Department Environmental Microbiology

Publications 2022

Van Riet, S., Tadesse, W., Mortier, J., Schlegel, S., Simoens, K., Bernaerts, K., … Aertsen, A. (2022). Heterogeneity and evolutionary tunability of Escherichia coli resistance against extreme acid stress. Microbiology Spectrum, 10(6), 1-13. doi:10.1128/spectrum.03757-22, Institutional Repository
Amin, M. B., Talukdar, P. K., Asaduzzaman, M., Roy, S., Flatgard, B. M., Islam, M. R., … Islam, M. A. (2022). Effects of chronic exposure to arsenic on the fecal carriage of antibiotic-resistant Escherichia coli among people in rural Bangladesh. PLoS Pathogens, 18(12), e1010952 (23 pp.). doi:10.1371/journal.ppat.1010952, Institutional Repository
Povolo, V. R. (2022). Causes and consequences of group formation during the degradation of carbon polymers by bacteria (Doctoral dissertation). ETH Zurich, Zurich, 165 p. , Institutional Repository
Montealegre, M. C., Greenwood, E. E., Teichmann, L., Nadimpalli, M. L., Caduff, L., Swarthout, J. M., … Julian, T. R. (2022). Drinking water chlorination impact on fecal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Bangladeshi children in a double-blind, cluster-randomized controlled trial. Environmental Health Perspectives, 130(11), 117702 (3 pp.). doi:10.1289/EHP11359, Institutional Repository
George, C. M., Birindwa, A., Beck, S., Julian, T. R., Kuhl, J., Williams, C., … Cirhuza, L. B. (2022). Fecal contamination in child play spaces and on child hands are associated with subsequent adverse child developmental outcomes in rural Democratic Republic of the Congo: REDUCE prospective cohort study. American Journal of Tropical Medicine and Hygiene, 106(4), 1141-1148. doi:10.4269/ajtmh.21-0706, Institutional Repository
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. doi:10.1016/j.cub.2022.11.009, Institutional Repository
Paoli, L., Robinson, S., & Moore, B. (2022). A wealth of new biosynthetic pathways from the global ocean microbiome. Nature (2 pp.). doi:10.1038/d41586-022-01545-x, Institutional Repository
Schubert, O. T., Bloom, J. S., Sadhu, M. J., & Kruglyak, L. (2022). Genome-wide base editor screen identifies regulators of protein abundance in yeast. eLife, 11, e79525 (29 pp.). doi:10.7554/eLife.79525, Institutional Repository
Huelsmann, M., & Ackermann, M. (2022). Community instability in the microbial world. Science, 378(6615), 29-30. doi:10.1126/science.ade2516, Institutional Repository
Cariti, F., Tuñas Corzon, A., Fernandez-Cassi, X., Ganesanandamoorthy, P., Ort, C., Julian, T. R., & Kohn, T. (2022). Wastewater reveals the spatiotemporal spread of SARS-CoV-2 in the Canton of Ticino (Switzerland) during the onset of the COVID-19 pandemic. ACS ES&T Water, 2(11), 2194-2200. doi:10.1021/acsestwater.2c00082, Institutional Repository
Nelson, T. F., Baumgartner, R., Jaggi, M., Bernasconi, S. M., Battagliarin, G., Sinkel, C., … Sander, M. (2022). Biodegradation of poly(butylene succinate) in soil laboratory incubations assessed by stable carbon isotope labelling. Nature Communications, 13(1), 5691 (16 pp.). doi:10.1038/s41467-022-33064-8, Institutional Repository
Wang, M., Chen, X., Liu, X., Fang, Y., Zheng, X., Huang, T., … Wu, X. L. (2022). Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor. Cell Reports, 40(13), 111410 (20 pp.). doi:10.1016/j.celrep.2022.111410, Institutional Repository
Wu, H., Wan, S., Ruan, C., Niu, X., Chen, G., Liu, Y., … Wang, G. (2022). Phage-bacterium interactions and nutrient availability can shape C and N retention in microbial biomass. European Journal of Soil Science, 73(4), e13296 (5 pp.). doi:10.1111/ejss.13296, Institutional Repository
Cavallaro, A., Rhoads, W. J., Huwiler, S. G., Stachler, E., & Hammes, F. (2022). Potential probiotic approaches to control Legionella in engineered aquatic ecosystems. FEMS Microbiology Ecology, 98(8), 1-9. doi:10.1093/femsec/fiac071, Institutional Repository
Jahn, K., Dreifuss, D., Topolsky, I., Kull, A., Ganesanandamoorthy, P., Fernandez-Cassi, X., … Beerenwinkel, N. (2022). Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nature Microbiology, 7, 1151-1160. doi:10.1038/s41564-022-01185-x, Institutional Repository
Schwartzman, J. A., Ebrahimi, A., Chadwick, G., Sato, Y., Roller, B. R. K., Orphan, V. J., & Cordero, O. X. (2022). Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Current Biology, 32(14), 3059-3069.e7. doi:10.1016/j.cub.2022.06.011, Institutional Repository
Conforti, S., & Costantini, F. (2022). Potential crypticity within two decapod (Crustacea) genera: Galathea Fabricius, 1793 and Eualus Thallwitz, 1891 suggested by integrative taxonomic approach. Mediterranean Marine Science, 23(3), 499-524. doi:10.12681/mms.27733, Institutional Repository
Smolander, N., Julian, T. R., & Tamminen, M. (2022). Prider: multiplexed primer design using linearly scaling approximation of set coverage. BMC Bioinformatics, 23(1), 174 (7 pp.). doi:10.1186/s12859-022-04710-1, Institutional Repository
Huisman, J. S., Scire, J., Caduff, L., Fernandez-Cassi, X., Ganesanandamoorthy, P., Kull, A., … Julian, T. R. (2022). Wastewater-based estimation of the effective reproductive number of SARS-CoV-2. Environmental Health Perspectives, 130(5), 057011 (12 pp.). doi:10.1289/EHP10050, Institutional Repository
Brandenberg, O. F., Schubert, O. T., & Kruglyak, L. (2022). Towards synthetic PETtrophy: engineering Pseudomonas putida for concurrent polyethylene terephthalate (PET) monomer metabolism and PET hydrolase expression. Microbial Cell Factories, 21(1), 119 (31 pp.). doi:10.1186/s12934-022-01849-7, Institutional Repository
Paoli, L., Ruscheweyh, H. J., Forneris, C. C., Hubrich, F., Kautsar, S., Bhushan, A., … Sunagawa, S. (2022). Biosynthetic potential of the global ocean microbiome. Nature, 607, 111-118. doi:10.1038/s41586-022-04862-3, Institutional Repository
Hemmerle, L., Maier, B. A., Bortfeld-Miller, M., Ryback, B., Gäbelein, C. G., Ackermann, M., & Vorholt, J. A. (2022). Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ. Nature Communications, 13(1), 2836 (14 pp.). doi:10.1038/s41467-022-30469-3, Institutional Repository
Bopp, C. E., Bernet, N. M., Kohler, H. P. E., & Hofstetter, T. B. (2022). Elucidating the role of O2 uncoupling in the oxidative biodegradation of organic contaminants by Rieske non-heme iron dioxygenases. ACS Environmental Au, 2(5), 428-440. doi:10.1021/acsenvironau.2c00023, Institutional Repository
Tagliavini, G., Khan, M. H., McCorquodale, M., Westbrook, C., & Holzner, M. (2022). Wake characteristics of complex-shaped snow particles: comparison of numerical simulations with fixed snowflakes to time-resolved particle tracking velocimetry experiments with free-falling analogs. Physics of Fluids, 34(5), 055112 (15 pp.). doi:10.1063/5.0089759, Institutional Repository
Pati, S. G., Bopp, C. E., Kohler, H. P. E., & Hofstetter, T. B. (2022). Substrate-specific coupling of O2 activation to hydroxylations of aromatic compounds by rieske non-heme iron dioxygenases. ACS Catalysis, 12(11), 6444-6456. doi:10.1021/acscatal.2c00383, Institutional Repository
Amin, M. B., Hoque, K. I., Roy, S., Saha, S. R., Islam, M. R., Julian, T. R., & Islam, M. A. (2022). Identifying the sources of intestinal colonization with extended-spectrum β-lactamase-producing Escherichia coli in healthy infants in the community. Frontiers in Microbiology, 13, 803043 (12 pp.). doi:10.3389/fmicb.2022.803043, Institutional Repository
Guo, F., McAuliffe, J. C., Bongiorni, C., Latone, J. A., Pepsin, M. J., Chow, M. S., … Whited, G. M. (2022). A procedure for removal of cyanuric acid in swimming pools using a cell-free thermostable cyanuric acid hydrolase. Journal of Industrial Microbiology and Biotechnology, 49(2), kuab084 (14 pp.). doi:10.1093/jimb/kuab084, Institutional Repository
Nadimpalli, M. L., Lanza, V. F., Montealegre, M. C., Sultana, S., Fuhrmeister, E. R., Worby, C. J., … Pickering, A. J. (2022). Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. Nature Microbiology, 7(5), 620-629. doi:10.1038/s41564-022-01101-3, Institutional Repository
Caduff, L., Dreifuss, D., Schindler, T., Devaux, A. J., Ganesanandamoorthy, P., Kull, A., … Julian, T. R. (2022). Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. Eurosurveillance: bulletin européen sur les maladies transmissibles, 27(10), 2100806 (20 pp.). doi:10.2807/1560-7917.ES.2022.27.10.2100806, Institutional Repository
Rhoads, W. J., Sindelar, M., Margot, C., Graf, N., & Hammes, F. (2022). Variable Legionella response to building occupancy patterns and precautionary flushing. Microorganisms, 10(3), 555 (18 pp.). doi:10.3390/microorganisms10030555, Institutional Repository
Mapili, K., Rhoads, W. J., Coughter, M., Pieper, K. J., Edwards, M. A., & Pruden, A. (2022). Occurrence of opportunistic pathogens in private wells after major flooding events: a four state molecular survey. Science of the Total Environment, 826, 153901 (11 pp.). doi:10.1016/j.scitotenv.2022.153901, Institutional Repository
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.). doi:10.1128/spectrum.01944-21, Institutional Repository
Bänziger, C., Schertenleib, A., Kunwar, B. M., Bhatta, M. R., & Marks, S. J. (2022). Assessing microbial water quality, users' perceptions and system functionality following a combined water safety intervention in rural Nepal. Frontiers in Water, 3, 750802 (14 pp.). doi:10.3389/frwa.2021.750802, Institutional Repository
Depetris, A., Tagliavini, G., Peter, H., Kühl, M., Holzner, M., & Battin, T. J. (2022). Biophysical properties at patch scale shape the metabolism of biofilm landscapes. npj Biofilms and Microbiomes, 8(1), 5 (12 pp.). doi:10.1038/s41522-022-00269-0, Institutional Repository
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. doi:10.1038/s41396-022-01189-9, Institutional Repository
