Research Scientist
Before joining UCSD I was co-founder and VP R&D of Marbis Corporation (Cardiff by the Sea, CA), a privately held biotechnology company focusing on the development of natural products for animal and human well being. Prior to this I was leading the microbial diversity team at Diversa Corporation (San Diego, CA), developing and applying novel cultivation approaches for anti-infective discovery as well as developing single cell technology for targeted whole-genome amplification combining FISH and MDA. Before "going into industry" I was working at the Max Planck Institute for Marine Microbiology (Bremen, Germany) on anaerobic degradation of aliphatic and aromatic hydrocarbons under various anoxic (phototropic, nitrate-reducing, iron-reducing, sulfate-reducing and methanogenic) conditions.
Current projects:
Transcription unit architecture and transcriptional regulatory network (TRN) elucidation
Community Systems Biology
Microbial electrosynthesis and direct electron transfer
Microbial ecology and cultivation of new microorganisms
Education
1999 Ph.D. Max-Planck-Institute for Marine Microbiology, Bremen (Germany); Advisor: Fritz Widdel "Microbial diversity and new capabilities during the anaerobic degradation of hydrocarbons"
1996 M.S. Georg-August University Goettingen (Germany); Advisor: Gerhard Gottschalk "Anaerobic oxidation of xylenes, other alkylbenzenes, and crude oil"
1992 B.A. University Hannover (Germany); Biology
Publications
Journal Articles:
The genome organization of Thermotoga maritima reflects its lifestyle. Latif, H., Lerman, J.A., Portnoy, V.A., Tarasova, Y., Nagarajan, H., Schrimpe-Rutledge, A.C., Smith, R.D., Adkins, J.H., Lee, D.H., Qiu, Y., Zengler, K. (2013) PLoS Genetics 9:e1003485
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Qiu, Y., Nagarana, J., Embree, M. Shieu, Abate, E., Juárez, K., Cho, B.-K., Elkins, J., Nevin, K.P., Barrett, C.L., Lovley, D.R., Palsson, B.O., Zengler, K. (2013) Nature Communications 4: 1755
The microbiome extends to subepidermal compartments of normal skin. Nakatsuji, T., Jian, S.B., Chiang, H.-I., Zengler, K., Gallo, R.L. (2013) Nature Communications 4:1431
Crystal ball – 2013. Curtis, T., Daran, J.-M., Pronk, J.T., Frey, J., Jansson, J.K., Robbins-Pianka, A., Knight, R., Schnürer, A., Smets, B.F., Smid, E.J., Abee, T., Vicente, M., Zengler, K. (2013) Microbial Biotechnology 6:3-16
Sulfide-driven microbial electrosynthesis. Gong, Y., Ebrahim, A., Feist, A.M., Embree, M., Zhang, T., Lovley, D.R., Zengler, K. (2013) Environmental Science & Technology 47:568-573
Anaerobic utilization of toluene by marine Alpha- and Gammaproteobacteria reducing nitrate. Alain, K., Harder, J., Widdel, F., Zengler, K. (2012) Microbiology 158:2946-2957
In silico method for modeling metabolism and gene product expression at genome scale. Lerman, J.A., Hyduke, D.R., Latif, H., Portnoy, V.A., Lewis, N.E., Orth, J.D., Schrimpe-Rutledge, A.C., Smith, R.D., Adkins, J.N., Zengler, K., Palsson, B.O. (2012) Nature Communications 3:929.
A road map for the development of community systems (CoSy) biology. Zengler, K. & Palsson, B.O. (2012) Nature Reviews Microbiology 10: 366-372.
Transcriptional regulation of hydrogen production and central metabolism in Thermotoga maritima by a redox-responsive Rex-family repressor. Ravcheev, D.A., Li, X., Portnoy, V.A., Zengler, K., Osterman, A.L., Rodionov, D.A. (2012) Journal of Bacteriology 194: 1145-1157.
Deciphering the transcriptional regulatory logic of amino acid metabolism. Cho, B.-K., Federowicz, S., Park, Y.S., Zengler, K., Palsson, B.O. (2012) Nature Chemical Biology 8: 65-71.
Deciphering the regulatory codes in bacterial genomes. Cho, B.-K., Palsson, B.O., Zengler, K. (2011) Biotechnology Journal 6: 1052-1063.
Adaptive laboratory evolution - harnessing the power of biology for metabolic engineering. Portnoy, V.A., Bezdan, D., Zengler, K. (2011) Current Opinion in Biotechnology 22: 590-594.
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. Thiele, I., Hyduke, D., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., Charusanti, P., Chen, F.-C., Fleming, R. M. T., Hsiung, C.A., De Keersmaecker, S.C.J., Liao, Y.-C., Marchal, K., Mo, M. L., Özdemir, E., Raghunathan, A., Reed, J.L., Shin, S.-I., Sigurbjörnsdóttir, S., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I. M., Zengler, K., Palsson, B. O., Adkins, J. N., Bumann, D. (2011) BMC Systems Biology 5:8.
The challenge of integrating multi-omic data sets. Palsson, B.O. & Zengler, K. (2010) Nature Chemical Biology doi:10.1038/nchembio.441.
Structural and operational complexity of the Geobacter sulfurreducens genome. Qiu Y., Cho B.K., Park Y.S., Lovley D., Palsson B.O., Zengler K. (2010) Genome Research doi:10.1101/gr.107540.110.
Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA. Klimes, A., Franks, A. E., Glaven, R. H. , Tran, H., Barrett, C. L, Qiu, Y., Zengler, K., Lovley, D.R. (2010) FEMS Microbiology Letters doi:10.1111/j.1574-6968.2010.02046.x
A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Tremblay, P.-l., Summers, Z. M., Glaven, R.H., Nevin, K.P., Zengler, K., Barrett, C.L., Qiu, Y., Palsson, B.O., Lovley, D.R. (2010) Environmental Microbiology doi:10.1111/j.1462-2920.2010.02302.x.
