publications

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ISME J (2016) 10

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Philos Trans Royal Soc B (2020) 375

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ISME J (2025) 19

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Commun Biol (2020) 3

Gu W, Richter XYL, Johnson DR (2026) Managing microbial interactions in environmental biotechnology: can we scale interaction principles? Trends in Microbiology. In press

Xiao D, Johnson DR, Zhang W, Xu Z, Hu P, Sun M, Zhao J, Chen H, Wang K (2026) Bedrock-soil geochemistry dominates free-living nitrogen fixation in soils but not in litter via interspecific microbial interactions. Communications Earth & Environment. In press.

Wang L, Ruan C, Huang D, Johnson DR, Wang D, Yu P (2026) Carrier bacteria motility determines efficacy of hitchhiking bacteriophages to control biofilm. Chemical Engineering Journal 536: 175902.

Xiao D, Zhang W, Johnson DR, Hu P, Xu L, Sun M, Tang L, He X, Zhao J, Liao X, Peng W, Chen H, Wang K (2026) Increased soil carbon and nitrogen stocks associate with stronger calcium-microbial and multi-trophic interactions under warming. Global Change Biology 32: e70826.

Takahashi K, Ohara K, Higuchi K, Ohmura T, Okabe S, Johnson DR, Oshiki M (2026) Horizontal and vertical gene transfer jointly shape the realized plasmid host range in surface-associated microbial systems. iScience 29: 115299.

Majumdar A, Johnson DR, Moulick D (2026) Managing environmental antimicrobial resistance (AMR) under climate change: current gaps and future needs. Integrated Environmental Assessment and Management 22: 329-330.

Tandler P, Johnson DR, Gogia G (2026) Sensitivity of microbial spatial self-organization to surface friction depends on metabolic interactions. The ISME Journal 20: wrag35 .

Dai J, Chen C, Zhai ZQ, Gao AX, Johnson DR, Kopittke PM, Zhao FJ, Wang P (2025) The balance between microbial arsenic methylation and demethylation in paddy soils underpins global arsenic risk and straighthead disease in rice. Proceedings of the National Academy of Sciences USA 122: e2508311122

Han M, Ruan C, Wang G, Johnson DR (2025) Fungal hyphae promote bacterial contact-dependent killing during surface-associated growth. The ISME Journal 19: wraf135

Ruan C, Vinod DP, Johnson DR (2025) Phage-mediated peripheral kill-the-winner facilitates the maintenance of costly antibiotic resistance. Nature Communications 16: 5839

Sam SB, Smith SK, Niederdorfer R, Scheidegger A, Ward BJ, Tembo JM, Kabika J, Johnson DR , Bürgmann H, Morgenroth E, Strande L (2025) Microbial community composition reflects water usage and storage conditions in a city-wide study of non-sewered wastewater (fecal sludge). PLOS Water 4: e0000386

Zhu C, Wu L, Ning D, Tian R, Gao S, Zhang B, Zhau J, Zhang Y, Xiao N, Wang Y, Brown MR, Tu Q, Global Water Microbiome Consortium, Ju F, Wells GF, Guo J, He Z, Nielsen PH, Wang A, Zhang Y, Chen T, He Q, Criddle CS, Wagner M, Tiedje JM, Curtis TP, Wen X, Yang Y, Alvarez-Cohen L, Stahl DA, Alvarez PJJ, Rittmann BE, Zhou J (2025) Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems. Nature Communications 16: 4006

Han M, Ruan C, Wang G, Johnson DR (2025) Evaporation controls contact-dependent bacterial killing during surface-associated growth. ISME Communications 5: ycaf034

Ma Y, Kan A, Johnson DR (2024) Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth. Cell Reports 45: 114653

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. 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 gargensis. Environmental 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 wittichii. BMC Microbiology 11: 250

Müller S, Johnson DR (2011) Application of cytomics to separate natural microbial communities by their physiological properties. In 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