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Berg, E.M., D.K. Dila, O. Schaul, A. Eros, S.L. McLellan, R.J. Newton, T.J. Hoellein, & J.J. Kelly. 2024. Anthropogenic particle concentrations and fluxes in an urban river are temporally variable and impacted by storm events. 

Folvarska, V., S.M. Thomson, Z. Lu, M. Adelgren, A. Schmidt, R.J. Newton, Y. Wang, & P.J. McNamara. 2024. The effects of lead, copper, and iron corrosion products on antibiotic resistant bacteria and antibiotic resistance genes. 

In Press


Skwor, T, D.C. Jones, C. Cahak, & R.J. Newton. 2024. First report and characterization of a plasmid-encoded blaSFO-1 in a multi-drug resistant Aeromonas hydrophila clinical isolate. Microorganisms 12(3): 494. Link


McMahon, K.D. & R.J. Newton. 2023. Pelagic Bacteria, Archaea, and Viruses in Wetzel's Limnology 4th edition. pp. 705-757. Academic Press.


Kimbell, L.K., E.L. LaMartina, S. Kohls, Y. Wang, R.J. Newton, & P.J. McNamara. 2023. Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water. mSphere e00307-23. Link

Jones, D.C., E.L. LaMartina, J.R. Lewis, A.J. Dahl, N. Nadig, A. Szabo, R.J. Newton, & T.A. Skwor. 2023. One health and global health view of antimicrobial susceptibility through the "eye" of Aeromonas: Systematic Review and Meta-Analysis. International Journal of Antimicrobial Agents 62(2): 106848. Link

Scarim, G., E.L. LaMartina, K. Venkiteshwaran, D.H. Zitomer, R.J. Newton, & P.J. McNamara. 2023. An inexpensive, reproducible method to quantify activated sludge foaming potential: Validation through lab-scale studies and year-long full-scale sampling campaign. Water Environment Research 95: e10856. Link



Burch, T.R., R.J. Newton, L.K. Kimbell, E.L. LaMartina, K. O'Malley, S.M. Thomson, C.W. Marshall, & P.J. McNamara. In Press. Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment. Environmental Science Water Research & Technology 8: 1787-1802. Link

Roguet, A.R., A.M. Eren, R.J. Newton, & S.L. McLellan. 2022. Guts of the urban ecosystem: Microbial ecology of sewer infrastructure. mSystems e00118-22. Link

LaMartina, E.L., A.L. Schmoldt, & R.J. Newton. 2022. Full-length 16S rRNA gene sequences from raw sewage spanning geographic and seasonal gradients in conveyance systems across the USA. Microbiology Resource Announcements e00319-22. Link

Podowski, J.C., S.F. Paver, R.J. Newton, & M.L. Coleman. Genome streamlining, proteorhodopsin, and organic nitrogen metabolism in freshwater nitrifiers. mBio e02379-21. Link

Lu, X., D-F. Deng, F. Huang, F. Casu, E. Kraco, R.J. Newton, M. Zohn, S.J. Teh, A.M. Watson, B. Sheperd, Y. Ma, M.A.O. Dawood, L.M. Rios Mendoza. 2022. Chronic exposure to high-density polyethylene microplastic through feeding alters the nutrient metabolism of juvenile yellow perch (Perca flavescens). Animal Nutrition 9: 143-158. Link

Lin, H., K. Matsui, R.J. Newton, & L. Guo. 2022. Disproportionate changes in the composition and molecular size spectra of dissolved organic matter between influent and effluent from a major metropolitan wastewater treatment system. ACS ES&T Water 2(1): 216-225. Link


LaMartina, E.L., A.A. Mohaimani, & R.J. Newton. 2021. Urban wastewater bacterial communities assemble into seasonal steady states. Microbiome 9(1):1-13. Link 

Deveneau, N.E., R.J. Newton, A. Agrawal, C.L. Kinman, G. Wu, Z. Lei, & S.L. Fancis. 2021. Shifts in vaginal bacterial community composition are associated with vaginal mesh exposure. Online Early. Link

