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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
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
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
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
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
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
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
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
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
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
Transcriptome analysis of the mobile genome ICE&lt;em&gt;clc&lt;/em&gt; in &lt;em&gt;Pseudomonas knackmussii&lt;/em&gt; 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
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
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
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
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
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
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
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
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