Hubrich, F., Bösch, N. M., Chepkirui, C., Morinaka, B. I., Rust, M., Gugger, M., … Piel, J. (2022). Ribosomally derived lipopeptides containing distinct fatty acyl moieties. Proceedings of the National Academy of Sciences of the United States of America PNAS, 119(3), e2113120119 (10 pp.). doi:10.1073/pnas.2113120119, Institutional Repository
Siegenthaler, M. B., Ramoneda, J., Frossard, E., & Mészáros, É. (2022). Microbial community responses to phosphorus and nitrogen inputs in the organic soil horizons of two contrasting temperate beech forests. Applied Soil Ecology, 172, 104357 (11 pp.). doi:10.1016/j.apsoil.2021.104357, Institutional Repository
Knobloch, M. C., Mathis, F., Fleischmann, T., Kohler, H. P. E., Kern, S., Bleiner, D., & Heeb, N. V. (2022). Enzymatic synthesis and formation kinetics of mono- and di-hydroxylated chlorinated paraffins with the bacterial dehalogenase LinB from Sphingobium indicum. Chemosphere, 291, 132939 (10 pp.). doi:10.1016/j.chemosphere.2021.132939, Institutional Repository
Tamminen, M., Spaak, J., Tlili, A., Eggen, R., Stamm, C., & Räsänen, K. (2022). Wastewater constituents impact biofilm microbial community in receiving streams. Science of the Total Environment, 807(3), 151080 (8 pp.). doi:10.1016/j.scitotenv.2021.151080, Institutional Repository
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.). doi:10.1016/j.bioelechem.2021.107989, Institutional Repository
Mason-Jones, K., Robinson, S. L., Veen, G. F. (C. ), Manzoni, S., & van der Putten, W. H. (2022). Microbial storage and its implications for soil ecology. ISME Journal, 16, 617-629. doi:10.1038/s41396-021-01110-w, Institutional Repository
Robinson, S. L. (2022). Artificial intelligence for microbial biotechnology: beyond the hype. Microbial Biotechnology, 15(1), 65-69. doi:10.1111/1751-7915.13943, Institutional Repository


Ahmed, W., Bibby, K., D'Aoust, P. M., Delatolla, R., Gerba, C. P., Haas, C. N., … Bivins, A. (2021). Differentiating between the possibility and probability of SARS-CoV-2 transmission associated with wastewater: empirical evidence is needed to substantiate risk. FEMS Microbes, 2, xtab007 (4 pp.). doi:10.1093/femsmc/xtab007, Institutional Repository
Bakkeren, E., Diard, M., Lentsch, V., Rocker, A., Bekele, N. A., Hoces, D., … Slack, E. (2021). A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nature Microbiology, 6, 830-841. doi:10.1038/s41564-021-00911-1, Institutional Repository
Beal, B., & Gogia, G. (2021). Cognition in moral space: a minimal model. Consciousness and Cognition, 92, 103134 (16 pp.). doi:10.1016/j.concog.2021.103134, Institutional Repository
Benz, F., Huisman, J. S., Bakkeren, E., Herter, J. A., Stadler, T., Ackermann, M., … Bonhoeffer, S. (2021). Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo. ISME Journal, 15, 862-878. doi:10.1038/s41396-020-00819-4, Institutional Repository
Burmeister, A. R., Sullivan, R. M., Gallie, J., & Lenski, R. E. (2021). Sustained coevolution of phage Lambda and Escherichia coli involves inner- as well as outer-membrane defences and counter-defences. Microbiology, 167(5), 001063 (9 pp.). doi:10.1099/mic.0.001063, Institutional Repository
Cavallaro, A., Rhoads, W. J., Rölli, F., Füchslin, H. P., Mäusezahl, D., Julian, T. R., … Hammes, F. (2021). Molekularbiologische Methoden. Charakterisierung von Legionellen. Aqua & Gas, 101(12), 34-38. , Institutional Repository
Chen, G., Hu, Z., Ebrahimi, A., Johnson, D. R., Wu, F., Sun, Y., … Wang, G. (2021). Chemotactic movement and zeta potential dominate Chlamydomonas microsphaera attachment and biocathode development. Environmental Technology. doi:10.1080/09593330.2021.2014575, Institutional Repository
Chen, C., Nadeau, S. A., Topolsky, I., Manceau, M., Huisman, J. S., Jablonski, K. P., … Stadler, T. (2021). Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics, 37, 100480 (8 pp.). doi:10.1016/j.epidem.2021.100480, Institutional Repository
Courcol, J. D., Invernizzi, C. F., Landry, Z. C., Minisini, M., Baumgartner, D. A., Bonhoeffer, S., … Schürmann, F. (2021). ARC: an open web-platform for request/supply matching for a prioritized and controlled COVID-19 response. Frontiers in Public Health, 9, 607677 (12 pp.). doi:10.3389/fpubh.2021.607677, Institutional Repository
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.). doi:10.1038/s42003-021-02023-2, Institutional Repository
D’Souza, G. G., Povolo, V. R., Keegstra, J. M., Stocker, R., & Ackermann, M. (2021). Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations. ISME Journal, 15, 2614-2626. doi:10.1038/s41396-021-00953-7, Institutional Repository
Fernandez-Cassi, X., Scheidegger, A., Bänziger, C., Cariti, F., Tuñas Corzon, A., Ganesanandamoorthy, P., … Kohn, T. (2021). Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high. Water Research, 200, 117252 (9 pp.). doi:10.1016/j.watres.2021.117252, Institutional Repository
Gallandat, K., Kolus, R. C., Julian, T. R., & Lantagne, D. S. (2021). A systematic review of chlorine-based surface disinfection efficacy to inform recommendations for low-resource outbreak settings. American Journal of Infection Control, 49(1), 90-103. doi:10.1016/j.ajic.2020.05.014, Institutional Repository
George, C. M., Cirhuza, L. B., Birindwa, A., Williams, C., Beck, S., Julian, T., … Mirindi, P. (2021). Child hand contamination is associated with subsequent pediatric diarrhea in rural Democratic Republic of the Congo (REDUCE Program). Tropical Medicine and International Health, 26(1), 102-110. doi:10.1111/tmi.13510, Institutional Repository
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. doi:10.1038/s41396-021-00942-w, Institutional Repository
Gorter, F. A., Tabares-Mafla, C., Kassen, R., & Schoustra, S. E. (2021). Experimental evolution of interference competition. Frontiers in Microbiology, 12, 613450 (10 pp.). doi:10.3389/fmicb.2021.613450, Institutional Repository
Harvey, A. P., Fuhrmeister, E. R., Cantrell, M. E., Pitol, A. K., Swarthout, J. M., Powers, J. E., … Pickering, A. J. (2021). Longitudinal monitoring of SARS-CoV-2 RNA on high-touch surfaces in a community setting. Environmental Science and Technology Letters, 8(2), 168-175. doi:10.1021/acs.estlett.0c00875, Institutional Repository
Heeb, N. V., Hubeli, J., Fleischmann, T., Lienemann, P., Nayyar, N., Lal, R., & Kohler, H. P. E. (2021). Transformation of ε-HBCD with the Sphingobium Indicum enzymes LinA1, LinA2 and LinATM, a triple mutant of LinA2. Chemosphere, 267, 129217 (12 pp.). doi:10.1016/j.chemosphere.2020.129217, Institutional Repository
Hess, A., Baum, C., Schiessl, K., Besmer, M. D., Hammes, F., & Morgenroth, E. (2021). Stagnation leads to short-term fluctuations in the effluent water quality of biofilters: a problem for greywater reuse?. Water Research X, 13, 100120 (9 pp.). doi:10.1016/j.wroa.2021.100120, Institutional Repository
Hockenberry, A. M., Micali, G., Takács, G., Weng, J., Hardt, W. D., & Ackermann, M. (2021). Microbiota-derived metabolites inhibit Salmonella virulent subpopulation development by acting on single-cell behaviors. Proceedings of the National Academy of Sciences of the United States of America PNAS, 118(31), e2103027118 (7 pp.). doi:10.1073/pnas.2103027118, Institutional Repository
Huemer, M., Shambat, S. M., Bergada-Pijuan, J., Söderholm, S., Boumasmoud, M., Vulin, C., … Zinkernagel, A. S. (2021). Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success. Proceedings of the National Academy of Sciences of the United States of America PNAS, 118(7), e2014920118 (12 pp.). doi:10.1073/pnas.2014920118, Institutional Repository
Knobloch, M. C., Schinkel, L., Kohler, H. P. E., Mathis, F., Kern, S., Bleiner, D., & Heeb, N. V. (2021). Transformation of short-chain chlorinated paraffins and olefins with the bacterial dehalogenase LinB from Sphingobium Indicum – Kinetic models for the homologue-specific conversion of reactive and persistent material. Chemosphere, 283, 131199 (12 pp.). doi:10.1016/j.chemosphere.2021.131199, Institutional Repository
Knobloch, M. C., Schinkel, L., Schilling, I., Kohler, H. P. E., Lienemann, P., Bleiner, D., & Heeb, N. V. (2021). Transformation of short-chain chlorinated paraffins by the bacterial haloalkane dehalogenase LinB – Formation of mono- and di-hydroxylated metabolites. Chemosphere, 262, 128288 (13 pp.). doi:10.1016/j.chemosphere.2020.128288, Institutional Repository
Mao, G., Wang, Y., & Hammes, F. (2021). Automated flow cytometry as a flexible tool for comparing disinfection characteristics of indigenous bacterial communities and pure cultures. Ecotoxicology and Environmental Safety, 225, 112799 (8 pp.). doi:10.1016/j.ecoenv.2021.112799, Institutional Repository
Margot, C., Rhoads, W. J., Graf, N., Rölli, F., & Hammes, F. (2021). Légionelles et eau potable. Une étude de cas de contrôle par la température. Aqua & Gas, 101(9), 78-83. , Institutional Repository
Moreno-Gámez, S., Dal Co, A., van Vliet, S., & Ackermann, M. (2021). Microfluidics for single-cell study of antibiotic tolerance and persistence induced by nutrient limitation. In N. Verstraeten & J. Michiels (Eds.), Methods in molecular biology: Vol. 2357. Bacterial persistence. Methods and protocols (pp. 107-124). doi:10.1007/978-1-0716-1621-5_8, Institutional Repository
Nguyen, J., Fernandez, V., Pontrelli, S., Sauer, U., Ackermann, M., & Stocker, R. (2021). A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations. Nature Communications, 12, 3662 (12 pp.). doi:10.1038/s41467-021-23439-8, Institutional Repository
Pieper, K. J., Jones, C. N., Rhoads, W. J., Rome, M. N., Gholson, D. M., Katner, A., … Beighley, R. E. (2021). Microbial contamination of drinking water supplied by private wells after hurricane harvey. Environmental Science and Technology, 55(12), 8382-8392. doi:10.1021/acs.est.0c07869, Institutional Repository
