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. 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. 2015. Antibiotics and antibiotic resistance in agroecosystems: State of the science. J. Environ. Qual. accepted.
  2. Luby, E., A. M. Ibekwe, J. Zilles, and A. Pruden. 2015. Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: Prospects and challenges. J Environ. Quality. accepted.
  3. 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
  4. 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. J Environ. Qual. 44(5):1366-1375 DOI:    10.2134/jeq2015.03.0141
  5. 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
  6. 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
  7. 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
  8. 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. 2014 Feb 12. [Epub ahead of print]
  9. 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. http://dx.doi.org/10.1007/s00248-013-0286-0 Epub 2013 Sept 29.
  10. 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.
  11. 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
  12. 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.
  13. 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
  14. Goetsch, H. E., S. E. Mylon, S. Butler, J. L. Zilles, and T. H. Nguyen. 2012. Adsorption of oxytetracycline to soil and its effects on natural transformation and growth inhibition of Azotobacter vinelandii. Environ. Toxicol. Chem.  2012 Jul 21. doi: 10.1002/etc.1945. [Epub ahead of print]
  15. 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.
  16. 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.
  17. 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
  18. 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.
  19. 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
  20. 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
  21. 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.
  22. 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.
  23. 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
  24. 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
  25. Shimada, T., J. Zilles, L. Raskin, and E. Morgenroth. 2007. Carbohydrate storage in anaerobic sequencing batch reactors. Water Res. 41(20):4721-4729.
  26. 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
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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
  32. 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.
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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.