2022

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• Chaudhary, A., ST Dunn, JJ Kelly, TJ Hoellein. 2022. Plastic microbiome development in a freshwater ecosystem. Sci Tot Environ 848: 157697. Full Text

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• Vincent, AES, A Chaudhary, JJ Kelly, TJ Hoellein. 2022. Biofilm assemblage and activity on plastic in urban streams at a continental scale: Site characteristics are more important than substrate type. Sci Total Environ 835: 155398. Full Text

• Rosi, E, M Fork, T Hoellein, JJ Kelly, E Richmond. 2022. Inputs, Occurrence and Effects of Pharmaceuticals and Microplastics in Freshwater Ecosystems. Encyclopedia of Inland Waters, 2nd edition, Elsevier. 
 

2021

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• Kelly, JJ, MG London, AR McCormick, M Rojas, JW Scott, TJ Hoellein. 2021. Wastewater treatment alters microbial colonization of microplastics. PLoS ONE 16(1): e0244443. Full Text

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2020

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• Kelly, JJ, MG London, N Oforji, A Ogunsola, TJ Hoellein. 2020. Microplastic selects for convergent microbiomes from distinct riverine sources. Freshwater Science 39: 281–291. Full Text

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• Griffin, JS, LA Haug, VA Rivera, LM Hernandez Gonzalez, JJ Kelly, WM Miller, GF Wells, AI Packman. 2020. Soil hydrology drives ecological niche differentiation in a native prairie microbiome. FEMS Microbiol Ecol 95: fiz163. Abstract

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2019

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• Hoellein TJ, AJ Shogren, JL Tank, P Risteca, JJ Kelly. 2019. Microplastic deposition velocity in streams follows patterns for naturally occurring allochthonous particles. Scientific Reports 9:3740. Full Text

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• Meschewski E, N Holm, BK Sharma, K Spokas, N Minalt, JJ Kelly. 2019. Pyrolysis biochar has negligible effects on soil greenhouse gas production, microbial communities, plant germination, and initial seedling growth. Chemosphere 228: 565-576. Full Text

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• Keyport S, BD Carson, O Johnson, BA Lawrence, SC Lishawa, NC Tuchman, JJ  Kelly. 2018. Effects of experimental harvesting of an invasive hybrid cattail on wetland structure and function. Restoration Ecology 27: 389-398. Full Text

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2018

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• McNeish, RE, LH Kim, HA Barrett, SA Mason, JJ Kelly, TJ Hoellein. 2018.  Microplastic in riverine fish is connected to species traits. Scientific Reports 8: 11639. Full Text

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• Volesky, LA, S Iqbal, JJ Kelly, P Geddes. 2018. Relationships of native and exotic strains of Phragmites australis to wetland ecosystem properties. Wetlands 38: 577-589. Full Text

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• Rosi, EJ, HA Bechtold, D Snow, M Rojas, AJ Reisinger, JJ Kelly. 2018. Urban stream microbial communities show resistance to pharmaceutical exposure. Ecosphere 9(1) e02041. Full Text

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2017

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• Craig, LS, JD Olden, AH Arthington, S Entrekin, CP Hawkins, JJ Kelly, TA Kennedy, BM Maitland,EJ Rosi, AH Roy, DL Strayer, JL Tank, AO West, MS Wooten. 2017.  Meeting the challenge of interacting threats in freshwater ecosystems: A call to scientists and managers. Elem Sci Anth 5:72. Full Text

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• Richmond EK, Grace MR, Kelly JJ, Reisinger AJ, Rosi EJ, Walters DM. 2017. Pharmaceuticals and personal care products (PPCPs) are ecological disrupting compounds (EcoDC). Elem Sci Anth 5:66. Full Text 

 

• Griffin, JS, N Lu, N Sangwan, A Li, M Dsouza, T Sevilla, A Culotti, AJ Stumpf, LL Keefer, JJ Kelly, JA Gilbert, GF Wells, AI Packman. 2017. Microbial diversity in an intensively managed landscape is structured by landscape connectivity. FEMS Microbiol Ecol 93: fix120. Abstract

