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Jeff Werner

Contact Information

From June 2017 to January 2018 I will be on sabbatical, doing research in the Helbling Lab at the Cornell University School of Civil & Environmental Engineering. During this time, email is the best way to contact me. 

Jeffrey J. Werner

Associate Professor
Chemistry Department
SUNY Cortland
Bowers Hall
PO Box 2000
Cortland, NY 13045

office: Bowers Hall, rm 1332 (3rd floor)
phone: 607-753-5471


Ph.D. (2006) University of Minnesota-Twin Cities :: Water Resources Science (Environmental Chemistry)

    Research advisors: Kris McNeill and Bill Arnold

B.S. (2002) University of Wisconsin-Madison :: Chemistry


  • 2015-presentAssociate Professor, Chemistry Department, SUNY-Cortland
  • June 2017 - Jan 2018. Visiting Associate Professor (sabbatical), Civil & Environmental Engineering, Cornell University (Helbling Lab)
  • 2011-2015. Assistant Professor, Chemistry Department, SUNY-Cortland
  • 2011-2017. Adjunct Assistant Professor, Biological and Environmental Engineering, Cornell University
  • 2009-2011. Research Associate, Biological & Environmental Engineering, Cornell University (Angenent Lab)
  • 2008-2009. Assistant Professor of Environmental Chemistry, Castleton State College
  • 2006-2008Postdoctoral Associate, Civil & Environmental Engineering, Cornell University (Richardson Lab)

Grants and Awards

External Funding

  • Werner JJ, Rossi F, Conklin P, Chatfield C, Fitzgerald T. "MRI: Acquisition of an LC-MS/MS to Enable Research and Training for Chemistry and Biology Students at SUNY Cortland." NSF 1337695, $270,807, Sept 2013 - Aug 2016.
  • Angenent LT (PI; Cornell University) and Werner JJ (co-PI, subaward to SUNY Cortland). "SusChEM: Converting Urban Wastes into Longer Chain Chemicals" NSF 1336186, $114,197 subaward to SUNY Cortland ($390,302 total), Sept 2013 - Aug 2016.

Undergraduate Student Summer Research Fellows Sponsored


Citations (via Google Scholar)

Jin Z, Di Rienzi SC, Janzon A, Werner JJ, Angenent LT, Fowler DM, Dangl JL, Ley RE (2016). Novel rhizosphere soil alleles for the enzyme ACC deaminase queried for function with an in-vivo competition assay. Applied and Environmental Microbiology, accepted.

Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley R, Walter MT and Angenent L (2015). Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics. Frontiers in Microbiology 6:1523. [link]

Regueiro L, Spirito CM, Usack JG, Hospodsky D, Werner JJ, Angenent LT (2015). Comparing the inhibitory thresholds of dairy manure co-digesters after prolonged acclimation periods: Part 2 - correlations between microbiomes and environment. Water Research 87: 458-466. [link]

Shrestha PM, Malvankar NS, Werner JJ, Elena-Rotaru A, Franks AE, Shrestha M, Liu F, Angenent LT, Lovley DR (2014). Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment. Bioresource Technology 174(1):306-310. [link]

Werner JJ, Garcia M, Perkins S, Yarasheski K, Smith S, Muegge B, Stadermann F, DeRito C, Floss C, Madsen E, Gordon J, Angenent LT (2014). Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation. Applied and Environmental Microbiology. 80(11): 3375-3383. [link]

Venkataraman A, Rosenbaum MA, Werner JJ, Winans SC, Angenent LT (2014). Metabolite transfer with the fermentation product 2,3-butanediol enhances virulence by Pseudomonas aeruginosa. The ISME Journal 8(6): 1210-1220. [link]

Zhang W, Werner JJ, Agler MT, Angenent LT (2014). Substrate type drives variation in reactor microbiomes of anaerobic digesters. Bioresource Technology 151(1): 397-401. [link]

Agler MT, Spirito CM, Usack JG, Werner JJ, Angenent LT (2014). Development of a highly specific and productive process for n-caproic acid production: applying lessons from methanogenic microbiomes. Water Science and Technology 69(1): 62-68. [link]

Cullender TC, Chassaing B, Janzon A, Kumar K, Muller CE, Werner JJ, Angenent LT, Bell E, Hay AG, Peterson DA, Walter J, Vijay-Kumar M, Gewirtz, Ley RE (2013). Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host & Microbe 14(15): 571-581. [link]

Agler MT, Werner JJ, Iten LB, Dekker A, Cotta MA, Dien BS, Angenent LT (2012). Shaping reactor microbiomes to produce the fuel precursor n-butyrate from pretreated cellulosic hydrolysates. Environmental Science & Technology 46(18): 10229-10238. [link]

Rowe A, Heavner G, Mansfeldt C, Werner JJ, Richardson RE (2012). Relating chloroethene respiration rates in Dehalococcoides to protein and mRNA biomarkers. Environmental Science & Technology 46(17): 9388-9397. [link]

Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Bäckhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Bäckhed F, Isolauri E, Salminen S, Ley RE (2012). Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150(3): 470-480. [link]

Agler MT, Spirito CM, Usack JG, Werner JJ and Angenent LT (2012). Chain elongation with reactor microbiomes: Upgrading dilute ethanol to medium-chain carboxylates. Energy & Environmental Science 5(8): 8189-8192. [link]

Werner JJ, Zhao D, Caporaso JG, Knight R, Angenent LT (2012). Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. The ISME Journal 6: 1273-1276. [link]

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE (2012). Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys. The ISME Journal 6:94-103. [link]

Venkataraman A, Rosenbaum MA, Perkins SD, Werner JJ, Angenent LT (2011). Metabolite-based mutualism between Pseudomonas aeruginosa PA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems. Energy & Environmental Science 4: 4550-4559. [link]

Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT (2011). Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proceedings of the National Academy of Sciences of the United States of America 108(10):4158-4163. [link]

Werner JJ, Ptak AC, Rahm BG, Zhang S, Richardson RE (2009). Absolute quantification of Dehalococcoides proteins: Enzyme bioindicators of chlorinated ethene dehalorespiration. Environmental Microbiology 11:2687-2697. [link]

Werner JJ, McNeill K, Arnold WA (2009). Photolysis of chlortetracycline on a clay surface. Journal of Agricultural and Food Chemistry 57:6932-6937. [link]

Werner JJ, Chintapalli M, Ludeen RA, Wammer KH, McNeill K, Arnold WA (2007). Environmental photochemistry of tylosin: efficient, reversible photoisomerization to a less-active isomer followed by photolysis. Journal of Agricultural and Food Chemistry 55:7062-7068. [link]

Werner JJ, Arnold WA, McNeill K (2006). Water hardness as a photochemical parameter: Photolysis of tetracycline as a function of pH, calcium concentration and magnesium concentration. Environmental Science & Technology 40:7236-7241 (Special Issue on Emerging Contaminants). [link]

Werner JJ, McNeill K, Arnold WA (2005). Environmental photodegradation of mefenamic acid. Chemosphere 58: 1339-1346. [link]

Packer JL, Werner JJ, Latch DE, McNeill K, Arnold WA (2003). Photochemical fate of pharmaceuticals in the environment: Naproxen, diclofenac, clofibric acid, and ibuprofen. Aquatic Science 64:342-351 (Special Issue on Photochemical Processes in the Hydrosphere). [link]