Please also check GoogleScholar for the most current list of publications

2026

Y. M. Vasquez, M. F. Romero, R. Bowers, R. R. Rohwer, K. D. McMahon, T. Woyke, F. Schulz (2026) “Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem” Nature Communications, in press
A. R. Rober, L. C. Reese, S. P. Brown, K. D. McMahon, S. Louca, J. Cieslik, E. S. Kane, M. R. Turetsky, and K. H. Wyatt (2026) “Hydrologic history regulates microbial biofilm diversity and ecosystem function” Environmental Microbiology, 28(4): e70300 https://doi.org/10.1111/1462-2920.70300
M. S. Sobol, C. Ané, K. D. McMahon, and B. Kaçar. (2026) “Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats” The ISME Journal 6(1):ycag007 https://doi.org/10.1093/ismeco/ycag007

2025

Venetz, N. Dotsios, O. M. Żygadłowska, W. K. Lenstra, N. A.G.M. van Helmond, C. Humborg, K. D. McMahon, D. in ‘t Zandt, C. P. Slomp, M. S.M. Jetten, and A. J. Veraart. (2025) “Long-term euxinia restricts microbial methane removal in eutrophic coastal basins” Environmental Science & Technology 59: 21988 https://pubs.acs.org/doi/10.1021/acs.est.5c05066
C. N. Olmsted, M. Gahler, E. Roden, B. Peterson, J. Lazarcik, P. Q. Tran, M. Berg, D. A. Bryant, D. Goudeau, R. R. Malmstrom, M. Qin, K. D. McMahon (2025) “Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake” Applied and Environmental Microbiology, 91: e01789-24 https://doi.org/10.1128/aem.01789-24
B. Peterson, S. Janssen, B. Poulin, J. Ogorek, A. White, E. McDaniel, R. Marick, G. Armstrong, N. Scheel, M. Tate, D. Krabbenhoft, K. D. McMahon (2025) “Sulfate reduction drives elevated methylmercury formation in the water column of a eutrophic freshwater lake” Environmental Science and Technology. 59 (13), 6799-6811. https://pubs.acs.org/doi/full/10.1021/acs.est.4c12759
R. R. Rohwer, M. Kirkpatrick, S. L. Garcia, M. Kellom, K. D. McMahon, B. J. Baker (2025) “Two decades of bacterial ecology and evolution in a freshwater lake” Nature Microbiology. 10(1):246–257 https://www.nature.com/articles/s41564-024-01888-3
Z. Zhou, P. Q. Tran, C. Martin, R. R. Rohwer, B. J. Baker, K. D. McMahon, K. Anantharaman (2025) “A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution” Nature Microbiology, 10(1):231-245. https://doi.org/10.1038/s41564-024-01876-7

2024

A. I. Krinos, R. M. Bowers, R. R. Rohwer, K. D. McMahon, T. Woyke and F. Schulz (2024) “Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake” Microbiome 12 (1): 13. https://doi.org/10.1186/s40168-024-01831-y
T. Oliver, N. Varghese, S. Roux, F. Schulz, M. Huntemann, A. Clum, B. Foster, B. Foster, R. Riley, Kurt LaButti, R. Egan, P. Hajek, S. Mukherjee, G. Ovchinnikova, T.B.K. Reddy, S. Calhoun, R. D. Hayes, R. R. Rohwer, Z. Zhou, C. Daum, A. Copeland, I. A. Chen, N. N. Ivanova, N. C. Kyrpides, N. J. Mouncey, T. Glavina del Rio, I. V. Grigoriev, S. Hofmeyr, L. Oliker^, K. Yelick, K. Anantharaman, K. D. McMahon, T. Woyke, E. A. Eloe-Fadrosh (2024) “Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota” Scientific Data 11:966 https://doi.org/10.1038/s41597-024-03826-8
R. D. Stewart, K. S. Myers, C. Amstadt, M. Seib, K. D. McMahon, D. R. Noguera (2024) “Refinement of the “CandidatusAccumulibacter” Genus based on a metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration” mSystems: e01188-23. https://journals.asm.org/doi/full/10.1128/msystems.01188-23
S. R. Van Frost, A. M. White, J. M. Jauquet, A. M. Magness, K. D. McMahon, C. K. Remucal (2024) “Laboratory measurements underestimate persistence of the aquatic herbicide fluridone in lakes” Environmental Science: Processes and Impacts. 26:368-379.