Wang, C., Y. Yang, B. Yang, H. Lin, T.R. Miller, R.J. Newton, & L. Guo. 2021. Relationship between alkaline phosphatase activities and phosphorus dynamics in a eutrophic coastal lagoon in Lake Michigan. Science of the Total Environment. 787:147681. Link 

McClary-Gutierrez, Z. Driscoll, C. Nenn, & R.J. Newton. 2021. Human fecal contamination corresponds to changes in the freshwater bacterial communities of a large river basin. Microbiology Spectrum 9(2):e01200-21. Link

Feng, S., A. Roguet, J.S. McClary-Gutierrez, R.J. Newton, N. Kloczko, J.G. Meiman, S.L. McLellan. 2021. Evaluation of sampling, analysis, and normalization methods for SARS-CoV-2 concentrations in wastewater to assess COVID-19 burdens in Wisconsin communities. ACS ES&T Water 1(8):1955-1965. Link

Kimbell, L.K., E.L. LaMartina, A.D. Kappell, J. Huo, Y. Wang, R.J. Newton, & P.J. McNamara. 2021. Cast iron drinking water pipe biofilm support diverse microbial communities containing antibiotic resistance genes, metal resistance genes, and class 1 integrons. Environmental Science: Water Research & Technology 7:584-598. Link



Bivins, A., D. North, A. Ahmad, et al., 2020. Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19. Environmental Science & Technology 54:7754-7757. Link

Jiang, M., H. Zhao, S.-W. Zhai, R.J. Newton, B. Shepherd, J. Tain, A.G. Lofald, S. Teh, F.P. Binkowski, & D.-F. Deng. 2020. Nutritional quality of different starches in feed fed to juvenile yellow perch, Perca flavescens. Aquaculture Nutrition. doi: 10.1111/anu.13026. Link

Roguet, A., Ö.C. Esen, A.M. Eren, R.J. Newton, & S.L. McLellan. 2020. FORENSIC: an online platform for fecal source identification. mSystems 5(2):e00869-19. Link

Paver, S.F., R.J. Newton, & M.L. Coleman. 2020. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environmental Microbiology 22:433-446. Link 


Newton, R.J. & J.S. McClary. 2019. The flux and impact of wastewater infrastructure microorganisms on human and ecosystem health. Current Opinion in Biotechnology. 57:145-150. doi: 10.1016.j.copbio.2019.03.015. Link

Bartelme, R.P., M.C. Smith, O.J. Sepulveda-Villet, & R.J. Newton. 2019. Component microenvironments and system biogeography structure microorganism distributions in recirculating aquaculture and aquaponic systems. mSphere 4: e00143-19. doi: 10.1128/mSphere.00143-19. Link


Roguet, A., A.M. Eren, R.J. Newton, & S.L. McLellan. 2018. Fecal source identification using random forest. Microbiome 6:185. doi: 10.1186/s40168-018-0568-3. 

Paver, S.F., D. Muratore, R.J. Newton, & M.L. Coleman. 2018. Reevaluating the salty divide: Phylogenetic specificity of transitions between marine and freshwater systems. mSystems 3(6): e00232-18. doi:10.1128/mSystems.00232-18.

Rohwer, R.R., J.J. Hamilton, R.J. Newton, & K.D. McMahon. 2018. TaxAss: Leveraging a custom database achieves fine-scale taxonomic resolution. mSphere 3:e00327-18. doi: 10.1128/mSphere.00327-18. Link

Bartelme, R.P., P. Barbier, R.S. Lipscomb, S.E. LaPatra, R.J. Newton, J.P. Evenhuis, M.J. McBride. 2018. Draft genome sequence of the fish pathogen Flavobacterium columnare strain MS-FC-4. Genome Announcements 6:20 e00429-18. doi: 10.1128/genomeA.00429-18. Link

Bartelme, R.P., B.O. Oyserman, J.E. Blom, O. J. Sepulveda-Villet, & R.J. Newton 2018. Stripping away the soil: Plant growth promoting microbiology opportunities in aquaponics. Frontiers in Microbiology 9: 8 doi: 10.3389/fmicb.2018.00008. Link



Bartelme, R.P., S.L. McLellan, & R.J. Newton 2017. Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing Archaea and comammox Nitrospria. Frontiers in Microbiology 8: 101 doi: 10.3389/fmicb.2017.00101. Link


