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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
Interaction-dependent effects of surface structure on microbial spatial self-organization
Ciccarese, D., Zuidema, A., Merlo, V., & Johnson, D. R. (2020). Interaction-dependent effects of surface structure on microbial spatial self-organization. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1798), 20190246 (11 pp.). https://doi.org/10.1098/rstb.2019.0246
A brief guide for the measurement and interpretation of microbial functional diversity
Johnson, D. R., & Pomati, F. (2020). A brief guide for the measurement and interpretation of microbial functional diversity. Environmental Microbiology, 22(8), 3039-3048. https://doi.org/10.1111/1462-2920.15147
Editorial overview: causes and biotechnological application of microbial metabolic specialization
Johnson, D. R., & Noack, S. (2020). Editorial overview: causes and biotechnological application of microbial metabolic specialization. Current Opinion in Biotechnology, 62, III-VI. https://doi.org/10.1016/j.copbio.2020.01.007
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
Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities
Mansfeldt, C., Achermann, S., Men, Y., Walser, J. C., Villez, K., Joss, A., … Fenner, K. (2019). Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. ISME Journal, 13(6), 1589-1601. https://doi.org/10.1038/s41396-019-0371-6
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
Global diversity and biogeography of bacterial communities in wastewater treatment plants
Wu, L., Ning, D., Zhang, B., Li, Y., Zhang, P., Shan, X., … Zhou, J. (2019). Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology, 4(7), 1183-1195. https://doi.org/10.1038/s41564-019-0426-5
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
Comparing the resistance, resilience, and stability of replicate moving bed biofilm and suspended growth combined nitritation–anammox reactors
Wells, G. F., Shi, Y., Laureni, M., Rosenthal, A., Szivák, I., Weissbrodt, D. G., … Morgenroth, E. (2017). Comparing the resistance, resilience, and stability of replicate moving bed biofilm and suspended growth combined nitritation–anammox reactors. Environmental Science and Technology, 51(9), 5108-5117. https://doi.org/10.1021/acs.est.6b05878
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