John J. Kelly
 |
Associate Professor Ph.D. 1998, Rutgers, The State Univ. of New Jersey, Microbial Ecology Phone: 773.508.7097 Fax: 773.508.3646 E-Mail: jkelly7@luc.edu My CV (PDF) |
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 various state-of-the-art methods, including molecular techniques, to gain insight into the structure and function of microbial communities. My lab has special interest in the structure and function of microbial communities involved in the nitrogen cycle.Current Projects:
DNA Microarray Development
We are working with collaborators from Argonne National Lab on the development of DNA microarrays for the assessment of bacterial functional guilds involved in the nitrogen cycle. We have used several different microarray approaches to assess nitrogen-cycling functional guilds, including direct hybridization of ribosomal RNAs as well as pre-hybridization PCR amplification of both ribosomal RNA genes and nitrogen-cycling functional genes. We are currently working with a new approach, Multiplex Microarray Enhanced PCR (MME-PCR) for the detection of nitrogen-cycling functional genes in complex communities.
Denitrification in Periphytic Biofilms
We are working with collaborators from Northwestern University and the Loyola University Department of Natural Sciences to explore the relationship between algal and bacterial communities in periphytic biofilms in order to understand how community dynamics influence the process of denitrification.
Impacts of Invasive Plant Species
We are working with collaborators from the Loyola University Department of Biology to examine the impacts of invasive plant species on nitrogen-cycling bacterial communities in freshwater wetland sediments.
Impacts of Soil Amendments
We have several projects examining the impacts of soil amendments on soil microbial communities. We are working with collaborators from the Illinois Department of Natural Resources to assess the use of Illinois River sediment as a soil amendment for the remediation of brownfield sites in the city of Chicago. We are also working with collaborators from the Metropolitan Water Reclamation District of Greater Chicago to examine the impacts on nitrogen cycling of biosolids additions to agricultural soils.
REPRESENTATIVE PUBLICATIONS
Kominoski, J.S., T.J. Hoellein, J.J. Kelly, C.M. Pringle. 2008. Does mixing litter of different qualities alter stream microbial diversity and functioning on individual litter species? Oikos (in press).Baniulyte, D., E. Favila, and J.J. Kelly. 2008. Shifts in microbial community composition following surface application of dredged river sediments. Microb. Ecol. (in press).
Kelly, J.J. 2008. Application of DNA microarrays to microbial ecology research: history, challenges, and recent developments. Env. Res. J. (in press).
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. (PDF available by e-mail request)
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. (PDF available by e-mail request)
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. (PDF available by e-mail request)
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. (PDF available by e-mail request)
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 of Bacillus 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. (Full Text PDF)
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.
 |
 |
 |
 |