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  • (-) Eawag Authors = Johnson, David R.
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Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations
Takahashi, K., Oshiki, M., Ruan, C., Morinaga, K., Toyofuku, M., Nomura, N., & Johnson, D. R. (2024). Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations. Environmental Microbiology Reports, 16(1), e13221 (14 pp.). https://doi.org/10.1111/1758-2229.13221
Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability
Dolinšek, J., Ramoneda, J., & Johnson, D. R. (2022). Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME Communications, 2(1), 77 (10 pp.). https://doi.org/10.1038/s43705-022-00160-1
Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia
Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023). Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia. Water Research, 247, 120756 (7 pp.). https://doi.org/10.1016/j.watres.2023.120756
Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria
Ge, Z. B., Zhai, Z. Q., Xie, W. Y., Dai, J., Huang, K., Johnson, D. R., … Wang, P. (2023). Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria. ISME Journal, 17, 2090-2102. https://doi.org/10.1038/s41396-023-01519-5
Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth
Ruan, C., Borer, B., Ramoneda, J., Wang, G., & Johnson, D. R. (2023). Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. npj Biofilms and Microbiomes, 9, 58 (10 pp.). https://doi.org/10.1038/s41522-023-00428-x
Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion
Ma, Y., Ramoneda, J., & Johnson, D. R. (2023). Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. Nature Communications, 14(1), 3530 (12 pp.). https://doi.org/10.1038/s41467-023-39354-z
Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion
Ruan, C., Ramoneda, J., Gogia, G., Wang, G., & Johnson, D. R. (2022). Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Current Biology, 32(24), 5285-5294. https://doi.org/10.1016/j.cub.2022.11.009
Type IV pilus shapes a 'bubble-burst' pattern opposing spatial intermixing of two interacting bacterial populations
Wang, M., Chen, X., Ma, Y., Tang, Y. Q., Johnson, D. R., Nie, Y., & Wu, X. L. (2022). Type IV pilus shapes a 'bubble-burst' pattern opposing spatial intermixing of two interacting bacterial populations. Microbiology Spectrum, 10(1), e01944-21 (7 pp.). https://doi.org/10.1128/spectrum.01944-21
Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment
Ciccarese, D., Micali, G., Borer, B., Ruan, C., Or, D., & Johnson, D. R. (2022). Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment. ISME Journal, 16, 1453-1463. https://doi.org/10.1038/s41396-022-01189-9
Chemotactic movement and zeta potential dominate <em>Chlamydomonas microsphaera</em> attachment and biocathode development
Chen, G., Hu, Z., Ebrahimi, A., Johnson, D. R., Wu, F., Sun, Y., … Wang, G. (2023). Chemotactic movement and zeta potential dominate Chlamydomonas microsphaera attachment and biocathode development. Environmental Technology, 44(12), 1838-1849. https://doi.org/10.1080/09593330.2021.2014575
Electrotaxis-mediated cell motility and nutrient availability determine <em>Chlamydomonas microsphaera</em>-surface interactions in bioelectrochemical systems
Chen, G., Hu, Z., Ebrahimi, A., Johnson, D. R., Wu, F., Sun, Y., … Wang, G. (2022). Electrotaxis-mediated cell motility and nutrient availability determine Chlamydomonas microsphaera-surface interactions in bioelectrochemical systems. Bioelectrochemistry, 143, 107989 (9 pp.). https://doi.org/10.1016/j.bioelechem.2021.107989
Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations
Ruan, C., Ramoneda, J., Chen, G., Johnson, D. R., & Wang, G. (2021). Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations. ISME Communications, 1(1), 54 (5 pp.). https://doi.org/10.1038/s43705-021-00057-5
Towards community systems microbiology for the optimization of aerobic-anaerobic ammonium oxidation processes
Weissbrodt, D. G., Wells, G. F., Johnson, D. R., Bürgmann, H., Joss, A., Laureni, M., & Morgenroth, E. (2014). Towards community systems microbiology for the optimization of aerobic-anaerobic ammonium oxidation processes. In Vol. 1. 87th annual water environment federation technical exhibition and conference (WEFTEC 2014) (pp. 2645-2649). https://doi.org/10.2175/193864714815942567
Challenges in microbial ecology: building predictive understanding of community function and dynamics
Widder, S., Allen, R. J., Pfeiffer, T., Curtis, T. P., Wiuf, C., Sloan, W. T., … Wilmes, P. (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal, 10(11), 2557-2568. https://doi.org/10.1038/ismej.2016.45
Causes and consequences of pattern diversification in a spatially self-organizing microbial community
Goldschmidt, F., Caduff, L., & Johnson, D. R. (2021). Causes and consequences of pattern diversification in a spatially self-organizing microbial community. ISME Journal, 15(8), 2415-2426. https://doi.org/10.1038/s41396-021-00942-w
Environmental connectivity controls diversity in soil microbial communities
Dubey, M., Hadadi, N., Pelet, S., Carraro, N., Johnson, D. R., & van der Meer, J. R. (2021). Environmental connectivity controls diversity in soil microbial communities. Communications Biology, 4(1), 492 (15 pp.). https://doi.org/10.1038/s42003-021-02023-2
Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages
Borer, B., Ciccarese, D., Johnson, D., & Or, D. (2020). Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages. Communications Biology, 3(1), 685 (10 pp.). https://doi.org/10.1038/s42003-020-01409-y
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
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
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