Publications

Invited book chapter:

Kumar, M., M. M. Payne, S. K. Poust and J. L. Zilles. 2012. Polymer-Based Biomimetic Membranes for Desalination, in Biomimetic membranes for sensor and separation applications, edited by Claus Helix Nielsen.

Peer-reviewed publications:

  1. Mobilia, K. C., J. M. Hutchison, and J. L. Zilles. 2017. Characterizing isozymes of chlorite dismutase for water treatment. Frontiers in Microbiology. accepted.
  2. Hutchison, J. M., J. S. Guest, and J. L. Zilles. 2017. Evaluating the development of biocatalytic technology for the targeted removal of perchlorate from drinking water. Environmental Science and Technology 51(12):7178-7186. doi: 10.1021/acs.est.7b00831 link
  3. Hathaway, S. K., N. A. Bartolerio, L. F. RodrÌguez, A. D. Kent, J. L. Zilles. 2017. Denitrifying bioreactors resist disturbance from fluctuating water levels. Frontiers in Environmental Science. Volume 5, article 35. doi: 10.3389/fenvs.2017.00035. full text
  4. Zilles, J. L., L. F. Rodríguez, N. A. Bartolerio, and A. D. Kent. 2016. Microbial community modeling using reliability theory. The ISME Journal 10:1809-1814. advance online publication 16 February 2016. doi: 10.1038/ismej.2016.1 full text through PubMed Central
  5. Williams-Nguyen, J., J. B. Sallach, S. Bartelt-Hunt, A. B. Boxall, L. M. Durso, J. E. McLain, R. S. Singer, D. D. Snow, J. L. Zilles. 2016. Antibiotics and antibiotic resistance in agroecosystems: State of the science. Journal of Environmental Quality 45:394-406. First Look posted: November 10, 2015. doi: 10.2134/jeq2015.07.0336. full text
  6. Luby, E., A. M. Ibekwe, J. Zilles, and A. Pruden. 2016. Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: Prospects and challenges. Journal of Environmental Quality 45:441-453. First Look posted: October 21, 2015. doi: 10.2134/jeq2015.07.0367. full text
  7. Hutchison, J. M., and J. L. Zilles. 2015. Biocatalytic perchlorate reduction: kinetics and effects of groundwater characteristics. Environmental Science: Water Research and Technology.  Advance Article available online 9 September 2015. DOI: 10.1039/C5EW00176E abstract
  8. Lu, N., A. Massoudieh, X. Liang, D. Hu, T. Kamai, T. R. Ginn, J. L. Zilles, T. H. Nguyen. 2015. Swimming motility reduces Azotobacter vinelandii deposition to silica surfaces. Journal of Environmental Quality 44(5):1366-1375 DOI:    10.2134/jeq2015.03.0141 abstract
  9. Hathaway, S. K., M. D. Porter, L. F. Rodri­guez, A. D. Kent, J. L. Zilles. 2015. Impact of the contemporary environment on denitrifying bacterial communities. Ecological Engineering 82:469-473. published online June 9, 2015 doi:10.1016/j.ecoleng.2015.05.005 link
  10. Porter, M. D., J. M. Andrus, N. A. Bartolerio, L. F. Rodriguez, Y. Zhang, J. L. Zilles, A. D. Kent. 2015. Seasonal patterns in microbial community composition in denitrifying bioreactors treating subsurface agricultural drainage. Microbial Ecology 70(3):710-23. published online April 26, 2015  DOI: 10.1007/s00248-015-0605-8 abstract
  11. Lu, N., A. Massoudieh, X. Liang, T. Kamai, J. L Zilles, T. H. Nguyen, T. R. Ginn. 2015. A kinetic model of gene transfer via natural transformation for Azotobacter vinelandii. Environmental Science: Water Research & Technology 1:363-374 DOI: 10.1039/C5EW00023H link
  12. Yoon, H., S. Leibeling, C. Zhang, R. H. Müller, C. J. Werth, and J. L. Zilles. 2014. Adaptation of Delftia acidovorans for herbicide degradation in a microfluidic porous medium. Biodegradation. 25(4):595-604. doi: 10.1007/s10532-014-9684-3. Epub 2014 Feb 12. abstract
