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publications

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ISME J (2016) 10

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Comm Biol (2020) 3

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Philos Trans Royal Soc B (2020)  375

Ma Y, Kan A, Johnson DR (2024) Metabolic interactions regulate the transfer and proliferation of plasmid-encoded antibiotic resistance during surface-associated microbial growth. Cell Reports. In press.

Gogia G, Johnson DR (2024) Bacteria spiral into control. Nature Physics 20: 897-898.

Ruan C, Ramoneda J, Kan A, Rudge TJ, Wang G, Johnson DR (2024) Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nature Communications 15: 5397.

Takahashi K, Oshiki M, Ruan C, Morinaga K, Toyofuku M, Nomura N, Johnson DR (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: e13221.

Ma Y, Ramoneda J, Johnson DR (2023) Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. Nature Communications 14: 3530.

Karakurt-Fischer S, Johnson DR, Fenner K, Hafner J (2023) Making Waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia. Water Research 247: 120756.

Ge ZB, Zhai ZQ, Xie WY, Dai J, Huang K, Johnson DR, Wang P (2023) Two-tiered mutualism improves survival and competitiveness of cross-feeding bacteria in soil. The ISME Journal 17: 2090-2102.

Ruan C, Borer B, Ramoneda J, Wang G, Johnson DR (2023) Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. npj Biofilms and Microbiomes 9: 58.

Chen G, Hu Z, Ebrahimi A, Johnson DR, Wu F, Sun Y, Shen R, Liu L, Wang G (2023) Chemotactic movement and zeta potential dominate Chlamydomonas microsphaera attachment and biocathode development. Environmental Technology 44: 1838-1849.

Ruan C, Ramoneda J, Gogia G, Wang G, Johnson DR (2022) Fungal hyphae regulate bacterial diversity and promote plasmid-mediated functional novelty during range expansion. Current BIology 32: 5285-5294.e4.

Dolinšek J, Ramoneda J, Johnson DR (2022) Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME Communications 2: 77.

Wang M, Chen X, Ma Y, Tang YQ, Johnson DR, Nie Y, Wu XL (2022) Type IV pilus shapes a 'bubble-jet' pattern opposing spatial intermixing of two interacting bacterial populations. Microbiology Spectrum 10: e01944-21.

Ciccarese D, Micali G, Borer B, Ruan C, Or D, Johnson DR (2022) Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment. The ISME Journal 16: 1453-1463.

Chen G, Hu Z, Ebrahimi A, Johnson DR, Wu F, Sun Y, Shen R, Liu L, Wang G (2022) Electrotaxis-mediated cell motility and nutrient availability determine Chlamydomonas microsphaera-surface interactions in bioelectrochemical systems. Bioelectrochemistry 143: 107989.

Ruan C, Ramoneda J, Chen G, Johnson DR, Wang G (2021) Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations. ISME Communications 1: 54.

Goldschmidt F, Caduff L, Johnson DR (2021) Causes and consequences of pattern diversification in a spatially self-organizing microbial community. The ISME Journal 15: 2415-2426.

Dubey M, Hadadi N, Pelet S, Carraro N, Johnson DR, van der Meer JR (2021) Environmental connectivity controls diversity in soil microbial communities. Communications Biology 4: 492.

Borer B, Ciccarese D, Johnson DR, Or D (2020) Spatial organization in microbial range expansion emerging from trophic dependencies and successful lineages. Communications Biology 3: 685.

Johnson DR, Pomati F (2020) A brief guide for the measurement and interpretation of microbial functional diversity. Environmental Microbiology 22: 3039-3048.

Ciccarese D, Zuidema A, Merlo V, Johnson DR (2020) Interaction-dependent effects of surface structure on microbial spatial self-organization. Philosophical Transactions of the Royal Society B 375: 20190246.

Johnson DR, Noack S (2020) Editorial overview: Causes and biotechnological application of microbial metabolic specialization. Current Opinion in Biotechnology 62: iii-vi.

Achermann S, Mansfeldt CB, Müller M, Johnson DR, Fenner K (2020) Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities. Environmental Science & Technology 54: 235-244.