Pitol, A. K., & Julian, T. R. (2021). Community transmission of SARS-CoV-2 by surfaces: risks and risk reduction strategies. Environmental Science and Technology Letters, 8(3), 263-269. doi:10.1021/acs.estlett.0c00966, Institutional Repository
Prest, E. I., Schaap, P. G., Besmer, M. D., & Hammes, F. (2021). Dynamic hydraulics in a drinking water distribution system influence suspended particles and turbidity, but not microbiology. Water, 13(1), 109 (18 pp.). doi:10.3390/w13010109, Institutional Repository
Qin, W., & Hammes, F. (2021). Substrate pre-loading influences initial colonization of GAC biofilter biofilms. Frontiers in Microbiology, 11, 596156 (13 pp.). doi:10.3389/fmicb.2020.596156, Institutional Repository
Ramoneda, J., Hawes, I., Pascual-García, A., MacKey, T. J., Sumner, D. Y., & Jungblut, A. D. (2021). Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system. FEMS Microbiology Ecology, 97(4), fiab044 (12 pp.). doi:10.1093/femsec/fiab044, Institutional Repository
Ramoneda, J., Le Roux, J., Stadelmann, S., Frossard, E., Frey, B., & Gamper, H. A. (2021). Soil microbial community coalescence and fertilization interact to drive the functioning of the legume-rhizobium symbiosis. Journal of Applied Ecology, 58(11), 2590-2602. doi:10.1111/1365-2664.13995, Institutional Repository
Rhoads, W., & Hammes, F. (2021). Growth of Legionella during COVID-19 lockdown stagnation. Environmental Science: Water Research and Technology, 7(1), 10 (6 pp.). doi:10.1039/D0EW00819B, Institutional Repository
Riechmann, M. E., Ndwandwe, B., Greenwood, E. E., Reynaert, E., Morgenroth, E., & Udert, K. M. (2021). On-site urine treatment combining Ca(OH)2 dissolution and dehydration with ambient air. Water Research X, 13, 100124 (12 pp.). doi:10.1016/j.wroa.2021.100124, Institutional Repository
Rodríguez-Verdugo, A., & Ackermann, M. (2021). Rapid evolution destabilizes species interactions in a fluctuating environment. ISME Journal, 15, 450-460. doi:10.1038/s41396-020-00787-9, Institutional Repository
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.). doi:10.1038/s43705-021-00057-5, Institutional Repository
Ruan, C., Niu, X., Xiong, G., Chen, G., Wu, H., Ma, Z., … Wang, G. (2021). Phenotypic and genotypic characterization of the new Bacillus cereus phage SWEP1. Archives of Virology, 166(11), 3183-3188. doi:10.1007/s00705-021-05222-8, Institutional Repository
Russo, S., Besmer, M. D., Blumensaat, F., Bouffard, D., Disch, A., Hammes, F., … Villez, K. (2021). The value of human data annotation for machine learning based anomaly detection in environmental systems. Water Research, 206, 117695 (10 pp.). doi:10.1016/j.watres.2021.117695, Institutional Repository
Song, Y., Pruden, A., Edwards, M. A., & Rhoads, W. J. (2021). Natural organic matter, orthophosphate, pH, and growth phase can limit copper antimicrobial efficacy for Legionella in drinking Water. Environmental Science and Technology, 55(3), 1759-1768. doi:10.1021/acs.est.0c06804, Institutional Repository
Springer, M. S., Guerrero-Juarez, C. F., Huelsmann, M., Collin, M. A., Danil, K., McGowen, M. R., … Gatesy, J. (2021). Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos. Current Biology, 31(10), 2124-2139. doi:10.1016/j.cub.2021.02.057, Institutional Repository
Stachler, E., Kull, A., & Julian, T. R. (2021). Bacteriophage treatment before chemical disinfection can enhance removal of plastic-surface-associated Pseudomonas aeruginosa. Applied and Environmental Microbiology, 87(20), e00980-21 (12 pp.). doi:10.1128/AEM.00980-21, Institutional Repository
Zumstein, M. T., & Fenner, K. (2021). Towards more sustainable peptide-based antibiotics: stable in human blood, enzymatically hydrolyzed in wastewater?. Chimia, 75(4), 267-271. doi:10.2533/chimia.2021.267, Institutional Repository
van Gestel, J., Bareia, T., Tenennbaum, B., Dal Co, A., Guler, P., Aframian, N., … Eldar, A. (2021). Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities. Nature Communications, 12(1), 2324 (11 pp.). doi:10.1038/s41467-021-22649-4, Institutional Repository


Achermann, S., Mansfeldt, C. B., Müller, M., Johnson, D. R., & Fenner, K. (2020). Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities. Environmental Science and Technology, 54(1), 235-244. doi:10.1021/acs.est.9b05421, Institutional Repository
Bopp, C. E., Kohler, H. P. E., & Hofstetter, T. B. (2020). Enzyme kinetics of organic contaminant oxygenations. Chimia, 74(3), 108-114. doi:10.2533/chimia.2020.108, Institutional Repository
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.). doi:10.1038/s42003-020-01409-y, Institutional Repository
Bosshard, L., Peischl, S., Ackermann, M., & Excoffier, L. (2020). Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics, 21(1), 253 (11 pp.). doi:10.1186/s12864-020-6676-z, Institutional Repository
Carratalà, A., Bachmann, V., Julian, T. R., & Kohn, T. (2020). Adaptation of human enterovirus to warm environments leads to resistance against chlorine disinfection. Environmental Science and Technology, 54(18), 11292-11300. doi:10.1021/acs.est.0c03199, Institutional Repository
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.). doi:10.1098/rstb.2019.0246, Institutional Repository
D'Souza, G. G. (2020). Phenotypic variation in spatially structured microbial communities: ecological origins and consequences. Current Opinion in Biotechnology, 62, 220-227. doi:10.1016/j.copbio.2019.12.013, Institutional Repository
Dal Co, A., van Vliet, S., Kiviet, D. J., Schlegel, S., & Ackermann, M. (2020). Short-range interactions govern the dynamics and functions of microbial communities. Nature Ecology & Evolution, 4, 366-375. doi:10.1038/s41559-019-1080-2, Institutional Repository
Domagała, K., Jacquin, C., Borlaf, M., Sinnet, B., Julian, T., Kata, D., & Graule, T. (2020). Efficiency and stability evaluation of Cu2O/MWCNTs filters for virus removal from water. Water Research, 179, 115879 (10 pp.). doi:10.1016/j.watres.2020.115879, Institutional Repository
Gorter, F. A., Manhart, M., & Ackermann, M. (2020). Understanding the evolution of interspecies interactions in microbial communities. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1798), 20190256 (13 pp.). doi:10.1098/rstb.2019.0256, Institutional Repository
Hernandez-Valdes, J. A., van Gestel, J., & Kuipers, O. P. (2020). A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium. Nature Communications, 11(1), 1203 (13 pp.). doi:10.1038/s41467-020-15017-1, Institutional Repository
Jacquin, C., Yu, D., Sander, M., Domagala, K. W., Traber, J., Morgenroth, E., & Julian, T. R. (2020). Competitive co-adsorption of bacteriophage MS2 and natural organic matter onto multiwalled carbon nanotubes. Water Research X, 9, 100058 (12 pp.). doi:10.1016/j.wroa.2020.100058, Institutional Repository
Johnson, D. R., & Pomati, F. (2020). A brief guide for the measurement and interpretation of microbial functional diversity. Environmental Microbiology, 22(8), 3039-3048. doi:10.1111/1462-2920.15147, Institutional Repository
Johnson, D. R., & Noack, S. (2020). Editorial overview: causes and biotechnological application of microbial metabolic specialization. Current Opinion in Biotechnology, 62, III-VI. doi:10.1016/j.copbio.2020.01.007, Institutional Repository
Liu, G., Zhang, Y., Liu, X., Hammes, F., Liu, W. T., Medema, G., … van der Meer, W. (2020). 360-degree distribution of biofilm quantity and community in an operational unchlorinated drinking water distribution pipe. Environmental Science and Technology, 54(9), 5619-5628. doi:10.1021/acs.est.9b06603, Institutional Repository
Marinkovic, Z. S., Vulin, C., Acman, M., Song, X., Di Meglio, J., Lindner, A. B., & Hersen, P. (2020). Observing nutrient gradients, gene expression and growth variation using the "yeast machine" microfluidic device. Bio-protocol, 10(13), e3668 (16 pp.). doi:10.21769/BioProtoc.3668, Institutional Repository
Mayr, M. J., Zimmermann, M., Dey, J., Brand, A., Wehrli, B., & Bürgmann, H. (2020). Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn. Communications Biology, 3, 108 (9 pp.). doi:10.1038/s42003-020-0838-z, Institutional Repository
Montealegre, M. C., Talavera Rodríguez, A., Roy, S., Hossain, M. I., Islam, M. A., Lanza, V. F., & Julian, T. R. (2020). High genomic diversity and heterogenous origins of pathogenic and antibiotic-resistant Escherichia coli in household settings represent a challenge to reducing transmission in low-income settings. mSphere, 5(1), e00704-19 (17 pp.). doi:10.1128/mSphere.00704-19, Institutional Repository
Moreno-Gámez, S., Kiviet, D. J., Vulin, C., Schlegel, S., Schlegel, K., van Doorn, G. S., & Ackermann, M. (2020). Wide lag time distributions break a trade-off between reproduction and survival in bacteria. Proceedings of the National Academy of Sciences of the United States of America PNAS, 117(31), 18729-18736. doi:10.1073/pnas.2003331117, Institutional Repository
Nadimpalli, M. L., Marks, S. J., Montealegre, M. C., Gilman, R. H., Pajuelo, M. J., Saito, M., … Pickering, A. J. (2020). Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nature Microbiology, 5(6), 787-795. doi:10.1038/s41564-020-0722-0, Institutional Repository
Neu, L., & Hammes, F. (2020). Feeding the building plumbing microbiome: the importance of synthetic polymeric materials for biofilm formation and management. Water, 12(6), 1774 (17 pp.). doi:10.3390/w12061774, Institutional Repository
Pitol, A. K., Kohn, T., & Julian, T. R. (2020). Retention of E. coli and water on the skin after liquid contact. PLoS One, 15(9), e0238998 (12 pp.). doi:10.1371/journal.pone.0238998, Institutional Repository
Reynaert, E., Greenwood, E. E., Ndwandwe, B., Riechmann, M. E., Sindall, R. C., Udert, K. M., & Morgenroth, E. (2020). Practical implementation of true on-site water recycling systems for hand washing and toilet flushing. Water Research X, 7, 100051 (13 pp.). doi:10.1016/j.wroa.2020.100051, Institutional Repository
