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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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). https://doi.org/10.1016/B978-0-444-64046-8.00472-9
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
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
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
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