Loyola University Chicago

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Loyola University Chicago

Institute of Environmental Sustainability

Faculty & Staff

John J. Kelly

Title/s: Associate Professor

Phone: 773.508.7097

E-mail: jkelly7@luc.edu

CV Link: John Kelly CV 2012


Ph.D., Microbial Ecology, Rutgers, The State Univ. of New Jersey, 1998

Research Interests

My research focus is microbial ecology and the analysis of complex microbial communities. Microbial communities are present in every ecosystem on earth, and they have a tremendous impact on the function of many of these ecosystems. Many current environmental problems as well as many of their potential solutions are closely linked to microbial communities and their activities, yet remarkably little is known about the diversity and function of microbial communities in the environment. My research uses state-of-the-art molecular techniques to gain insight into the structure and function of microbial communities in both aquatic and terrestrial ecosystems.

Current Projects:

Environmental Impacts of Nanomaterials

Nanomaterials (NM) are engineered particles of extremely small size (at least one dimension of 100 nm or less). The small size of NM gives them many novel and useful properties and has led to their rapid incorporation into a wide variety of consumer products ranging from pharmaceuticals and cosmetics to tools and electronics. There is growing concern about the potential for unanticipated environmental consequences of these materials. We are working with collaborators from Northwestern University and the Loyola University Department of Environmental Sciences to assess the potential impacts of NM on microbial communities in aquatic ecosystems.

Environmental Impacts of Pharmaceuticals and Personal Care Products

Recent research has documented the presence of a variety of pharmaceuticals and personal care products (PPCPs) in rivers and streams in the United States. PPCPs include prescription and over-the counter therapeutic drugs, antibacterial products such as soaps and detergents, as well as fragrances and cosmetics. The potential effects of these PPCPs on stream ecosystems remain largely unknown. We are working with collaborators from the Cary Institute of Ecosystem Studies to investigate the potential ecological effects of a popular antibacterial agent, triclosan, on bacterial communities in rivers and streams in the Chicago region.

Interactions Between Pathogens and Biofilms in Drinking Water Distribution Systems

The pipes within drinking water distribution systems are commonly inhabited by microbial biofilms. These biofilms are generally composed of non-pathogenic bacteria, but recent research has suggested that these biofilms can serve as a refuge for pathogenic organisms, enhancing the survival of pathogens within these systems. We are working with a collaborator from Northwestern University to examine the interactions between pathogens and biofilms in drinking water distribution systems.

Nanoarray Development

We are working with collaborators from the Loyola University Department of Chemistry on the development of carbohydrate-based nanoarrays as a tool for the rapid detection of pathogenic bacteria. We have used dip pen nanolithography (DPN) and polymer pen lithography (PPL) to pattern carbohydrates on solid substrates and are currently testing the ability of these carbohydrate arrays to specifically bind pathogenic bacteria.

Ecology of Periphytic Biofilms

Periphytic biofilms are communities of algae and bacteria attached to solid surfaces within photic zones of aquatic systems. These biofilms are an excellent system for the study of algal-bacterial interactions in aquatic ecosystems. We are working with collaborators from Northwestern University and the Loyola University Department of Environmental Sciences to explore the relationship between algal and bacterial communities in periphytic biofilms in order to understand how population dynamics influence the function of these communities.

Impacts of Elevated Atmospheric Carbon Dioxide on Microbial Communities

The concentration of carbon dioxide in the Earth’s atmosphere has increased dramatically over the last 150 years due primarily to human activities, including the burning of fossil fuels and changes in land use patterns. Increasing atmospheric carbon dioxide has significant implications for global climate due to the role of carbon dioxide in the greenhouse effect. Elevated carbon dioxide can also have significant implications for ecosystems due to the direct effect of carbon dioxide on plants. We are working with a collaborator from the Loyola University Center for Urban Environmental Research and Policy to assess the effects of elevated carbon dioxide on microbial communities in terrestrial and aquatic ecosystems.