Rölli, F., Kötzsch, S., Kunz, I., & Hammes, F. (2020). Mal schnell eine Wasserprobe nehmen. Untersuchung von Gebäude-Trinkwasser-Installationen auf Legionellen. Aqua & Gas, 100(12), 26-32. , Institutional Repository
Schreiber, F., & Ackermann, M. (2020). Environmental drivers of metabolic heterogeneity in clonal microbial populations. Current Opinion in Biotechnology, 62, 202-211. doi:10.1016/j.copbio.2019.11.018, Institutional Repository
Scotoni, M., Koch, J., Julian, T. R., Clack, L., Pitol, A. K., Wolfensberger, A., … Sax, H. (2020). Silica nanoparticles with encapsulated DNA (SPED) - a novel surrogate tracer for microbial transmission in healthcare. Antimicrobial Resistance & Infection Control, 9, 152 (10 pp.). doi:10.1186/s13756-020-00813-7, Institutional Repository
Sun, L., Ashcroft, P., Ackermann, M., & Bonhoeffer, S. (2020). Stochastic gene expression influences the selection of antibiotic resistance mutations. Molecular Biology and Evolution, 37(1), 58-70. doi:10.1093/molbev/msz199, Institutional Repository
Tamminen, M., Spaak, J., Caduff, L., Schiff, H., Lang, R., Schmid, S., … Julian, T. R. (2020). Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates. Communications Biology, 3, 264 (6 pp.). doi:10.1038/s42003-020-0980-7, Institutional Repository
Watts, S., Julian, T. R., Maniura-Weber, K., Graule, T., & Salentinig, S. (2020). Colloidal transformations in MS2 virus particles: driven by pH, influenced by natural organic matter. ACS Nano, 14(2), 1879-1887. doi:10.1021/acsnano.9b08112, Institutional Repository
Wilson, A. M., King, M. F., López-García, M., Weir, M. H., Sexton, J. D., Canales, R. A., … Reynolds, K. A. (2020). Evaluating a transfer gradient assumption in a fomite-mediated microbial transmission model using an experimental and Bayesian approach. Journal of the Royal Society Interface, 17(167), 20200121 (12 pp.). doi:10.1098/rsif.2020.0121, Institutional Repository
van Gestel, J. (2020). Slow lane to collectivity. Nature Ecology & Evolution, 4(3), 292-293. doi:10.1038/s41559-020-1116-7, Institutional Repository


Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., … Zinkernagel, A. (2019). Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology, 17, 441-448. doi:10.1038/s41579-019-0196-3, Institutional Repository
Bibby, K., Crank, K., Greaves, J., Li, X., Wu, Z., Hamza, I. A., & Stachler, E. (2019). Metagenomics and the development of viral water quality tools. npj Clean Water, 2(1), 9 (13 pp.). doi:10.1038/s41545-019-0032-3, Institutional Repository
Bischel, H. N., Caduff, L., Schindelholz, S., Kohn, T., & Julian, T. R. (2019). Health risks for sanitation service workers along a container-based urine collection system and resource recovery value chain. Environmental Science and Technology, 7055-7067. doi:10.1021/acs.est.9b01092, Institutional Repository
Bosshard, L., Peischl, S., Ackermann, M., & Excoffier, L. (2019). Mutational and selective processes involved in evolution during bacterial range expansions. Molecular Biology and Evolution, 36(10), 2313-2327. doi:10.1093/molbev/msz148, Institutional Repository
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). doi:10.1016/B978-0-444-64046-8.00472-9, Institutional Repository
Cossey, S. M., Yu, Y. T. N., Cossu, L., & Velicer, G. J. (2019). Kin discrimination and outer membrane exchange in Myxococcus xanthus: experimental analysis of a natural population. PLoS One, 14(11), e0224817 (24 pp.). doi:10.1371/journal.pone.0224817, Institutional Repository
Czechowska, K., Lannigan, J., Wang, L., Arcidiacono, J., Ashhurst, T. M., Barnard, R. M., … Tárnok, A. (2019). Cyt-Geist: current and future challenges in cytometry: reports of the CYTO 2018 conference workshops. Cytometry Part A, 95(6), 598-644. doi:10.1002/cyto.a.23777, Institutional Repository
Dal Co, A., van Vliet, S., & Ackermann, M. (2019). Emergent microscale gradients give rise to metabolic cross-feeding and antibiotic tolerance in clonal bacterial populations. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1786), 20190080 (10 pp.). doi:10.1098/rstb.2019.0080, Institutional Repository
Dal Co, A., Ackermann, M., & van Vliet, S. (2019). Metabolic activity affects the response of single cells to a nutrient switch in structured populations. Journal of the Royal Society Interface, 16(156), 20190182 (10 pp.). doi:10.1098/rsif.2019.0182, Institutional Repository
De Hoe, G. X., Zumstein, M. T., Getzinger, G. J., Rüegsegger, I., Kohler, H. P. E., Maurer-Jones, M. A., … McNeill, K. (2019). Photochemical transformation of poly(butylene adipate-co-terephthalate) and its effects on enzymatic hydrolyzability. Environmental Science and Technology, 53(5), 2472-2481. doi:10.1021/acs.est.8b06458, Institutional Repository
Dengler Haunreiter, V., Boumasmoud, M., Häffner, N., Wipfli, D., Leimer, N., Rachmühl, C., … Zinkernagel, A. S. (2019). In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance. Nature Communications, 10(1), 1149 (14 pp.). doi:10.1038/s41467-019-09053-9, Institutional Repository
Genter, F., Marks, S. J., Clair-Caliot, G., Mugume, D. S., Johnston, R. B., Bain, R. E. S., & Julian, T. R. (2019). Evaluation of the novel substrate RUG for the detection of Escherichia coli in water from temperate (Zurich, Switzerland) and tropical (Bushenyi, Uganda) field sites. Environmental Science: Water Research and Technology, 5(6), 1082-1091. doi:10.1039/C9EW00138G, Institutional Repository
Gostic, K. M., Wunder, E. A., Bisht, V., Hamond, C., Julian, T. R., Ko, A. I., & Lloyd-Smith, J. O. (2019). Mechanistic dose–response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1782), 20190367 (10 pp.). doi:10.1098/rstb.2019.0367, Institutional Repository
Hammes, F., Velten, S., Egli, T., & Juhna, T. (2019). Biotreatment of drinking water. In M. Y. Murray (Ed.), Comprehensive biotechnology: Vol. 6. Environmental and related biotechnologies (pp. 463-476). doi:10.1016/B978-0-444-64046-8.00374-8, Institutional Repository
Hammes, F. (2019). Editorial Perspectives: using bacteria in rubber ducks to improve scientific literacy, advance citizen science, and expand fundamental science. Environmental Science: Water Research and Technology, 5(3), 442-443. doi:10.1039/c9ew90008j, Institutional Repository
Heeb, N. V., Schalles, S., Lehner, S., Schinkel, L., Schilling, I., Lienemann, P., … Kohler, H. P. E. (2019). Biotransformation of short-chain chlorinated paraffins (SCCPs) with LinA2: a HCH and HBCD converting bacterial dehydrohalogenase. Chemosphere, 226, 744-754. doi:10.1016/j.chemosphere.2019.03.169, Institutional Repository
Huelsmann, M., Hecker, N., Springer, M. S., Gatesy, J., Sharma, V., & Hiller, M. (2019). Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances, 5(9), eaaw6671 (12 pp.). doi:10.1126/sciadv.aaw6671, Institutional Repository
Islam, M. A., Amin, M. B., Roy, S., Asaduzzaman, M., Islam, M. R., Navab-Daneshmand, T., … Julian, T. R. (2019). Fecal colonization with multidrug-resistant E. coli among healthy infants in rural Bangladesh. Frontiers in Microbiology, 10, 640 (9 pp.). doi:10.3389/fmicb.2019.00640, Institutional Repository
Ju, F., Beck, K., Yin, X., Maccagnan, A., McArdell, C. S., Singer, H. P., … Bürgmann, H. (2019). Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes. ISME Journal, 13(2), 346-360. doi:10.1038/s41396-018-0277-8, Institutional Repository
Leventhal, G. E., Ackermann, M., & Schiessl, K. T. (2019). Why microbes secrete molecules to modify their environment: the case of iron-chelating siderophores. Journal of the Royal Society Interface, 16(150), 20180674 (13 pp.). doi:10.1098/rsif.2018.0674, Institutional Repository
Lilja, E. E., & Johnson, D. R. (2019). Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage. BMC Evolutionary Biology, 19(1), 129 (11 pp.). doi:10.1186/s12862-019-1458-4, Institutional Repository
Liu, L., Helbling, D. E., Kohler, H. P. E., & Smets, B. F. (2019). Modelling carbofuran biotransformation by: Novosphingobium sp. KN65.2 in the presence of coincidental carbon and indigenous microbes. Environmental Science: Water Research and Technology, 5(4), 798-807. doi:10.1039/c8ew00929e, Institutional Repository
Mansfeldt, C., Achermann, S., Men, Y., Walser, J. C., Villez, K., Joss, A., … Fenner, K. (2019). Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. ISME Journal, 13(6), 1589-1601. doi:10.1038/s41396-019-0371-6, Institutional Repository
Marinkovic, Z. S., Vulin, C., Acman, M., Song, X., Di Meglio, J. M., Lindner, A. B., & Hersen, P. (2019). A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies. eLife, 8, e47951 (21 pp.). doi:10.7554/eLife.47951, Institutional Repository
Micali, G., & Endres, R. G. (2019). Maximal information transmission is compatible with ultrasensitive biological pathways. Scientific Reports, 9(1), 16898 (13 pp.). doi:10.1038/s41598-019-53273-4, Institutional Repository
Nelson, T. F., Remke, S. C., Kohler, H. P. E., McNeill, K., & Sander, M. (2019). Quantification of synthetic polyesters from biodegradable mulch films in soils. Environmental Science and Technology, 54(1), 266-275. doi:10.1021/acs.est.9b05863, Institutional Repository
Neu, L., Proctor, C. R., Walser, J. C., & Hammes, F. (2019). Small-scale heterogeneity in drinking water biofilms. Frontiers in Microbiology, 10, 2446 (14 pp.). doi:10.3389/fmicb.2019.02446, Institutional Repository
Nguyen, T. M. H., Suwan, P., Koottatep, T., & Beck, S. E. (2019). Application of a novel, continuous-feeding ultraviolet light emitting diode (UV-LED) system to disinfect domestic wastewater for discharge or agricultural reuse. Water Research, 153, 53-62. doi:10.1016/j.watres.2019.01.006, Institutional Repository