2023

B. D. Peterson, B. A. Poulin, D. P. Krabbenhoft, M. T. Tate, A. K. Baldwin, J. Naymik, N. Gastelecutto, K. D. McMahon (2023) “Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in dynamic hydroelectric reservoir” ISME Journal (17)1705-1718. https://doi.org/10.1038/s41396-023-01482-1
A. M. White, S. R. van Frost, J. M. Jauquet, A. M. Magness, K. D. McMahon, C. K. Remucal (2023) “Quantifying the Role of Simultaneous Transformation Pathways in the Fate of the Novel Aquatic Herbicide Florpyrauxifen-Benzyl” Environmental Chemistry and Technology, 57: 12421–12430.
P. Q. Tran, S. B. Bachand, J. C. Hotvedt, K. Kieft, K., E. A. McDaniel, K. D. McMahon, K. Anantharaman (2023). “Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria”. mSystems e00201-23. https://journals.asm.org/doi/full/10.1128/msystems.00201-23
S. He, A.M. Linz, S.L.R Stevens, P.Q. Tran, F. Moya-Flores, B. O. Oyserman, J. R. Dwulit-Smith, K. T. Forest, K. D. McMahon (2023) “Diversity, distribution and expression of opsin genes in freshwater lakes” Molecular Ecology 32: 2798-2817. https://doi.org/10.1111/mec.16891
B. D. Peterson, D. P. Krabbenhoft, K. D. McMahon, J. M. Ogorek, M. T. Tate, W. H. Orem, B. A. Poulin(2023) “Environmental formation of methylmercury is controlled by synergy of inorganic mercury bioavailability and microbial mercury-methylation capacity” Environmental Microbiology 25:1409-1423. https://doi.org/10.1111/1462-2920.16364
R. R. Rohwer, R. J. Hale, T. R. Miller, K. D. McMahon (2023) “Species invasions shift microbial phenology in a two-decade freshwater time series” PNAS 120(11): e2211796120. https://doi.org/10.1073/pnas.2211796120
C. N. Olmsted, R. Ort, P. Q. Tran, E. A. McDaniel, E. E. Roden, D. R. Bond, S. He, K. D. McMahon (2023) “Environmental predictors of electroactive bacterioplankton in small boreal lakes” Environmental Microbiology. 25(3):705-720. DOI: 10.1111/1462-2920.16314.

2022

White AM, Nault ME, McMahon KD, Remucal CK. Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments. Environmental Science & Technology 2022, 56((15)), 10838-10848
Petriglieri F, Singleton CM, Kondrotaite Z, Dueholm MKD, McDaniel EA, McMahon KD, Nielsen PH. Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus ” Candidatus Accumulibacter”. mSystems, 2022 7((3)), e0001622
Stewart RD, Bashar R, Amstadt C, Uribe-Santos GA, McMahon KD, Seib M, Noguera DR. Pilot-scale comparison of biological nutrient removal (BNR) using intermittent and continuous ammonia-based low dissolved oxygen aeration control systems. Water science and technology, 2022 85((2)), 578-590

2021

McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. Water Research, 2021 205(), 117608
McDaniel EA, Moya-Flores F, Keene Beach N, Camejo PY, Oyserman BO, Kizaric M, Khor EH, Noguera DR, McMahon KD. Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics. mSystems, 2021 6((4)), e0047421
Garcia SL, Mehrshad M, Buck M, Tsuji JM, Neufeld JD, McMahon KD, Bertilsson S, Greening C, Peura S. Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations. mSystems, 2021 6((3)),
McDaniel EA, Wever R, Oyserman BO, Noguera DR, McMahon KD. Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal. Microbiology Resource Snnouncements, 2021 10((18)),
Tran PQ, Bachand SC, McIntyre PB, Kraemer BM, Vadeboncoeur Y, Kimirei IA, Tamatamah R, McMahon KD, Anantharaman K. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. The ISME Journal 2021 15((7)), 1971-1986
Berg M, Goudeau D, Olmsted C, McMahon KD, Yitbarek S, Thweatt JL, Bryant DA, Eloe-Fadrosh EA, Malmstrom RR, Roux S. Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. The ISME Journal 2021 15((6)), 1569-1584