Rosi-Marshall, E.J., D. Kincaid, H. Bechtold, T.V. Royer, M. Rojas and J.J. Kelly. 2013. In situ exposure to pharmaceutical compounds suppresses algal growth, microbial respiration and bacterial communities in streams. Ecol. Appl. In Press. (PDF available by e-mail request)

Kelly, J.J., E. Peterson, J. Winkelman, T.J. Walter, S.T. Rier, N.C. Tuchman. 2012. Elevated atmospheric CO2 impacts abundance and diversity of nitrogen cycling functional genes in soil. Microbial Ecol. DOI 10.1007/s00248-012-0122-y. (PDF available by e-mail request)

Kalscheur, K.N., M. Rojas, C.G. Peterson, J.J. Kelly, and K.A. Gray. 2012. Algal exudates and stream organic matter influence the structure and function of denitrifying bacterial communities. Microbial Ecol. 64: 881-892. (PDF available by e-mail request)

Kalscheur, K.N., R.R. Penskar, A.D. Daley, S.M. Pechauer, J.J. Kelly, C.G. Peterson and K.A. Gray. 2012. Effects of anthropogenic inputs on the organic quality of urbanized streams. Water Res. 46: 2515-2524. (PDF available by e-mail request)

Kelly, J.J., K. Policht, T. Grancharova, and L.S. Hundal. 2011. Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil. Appl. Environ. Microbiol. 77:6551-6558. (PDF available by e-mail request)

Peterson, C.G., A.D. Daley, S.M. Pechauer, K.N. Kalscheur, M.J. Sullivan, S.L. Kufta, M. Rojas, K.A. Gray, and J.J. Kelly. 2011. Development of associations between microalgae and denitrifying bacteria in streams of contrasting anthropogenic influence. FEMS Microbiol. Ecol. 77: 477-492. (PDF available by e-mail request)

Kelly, J.J., A. Bansal, J. Winkelman, L.R. Janus, S. Hell, M. Wencel, P. Belt, K.A. Kuehn, S.T. Rier, and N.C. Tuchman. 2010. Alteration of Microbial Communities Colonizing Leaf Litter in a Temperate Woodland Stream by Growth of Trees under Conditions of Elevated Atmospheric CO2. Appl. Environ. Microbiol. 76: 4950-4959.  (Full Text PDF)

Hoellein, T.J., J.L. Tank, J.J. Kelly, and E.J. Rosi-Marshall. 2010. Seasonal variation in nutrient limitation of microbial biofilms colonizing organic and inorganic substrata in streams. Hydrobiologia 649: 331–345.   (Full Text PDF)

Kominoski, J.S., T.J. Hoellein, J.J. Kelly, C.M. Pringle. 2009. Does mixing litter of different qualities alter stream microbial diversity and functioning on individual litter species? Oikos 118: 457-463. (Full Text PDF)

Baniulyte, D., E. Favila, and J.J. Kelly. 2009. Shifts in microbial community composition following surface application of dredged river sediments. Microb. Ecol. 57: 160–169.   (Full Text PDF)

Kelly, J.J. 2009. Application of DNA microarrays to microbial ecology research: history, challenges, and recent developments. Env. Res. J. 3: 357-384.   (Full Text PDF)

Bavykin, S.G., V.M. Mikhailovich, V.M. Zakharyev, Y.P. Lysov, J.J. Kelly, O.S. Alferov, I.M. Gavin, A.V. Kukhtin, J. Jackman, D.A. Stahl, D. Chandler, and A.D. Mirzabekov. 2008. Discrimination of Bacillus anthracis and Closely Related Microorganisms by Analysis of 16S and 23S rRNA with Oligonucleotide Microarray. Chem. Bio. Interact. 171: 212-235.   (Full Text PDF)

Ishida, C.K., S. Arnon, C.G. Peterson, J.J. Kelly, and K.A. Gray. 2008. Influence of algal community structure on denitrification rates in periphyton cultivated on artificial substrates. Microb. Ecol. 56: 140–152.   (Full Text PDF)

J.J. Kelly, E. Favila, L.S. Hundal, and J.C. Marlin. 2007. Assessment of soil microbial communities in surface applied mixtures of Illinois River sediments and biosolids. Appl. Soil Ecol. 36: 176-183.   (PDF available by e-mail request)

Angeloni, N.L., K.J. Jankowski, N.C. Tuchman, and J.J. Kelly. 2006. Effects of an invasive cattail species (Typha x glauca) on sediment nitrogen and microbial community composition in a freshwater wetland. FEMS Microbiol. Lett. 263: 86-92. (Full Text PDF)

Ishida, C.K., J.J. Kelly, and K.A. Gray. 2006. Effects of variable hydroperiods and water level fluctuations on denitrification capacity, nitrate removal, and benthic microbial community structure in constructed wetlands. Ecol. Eng. 28: 363-373. (Full Text PDF)

