top of page

Past Research

Here is a compilation of previous research that has been completed by the Newton Lab. These projects are no longer funded and/or actively being researched. 

Aquaculture - biofilters

Many recirculating aquaculture systems (RAS) employ a nitrifying biofilter to remove nitrogenous waste from fish excreta and undigested feed. We characterized the microbial communities in these biofilters, identified what organisms were carrying out ammonia- and nitrite-oxidation, and examined whether the life traits of these organisms impact system start-up and typical operation conditions.

Publications on this work

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

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

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


Bartelme, R.P. 2018. Cultivating Ecosystems: Microbial commuities in recirculating aquaculture systems. Ph.D. Dissertation, UW-Milwaukee. 


In collaboration with Dr. Tim Gundl, we investigated how macronutrients from wastewater treatment systems enter shallow groundwater aquifers and whether this nutrient input alters the microbial community composition and bioactive processes carried out in these ecosystems. The studied groundwater systems are used as a drinking water source and were once isolated from surface water infiltration, but changes in river flow resulting from wastewater discharge have allowed river water containing relatively high concentrations of macronutrients to enter the system. Yet some aquifers nearby remain un-impacted.


In this project, we examined how alteration to surface water nutrient concentrations can impact microbial energetics in aquifers and whether this process could impact drinking water quality. 


Gayner, Natalie. J. 2018. Riverbank inducement influence on a shallow groundwater microbial community and its effects on aquifer reactivity. M.S. Thesis, UW-Milwaukee

bottom of page