2020

Peterson BD, McDaniel EA, Schmidt AG, Lepak RF, Janssen SE, Tran PQ, Marick RA, Ogorek JM, DeWild JF, Krabbenhoft DP, McMahon KD. Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake. Environmental Science & Technology 2020 54((24)), 15840-15851
Lawson CE, Nuijten GHL, de Graaf RM, Jacobson TB, Pabst M, Stevenson DM, Jetten MSM, Noguera DR, McMahon KD, Amador-Noguez D, Lücker S. Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo C and H metabolic network mapping. The ISME Journal 2020 15((3)), 673-687
Chen LX, Méheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, Warren LA, Banfield JF. Large freshwater phages with the potential to augment aerobic methane oxidation. Nature Microbiology 2020 5((12)), 1504-1515
McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD. Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. mSystems 2020 5((4)),
Fernandez L, Peura S, Eiler A, Linz AM, McMahon KD, Bertilsson S. Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake. Frontiers in Microbiology 2020 11(), 1500
Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. Giant virus diversity and host interactions through global metagenomics. Nature 2020 578((7795)), 432-436

2019

Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC. Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 2019 7((1)), 157
Chen LX, Zhao Y, McMahon KD, Mori JF, Jessen GL, Nelson TC, Warren LA, Banfield JF. Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. mSystems 2019 4((5)),
Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O’Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. Common principles and best practices for engineering microbiomes. Nature Reviews – Microbiology 2019 17((12)), 725-741
Camejo PY, Oyserman BO, McMahon KD, Noguera DR. Integrated Omic Analyses Provide Evidence that a ” Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions. mSystems 2019 4((1)),
He S, Lau MP, Linz AM, Roden EE, McMahon KD. Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes. mSphere 2019 4((1)),

2018

Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 2018 6(), e6075
Dwulit-Smith JR, Hamilton JJ, Stevenson DM, He S, Oyserman BO, Moya-Flores F, Garcia SL, Amador-Noguez D, McMahon KD, Forest KT. acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal. Applied and Environmental Microbiology 2018 84((24)),
Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD. TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution. mSphere 2018 3((5)),
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, , Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 2018 36((7)), 660
Garcia SL, Buck M, Hamilton JJ, Wurzbacher C, Grossart HP, McMahon KD, Eiler A. Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria. mSphere 2018 3((3)),
Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environmental Microbiology 2018 20((6)), 2207-2217
Korosh TC, Dutcher A, Pfleger BF, McMahon KD. Inhibition of Cyanobacterial Growth on a Municipal Wastewater Sidestream Is Impacted by Temperature. mSphere 2018 3((1)),
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, , Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature biotechnology 2018 36((2)), 196

2017

Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. The ISME journal 2017 12((3)), 742-755
Camejo PY, Owen BR, Martirano J, Ma J, Kapoor V, Domingo JS, McMahon KD, Noguera DR. Corrigendum to “Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors” [Water Res. 102 (2016) 125-137]. Water research 2017 127(), 258
Korosh TC, Markley AL, Clark RL, McGinley LL, McMahon KD, Pfleger BF. Engineering photosynthetic production of L-lysine. Metabolic engineering 2017 44(), 273-283
Tiede J, Scherber C, Mutschler J, McMahon KD, Gratton C. Gut microbiomes of mobile predators vary with landscape context and species identity. Ecology and evolution 2017 7((20)), 8545-8557
Roux S, Chan LK, Egan R, Malmstrom RR, McMahon KD, Sullivan MB. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature communications 2017 8((1)), 858
Hall MW, Rohwer RR, Perrie J, McMahon KD, Beiko RG. Ananke: temporal clustering reveals ecological dynamics of microbial communities. PeerJ 2017 5(), e3812
He S, Stevens SLR, Chan LK, Bertilsson S, Glavina Del Rio T, Tringe SG, Malmstrom RR, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2017 2((5)),
Camejo PY, Santo Domingo J, McMahon KD, Noguera DR. Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium ” Candidatus Nitrospira nitrosa”. mSystems 2017 2((5)),
Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, Malmstrom RR, Forest KT, McMahon KD. Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems 2017 2((4)),
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, , Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature biotechnology 2017 35((8)), 725-731
Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD. Erratum for Linz et al., “Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes”. mSphere 2017 2((4)),
Herren CM, McMahon KD. Cohesion: a method for quantifying the connectivity of microbial communities. The ISME journal 2017 11((11)), 2426-2438
Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. mSphere 2017 2((3)),
Lawson CE, Wu S, Bhattacharjee AS, Hamilton JJ, McMahon KD, Goel R, Noguera DR. Metabolic network analysis reveals microbial community interactions in anammox granules. Nature communications 2017 8(), 15416
Bhattacharjee AS, Wu S, Lawson CE, Jetten MSM, Kapoor V, Domingo JWS, McMahon KD, Noguera DR, Goel R. Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure. Environmental science & technology 2017 51((8)), 4317-4327
Oyserman BO, Martirano JM, Wipperfurth S, Owen BR, Noguera DR, McMahon KD. Community Assembly and Ecology of Activated Sludge under Photosynthetic Feast-Famine Conditions. Environmental science & technology 2017 51((6)), 3165-3175