Siripong, S., J.J. Kelly, D.A. Stahl, and B.E. Rittmann. 2006. Impact of Pre-Hybridization PCR Amplification on Microarray Detection of Nitrifying Bacteria in Wastewater Treatment Plant Samples. Env. Microbiol. 8: 1564-1574. (Full Text PDF)

Kelly, J.J., S. Siripong, J. McCormack, L.R. Janus, H. Urakawa, S. El Fantroussi, P.A. Noble, L. Sappelsa, B.E. Rittmann, and D.A. Stahl. 2005. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Res. 39: 3229-3238. (Full Text PDF)

Janus, L.R., N.L. Angeloni, J. McCormack, S.T. Rier, N.C. Tuchman, and J.J. Kelly. 2005. Elevated atmospheric CO2 alters soil microbial communities associated with trembling aspen (Populus tremuloides) roots. Microb. Ecol. 50: 102-109. (Full Text PDF)

Bavykin, S. G. , Y. P. Lysov, V. Zakhariev, J. J. Kelly, J. Jackman, D. A. Stahl, A. Cherni. 2004. Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships ofBacillus cereus group microorganisms J. Clin. Microbiol. 42:3711-3730. (Full Text PDF)

Kelly, J. J. 2003. Molecular Techniques for the Analysis of Soil Microbial Processes: Functional Gene Analysis and the Utility of DNA Microarrays. Soil Sci. 168:597-605. (Full Text PDF)

Kelly, J. J., M. Haggblom, and R. L. Tate. 2003. Effects of heavy metal contamination and remediation on soil microbial communities in the vicinity of a zinc smelter as indicated by analysis of microbial community phospholipid fatty acid profiles. Biol. Fertil. Soils 38: 65-71. (Full Text PDF)

Urakawa, H., S. El Fantroussi, H. Smidt, J. C. Smoot, E. H. Tribou, J. J. Kelly, P. A. Noble, and D. A. Stahl. 2003. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Environ. Microbiol. 69: 2848-2856. ()

El Fantroussi, S., H. Urakawa, A.E. Bernhard, J.J. Kelly, P.A. Noble, H. Smidt, G.M. Yershov, and D.A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal RNAs hybridized to oligonucleotide microarrays. Appl. Environ. Microbiol. 69: 2377-2382. (Full Text PDF)

Kelly, J. J., B. K. Chernov, I. Tovstanovsky, A. D. Mirzabekov, and S. G. Bavykin. 2002. Radical generating coordination complexes as tools for rapid and effective fragmentation and fluorescent labeling of nucleic acids for microchip hybridization. Analyt. Biochem. 311: 103-118. (Full Text PDF)

Koizumi, Y., J.J. Kelly, T. Nakagawa, H. Urakawa, S. El-Fantroussi, S. Al-Muzaini, M. Fukui, Y. Urushigawa, and D.A. Stahl. 2002. Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology. Appl. Environ. Microbiol. 68: 3215-3225. (Full Text PDF)

Urakawa, H., P. A. Noble, S. El Fantroussi, J. J. Kelly, D. A. Stahl. 2002. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network anlayses. Appl. Environ. Microbiol. 68: 235-244. (Full Text PDF)

Kelly, J. J., R. L. Tate, and M. Haggblom. 1999. Changes in soil microbial communities over time resulting from one time application of zinc: a laboratory microcosm study. Soil Biol. Biochem. 31: (10) 1455-1465. (Full Text PDF)

Kelly, J. J., M. Haggblom, and R. L. Tate. 1999. Effects of the land application of sewage sludge on soil heavy metal concentrations and soil microbial communities. Soil Biol. Biochem. 31: (10) 1467-1470. (Full Text PDF)

Kelly, J. J., and R. L. Tate. 1998. Effects of heavy metal contamination and remediation on soil microbial communities in the vicinity of a zinc smelter. J. Environ. Qual. 27: 609-617. (Full Text PDF)

Kelly, J. J., and R. L. Tate. 1998. Use of BIOLOG for the analysis of microbial communities from zinc contaminated soils. J. Environ. Qual. 27: 600-608.


Institute of Environmental Sustainability
Loyola University Chicago · 1032 W. Sheridan Road
Chicago, IL 60660 · Phone: 773-508-2130 · IES@luc.edu

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