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Submitted

Paver, S.F., R.J. Newton, & M.L. Coleman. Connectivity and local biogeochemistry shape microbial communities of the Laurentian Great Lakes.  

 

2019

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

2018

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

 

2017

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

2016

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

 

2015

 

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 

2014

 

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 

 

2013

 

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 

 

2012

 

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 

 

2011

 

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 

 

2010

 

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 

 

2009

 

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 

 

2008

 

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 

 

2007

 

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 

 

2006

 

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 

 

2005

 

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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