2016

Herren CM, Webert KC, McMahon KD. Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton. mSystems 2016 1(3),
Camejo PY, Owen BR, Martirano J, Ma J, Kapoor V, Santo Domingo J, McMahon KD, Noguera DR. Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors. Water Res. 2016 102(), 125-137
Oyserman BO, Moya F, Lawson CE, Garcia AL, Vogt M, Heffernen M, Noguera DR, McMahon KD. Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria. ISME J 2016 10(12), 2931-2945
Eiler A, Mondav R, Sinclair L, Fernandez-Vidal L, Scofield DG, Schwientek P, Martinez-Garcia M, Torrents D, McMahon KD, Andersson SG, Stepanauskas R, Woyke T, Bertilsson S. Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME J 2016 10(8), 1902-14
Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J 2016 10(7), 1589-601

2015

Srivastava A, McMahon KD, Stepanauskas R, Grossart HP. De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany). Int. Microbiol. 2015 18(4), 39-47
Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J 2015 10(4), 810-22
Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F. Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community. Mol. Ecol. 2015 24(17), 4449-59
Beversdorf LJ, Miller TR, McMahon KD. Long-term monitoring reveals carbon-nitrogen metabolism key to microcystin production in eutrophic lakes. Front Microbiol 2015 6(), 456
Beversdorf LJ, Chaston SD, Miller TR, McMahon KD. Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes. PLoS ONE 2015 10(5), e0125353

2014

Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J 2014 8(12), 2503-16
Read EK, Ivancic M, Hanson P, Cade-Menun BJ, McMahon KD. Phosphorus speciation in a eutrophic lake by ³¹P NMR spectroscopy. Water Res. 2014 62(), 229-40
Eiler A, Zaremba-Niedzwiedzka K, Martínez-García M, McMahon KD, Stepanauskas R, Andersson SG, Bertilsson S. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environ. Microbiol. 2014 16(9), 2682-98
Garcia SL, McMahon KD, Grossart HP, Warnecke F. Successful enrichment of the ubiquitous freshwater acI Actinobacteria. Environ Microbiol Rep 2014 6(1), 21-7

2013

Flowers JJ, He S, Malfatti S, del Rio TG, Tringe SG, Hugenholtz P, McMahon KD. Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal. ISME J 2013 7(12), 2301-14
Flowers JJ, Cadkin TA, McMahon KD. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant. Water Res. 2013 47(19), 7019-31
Bareither CA, Wolfe GL, McMahon KD, Benson CH. Microbial diversity and dynamics during methane production from municipal solid waste. Waste Manag 2013 33(10), 1982-92
Miller TR, Beversdorf L, Chaston SD, McMahon KD. Spatiotemporal molecular analysis of cyanobacteria blooms reveals Microcystis–Aphanizomenon interactions. PLoS ONE 2013 8(9), e74933
McMahon KD, Read EK. Microbial contributions to phosphorus cycling in eutrophic lakes and wastewater. Annu. Rev. Microbiol. 2013 67(), 199-219
Kara EL, Hanson PC, Hu YH, Winslow L, McMahon KD. A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA. ISME J 2013 7(3), 680-4
Beversdorf LJ, Miller TR, McMahon KD. The role of nitrogen fixation in cyanobacterial bloom toxicity in a temperate, eutrophic lake. PLoS ONE 2013 8(2), e56103
Youngblut ND, Shade A, Read JS, McMahon KD, Whitaker RJ. Lineage-specific responses of microbial communities to environmental change. Appl. Environ. Microbiol. 2013 79(1), 39-47
Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J 2013 7(1), 137-47