Povolo, V. R., & Ackermann, M. (2019). Disseminating antibiotic resistance during treatment. A multidrug efflux pump can help bacteria acquire antibiotic resistance through plasmid transfer. Science, 364(6442), 737-738. doi:10.1126/science.aax6620, Institutional Repository
Raes, B., Horemans, B., Rentsch, D., T'Syen, J., Ghequire, M. G. K., De Mot, R., … Springael, D. (2019). Aminobacter sp. MSH1 mineralises the groundwater micropollutant 2,6-dichlorobenzamide through a unique chlorobenzoate catabolic pathway.. Environmental Science and Technology, 53(17), 10146-10156. doi:10.1021/acs.est.9b02021, Institutional Repository
Ramos, Y., Rocha, J., Hael, A. L., van Gestel, J., Vlamakis, H., Cywes-Bentley, C., … Morales, D. K. (2019). PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis. PLoS Pathogens, 15(2), e1007571 (32 pp.). doi:10.1371/journal.ppat.1007571, Institutional Repository
Rodríguez-Verdugo, A., Vulin, C., & Ackermann, M. (2019). The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system. Ecology Letters, 22(5), 838-846. doi:10.1111/ele.13241, Institutional Repository
Sander, M., Kohler, H. P. E., & McNeill, K. (2019). Assessing the environmental transformation of nanoplastic through 13C-labelled polymers. Nature Nanotechnology, 14(4), 301-303. doi:10.1038/s41565-019-0420-3, Institutional Repository
Schertenleib, A., Sigrist, J., Friedrich, M. N. D., Ebi, C., Hammes, F., & Marks, S. J. (2019). Construction of a low-cost mobile incubator for field and laboratory use. Journal of Visualized Experiments (145), e58443 (17 pp.). doi:10.3791/58443, Institutional Repository
Schiessl, K., Ross-Gillespie, A., Cornforth, D. M., Weigert, M., Bigosch, C., Brown, S. P., … Kümmerli, R. (2019). Individual- versus group-optimality in the production of secreted bacterial compounds. Evolution, International Journal of Organic Evolution, 73(4), 675-688. doi:10.1111/evo.13701, Institutional Repository
Schilling, I. E., Bopp, C. E., Lal, R., Kohler, H. P. E., & Hofstetter, T. B. (2019). Assessing aerobic biotransformation of hexachlorocyclohexane isomers by compound-specific isotope analysis. Environmental Science and Technology, 53(13), 7419-7431. doi:10.1021/acs.est.9b01007, Institutional Repository
Schilling, I. E., Hess, R., Bolotin, J., Lal, R., Hofstetter, T. B., & Kohler, H. P. E. (2019). Kinetic isotope effects of the enzymatic transformation of γ-hexachlorocyclohexane by the lindane dehydrochlorinase variants LinA1 and LinA2. Environmental Science and Technology, 53(5), 2353-2363. doi:10.1021/acs.est.8b04234, Institutional Repository
Stachler, E., Crank, K., & Bibby, K. (2019). Co-occurrence of crAssphage with antibiotic resistance genes in an impacted urban watershed. Environmental Science and Technology Letters, 6(4), 216-221. doi:10.1021/acs.estlett.9b00130, Institutional Repository
Staps, M., van Gestel, J., & Tarnita, C. E. (2019). Emergence of diverse life cycles and life histories at the origin of multicellularity. Nature Ecology & Evolution, 3(8), 1197-1205. doi:10.1038/s41559-019-0940-0, Institutional Repository
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.). doi:10.1128/mSystems.00265-18, Institutional Repository
Verbyla, M. E., Pitol, A. K., Navab-Daneshmand, T., Marks, S. J., & Julian, T. R. (2019). Safely managed hygiene: a risk-based assessment of handwashing water quality. Environmental Science and Technology, 53(5), 2852-2861. doi:10.1021/acs.est.8b06156, Institutional Repository
Woo, H., Beck, S. E., Boczek, L. A., Carlson, K. M., Brinkman, N. E., Linden, K. G., … Ryu, H. (2019). Efficacy of inactivation of human enteroviruses by dual-wavelength germicidal ultraviolet (UV-C) light emitting diodes (LEDs). Water, 11(6), 1131 (8 pp.). doi:10.3390/w11061131, Institutional Repository
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. doi:10.1038/s41564-019-0426-5, Institutional Repository
Zimmermann, M. (2019). Modelling perspectives on microbial methane oxidation in stratified lakes (Doctoral dissertation). doi:10.3929/ethz-b-000423771, Institutional Repository
Zumstein, M. T., Narayan, R., Kohler, H. P. E., McNeill, K., & Sander, M. (2019). Dos and do nots when assessing the biodegradation of plastics. Environmental Science and Technology, 53(17), 9967-9969. doi:10.1021/acs.est.9b04513, Institutional Repository
van Gestel, J., Ackermann, M., & Wagner, A. (2019). Microbial life cycles link global modularity in regulation to mosaic evolution. Nature Ecology & Evolution, 3(8), 1184-1196. doi:10.1038/s41559-019-0939-6, Institutional Repository


Afrooz, A. R. M. N., Pitol, A. K., Kitt, D., & Boehm, A. B. (2018). Role of microbial cell properties on bacterial pathogen and coliphage removal in biochar-modified stormwater biofilters. Environmental Science: Water Research and Technology, 4(12), 2160-2169. doi:10.1039/c8ew00297e, Institutional Repository
Beck, S. E., Hull, N. M., Poepping, C., & Linden, K. G. (2018). Wavelength-dependent damage to adenoviral proteins across the germicidal UV spectrum. Environmental Science and Technology, 52(1), 223-229. doi:10.1021/acs.est.7b04602, Institutional Repository
Bircher, L., Geirnaert, A., Hammes, F., Lacroix, C., & Schwab, C. (2018). Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes. Microbial Biotechnology, 11(4), 721-733. doi:10.1111/1751-7915.13265, Institutional Repository
Csilléry, K., Rodríguez-Verdugo, A., Rellstab, C., & Guillaume, F. (2018). Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution. Molecular Ecology, 27(3), 606-612. doi:10.1111/mec.14499, Institutional Repository
D'Souza, G., Shitut, S., Preussger, D., Yousif, G., Waschina, S., & Kost, C. (2018). Ecology and evolution of metabolic cross-feeding interactions in bacteria. Natural Product Reports, 35(5), 455-488. doi:10.1039/C8NP00009C, Institutional Repository
Dai, D., Proctor, C. R., Williams, K., Edwards, M. A., & Pruden, A. (2018). Mediation of effects of biofiltration on bacterial regrowth, Legionella pneumophila, and the microbial community structure under hot water plumbing conditions. Environmental Science: Water Research and Technology, 4(2), 183-194. doi:10.1039/c7ew00301c, Institutional Repository
Dal Co, A., Brannon, C., & Ackermann, M. (2018). Division of labor in bacteria. eLife, 7, e38578 (3 pp.). doi:10.7554/eLife.38578, Institutional Repository
Epting, J., Huggenberger, P., Radny, D., Hammes, F., Hollender, J., Page, R. M., … Auckenthaler, A. (2018). Spatiotemporal scales of river-groundwater interaction – The role of local interaction processes and regional groundwater regimes. Science of the Total Environment, 618, 1224-1243. doi:10.1016/j.scitotenv.2017.09.219, Institutional Repository
Farhat, N., Hammes, F., Prest, E., & Vrouwenvelder, J. (2018). A uniform bacterial growth potential assay for different water types. Water Research, 142, 227-235. doi:10.1016/j.watres.2018.06.010, Institutional Repository
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. doi:10.1038/ismej.2017.147, Institutional Repository
Gorter, F. A., Aarts, M. G. M., Zwaan, B. J., & de Visser, J. A. G. M. (2018). Local fitness landscapes predict yeast evolutionary dynamics in directionally changing environments. Genetics, 208(1), 307-322. doi:10.1534/genetics.117.300519, Institutional Repository
Grilli, J., Cadart, C., Micali, G., Osella, M., & Cosentino Lagomarsino, M. (2018). The empirical fluctuation pattern of E. coli division control. Frontiers in Microbiology, 9, 1541 (10 pp.). doi:10.3389/fmicb.2018.01541, Institutional Repository
Guggenheim, C. S. (2018). The role of copper for methane-oxidizing bacteria in lakes (Doctoral dissertation). doi:10.3929/ethz-b-000337932, Institutional Repository
Gulde, R., Anliker, S., Kohler, H. P. E., & Fenner, K. (2018). Ion trapping of amines in protozoa: a novel removal mechanism for micropollutants in activated sludge. Environmental Science and Technology, 52(1), 52-60. doi:10.1021/acs.est.7b03556, Institutional Repository
Heeb, N. V., Mazenauer, M., Wyss, S., Geueke, B., Kohler, H. P. E., & Lienemann, P. (2018). Kinetics and stereochemistry of LinB-catalyzed δ-HBCD transformation: comparison of in vitro and in silico results. Chemosphere, 207, 118-129. doi:10.1016/j.chemosphere.2018.05.057, Institutional Repository
Hong, P. Y., Julian, T. R., & Jumat, M. R. (2018). Editorial: Microbial safety in water resources. Frontiers in Microbiology, 9, 3064 (3 pp.). doi:10.3389/fmicb.2018.03064, Institutional Repository
Hong, P. Y., Julian, T. R., Pype, M. L., Jiang, S. C., Nelson, K. L., Graham, D., … Manaia, C. M. (2018). Reusing treated wastewater: consideration of the safety aspects associated with antibiotic-resistant bacteria and antibiotic resistance genes. Water, 10(3), 244 (22 pp.). doi:10.3390/w10030244, Institutional Repository
Julian, T. R. (2018). Escherichia coli in Harare - Wie gelangt das Bakterium in die Haushalte und woher stammt es?. Aqua & Gas, 98(5), 60-64. , Institutional Repository
Julian, T. R., Vithanage, H. S. K., Chua, M. L., Kuroda, M., Pitol, A. K., Nguyen, P. H. L., … Harada, H. (2018). High time-resolution simulation of E. coli on hands reveals large variation in microbial exposures amongst Vietnamese farmers using human excreta for agriculture. Science of the Total Environment, 635, 120-131. doi:10.1016/j.scitotenv.2018.04.100, Institutional Repository
Julian, T. R., Bustos, C., Kwong, L. H., Badilla, A. D., Lee, J., Bischel, H. N., & Canales, R. A. (2018). Quantifying human-environment interactions using videography in the context of infectious disease transmission. Geospatial Health, 13(1), 195-197. doi:10.4081/gh.2018.631, Institutional Repository
Kolesinska, B., Wasko, J., Kaminski, Z., Geueke, B., Kohler, H. P. E., & Seebach, D. (2018). Labeling and protecting N-terminal protein positions by β-peptidyl aminopeptidase-catalyzed attachment of β-amino-acid residues – insulin as a first example. Helvetica Chimica Acta, 101(1), e1700259 (10 pp.). doi:10.1002/hlca.201700259, Institutional Repository