Newton, R.J. & A. Shade. 2016. Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere. Aquatic Microbial Ecology. 78: 51-63. doi: 10.3354/ame0181. Link

Bartelme, R.P., R.J. Newton, Y. Zhu, N. Li, B.R. LaFrentz, & M.J. McBride. 2016. Complete genome sequences of the fish pathogen Flavobacterium columnare Strain C#2. Genome Announcements 4:e00624-16. doi:10.1128/genomeA.00624-16. Link

Bendall, M.L., S.L.R. Stevens, L.-K. Chan, S. Malfatti, P. Schwientek, J. Tremblay, W. Schackwitz, J. Martin, A. Pati, B. Bushnell, J. Froula, D. Kang, S.G. Tringe, S. Bertilsson, M.A. Moran, A. Shade, R.J. Newton, K.D. McMahon, & R.R. Malmstrom. 2016. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME Journal 10: 1589-1601. doi:10.1038/ismej.2015.241 Link

McLellan, S.L., J.C. Fisher, & R.J. Newton. 2016. The microbiome of urban waters. International Microbiology 18: 141-149. doi:10.2436/20.1501.01.244. Link

Graham, E.B., J.E. Knelman, A. Schindlbacher, S. Siciliano, M. Breulmann, A. Yannarell, J.M. Beman, G. Abell, L. Philippot, J. Prosser, A. Foulquier, J. Yuste, H.C. Glanville, D.L. Jones, R. Angel, J. Salminen, R.J. Newton, et al. 2016. Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?  Frontiers in Microbiology 7:214. doi: 10.3389/fmicb.2016.00214. Link




Newton, R.J. & S.L. McLellan. 2015. A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan. Frontiers in Microbiology 6:1028. doi: 10.3389/fmicb.2015.01028. Link


Fisher, J.C., R.J. Newton, D.K. Dila, & S.L. McLellan. 2015. Urban microbial ecology of a freshwater estuary of Lake Michigan. Elementa: Science of the Anthropocene 3:000064. doi.10.12952/journal.elementa.000064. Link 

Newton, R.J., S.L. McLellan, D.K. Dila, J.H. Vineis, H.G. Morrison, A.M. Eren, & M.L. Sogin. 2015. Sewage reflects the microbiomes of human populations. mBio 6(2): e02574-14. doi: 10.1128/mBio.02574-14. Link 

Kappell, A.D., M.S. DeNies, N.H. Ahuja, N.A. Ledeboer, R.J. Newton, & K.R. Hristova. 2015. Detection of multi-drug resistant Escherichia coli in the urban waterways of Milwaukee, WI. Frontiers in Microbiology 6:336 doi: 10.3389/fmicb.2015.00336. Link 

Eren, A.M., M.L. Sogin, H.G. Morrison, J.H. Vineis, J.C. Fisher, R.J. Newton, & S.L. McLellan. 2015. A single genus in the gut microbiome reflects host preference and specificity. ISME Journal 9: 90-100. Link 



Kappell, A.D., Y. Wei, R.J. Newton, J.D. Van Nostrand, J. Zhou, S.L. McLellan & K.R. Hristova. 2014. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill. Frontiers in Microbiology 5: doi: 10.3389/fmicb.2014.00205. Link 


Koskey, A.M., J.C. Fisher, M.F. Traudt, R.J. Newton, & S.L. McLellan. 2014. Analysis of gull fecal microbial community reveals dominance of Catellicoccus marimammalium in relation to cultureable enterococci. Applied and Environmental Microbiology 80: 757-765. Link 




Newton, R.J., S.M. Huse, H.G. Morrison, C.S. Peake, M.L. Sogin, & S.L. McLellan. 2013. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling. PLoS ONE 8: e74265, doi: 10.1371/journal/pone.0074265. Link 


Shanks, O.C., R.J. Newton, C.A. Kelty, S.M. Huse, M.L. Sogin, & S.L. McLellan. 2013. Comparison of microbial community structure in untreated wastewater from different geographic locales. Applied and Environmental Microbiology 79: 2906-2913. Link 