2012

Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J, Whitaker RJ, Wu CH, McMahon KD. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J 2012 6(12), 2153-67
Jones SE, Cadkin TA, Newton RJ, McMahon KD. Spatial and temporal scales of aquatic bacterial beta diversity. Front Microbiol 2012 3(), 318
Ghai R, Hernandez CM, Picazo A, Mizuno CM, Ininbergs K, Díez B, Valas R, DuPont CL, McMahon KD, Camacho A, Rodriguez-Valera F. Metagenomes of Mediterranean coastal lagoons. Sci Rep 2012 2(), 490
Ghai R, McMahon KD, Rodriguez-Valera F. Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environ Microbiol Rep 2012 4(1), 29-35
Ghai R(1), Pasic L, Fernandez AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F.. New abundant microbial groups in aquatic hypersaline environments. Sci Rep 2012 1(), 135

2011

Miller TR, McMahon KD. Genetic diversity of cyanobacteria in four eutrophic lakes. FEMS Microbiol. Ecol. 2011 78(2), 336-48
Shade A, Read JS, Welkie DG, Kratz TK, Wu CH, McMahon KD. Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ. Microbiol. 2011 13(10), 2752-67
He S, McMahon KD. Microbiology of ‘Candidatus Accumulibacter’ in activated sludge. Microb Biotechnol 2011 4(5), 603-19
Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS ONE 2011 6(8), e23785
Hoover SW, Marner WD, Brownson AK, Lennen RM, Wittkopp TM, Yoshitani J, Zulkifly S, Graham LE, Chaston SD, McMahon KD, Pfleger BF. Bacterial production of free fatty acids from freshwater macroalgal cellulose. Appl. Microbiol. Biotechnol. 2011 91(2), 435-46
Skennerton CT, Angly FE, Breitbart M, Bragg L, He S, McMahon KD, Hugenholtz P, Tyson GW. Phage encoded H-NS: a potential achilles heel in the bacterial defence system. PLoS ONE 2011 6(5), e20095
Newton RJ, McMahon KD. Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environ. Microbiol. 2011 13(4), 887-99
Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 2011 75(1), 14-49
He S, McMahon KD. ‘Candidatus Accumulibacter’ gene expression in response to dynamic EBPR conditions. ISME J 2011 5(2), 329-40

2010

He S, Bishop FI, McMahon KD. Bacterial community and “Candidatus Accumulibacter” population dynamics in laboratory-scale enhanced biological phosphorus removal reactors. Appl. Environ. Microbiol. 2010 76(16), 5479-87
He S, Kunin V, Haynes M, Martin HG, Ivanova N, Rohwer F, Hugenholtz P, McMahon KD. Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge. Environ. Microbiol. 2010 12(5), 1205-17
Seyfried EE, Newton RJ, Rubert KF, Pedersen JA, McMahon KD. Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline. Microb. Ecol. 2010 59(4), 799-807
Shade A, Chiu CY, McMahon KD. Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics. Microb. Ecol. 2010 59(3), 546-54
Shade A, Chiu CY, McMahon KD. Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment. Environ. Microbiol. 2010 12(2), 455-66

2009

Flowers JJ, He S, Yilmaz S, Noguera DR, McMahon KD. Denitrification capabilities of two biological phosphorus removal sludges dominated by different “Candidatus Accumulibacter” clades. Environ Microbiol Rep 2009 1(6), 583-588
Jones SE, Newton RJ, McMahon KD. Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes. Environ. Microbiol. 2009 11(9), 2463-72
Shade A, Carey CC, Kara E, Bertilsson S, McMahon KD, Smith MC. Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies. ISME J 2009 3(8), 881-8
Jones SE, McMahon KD. Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics. Environ. Microbiol. 2009 11(4), 905-13

