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Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities
Achermann, S., Mansfeldt, C. B., Müller, M., Johnson, D. R., & Fenner, K. (2020). Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities. Environmental Science and Technology, 54(1), 235-244. https://doi.org/10.1021/acs.est.9b05421
Functional microbial landscapes
Ciccarese, D., & Johnson, D. R. (2019). Functional microbial landscapes. In S. Agathos & B. Stenuit (Eds.), Comprehensive biotechnology: Vol. 6. Environmental and related biotechnologies (pp. 42-51). Elsevier.
Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes
Ju, F., Beck, K., Yin, X., Maccagnan, A., McArdell, C. S., Singer, H. P., … Bürgmann, H. (2019). Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes. ISME Journal, 13(2), 346-360. https://doi.org/10.1038/s41396-018-0277-8
Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage
Lilja, E. E., & Johnson, D. R. (2019). Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage. BMC Evolutionary Biology, 19(1), 129 (11 pp.). https://doi.org/10.1186/s12862-019-1458-4
Bridging the holistic-reductionist divide in microbial ecology
Tecon, R., Mitri, S., Ciccarese, D., Or, D., van der Meer, J. R., & Johnson, D. R. (2019). Bridging the holistic-reductionist divide in microbial ecology. mSystems, 4(1), e00265-18 (5 pp.). https://doi.org/10.1128/mSystems.00265-18
Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community
Goldschmidt, F., Regoes, R. R., & Johnson, D. R. (2018). Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community. ISME Journal, 12(1), 136-144. https://doi.org/10.1038/ismej.2017.147
Generality of associations between biological richness and the rates of metabolic processes across microbial communities
Patsch, D., van Vliet, S., Garbani Marcantini, L., & Johnson, D. R. (2018). Generality of associations between biological richness and the rates of metabolic processes across microbial communities. Environmental Microbiology, 20(12), 4356-4368. https://doi.org/10.1111/1462-2920.14352
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
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
A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations
Marchal, M., Goldschmidt, F., Derksen-Müller, S. N., Panke, S., Ackermann, M., & Johnson, D. R. (2017). A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evolutionary Biology, 17, 106 (14 pp.). https://doi.org/10.1186/s12862-017-0950-y
Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation
Men, Y., Achermann, S., Helbling, D. E., Johnson, D. R., & Fenner, K. (2017). Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation. Water Research, 109, 217-226. https://doi.org/10.1016/j.watres.2016.11.048
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
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
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
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
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 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
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
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