  13. Andrus, J. M., M. D. Porter, L. F. Rodriguez, T. Kuehlhorn, R. A. C. Cooke, Y. Zhang, A. D. Kent, and J. L. Zilles. 2014. Spatial variation in the total and denitrifying bacterial community in a denitrifying biofilter treating subsurface agricultural drainage. Microbial Ecology 67(2):265-272. Epub 2013 Sept 29. link
  14. Hutchison, J. M., S. K. Poust, M. Kumar, D. M. Cropek, I. E. MacAllister, C. M. Arnett, J. L. Zilles. 2013. Perchlorate reduction using free and encapsulated Azospira oryzae enzymes. Environ. Sci. Technol. 47(17):9934-9941. doi: 10.1021/es402081b. Epub 2013 Aug 23. abstract
  15. Zhang, X., X. Ye, K. T. Finneran, J. L. Zilles, B. Guo, and E. Morgenroth. 2013. Lignocellulosic hydrolysates and alternative electron shuttles for H2 production using co-culture fermentation with Clostridium beijerinckii and Geobacter metallireducens. Bioresource Technol. 147:89-95 abstract
  16. Lu, N., T. Bevard, A. Massoudieh, C. Zhang, A. C. Dohnalkova, J. L. Zilles, T. H. Nguyen. 2013. Flagella-mediated differences in deposition dynamics for Azotobacter vinelandii in porous media. Environ. Sci. Technol. 47(10):5162–5170. link
  17. Zhang, X., X. Ye, K. T. Finneran, J. L. Zilles, and E.  Morgenroth. 2012. Interactions between Clostridium beijerinckii and Geobacter metallireducens in co-culture fermentation with anthrahydroquinone-2, 6-disulfonate (AH2QDS) for enhanced biohydrogen production from xylose. Biotechnol. Bioeng. 110(1):164-72. doi: 10.1002/bit.24627 abstract
  18. Goetsch, H. E., S. E. Mylon, S. Butler, J. L. Zilles, and T. H. Nguyen. 2012. Oxytetracycline interactions at the soil–water interface: Effects of environmental surfaces on natural transformation and growth inhibition of Azotobacter vinelandii. Environ. Toxicol. Chem.  2012 Jul 21. doi: 10.1002/etc.1945. [Epub ahead of print] link
  19. Lu, N., S. E. Mylon, R. Kong, R. Bhargava, J. L. Zilles, and T. H. Nguyen. 2012. Interactions between dissolved natural organic matter and adsorbed DNA and their effect on natural transformation of Azotobacter vinelandii. Sci. Total Environ. 426:430-435. abstract
  20. Shimada, T., X. Li, J. L. Zilles, E. Morgenroth, and L. Raskin. 2011. Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor. Biotechnol. Bioeng. 108(2):296-305. abstract
  21. Lu, N., J. L. Zilles, and T. H. Nguyen. 2010. Adsorption of extracellular chromosomal DNA and its effects on natural transformation of Azotobacter vinelandii. Appl. Environ. Microbiol. 76(13):4179-84. free full text through PubMed
  22. Zhang, C., Q. Kang, X. Wang, J. L. Zilles, R. H. Müller, and C. J. Werth. 2010. Effects of porous media heterogeneity and transverse mixing on bacterial growth. Environ. Sci. Tech. 44(8):3085-3092. abstract
  23. Zhou, Z., L. Raskin, and J. L. Zilles. 2010. Effects of swine manure on macrolide, lincosamide, and streptogramin B (MLSB) antimicrobial resistance in soils. Appl. Environ. Microbiol. 76(7):2218-2224.   free full text through PubMed
  24. Zhou, Z., L. Raskin, and J. L. Zilles. 2009. Macrolide Resistance in Microorganisms at Antimicrobial-Free Swine Farms. Appl. Environ. Microbiol. 75(18):5814-5820. free full text through PubMed
  25. Shimada, T., J. L. Zilles, E. Morgenroth, and L. Raskin. 2008. Modeling the effect of the antimicrobial tylosin on the performance of an anaerobic sequencing batch reactor. Water Sci Technol. 57(11):1699-704.