2008

Peterson SB, Warnecke F, Madejska J, McMahon KD, Hugenholtz P. Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ. Microbiol. 2008 10(10), 2692-703
Hinckley GT, Johnson CJ, Jacobson KH, Bartholomay C, McMahon KD, McKenzie D, Aiken JM, Pedersen JA. Persistence of pathogenic prion protein during simulated wastewater treatment processes. Environ. Sci. Technol. 2008 42(14), 5254-9
Jones SE, Newton RJ, McMahon KD. Potential for atmospheric deposition of bacteria to influence bacterioplankton communities. FEMS Microbiol. Ecol. 2008 64(3), 388-94
Shade A, Jones SE, McMahon KD. The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ. Microbiol. 2008 10(4), 1057-67
Cho YK, Donohue TJ, Tejedor I, Anderson MA, McMahon KD, Noguera DR. Development of a solar-powered microbial fuel cell. J. Appl. Microbiol. 2008 104(3), 640-50
Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD, Hugenholtz P. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 2008 18(2), 293-7
He S, Gu AZ, McMahon KD. Progress toward understanding the distribution of Accumulibacter among full-scale enhanced biological phosphorus removal systems. Microb. Ecol. 2008 55(2), 229-36

2007

Newton RJ, Jones SE, Helmus MR, McMahon KD. Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl. Environ. Microbiol. 2007 73(22), 7169-76
McMahon KD, Yilmaz S, He S, Gall DL, Jenkins D, Keasling JD. Polyphosphate kinase genes from full-scale activated sludge plants. Appl. Microbiol. Biotechnol. 2007 77(1), 167-73
He S, Gall DL, McMahon KD. “Candidatus Accumulibacter” population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Appl. Environ. Microbiol. 2007 73(18), 5865-74
McMahon KD, Martin HG, Hugenholtz P. Integrating ecology into biotechnology. Curr. Opin. Biotechnol. 2007 18(3), 287-92
Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD. Synchrony in aquatic microbial community dynamics. ISME J 2007 1(1), 38-47
Auerbach EA, Seyfried EE, McMahon KD. Tetracycline resistance genes in activated sludge wastewater treatment plants. Water Res. 2007 41(5), 1143-51
Jones SE, Shade AL, McMahon KD, Kent AD. Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective. Appl. Environ. Microbiol. 2007 73(2), 659-62

2006

García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 2006 24(10), 1263-9
He S, Gu AZ, McMahon KD. Fine-scale differences between Accumulibacter-like bacteria in enhanced biological phosphorus removal activated sludge. Water Sci. Technol. 2006 54(1), 111-7
Kent AD, Jones SE, Lauster GH, Graham JM, Newton RJ, McMahon KD. Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure. Environ. Microbiol. 2006 8(8), 1448-59
Newton RJ, Kent AD, Triplett EW, McMahon KD. Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes. Environ. Microbiol. 2006 8(6), 956-70

2004

McMahon KD, Zheng D, Stams AJ, Mackie RI, Raskin L. Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnol. Bioeng. 2004 87(7), 823-34

2002

McMahon KD, Dojka MA, Pace NR, Jenkins D, Keasling JD. Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal. Appl. Environ. Microbiol. 2002 68(10), 4971-8
McMahon KD, Jenkins D, Keasling JD. Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal. Water Sci. Technol. 2002 46(1-2), 155-62
Renninger N, McMahon KD, Knopp R, Nitsche H, Clark DS, Keasling JD. Uranyl precipitation by biomass from an enhanced biological phosphorus removal reactor. Biodegradation 2002 12(6), 401-10

2001

McMahon KD, Stroot PG, Mackie RI, Raskin L. Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions–II: Microbial population dynamics. Water Res. 2001 35(7), 1817-27
Stroot PG, McMahon KD, Mackie RI, Raskin L. Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions–I. Digester performance. Water Res. 2001 35(7), 1804-16

1998

McMahon KD, Stahl DA, Raskin L. A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment. Microb. Ecol. 1998 36(3), 362-371
Griffin ME, McMahon KD, Mackie RI, Raskin L. Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids. Biotechnol. Bioeng. 1998 57(3), 342-55