Newton, R.J., M.J. Bootsma, H.G. Morrison, M.L. Sogin, & S.L. McLellan. 2013. A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan. Microbial Ecology 65: 1011-1023. Link 

McLellan, S.L., R.J. Newton, J.L. VandeWalle, O.C. Shanks, S.M. Huse, A.M. Eren, & M.L. Sogin. 2013. Sewage reflects the distribution of human fecal Lachnospiraceae. Environmental Microbiology 15: 2213-2227. Link 




Jones, S.E., T.A. Cadkin, R.J. Newton, & K.D. McMahon. 2012. Spatial and temporal scales of aquatic bacterial beta diversity. Frontiers in Microbiology doi: 10.33389/fmicb.2012.00318. Link 


Chan, L.-K.†, R.J. Newton†, S. Sharma, P. Rayapati, A.J. Limardo, C.B. Smith, C. Meile, & M.A. Moran. 2012. Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Frontiers in Microbiology doi: 10.3389/fmicb.2012.00159. Link 




Newton R.J., J.L. VandeWalle, M.A. Borchardt, M.H. Gorelick, & S.L. McLellan. 2011. Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Applied and Environmental Microbiology, 77: 6972-6981. Link 


Newton R.J.* & K.D. McMahon. 2011. Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environmental Microbiology, 13: 887-899. Link 

Shanks, O.C., C.A. Kelty, S. Archibeque, M. Jenkins, R.J. Newton, S.L. McLellan, S.M. Huse, & M.L. Sogin. 2011. Community structure of cattle fecal bacteria from animal feeding operations. Applied and Environmental Microbiology, 77: 2992-3001. Link 

Newton, R.J., S.E. Jones, A. Eiler, K.D. McMahon, and S. Bertilsson. 2011. A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews, 75: 14-49. Link 




Newton R.J., L.E. Griffin, K.M. Bowles, C. Meile, S. Gifford, C.E. Givens, E.C. Howard, E. King, C.A. Oakley, C.R. Reisch, J.M. Rinta-Kanto, S. Sharma, S. Sun, V. Varaljay, M. Vila-Costa, J.R. Westrich, and M.A. Moran. 2010. Genome characteristics of a generalist marine bacterial lineage. ISME Journal, 4: 784-798. Link 


Seyfried E.E., R.J. Newton, K.F. Rubert IV, J.A. Pedersen, and K.D. McMahon. 2010. Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline. Microbial Ecology, 59: 799-807. Link 




Jones S.E., R.J. Newton, and K.D. McMahon. 2009. Evidence for structuring bacterial community composition by organic carbon source in temperate lakes. Environmental Microbiology, 11: 2463-2472. Link 




Jones S.E., R.J. Newton, KD McMahon. 2008. Potential for atmospheric deposition of bacteria to influence bacterioplankton communities. FEMS Microbiology Ecology, 64: 388-394. Link 




Newton R.J., S.E. Jones, M.R. Helmus, and K.D. McMahon. 2007. Phylogenetic Ecology of the Freshwater acI Lineage. Applied and Environmental Microbiology, 73: 7169-7176. Link 




Shade A., A.D. Kent, S.E. Jones, R.J. Newton, E.W. Triplett, & K.D. McMahon. 2006. Interannual dynamics and phenology of bacterial communities in a eutrophic lake. Limnology and Oceanography, 52: 487-494. Link 


Kent A.D., S. E. Jones, G.H. Lauster, J.M. Graham, R.J. Newton, and K.D. McMahon. 2006. Experimental Manipulations of Microbial Food Web Interactions in a Humic Lake: Shifting Biological Drivers of Bacterial Community Structure. Environmental Microbiology, 8: 1448-1459. Link 

Newton R.J., A.D. Kent, E.W. Triplett, and K.D. McMahon. 2006. Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes. Environmental Microbiology, 8: 956-970. Link 




Jacob C., A.D. Kent, B.J. Benson, R.J. Newton, E.W. Triplett, and K.D. McMahon 2005. Biological databases for linking large microbial and environmental datasets. In Proceedings of the 9th World Multiconference on Systemics, Cybernetics and Informatics. Vol VI: 279-282. July 10-13, 2005, Orlando, Fl. Link 




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