 

• Hoellein, TJ, AR McCormick, J Hittie, MG London, JW Scott, JJ Kelly. 2017. Longitudinal patterns of microplastic concentration and bacterial assemblages in surface and benthic habitats of an urban river. Freshwater Science 36: 491-507. Abstract

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• Hartzog, PE, M Sladek, JJ Kelly, DJ Larkin. 2017. Bottle effects alter taxonomic composition of wetland soil bacterial communities during the denitrification enzyme activity assay. Soil Biol Biochem 110: 87–94. Full Text

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2016

 

• McCormick, AR, TJ Hoellein, MG London, J Hittie, JW Scott, JJ Kelly. 2016. Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages. Ecosphere 7(11) e01556. Full Text

 

• Lee, SS, AM Paspalof, DD Snow, EK Richmond, EJ Rosi-Marshall, JJ Kelly. 2016. Occurrence and potential biological effects of amphetamine on stream communities. Environ Sci Technol 50: 9727-9735. Full Text

 

           * Lee at el. 2016 paper was reported on by CNN (link) and US News (link) and was discussed on Scientific American's 60

              Second Science podcast (link).

 

• Bernhard, AE, JJ Kelly. 2016. Editorial: Linking Ecosystem Function to Microbial Diversity. Frontiers Microbiol 7:1041. Full Text

 

• Binh, CTT, E Adams, E Vigen, T Tong, MA Alsina, J-F Gaillard, KA Gray, C Peterson, JJ Kelly. 2016. Chronic addition of a common engineered nanomaterial alters biomass, activity and composition of stream biofilm communities. Environmental Science: Nano. 3: 619-620. Full Text

 

• Costello DM, EJ Rosi-Marshall, LE Shaw, MR Grace, JJ Kelly. 2016. A novel method to assess the effects of chemical stressors on natural biofilm structure and function. Freshwater Biol 61: 2129-2140. Full Text

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• Ozaki, A, E Adams, CTT Binh, T Tong, J-F Gaillard, KA Gray, JJ Kelly. 2015. One-time addition of nano-TiO2 triggers short-term responses in benthic bacterial communities in artificial streams. Microb Ecol 71: 266-275. Abstract

 

2015

 

• Tong T, CM Wilke, J Wu, CTT Binh, JJ Kelly, J-F Gaillard, KA Gray. 2015. Combined toxicity of nano-ZnO and nano-TiO2: From single- to multi-nanomaterials systems. Environ Sci Technol 49: 8113-8123. Full Text

 

• Mikita RA, JJ Kelly, RL Tate. 2015. Wildfire effects on the properties and microbial community structure of organic horizon soils in the New Jersey Pinelands. Soil Biol Biochem.  86: 67-76. Abstract 

 

​•  Binh CTT, CG Peterson, T Tong, J-F Gaillard, KA Gray, JJ Kelly. 2015. Comparing acute effects of a nano-TiO2 pigment on cosmopolitan freshwater phototrophic microbes using high-throughput screening. PLoS ONE 10(4): e0125613. Full Text

 

​•  Rosi-Marshall EJ, and JJ Kelly. 2015. Antibiotic stewardship should consider environmental fate of antibiotics. Environ Sci Technol 49: 5257–5258.  Full Text

 

​•  Tong T, AN Hill, MA Alsina, J Wu, KY Shang, JJ Kelly, KA Gray, and J-F Gaillard. 2015 Spectroscopic characterization of TiO2 polymorphs in wastewater treatment and sediment samples. Environ Sci Technol Letters 2: 12−18. Abstract

 

2014

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​•  McCormick A, TJ Hoellein, SA Mason, J Schluep, and JJ Kelly. 2014. Microplastic is an abundant and distinct microbial habitat in an urban river. Environ Sci Technol 48: 11863–11871. Abstract