Louca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A., O'Connor, M. I., … Wegener Parfrey, L. (2018). Function and functional redundancy in microbial systems. Nature Ecology & Evolution, 2, 936-943. doi:10.1038/s41559-018-0519-1, Institutional Repository
Manjarrez Casas, A. M. (2018). Effects of antibiotics on individual bacterial cells (Doctoral dissertation). doi:10.3929/ethz-b-000309075, Institutional Repository
Mao, G., Wang, Y., & Hammes, F. (2018). Short-term organic carbon migration from polymeric materials in contact with chlorinated drinking water. Science of the Total Environment, 613-614, 1220-1227. doi:10.1016/j.scitotenv.2017.09.166, Institutional Repository
Marchant, H. K., Tegetmeyer, H. E., Ahmerkamp, S., Holtappels, M., Lavik, G., Graf, J., … Kuypers, M. M. M. (2018). Metabolic specialization of denitrifiers in permeable sediments controls N2O emissions. Environmental Microbiology, 20(12), 4486-4502. doi:10.1111/1462-2920.14385, Institutional Repository
Micali, G., Grilli, J., Osella, M., & Cosentino Lagomarsino, M. (2018). Concurrent processes set E. coli cell division. Science Advances, 4(11), eaau3324 (7 pp.). doi:10.1126/sciadv.aau3324, Institutional Repository
Micali, G., Grilli, J., Marchi, J., Osella, M., & Cosentino Lagomarsino, M. (2018). Dissecting the control mechanisms for DNA replication and cell division in E. coli. Cell Reports, 25(3), 761-771. doi:10.1016/j.celrep.2018.09.061, Institutional Repository
Montealegre, M. C., Roy, S., Böni, F., Hossain, M. I., Navab-Daneshmand, T., Caduff, L., … Julian, T. R. (2018). Risk factors for detection, survival, and growth of antibiotic-resistant and pathogenic Escherichia coli in household soils in rural Bangladesh. Applied and Environmental Microbiology, 84(24), e01978-18 (14 pp.). doi:10.1128/AEM.01978-18, Institutional Repository
Navab-Daneshmand, T., Friedrich, M. N. D., Gächter, M., Montealegre, M. C., Mlambo, L. S., Nhiwatiwa, T., … Julian, T. R. (2018). Escherichia coli contamination across multiple environmental compartments (soil, hands, drinking water, and handwashing water) in urban Harare: correlations and risk factors. American Journal of Tropical Medicine and Hygiene, 98(3), 803-813. doi:10.4269/ajtmh.17-0521, Institutional Repository
Nescerecka, A., Juhna, T., & Hammes, F. (2018). Identifying the underlying causes of biological instability in a full-scale drinking water supply system. Water Research, 135, 11-21. doi:10.1016/j.watres.2018.02.006, Institutional Repository
Neu, L., Proctor, C. R., & Hammes, F. (2018). Der finale Meter. Biofilme in Duschschläuchen. Aqua & Gas, 98(5), 42-45. , Institutional Repository
Neu, L., Bänziger, C., Proctor, C. R., Zhang, Y., Liu, W. T., & Hammes, F. (2018). Ugly ducklings - the dark side of plastic materials in contact with potable water. npj Biofilms and Microbiomes, 4(1), 7 (11 pp.). doi:10.1038/s41522-018-0050-9, Institutional Repository
Oh, S., Hammes, F., & Liu, W. T. (2018). Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Research, 128, 278-285. doi:10.1016/j.watres.2017.10.054, Institutional Repository
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. doi:10.1111/1462-2920.14352, Institutional Repository
Pitol, A. K., Bischel, H. N., Boehm, A. B., Kohn, T., & Julian, T. R. (2018). Transfer of enteric viruses adenovirus and coxsackievirus and bacteriophage MS2 from liquid to human skin. Applied and Environmental Microbiology, 84(22), e01809-18 (13 pp.). doi:10.1128/AEM.01809-18, Institutional Repository
Prest, E. I., Schaap, P. G., & Hammes, F. (2018). Analyse microbiologique en ligne. Étude des variations de la qualité microbiologique de l'eau potable dans une usine de traitement. Aqua & Gas, 98(5), 20-24. , Institutional Repository
Proctor, C. R., Reimann, M., Vriens, B., & Hammes, F. (2018). Biofilms in shower hoses. Water Research, 131, 274-286. doi:10.1016/j.watres.2017.12.027, Institutional Repository
Proctor, C. R., Besmer, M. D., Langenegger, T., Beck, K., Walser, J. C., Ackermann, M., … Hammes, F. (2018). Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems. ISME Journal, 12, 1344-1359. doi:10.1038/s41396-018-0070-8, Institutional Repository
Props, R., Rubbens, P., Besmer, M., Buysschaert, B., Sigrist, J., Weilenmann, H., … Hammes, F. (2018). Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data. Water Research, 145, 73-82. doi:10.1016/j.watres.2018.08.013, Institutional Repository
Rotem, A., Serohijos, A. W. R., Chang, C. B., Wolfe, J. T., Fischer, A. E., Mehoke, T. S., … Shakhnovich, E. I. (2018). Evolution on the biophysical fitness landscape of an RNA virus. Molecular Biology and Evolution, 35(10), 2390-2400. doi:10.1093/molbev/msy131, Institutional Repository
Savio, D., Stadler, P., Reischer, G. H., Kirschner, A. K. T., Demeter, K., Linke, R., … Farnleitner, A. H. (2018). Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management. Wiley Interdisciplinary Reviews: Water, 5(3), e1282 (20 pp.). doi:10.1002/wat2.1282, Institutional Repository
Shettigar, M., Balotra, S., Cahill, D., Warden, A. C., Lacey, M. J., Kohler, H. P. E., … Pandey, G. (2018). Isolation of the (+)-pinoresinol-mineralizing Pseudomonas sp. strain SG-MS2 and elucidation of its catabolic pathway. Applied and Environmental Microbiology, 84(4), e02531-17 (14 pp.). doi:10.1128/AEM.02531-17, Institutional Repository
Sun, L., Alexander, H. K., Bogos, B., Kiviet, D. J., Ackermann, M., & Bonhoeffer, S. (2018). Effective polyploidy causes phenotypic delay and influences bacterial evolvability. PLoS Biology, 16(2), e2004644 (24 pp.). doi:10.1371/journal.pbio.2004644, Institutional Repository
T'Syen, J., Raes, B., Horemans, B., Tassoni, R., Leroy, B., Lood, C., … Springael, D. (2018). Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1. Applied Microbiology and Biotechnology, 102(18), 7963-7979. doi:10.1007/s00253-018-9189-9, Institutional Repository
Vignola, M., Werner, D., Hammes, F., King, L. C., & Davenport, R. J. (2018). Flow-cytometric quantification of microbial cells on sand from water biofilters. Water Research, 143, 66-76. doi:10.1016/j.watres.2018.05.053, Institutional Repository
Vulin, C., Leimer, N., Huemer, M., Ackermann, M., & Zinkernagel, A. S. (2018). Prolonged bacterial lag time results in small colony variants that represent a sub-population of persisters. Nature Communications, 9(1), 4074 (8 pp.). doi:10.1038/s41467-018-06527-0, Institutional Repository
Zimmermann, M., Escrig, S., Lavik, G., Kuypers, M. M. M., Meibom, A., Ackermann, M., & Schreiber, F. (2018). Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium. Environmental Microbiology Reports, 10(2), 179-183. doi:10.1111/1758-2229.12616, Institutional Repository
Zumstein, M. T., Schintlmeister, A., Nelson, T. F., Baumgartner, R., Woebken, D., Wagner, M., … Sander, M. (2018). Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass. Science Advances, 4(7), eaas9024 (8 pp.). doi:10.1126/sciadv.aas9024, Institutional Repository
van Vliet, S., Dal Co, A., Winkler, A. R., Spriewald, S., Stecher, B., & Ackermann, M. (2018). Spatially correlated gene expression in bacterial groups: the role of lineage history, spatial gradients, and cell-cell interactions. Cell Systems, 6(4), 496-507. doi:10.1016/j.cels.2018.03.009, Institutional Repository


Ackermann, M., & van Vliet, S. (2017). Stochastic gene expression: bacterial elites in chemotaxis. Molecular Systems Biology, 13(1), 909-910. doi:10.15252/msb.20167458, Institutional Repository
Bayramoglu, B., Toubiana, D., van Vliet, S., Inglis, R. F., Shnerb, N., & Gillor, O. (2017). Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective. Scientific Reports, 7, 1-10. doi:10.1038/srep42068, Institutional Repository
Bergmiller, T., Andersson, A. M. C., Tomasek, K., Balleza, E., Kiviet, D. J., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Science, 356(6335), 311-315. doi:10.1126/science.aaf4762, Institutional Repository
Besmer, M. D., Hammes, F., Sigrist, J. A., & Ort, C. (2017). Evaluating monitoring strategies to detect precipitation-induced microbial contamination events in karstic springs used for drinking water. Frontiers in Microbiology, 8, 2229 (12 pp.). doi:10.3389/fmicb.2017.02229, Institutional Repository
Besmer, M. D., Sigrist, J. A., Props, R., Buysschaert, B., Mao, G., Boon, N., & Hammes, F. (2017). Laboratory-scale simulation and real-time tracking of a microbial contamination event and subsequent shock-chlorination in drinking water. Frontiers in Microbiology, 8, 1900 (11 pp.). doi:10.3389/fmicb.2017.01900, Institutional Repository
Bosshard, L., Dupanloup, I., Tenaillon, O., Bruggmann, R., Ackermann, M., Peischl, S., & Excoffier, L. (2017). Accumulation of deleterious mutations during bacterial range expansions. Genetics, 207(2), 669-684. doi:10.1534/genetics.117.300144, Institutional Repository
Böhler, M., Fleiner, J., Siegrist, H., McArdell, C. S., Teichler, R., Bourgin, M., … Blunschi, M. (2017). Biologische Nachbehandlung von kommunalem Abwasser nach Ozonung – ReTREAT. Schlussbericht. Dübendorf: Eawag. , Institutional Repository
Casotti, R., Balestra, C., Van Dijk, M., Passarelli, A., Sigrist, J., & Hammes, F. (2017). Real-time microbial concentrations by automated on-line flow cytometry for marine coastal monitoring. In IMEKO TC19 workshop on metrology for the sea (MetroSea 2017). Learning to measure sea health parameters (pp. 50-53). Budapest: International Measurement Confederation (IMEKO). , Institutional Repository
Diard, M., Bakkeren, E., Cornuault, J. K., Moor, K., Hausmann, A., Sellin, M. E., … Hardt, W. D. (2017). Inflammation boosts bacteriophage transfer between Salmonella spp.. Science, 355(6330), 1211-1215. doi:10.1126/science.aaf8451, Institutional Repository