Ciccarese D, Johnson DR (2019) Functional microbial landscapes. In Comprehensive Biotechnology 3rd Ed. Moo-Young M. Elsevier.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A, Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J (2019) Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology 4: 1183-1195.

Mansfeldt C, Achermann S, Men Y, Walser JC, Villez K, Joss A, Johnson DR, Fenner K (2019) Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. The ISME Journal 13: 1589-1601.

Ju F, Beck K, Yin X, Maccagnan A, McArdell CS, Singer H, Johnson DR, Zhang T, Bürgmann H (2019) Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes. The ISME Journal 13: 346-360.

Lilja EE, Johnson DR (2019) Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage. BMC Evolutionary Biology 19: 129.

Tecon R, Mitri S, Ciccarese D, Or D, van der Meer JR, Johnson DR (2019) Bridging the holistic-reductionist divide in microbial ecology. mSystems 4: e00265-18.

Patsch D, van Vliet S, Marcantini LG, Johnson DR (2018) Generality of associations between biological richness and the rates of metabolic processes across microbial communities. Environmental Microbiology 20: 4356-4368.

Goldschmidt F, Regoes R, Johnson DR (2018) Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community. The ISME Journal 12: 136-144.

Wells GF, Shi YJ, Laureni M, Weissbrodt DG, Joss A, Bürgmann H, Johnson DR, Morgenroth E (2017) Comparing the resistance, resilience, and stability of replicate moving bed biofilm and suspended growth combined nitritation-anammox reactors. Environmental Science & Technology 51: 5108-5117.

Goldschmidt F, Regoes R, Johnson DR (2017) Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations. The ISME Journal 11: 2112-2123.

Marchal M, Selina Derksen, Sven Panke, Ackermann M, Johnson DR (2017) A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evolutionary Biology 17: 106.

Lilja EE, Johnson DR (2017) Metabolite toxicity determines the pace of molecular evolution within microbial populations. BMC Evolutionary Biology 17: 52.

Men Y, Achermann S, Helbling DE, Johnson DR, 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.

Men Y, Han P, Helbling DE, Jehmlich N, Herbold C, Guide R, Onnis-Hayden A, Gu AZ, Johnson DR, Wagner M, Fenner K (2016) Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon Nitrososphaera gargensisEnvironmental Science & Technology 50: 4682-4692.

Filippidou S, Bueche M, Wunderlin T, Junier T, Roussel-Delif L, Jeanneret N, Dorador C, Molina V, Ioannidou A, Vargemezis G, Johnson DR, Junier P (2016) A combination of extreme environmental conditions favor the prevalence of endospore-forming firmicutes. Frontiers in Microbiology 7: 1707.

Dolinšek J, Goldschmidt F, Johnson DR (2016) Synthetic microbial assemblages and the dynamic interplay between microbial genotypes. FEMS Microbiology Reviews 40: 961-979.

Kinnunen M, Dechesne A, Proctor C, Hammes F, Johnson DR, Quintela-Baluja M, Graham D, Daffonchio D, Fodelianakis S, Hahn N, Boon N, Smets BF (2016) A conceptual framework for invasion in microbial communities. The ISME Journal 10: 2773-2775.

Widder S, Allen R, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Grosskopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME Journal 10: 2557-2568.

Lindemann SR, Bernstein HC, Song HS, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS (2016) Engineering microbial consortia for controllable outputs. The ISME Journal 10: 2077-2084.

Lilja EL, Johnson DR (2016) Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. The ISME Journal 10: 1568-1578.

Johnson DR, Lee TK, Park J, Fenner K, Helbling DE (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: 4851-4860.

Johnson DR, Helbling DE, Men Y, Fenner K (2015) Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products? Environmental Science: Water Research & Technology 1: 272-278.

Johnson DR, Helbling DE, Lee TK, Park J, Fenner K, Kohler HPE, Ackermann M (2015) Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities. Applied and Environmental Microbiology 81: 666-675.

Helbling DE, Johnson DR, Lee TK, 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.

West KA, Lee PKH, Johnson DR, Zinder SH, Alvarez-Cohen L (2013) Global gene expression of Dehalococcoideswithin a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply. Biotechnology & Bioengineering 110: 1333-1341.