  26. Shimada, T., J. L. Zilles, E. Morgenroth, and L. Raskin. 2008. Inhibitory effects of the macrolide antimicrobial tylosin on anaerobic treatment. Biotechnol. & Bioeng. 101(1):73-82. abstract
  27. Kumar, M., M. Grzelakowski, J. Zilles, M. Clark, and W. Meier. 2007. Highly permeable polymeric membranes based on functional water channel protein incorporation. Proc. Nat. Acad. Sci. 104(52):20719-20724. free full text through PubMed
  28. Zhou, Z., M.-N. Pons, L. Raskin, and J. L. Zilles. 2007. Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples. Appl. Environ. Microbiol. 73(9):2956-2962. free full text through PubMed
  29. Shimada, T., J. Zilles, L. Raskin, and E. Morgenroth. 2007. Carbohydrate storage in anaerobic sequencing batch reactors. Water Res. 41(20):4721-4729. abstract
  30. Jindal, A., S. Kocherginskaya, A. Mehboob, M. Robert, R. I. Mackie, L. Raskin, and J. L. Zilles. 2006. Antimicrobial use and resistance in swine waste treatment systems. Appl. Environ. Microbiol. 72(12):7813-7820. free full text through PubMed
  31. Amin, M. M., J. L. Zilles, J. Greiner, S. Charbonneau, L. Raskin, E. Morgenroth. 2006. Influence of the antibiotic erythromycin on anaerobic treatment of a pharmaceutical wastewater. Environ. Sci. Technol., 40 (12), 3971-3977. abstract
  32. Zilles, J., T. Shimada, A. Jindal, M. Robert, and L. Raskin. 2005. Presence of macrolide-lincosamide-streptogramin B and tetracycline antimicrobials in swine waste treatment processes and amended soil. Water Environ. Res. 77(1):57-62.
  33. Hung, C.-H., J. Peccia, J. L. Zilles, and D. R. Noguera. 2002. Physical enrichment of polyphosphate-accumulating organisms in activated sludge. Water Environ. Res. 74(4):354-361.
  34. Zilles, J. L., C.-H. Hung, and D. R. Noguera. 2002. Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal. Water Sci. Technol. 46(1-2):123-128.
  35. Zilles, J. L., J. Peccia, M.-W. Kim, C.-H. Hung, and D. R. Noguera. 2002. Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants. Appl. Environ. Microbiol. 68(6):2763-2769. free full text through PubMed
  36. Zilles, J. L., J. Peccia, and D. R. Noguera. 2002. Microbiology of enhanced biological phosphorus removal in aerated-anoxic Orbalô processes. Water Environ. Res. 74(5):428-436.
  37. Allen, Shara, Julie L. Zilles, and Diana M. Downs. 2002. Metabolic flux in both the purine mononucleotide and histidine biosynthetic pathways can influence synthesis of the hydroxymethyl pyrimidine moiety of thiamine in Salmonella enterica. J. Bacteriol. 184(22):6130-6137. free full text through PubMed
  38. Zilles, Julie L., T. Joseph Kappock, JoAnne Stubbe, and Diana M. Downs. 2001. Altered pathway routing in a class of Salmonella enterica Serovar typhimurium mutants defective in aminoimidazole ribonucleotide synthetase. J. Bacteriol. 183: 2234-2240. free full text through PubMed
  39. Zilles, Julie L., Laura R. Croal, and Diana M. Downs. 2000. Action of the thiamine antagonist bacimethrin on thiamine biosynthesis. J. Bacteriol. 182: 5606-5610. free full text through PubMed
  40. Zilles, Julie L., and Diana M. Downs. 1996. A novel involvement of the PurG and PurI proteins in thiamine synthesis via the alternative pyrimidine biosynthetic (APB) pathway in Salmonella typhimurium. Genetics 144:883-892. free full text through PubMed
  41. Krumholz, Lee R., Julie L. Hollenback, Sanford J. Roskes, and David B. Ringelberg. 1995. Methanogenesis and methanotrophy within a Sphagnum peatland. FEMS Microbiol. Ecol. 18:215-224.