 

​•  Binh CTT, T Tong, J-F Gaillard, KA Gray, and JJ Kelly. 2014. Acute effects of TiO2 nanomaterials on the viability and taxonomic composition of aquatic bacterial communities assessed via high-throughput screening and next generation sequencing. PLoS ONE 9(9): e106280.  Full Text

 

•  Tong T, K Fang, SA Thomas, JJ Kelly, KA Gray, and J-F Gaillard. 2014. Chemical interactions between nano-ZnO and nano-TiO2 in a natural aqueous medium. Environ Sci Technol 48: 7924-7932.  Abstract

 

•  Hoellein T, M Rojas, A Pink, J Gasior, and J Kelly. 2014. Anthropogenic litter in urban freshwater ecosystems: distribution and microbial interactions. PLoS ONE 9(6): e98485. Full Text 

 

•  Kelly JJ, N Minalt, A Culotti, M Pryor, and A Packman. 2014. Temporal variations in the abundance and composition of biofilm communities colonizing drinking water distribution pipes. PLoS ONE 9(5): e98542. Full Text

 

•  Geddes P, T Grancharova, JJ Kelly, D Treering, and NC Tuchman. 2014. Effects of invasive Typha x glauca on wetland nutrient pools, denitrification, and bacterial communities are influenced by time since invasion. Aquat Ecol  48: 247-258. Full Text

 

•  Binh CTT, T Tong, J-F Gaillard, KA Gray, and JJ Kelly. 2014. Common freshwater bacteria vary in their responses to short-term exposure to  nano-TiO2. Environ Toxicol Chem 33: 317-327. Abstract

 

2013

 

•  Tong T, A Shereef, J Wu, CTT Binh, JJ Kelly, J-F Gaillard, and KA Gray. 2013. Effects of material morphology on the phototoxicity of nano-TiO2 to bacteria. Environ. Sci. Technol. 47: 12486–12495. Abstract

 

•  Drury, B, J Scott, EJ Rosi-Marshall, and JJ Kelly. 2013. Triclosan exposure increases triclosan resistance and influences taxonomic composition of benthic bacterial communities. Environ. Sci. Technol. 47: 8923−8930. Abstract

 

• Tong, T., C.T.T. Binh, J.J. Kelly, J.-F. Gaillard, and K.A. Gray. 2013. Cytotoxicity of commercial nano-TiO2 to Escherichia coli assessed by high-throughput screening: Effects of environmental factors. Water Res. 47: 2352-2362. ​Abstract

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• 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.23: 583-593. ​PDF

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​              * Rosi-Marshall et al 2013 paper was highlighted in Science Now Link

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• Drury, B, E. Rosi-Marshall  and J.J. Kelly. 2013. Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers. Appl. Environ. Microbiol. 79: 1897-1905. ​PDF

 

              * Drury et al 2013 paper was  highlighted as an Editor's Choice  in Feb 1, 2013 issue of Science PDF​

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• Kelly, J.J., E. Peterson, J. Winkelman, T.J. Walter, S.T. Rier, N.C. Tuchman. 2013. Elevated atmospheric CO2 impacts abundance and diversity of nitrogen cycling functional genes in soil. Microbial Ecol. 65: 394-404. PDF

2012

 

• 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

• 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

 

2011

 

• 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

• 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

2010

 

• 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. 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. PDF​

 

2009

 

• 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. 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. PDF​

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

2008

 

• 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​

• 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​

2007

 

• Kelly, J.J., 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. ​

2006

 

• 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.

• 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.

• 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.

2005

 

• 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.

• 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.

2004

 

• 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.

2003

 

• 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.

• 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.

• 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.

2002

 

• 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.

• 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.​

• 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 analyses. Appl. Environ. Microbiol. 68: 235-244.

 

1999

 

• Kelly,  J. J., M. Haggblom, and R. L. Tate. 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.

• 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.

 

1998

• 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.

• 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. PDF