degrading Comamonas testosteroni strain I2gfp. Appl. Environ. Microbiol. 66: 2906-2913.
  93. Smalla, K., E. Krögerrecklenfort, H. Heuer, W. Dejonghe, Top, M. Osborn, J. Niewint, C. Tebbe, M. Barr, M. Bailey, A. Greated, C. Thomas, S. Turner, P. Young, D. Nikolakopoulou, A. Karagouni, A. Wolters, J.D. van Elsas, K. Drønen, R. Sandaa, S. Borin, J. Brahbu, E. Grohmann, and P. Sobecky. 2000. PCR-based detection of mobile genetic elements in total community DNA. Microbiology 164: 1256-1257.
  94. Boon, N., C. Marlé, M. Top, and W. Verstraete. 2000. Comparison of the spatial homogeneity of physico-chemical parameters and bacterial 16S rRNA genes in sediment samples of a dumping site of dredging sludge. Appl. Microbiol. Biotechnol. 53: 742-747.
  95. Bossier, P., M. Top, G. Huys, K. Kersters, C.J.P. Boonaert, P.G. Rouxhet, and W. Verstraete. 2000. Modification of the aggregation behaviour of the environmental Ralstonia eutropha-like strain AE815 is reflected by both surface hydrophobicity and AFLP-patterns. Environmental Microbiology 2: 51-58.
  96. Top, E.M., P. Maila, M. Clerinx, J. Goris, P. De Vos, and W. Verstraete. 1999. Methane oxidation as a method to evaluate the removal of 2,4-dichlorophenoxyactic acid (2,4-D) from soil by plasmid mediated bioaugmentation. FEMS Microbiol. Ecol. 28: 203-213.
  97. El Fantroussi, S., L. Verschuere, W. Verstraete, and M. Top. 1999. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65: 982-988.
  98. Drønen, A.K., V. Torsvik, and M. Top. 1999. Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil. FEMS Microbiol. Letters 176: 105-110.
  99. Verstraete, W., and M. Top. 1999. Soil clean-up: lessons to remember. Int. Biodeter. Biodegr. 43:147-153
  100. El Fantroussi, S., M. Belkacemi, M. Top, J. Mahillon, H. Naveau, and S. N. Agathos. 1999. Bioaugmentation of a soil bioreactor designed for pilot scale anaerobic bioremediation studies. Environ. Sci. Technol. 33:2992-3001.
  101. Szpirer, C., Top, M. Couturier and M. Mergeay. 1999. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology 145: 3321-3329
  102. Top, E.M., Van Daele, N. De Saeyer, and L.J. Forney. 1998. Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids. Anton. Leeuw. Int. J. Gen. Mol. Microbiol.73:87-94.
  103. K.E., and E.M. Top. 1998. Gene transfer in soil systems using microcosms. FEMS Microbiol. Ecol. 25: 3 19-329
  104. Drønen, A.K., V. Torsvik, J. Goksøyr, and M. Top. 1998. Effect of mercury addition on plasmid incidence and gene mobilising capacity in bulk soil. FEMS Microbiol. Ecol. 27: 381-394.
  105. Van Limbergen, H., M. Top, and W. Verstraete. 1998. Bioaugmentation in activated sludge: current features and future perspectives. Appl. Microbiol. Biotechnol. 50: 16-23
  106. Top, E.M., O. Maltseva, and L.J. Forney. 1996. Capture of a catabolic plasmid that only encodes 2,4-dichlorophenoxyacetic acid:a-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. Appl. Environ. Microbiol. 62:1470-1476.
  107. Top, E.M.,E. Holben, and L.J. Forney. 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid- degradative plasmids isolated from soil by complementation. Appl. Environ. Microbiol. 61: 1691-1698.
  108. Top, E.M., H. De Rore, J.-M. Collard, V. Gellens, G. Slobodkina, W. Verstraete, and M. Mergeay. 1995. Retromobilization of heavy metal resistance genes in unpolluted and heavy metal polluted soil. FEMS Microbiol. Ecol. 18:191-203.
  109. De Rore, H., Top, F. Houwen, M. Mergeay, and W. Verstraete. 1994. Evolution of heavy metal resistant transconjugants in a soil environment with a concomitant selective pressure. FEMS Microbiol. Ecol 14:263-274.
  110. De Rore, H., K. Demolder, K. De Wilde, Top, F. Houwen, and W. Verstraete. 1994. Transfer of the catabolic plasmid RP4::Tn4371 to indigenous soil bacteria and its effect on respiration and biphenyl breakdown. FEMS Microbiol. Ecol. 15:71-81.
  111. Top, E., De Smet, W. Verstraete, R. Dijkmans, and M. Mergeay. 1994. Exogenous isolation of mobilizing plasmids from polluted soils and sludges. Appl. Environ. Microbiol. 60:831-839.
  112. Diels, L., D. Springael, D. van der Lelie, Top, and M. Mergeay. 1993. Use of DNA probes and plasmid capture in a search for new interesting environmental genes. The Science of the total environment 139/140:471-478.
  113. Top, E., P. Vanrolleghem, M. Mergeay, and W. Verstraete. 1992. Determination of the mechanism of retrotransfer by mechanistic mathematical modeling. J. Bacteriol. 174:5953-5960.
  114. Top, E., Mergeay, D. Springael, and W. Verstraete. 1990. Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples. Appl. Environ. Microbiol. 56:2471-2479.