Coronado E, Roggo C, Johnson DR, van der Meer JR (2012) Genome-wide analysis of salicylate and dibenzofuran metabolism in Sphingomonas wittichii RW1. Frontiers in Microbiology 3: 300.

Fida TT, Breugelmans P, Lavigne R, Coronado E, Johnson DR, van der Meer JR, Mayer AP, Heipieper HJ, Hofkens J, Springael D (2012) Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. LH128 in biofilms. Applied and Environmental Microbiology 78: 8311-8320.

Helbling DE, Ackermann M, Fenner K, Kohler HPE, Johnson DR (2012) The activity level of a microbial community function can be predicted from its metatranscriptome. The ISME Journal 6: 902-904.

Helbling DE, Johnson DR, Honti M, Fenner K (2012) Micropollutant biotransformation kinetics associate with WWTP process parameters and microbial community characteristics. Environmental Science & Technology 46: 10579-10588,

Johnson DR, Goldschmidt F, Lilja EE, Ackermann M (2012) Metabolic specialization and the assembly of microbial communities. The ISME Journal 6: 1985-1991.

Men Y, Feil H, VerBerkmoes NC, Shah MB, Johnson DR, Lee PK, West KA, Zinder SH, Andersen GL, Alvarez-Cohen L (2012) Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analysis. The ISME Journal 6: 410-421.

Johnson DR, Coronado E, Moreno-Forero SK, Heipieper HJ, van der Meer JR (2011) Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichiiBMC Microbiology 11: 250.

Müller S, Johnson DR (2011) Application of cytomics to separate natural microbial communities by their physiological propertiesIn Handbook of Molecular Microbial Ecology Vol I: Metagenomics and Complementary Approaches. Ed. de Bruijn FJ. Wiley-Blackwell.

 

Gaillard M, Pradervand N, Minoia M, Sentchilo V, Johnson DR, van der Meer JR (2010) Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiology 10: 153.

Johnson DR (2009) Transcriptome analysis using high-density oligonucleotide microarrays. In Handbook of Hydrocarbon and Lipid Microbiology Vol 5: Experimental Protocols and Appendices. Eds. Timmis KN, McGenity T, van der Meer JR, de Lorenzo V. Springer.

 

Johnson DR, Czechowska K, Chèvre N, van der Meer JR (2009) Toxicity of triclosan, penconazole, and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry. Environmental Microbiology 11: 1682-1691.

Johnson DR, Nemir A, Andersen GL, Zinder SH, Alvarez-Cohen L (2009) Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiology Letters 294: 198-206.

 

Czechowska K, Johnson DR, van der Meer JR (2008) Use of flow cytometric methods for single-cell analysis in environmental microbiology. Current Opinion in Microbiology 11: 205-212.

 

Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Temporal transcriptomic microarray analysis of “Dehalococcoides ethenogenes” strain 195 during the transition into stationary phase. Applied and Environmental Microbiology 74: 2864-2872.

 

West KA, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PKH, Feil H, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Comparative genomics of “Dehalococcoides ethenogenes” 195 and an enrichment culture containing unsequenced “Dehalococcoides” strains. Applied and Environmental Microbiology 74: 3490-3496.

Johnson DR, Park J, Kukor JJ, Abriola LM (2006) Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation 17: 437-445.

 

Lee PKH, Johnson DR, Holmes VF, He J, Alvarez-Cohen L (2006) Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Applied and Environmental Microbiology 72: 6161-6168.

 

Pecson BM, Barrios JA, Johnson DR, Nelson KL (2006) A real-time PCR method for quantifying viable Ascaris eggs using the first internally-transcribed spacer region of rRNA. Applied and Environmental Microbiology 72: 7864-7872.

 

Johnson DR, Lee PKH, Holmes VF, Alvarez-Cohen L (2005) An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Applied and Environmental Microbiology 71: 3866-3871.

 

Johnson DR, Lee PKH, Holmes VF, Fortin AC, Alvarez-Cohen L (2005) Transcriptional expression of the tceAgene in a Dehalococcoides-containing microbial enrichment. Applied and Environmental Microbiology 71: 7145-7151.

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