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Transcriptome analysis of the mobile genome ICE<i>clc</i> in <i>Pseudomonas knackmussii</i> B13
Gaillard, M., Pradervand, N., Minoia, M., Sentchilo, V., Johnson, D. R., & van der Meer, J. R. (2010). Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiology, 10, 153 (14 pp.). https://doi.org/10.1186/1471-2180-10-153
Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium <I>Sphingomonas wittichii</I>
Johnson, D. R., Coronado, E., Moreno-Forero, S. K., Heipieper, H. J., & van der Meer, J. R. (2011). Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii. BMC Microbiology, 11, 250 (12 pp.). https://doi.org/10.1186/1471-2180-11-250
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of <I>Sphingomonas</I> sp. strain LH128 in biofilms
Fida, T. T., Breugelmans, P., Lavigne, R., Coronado, E., Johnson, D. R., van der Meer, J. R., … Springael, D. (2012). Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. Applied and Environmental Microbiology, 78(23), 8311-8320. https://doi.org/10.1128/AEM.02516-12
The activity level of a microbial community function can be predicted from its metatranscriptome
Helbling, D. E., Ackermann, M., Fenner, K., Kohler, H. P. E., & Johnson, D. R. (2012). The activity level of a microbial community function can be predicted from its metatranscriptome. ISME Journal, 6(4), 902-904. https://doi.org/10.1038/ismej.2011.158
Genome-wide analysis of salicylate and dibenzofuran metabolism in &lt;em&gt;Sphingomonas wittichii&lt;/em&gt; RW1
Coronado, E., Roggo, C., Johnson, D. R., & van der Meer, J. R. (2012). Genome-wide analysis of salicylate and dibenzofuran metabolism in Sphingomonas wittichii RW1. Frontiers in Microbiology, 3, 300 (13 pp.). https://doi.org/10.3389/fmicb.2012.00300
Micropollutant biotransformation kinetics associate with WWTP process parameters and microbial community characteristics
Helbling, D. E., Johnson, D. R., Honti, M., & Fenner, K. (2012). Micropollutant biotransformation kinetics associate with WWTP process parameters and microbial community characteristics. Environmental Science and Technology, 46(19), 10579-10588. https://doi.org/10.1021/es3019012
Metabolic specialization and the assembly of microbial communities
Johnson, D. R., Goldschmidt, F., Lilja, E. E., & Ackermann, M. (2012). Metabolic specialization and the assembly of microbial communities. ISME Journal, 6(11), 1985-1991. https://doi.org/10.1038/ismej.2012.46
Sustainable syntrophic growth of <I>Dehalococcoides ethenogenes</I> strain 195 with <I>Desulfovibrio vulgaris</I> Hildenborough and <I>Methanobacterium congolense</I>: global transcriptomic and proteomic analyses
Men, Y., Feil, H., Verberkmoes, N. C., Shah, M. B., Johnson, D. R., Lee, P. K. H., … Alvarez-Cohen, L. (2012). Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME Journal, 6(2), 410-421. https://doi.org/10.1038/ismej.2011.111
Global gene expression of <I>Dehalococcoides</I> within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply
West, K. A., Lee, P. K. H., Johnson, D. R., Zinder, S. H., & Alvarez-Cohen, L. (2013). Global gene expression of Dehalococcoides within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply. Biotechnology and Bioengineering, 110(5), 1333-1341. https://doi.org/10.1002/bit.24819
Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?
Johnson, D. R., Helbling, D. E., Men, Y., & Fenner, K. (2015). Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products? Environmental Science: Water Research and Technology, 1(3), 272-278. https://doi.org/10.1039/c5ew00016e
A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates
Helbling, D. E., Johnson, D. R., Lee, T. K., Scheidegger, A., & Fenner, K. (2015). A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. Water Research, 70, 471-484. https://doi.org/10.1016/j.watres.2014.12.013
Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities
Johnson, D. R., Helbling, D. E., Lee, T. K., Park, J., Fenner, K., Kohler, H. P. E., & Ackermann, M. (2015). Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities. Applied and Environmental Microbiology, 81(2), 666-675. https://doi.org/10.1128/AEM.03286-14
The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability
Johnson, D. R., Lee, T. K., Park, J., Fenner, K., & Helbling, D. E. (2015). The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability. Environmental Microbiology, 17(12), 4851-4860. https://doi.org/10.1111/1462-2920.12429
Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates
Lilja, E. E., & Johnson, D. R. (2016). Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. ISME Journal, 10, 1568-1578. https://doi.org/10.1038/ismej.2015.243
A combination of extreme environmental conditions favor the prevalence of endospore-forming firmicutes
Filippidou, S., Wunderlin, T., Junier, T., Jeanneret, N., Dorador, C., Molina, V., … Junier, P. (2016). A combination of extreme environmental conditions favor the prevalence of endospore-forming firmicutes. Frontiers in Microbiology, 7, 1707 (11 pp.). https://doi.org/10.3389/fmicb.2016.01707
Synthetic microbial ecology and the dynamic interplay between microbial genotypes
Dolinšek, J., Goldschmidt, F., & Johnson, D. R. (2016). Synthetic microbial ecology and the dynamic interplay between microbial genotypes. FEMS Microbiology Reviews, 40(6), 961-979. https://doi.org/10.1093/femsre/fuw024
Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon <I>Nitrososphaera gargensis</I>
Men, Y., Han, P., Helbling, D. E., Jehmlich, N., Herbold, C., Gulde, R., … Fenner, K. (2016). Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon Nitrososphaera gargensis. Environmental Science and Technology, 50(9), 4682-4692. https://doi.org/10.1021/acs.est.5b06016
A conceptual framework for invasion in microbial communities
Kinnunen, M., Dechesne, A., Proctor, C., Hammes, F., Johnson, D., Quintela-Baluja, M., … Smets, B. F. (2016). A conceptual framework for invasion in microbial communities. ISME Journal, 10, 2773-2779. https://doi.org/10.1038/ismej.2016.75
Metabolite toxicity determines the pace of molecular evolution within microbial populations
Lilja, E. E., & Johnson, D. R. (2017). Metabolite toxicity determines the pace of molecular evolution within microbial populations. BMC Evolutionary Biology, 17, 52 (12 pp.). https://doi.org/10.1186/s12862-017-0906-2
Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Goldschmidt, F., Regoes, R. R., & Johnson, D. R. (2017). Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations. ISME Journal, 11(9), 2112-2123. https://doi.org/10.1038/ismej.2017.76