Isotopic fingerprinting of methane and CO2 formation from aliphatic and aromatic hydrocarbons. Feisthauer, S., Siegert, M., Seidel, M., Richnow, H.H., Zengler, K., Gründger, F., Krüger, M. (2010) Organic Geochemistry, doi:10.1016/j.orggeochem.2010.01.00.
De novo assembly of a complete microbial genome using short reads: The case of an enhanced electricity-producing variant of Geobacter sulfurreducens. Nagarajan, H., Butler, J., Klimes, A., Qiu, Y., Zengler, K., Methe, B.A., Palsson, B.O., Lovley, D.R., Barrett, C.L. (2010) PLoS ONE 5: e10922. doi:10.1371/journal.pone.0010922.
Elucidation of the transcription unit architecture of the Escherichia coli K-12 MG1655 genome. Cho, B.-K., Zengler, K., Qiu, Y., Park, Y.S., Knight, E.M., Barrett, C., Gao, Y., Palsson, B.O. (2009) Nature Biotechnology 27:1043-1049.
Central role of the cell in microbial ecology. Zengler, K. (2009). Microbiology and Molecular Biology Reviews 73: 712-729.
Targeted access to the genomes of low abundance organisms in complex microbial communities. Podar, M., Abulencia, C., Walcher, M., Hutchinson, D., Zengler, K., Garcia, J., Holland, T., Cotton, D., Hauser, L., Keller, M. (2007) Applied and Environmental Microbiology 73: 3205-3214
Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka. Vadim, V.K., Zengler, K., Lysenko, A.M., Wiegel, J. (2005) Extremophiles 9: 391-398
Tapping into microbial diversity. Keller, M. & Zengler, K. (2004) Nature Reviews Microbiology 2: 141-150
Cultivating the uncultured. Zengler, K., Toledo, T., Rappé, M., Elkins, J., Mathur, E.J., Short, J.M., Keller, M. (2002) PNAS, U.S.A. 99: 15681-15686
Anaerobic degradation and carbon isotopic fractionation of alkylbenzenes in crude oil by sulphate-reducing bacteria. Wilkes, H., Boreham, C., Harms, G., Zengler, K., Rabus, R. (2000) Organic Geochemistry 21: 101-115
Methane formation from long-chain alkanes by anaerobic microorganisms. Zengler, K., Richnow, H.H., Rosselló-Mora, R., Michaelis, W., Widdel, F. (1999) Nature 401: 266-269
Phototrophic utilization of toluene under anoxic conditions by a new strain of Blastochloris sulfoviridis. Zengler, K., Heider, J., Rosselló-Mora, R., Widdel, F. (1999) Archives of Microbiology 172: 204-212
Anaerobic oxidation of o xylene, m xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Harms, G., Zengler, K., Rabus, R., Aeckersberg, F., Minz, D., Rosselló-Mora, R., Widdel, F. (1999) Applied and Environmental Microbiology 65: 999-1004 (first two authors contributed equally to the work)
Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. Champion, K.M., Zengler, K., Rabus, R. (1999) Journal of Molecular Microbiology and Biotechnology 1: 157-164
Books:
Zengler, K. (ed) Accessing Uncultivated Microorganisms: From the environment to organisms and genomes and back, (2008) ASM Press
Book Chapters:
Genome and post-genome technology. Pappas Jr, G., Barreto, C.C., Ferraz Quirino, B., Krüger, R.H., Zengler, K. Krampis, K. In: Rosenberg, E., DeLong, E.F., Thompson, F., Lory, S., Stackebrand, E. (Eds) The Prokaryotes, 4th Edition (in press)
To grow or not to grow: Isolation and cultivation procedures in the genomic age: Zengler, K. (2010). In: Fredricks, D.N. (ed) The Human Microbiota: How Microbial Communities Affect Health and Disease, p. 289-302
Does cultivation still matter? Zengler, K. (2008) In: Zengler, K. (ed) Accessing Uncultivated Microorganisms: From the environment to organisms and genomes and back, p. 3-10
High throughput cultivation of oligotrophic microorganisms. Zengler, K., Walcher, M., Clark, G., Toledo, G., Haller, I., Holland, T., Mathur, E.J., Woodnutt, G., Short, J.M., Keller, M. (2005). In: Leadbetter, J.R. (ed) Methods in Enzymology 397: 124-130
New methods to access microbial diversity for small molecule discovery. Zengler, K., Paradkar, A., Keller, M. (2005). In: Zhang, L., Demain, A.L. (eds) Natural Products: Drug Discovery, Therapeutics and Preventive Medicine, p. 275-293
Proceedings:
High throughput cultivation: a new cultivation-based approach for mining the metabolic potential of microorganisms. Zengler, K., Clark, C., Haller, I., Toledo, G., Walcher, M., Keller, M. (2004) Proceedings of the Tenth International Congress for Culture Collections, p. 113-116
Anaerobic degradation of oil hydrocarbons by sulfate-reducing and nitrate-reducing bacteria. Fukui, M., Harms, G., Rabus, R., Schramm, A., Widdel, F., Zengler, K., Boreham, C., Wilkes, H. (2000). In: Bell, CR, Brylinsky, M, Johnson-Green, P (eds) Microbial biosystems: new frontiers, Proceedings of the 8th International Symposium on Microbial Ecology, p. 359-367
Contact Information
Email Address: kzengler@bioeng.ucsd.edu
Phone: (858)534-5758
Mailing Address: 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412