Epting, J., Huggenberger, P., Page, R. M., Besmer, M. D., Hammes, F., Radny, D., … Borer, P. (2017). Variabilität der grundwasserqualität. Einflussfaktoren für die Grundwasserqualität Flussnaher Trinkwasserfassungen. Aqua & Gas, 97(2), 30-39. , Institutional Repository
Friedrich, M. N. D., Julian, T. R., Kappeler, A., Nhiwatiwa, T., & Mosler, H. J. (2017). Handwashing, but how? Microbial effectiveness of existing handwashing practices in high-density suburbs of Harare, Zimbabwe. American Journal of Infection Control, 45(3), 228-233. doi:10.1016/j.ajic.2016.06.035, Institutional Repository
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. doi:10.1038/ismej.2017.76, Institutional Repository
González-González, A., Hug, S. M., Rodríguez-Verdugo, A., Patel, J. S., & Gaut, B. S. (2017). Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression. Molecular Biology and Evolution, 34(11), 2839-2855. doi:10.1093/molbev/msx216, Institutional Repository
Heeb, N. V., Grubelnik, A., Geueke, B., Kohler, H. P. E., & Lienemann, P. (2017). Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26. Chemosphere, 182, 491-500. doi:10.1016/j.chemosphere.2017.05.047, Institutional Repository
König, B., Bochet, C., Egli, T., Kling, S., Norton, B., & Wehrli, B. (2017). Uses of daylight. In S. Sanders & J. Oberst (Eds.), Changing perspectives on daylight: science, technology, and culture (pp. 38-42). Retrieved from, Institutional Repository
Kötzsch, S., Rölli, F., & Hammes, F. (2017). Trinkwasserqualität in Gebäuden. Synthesebericht: KTI-Projekt «Materialien in Kontakt mit Trinkwasser». Aqua & Gas, 97(10), 74-78. , Institutional Repository
Lilja, E. E., & Johnson, D. R. (2017). Metabolite toxicity determines the pace of molecular evolution within microbial populations. BMC Evolutionary Biology, 17, 52 (12 pp.). doi:10.1186/s12862-017-0906-2, Institutional Repository
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.). doi:10.1186/s12862-017-0950-y, Institutional Repository
Mathis, R., & Ackermann, M. (2017). Asymmetric cellular memory in bacteria exposed to antibiotics. BMC Evolutionary Biology, 17, 73 (14 pp.). doi:10.1186/s12862-017-0884-4, Institutional Repository
Men, Y., Achermann, S., Helbling, D. E., Johnson, D. R., & 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. doi:10.1016/j.watres.2016.11.048, Institutional Repository
Micali, G., Colin, R., Sourjik, V., & Endres, R. G. (2017). Drift and behavior of E. coli cells. Biophysical Journal, 113(11), 2321-2325. doi:10.1016/j.bpj.2017.09.031, Institutional Repository
Montealegre, M. C., Roh, J. H., Rae, M., Davlieva, M. G., Singh, K. V., Shamoo, Y., & Murray, B. E. (2017). Differential Penicillin-Binding Protein 5 (PBP5) levels in the Enterococcus faecium clades with different levels of ampicillin resistance. Antimicrobial Agents and Chemotherapy, 61(1), e02034 (10 pp.). doi:10.1128/AAC.02034-16, Institutional Repository
Moor, K., Diard, M., Sellin, M. E., Felmy, B., Wotzka, S. Y., Toska, A., … Slack, E. (2017). High-avidity IgA protects the intestine by enchaining growing bacteria. Nature, 544(7651), 498-502. doi:10.1038/nature22058, Institutional Repository
Nguyen, M. T., Allemann, L., Ziemba, C., Larivé, O., Morgenroth, E., & Julian, T. R. (2017). Controlling bacterial pathogens in water for reuse: treatment technologies for water recirculation in the Blue Diversion Autarky Toilet. Frontiers in Environmental Science, 5, 90 (13 pp.). doi:10.3389/fenvs.2017.00090, Institutional Repository
Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D. J., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics, 13(12), e1007122 (24 pp.). doi:10.1371/journal.pgen.1007122, Institutional Repository
Page, R. M., Besmer, M. D., Epting, J., Sigrist, J. A., Hammes, F., & Huggenberger, P. (2017). Online analysis: deeper insights into water quality dynamics in spring water. Science of the Total Environment, 599-600, 227-236. doi:10.1016/j.scitotenv.2017.04.204, Institutional Repository
Pati, S. G., Kohler, H. P. E., & Hofstetter, T. B. (2017). Characterization of substrate, cosubstrate, and product isotope effects associated with enzymatic oxygenations of organic compounds based on compound-specific isotope analysis. In M. E. Harris & V. E. Anderson (Eds.), Methods in enzymology: Vol. 596. Measurement and analysis of kinetic isotope effects (pp. 291-329). doi:10.1016/bs.mie.2017.06.044, Institutional Repository
Pitol, A. K., Bischel, H. N., Kohn, T., & Julian, T. R. (2017). Virus transfer at the skin−liquid interface. Environmental Science and Technology, 51, 14417-14425. doi:10.1021/acs.est.7b04949, Institutional Repository
Probst-Rüd, S., McNeill, K., & Ackermann, M. (2017). Thiouridine residues in tRNAs are responsible for a synergistic effect of UVA and UVB light in photoinactivation of Escherichia coli. Environmental Microbiology, 19(2), 434-442. doi:10.1111/1462-2920.13319, Institutional Repository
Proctor, C. R., Dai, D., Edwards, M. A., & Pruden, A. (2017). Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems. Microbiome, 5, 130-146. doi:10.1186/s40168-017-0348-5, Institutional Repository
Proctor, C. R. (2017). Microbiology of household plumbing causes and consequences (Doctoral dissertation). doi:10.3929/ethz-b-000255592, Institutional Repository
Props, R., Kerckhof, F. M., Rubbens, P., De Vrieze, J., Hernandez Sanabria, E., Waegeman, W., … Boon, N. (2017). Absolute quantification of microbial taxon abundances. ISME Journal, 11(587), 584-587. doi:10.1038/ismej.2016.117, Institutional Repository
Ricken, B., Kolvenbach, B. A., Bergesch, C., Benndorf, D., Kroll, K., Strnad, H., … Corvini, P. F. X. (2017). FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp strain BR1 subsisting on sulfonamide antibiotics. Scientific Reports, 7, 15783 (11 pp.). doi:10.1038/s41598-017-16132-8, Institutional Repository
Rodriguez-Verdugo, A., Buckley, J., & Stapley, J. (2017). The genomic basis of eco-evolutionary dynamics. Molecular Ecology, 26(6), 1456-1464. doi:10.1111/mec.14045, Institutional Repository
Schiessl, K. T., Janssen, E. M. L., Kraemer, S. M., McNeill, K., & Ackermann, M. (2017). Magnitude and mechanism of siderophore-mediated competition at low iron solubility in the Pseudomonas aeruginosa pyochelin system. Frontiers in Microbiology, 8, 1964 (11 pp.). doi:10.3389/fmicb.2017.01964, Institutional Repository
Schiff, H. (2017). Development of a massively multiplexed ligation-dependent assay for antibiotic resistance gene detection (Master thesis). 70 p. , Institutional Repository
Shrivastava, N., Macwan, A. S., Kohler, H. P. E., & Kumar, A. (2017). Important amino acid residues of hexachlorocyclohexane dehydrochlorinases (LinA) for enantioselective transformation of hexachlorocyclohexane isomers. Biodegradation, 28(2-3), 171-180. doi:10.1007/s10532-017-9786-9, Institutional Repository
Van Nevel, S., Koetzsch, S., Proctor, C. R., Besmer, M. D., Prest, E. I., Vrouwenvelder, J. S., … Hammes, F. (2017). Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring. Water Research, 113, 191-206. doi:10.1016/j.watres.2017.01.065, Institutional Repository
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. doi:10.1021/acs.est.6b05878, Institutional Repository
Zumstein, M. T., Rechsteiner, D., Roduner, N., Perz, V., Ribitsch, D., Guebitz, G. M., … Sander, M. (2017). Enzymatic hydrolysis of polyester thin films at the nanoscale: effects of polyester structure and enzyme active-site accessibility. Environmental Science and Technology, 51(13), 7476-7485. doi:10.1021/acs.est.7b01330, Institutional Repository
Zumstein, M. T., Kohler, H. P. E., McNeill, K., & Sander, M. (2017). High-throughput analysis of enzymatic hydrolysis of biodegradable polyesters by monitoring cohydrolysis of a polyester-embedded fluorogenic probe. Environmental Science and Technology, 51(8), 4358-4367. doi:10.1021/acs.est.6b06060, Institutional Repository
van Gestel, J., & Tarnita, C. E. (2017). On the origin of biological construction, with a focus on multicellularity. Proceedings of the National Academy of Sciences of the United States of America PNAS, 114(42), 11018-11026. doi:10.1073/pnas.1704631114, Institutional Repository
van Vliet, S. (2017). Individuality and collective behavior in bacterial populations (Doctoral dissertation). doi:10.3929/ethz-b-000247119, Institutional Repository


Avalos Vizcarra, I., Hosseini, V., Kollmannsberger, P., Meier, S., Weber, S. S., Arnoldini, M., … Vogel, V. (2016). How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics. Scientific Reports, 6, 18109 (13 pp.). doi:10.1038/srep18109, Institutional Repository
Baumgartner, A., Niederhauser, I., Diston, D., & Moor, D. (2016). Enterohemorrhagic Escherichia coli (EHEC) in water from karst springs: detection with real-time PCR and isolation of strains. Journal of Consumer Protection and Food Safety, 11(4), 353-357. doi:10.1007/s00003-016-1053-1, Institutional Repository
Besmer, M. D. (2016). Monitoring short-term dynamics of bacterial concentrations in natural and engineered aquatic ecosystems (Doctoral dissertation). ETH Zürich, Zürich, 189 p. , Institutional Repository
Besmer, M. D., Epting, J., Page, R. M., Sigrist, J. A., Huggenberger, P., & Hammes, F. (2016). Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment. Scientific Reports, 6, 1-10. doi:10.1038/srep38462, Institutional Repository
Besmer, M. D., Sigrist, J. A., Hammes, F., & Auckenthaler, A. (2016). Online-Durchflusszytometrie in der Praxis. Fenster in die Welt mikrobiologischer Dynamiken in Wasser - von der Quelle bis zum Wasserhahn. Aqua & Gas, 96(7-8), 73-77. , Institutional Repository
Besmer, M. D., & Hammes, F. (2016). Short-term microbial dynamics in a drinking water plant treating groundwater with occasional high microbial loads. Water Research, 107, 11-18. doi:10.1016/j.watres.2016.10.041, Institutional Repository
Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E. coli. PLoS Genetics, 12(4), 1-17. doi:10.1371/journal.pgen.1005974, Institutional Repository
Bürgmann, H., & Imminger, S. (2016). FOWA Projekt "Antibiotikaresistenz" (Report No.: 012-15). Kastanienbaum, Switzerland: Eawag. , Institutional Repository
Czekalski, N., Imminger, S., Salhi, E., Veljkovic, M., Kleffel, K., Drissner, D., … Von Gunten, U. (2016). Inactivation of antibiotic resistant bacteria and resistance genes by ozone: from laboratory experiments to full-scale wastewater treatment. Environmental Science and Technology, 50(21), 11862-11871. doi:10.1021/acs.est.6b02640, Institutional Repository
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. doi:10.1093/femsre/fuw024, Institutional Repository
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.). doi:10.3389/fmicb.2016.01707, Institutional Repository
Frossard, A., Hammes, F., & Gessner, M. O. (2016). Flow cytometric assessment of bacterial abundance in soils, sediments and sludge. Frontiers in Microbiology, 7, 903 (8 pp.). doi:10.3389/fmicb.2016.00903, Institutional Repository
Garg, N., Lata, P., Jit, S., Sangwan, N., Singh, A. K., Dwivedi, V., … Lal, R. (2016). Laboratory and field scale bioremediation of hexachlorocyclohexane (HCH) contaminated soils by means of bioaugmentation and biostimulation. Biodegradation, 27(2), 179-193. doi:10.1007/s10532-016-9765-6, Institutional Repository
Gulde, R., Meier, U., Schymanski, E. L., Kohler, H. P. E., Helbling, D. E., Derrer, S., … Fenner, K. (2016). Systematic exploration of biotransformation reactions of amine-containing micropollutants in activated sludge. Environmental Science and Technology, 50(6), 2908-2920. doi:10.1021/acs.est.5b05186, Institutional Repository
Happe, M., Sugnaux, M., Cachelin, C. P., Stauffer, M., Zufferey, G., Kahoun, T., … Fischer, F. (2016). Scale-up of phosphate remobilization from sewage sludge in a microbial fuel cell. Bioresource Technology, 200, 435-443. doi:10.1016/j.biortech.2015.10.057, Institutional Repository
Hering, J. G., Giger, W., Hug, S. J., Kohler, H. P. E., Kretzschmar, R., Schwarzenbach, R., … Zobrist, J. (2016). An American in Zurich: Jerry Schnoor as an ambassador for U.S. environmental science and engineering. Environmental Science and Technology, 50(13), 6597-6598. doi:10.1021/acs.est.5b06233, Institutional Repository
Inglis, R. F., Biemaskie, J. M., Gardner, A., & Kümmerli, R. (2016). Presence of a loner strain maintains cooperation and diversity in well-mixed bacterial communities. Proceedings of the Royal Society B: Biological Sciences, 283(1822), 20152682 (9 pp.). doi:10.1098/rspb.2015.2682, Institutional Repository
Julian, T. R. (2016). Environmental transmission of diarrheal pathogens in low and middle income countries. Environmental Science: Processes and Impacts, 18(8), 944-955. doi:10.1039/c6em00222f, Institutional Repository
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. doi:10.1038/ismej.2016.75, Institutional Repository
Kötzsch, S., Rölli, F., Sigrist, R., & Hammes, F. (2016). Kunststoffe in Kontakt mit Trinkwasser. Hygienetests im Vergleich. Aqua & Gas, 96(12), 42-52. , Institutional Repository
Kötzsch, S., Sigrist, R., Rölli, F., & Hammes, F. (2016). Wenn der Start zum Problemfall wird. Hygienische Inbetriebnahme von Trinkwasserinstallationen. Aqua & Gas, 96(6), 74-81. , Institutional Repository
Lacanna, E., Bigosch, C., Kaever, V., Boehm, A., & Becker, A. (2016). Evidence for Escherichia coli diguanylate cyclase DgcZ interlinking surface sensing and adhesion via multiple regulatory routes. Journal of Bacteriology, 198(18), 2524-2535. doi:10.1128/JB.00320-16, Institutional Repository
Lee, Y., Imminger, S., Czekalski, N., von Gunten, U., & Hammes, F. (2016). Inactivation efficiency of Escherichia coli and autochthonous bacteria during ozonation of municipal wastewater effluents quantified with flow cytometry and adenosine tri-phosphate analyses. Water Research, 101, 617-627. doi:10.1016/j.watres.2016.05.089, Institutional Repository
Lilja, E. E., & Johnson, D. R. (2016). Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. ISME Journal, 10, 1568-1578. doi:10.1038/ismej.2015.243, Institutional Repository
Manjarrez-Casas, A. M., Bagheri, H. C., & Dobay, A. (2016). Transition from one- to two-dimensional development facilitates maintenance of multicellularity. Royal Society Open Science, 3(9), 160554 (11 pp.). doi:10.1098/rsos.160554, Institutional Repository
Mathis, R., & Ackermann, M. (2016). Response of single bacterial cells to stress gives rise to complex history dependence at the population level. Proceedings of the National Academy of Sciences of the United States of America PNAS, 113(15), 4224-4229. doi:10.1073/pnas.1511509113, Institutional Repository
Men, Y., Han, P., Helbling, D. E., Jehmlich, N., Herbold, C., Gulde, R., … Fenner, K. (2016). Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon Nitrososphaera gargensis. Environmental Science and Technology, 50(9), 4682-4692. doi:10.1021/acs.est.5b06016, Institutional Repository
Nelson, M. B., Chase, A. B., Martiny, J. B. H., Stocker, R., Nguyen, J., Lloyd, K., … Jermy, A. J. (2016). The microbial olympics 2016. Nature Microbiology, 1, 1-5. doi:10.1038/NMICROBIOL.2016.122, Institutional Repository
Nescerecka, A., Hammes, F., & Juhna, T. (2016). A pipeline for developing and testing staining protocols for flow cytometry, demonstrated with SYBR Green I and propidium iodide viability staining. Journal of Microbiological Methods, 131, 172-180. doi:10.1016/j.mimet.2016.10.022, Institutional Repository
Nescerecka, A., Juhna, T., & Hammes, F. (2016). Behavior and stability of adenosine triphosphate (ATP) during chlorine disinfection. Water Research, 101, 490-497. doi:10.1016/j.watres.2016.05.087, Institutional Repository
Oswald, K. (2016). Methane oxidation in suboxic and anoxic zones of freshwater lakes (Doctoral dissertation). ETH Zürich, Zürich, 142 p. , Institutional Repository
Pati, S. G., Bolotin, J., Brennwald, M. S., Kohler, H. P. E., Werner, R. A., & Hofstetter, T. B. (2016). Measurement of oxygen isotope ratios (18O/16O) of aqueous O2 in small samples by gas chromatography/isotope ratio mass spectrometry. Rapid Communications in Mass Spectrometry, 30(6), 684-690. doi:10.1002/rcm.7481, Institutional Repository
Pati, S. G., Kohler, H. P. E., Pabis, A., Paneth, P., Parales, R. E., & Hofstetter, T. B. (2016). Substrate and enzyme specificity of the kinetic isotope effects associated with the dioxygenation of nitroaromatic contaminants. Environmental Science and Technology, 50(13), 6708-6716. doi:10.1021/acs.est.5b05084, Institutional Repository
Petersen, E. J., Flores-Cervantes, D. X., Bucheli, T. D., Elliott, L. C. C., Fagan, J. A., Gogos, A., … Winchester, M. R. (2016). Quantification of carbon nanotubes in environmental matrices: current capabilities, case studies, and future prospects. Environmental Science and Technology, 50(9), 4587-4605. doi:10.1021/acs.est.5b05647, Institutional Repository
Prest, E. I., Hammes, F., Kötzsch, S., van Loosdrecht, M. C. M., & Vrouwenvelder, J. S. (2016). A systematic approach for the assessment of bacterial growth-controlling factors linked to biological stability of drinking water in distribution systems. Water Science and Technology: Water Supply, 16(4), 865-880. doi:10.2166/ws.2016.001, Institutional Repository
Prest, E. I., Hammes, F., van Loosdrecht, M. C. M., & Vrouwenvelder, J. S. (2016). Biological stability of drinking water: controlling factors, methods, and challenges. Frontiers in Microbiology, 7, 45 (24 pp.). doi:10.3389/fmicb.2016.00045, Institutional Repository
Prest, E. I., Weissbrodt, D. G., Hammes, F., van Loosdrecht, M. C. M., & Vrouwenvelder, J. S. (2016). Long-term bacterial dynamics in a full-scale drinking water distribution system. PLoS One, 11(10), 1-20. doi:10.1371/journal.pone.0164445, Institutional Repository
Proctor, C. R., Gächter, M., Kötzsch, S., Rölli, F., Sigrist, R., Walser, J. C., & Hammes, F. (2016). Biofilms in shower hoses-choice of pipe material influences bacterial growth and communities. Environmental Science: Water Research and Technology, 2(4), 670-682. doi:10.1039/c6ew00016a, Institutional Repository
Rölli, F., Sigrist, R., & Kötzsch, S. (2016). Hyienische Beurteilung von Materialien in Kontakt mit Trinkwasser. Energie-, Wasser-Praxis, 5, 92-96. , Institutional Repository
Schreiber, F., Littmann, S., Lavik, G., Escrig, S., Meibom, A., Kuypers, M. M. M., & Ackermann, M. (2016). Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments. Nature Microbiology, 1(6), 16055 (7 pp.). doi:10.1038/nmicrobiol.2016.55, Institutional Repository
Stamm, C., Räsänen, K., Burdon, F. J., Altermatt, F., Jokela, J., Joss, A., … Eggen, R. I. L. (2016). Unravelling the impacts of micropollutants in aquatic ecosystems: interdisciplinary studies at the interface of large-scale ecology. In A. J. Dumbrell, R. L. Kordas, & G. Woodward (Eds.), Advances in Ecological Research: Vol. 55. Large-Scale Ecology: Model Systems to Global Perspectives (pp. 183-223). doi:10.1016/bs.aecr.2016.07.002, Institutional Repository
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. doi:10.1038/ismej.2016.45, Institutional Repository
Zumstein, M. T., Kohler, H. P. E., McNeill, K., & Sander, M. (2016). Enzymatic hydrolysis of polyester thin films: real-time analysis of film mass changes and dissipation dynamics. Environmental Science and Technology, 50(1), 197-206. doi:10.1021/acs.est.5b04103, Institutional Repository
von Euw, R., Suter, J. M., Kötzsch, S., & Arnold, F. (2016). Hygiene bei der Warmwasserversorgung. Eine Herausforderung. Aqua & Gas, 96(9), 40-47. , Institutional Repository

All Eawag publications are available in the library.