Skip to Main Content U.S. Department of Energy

Biological Sciences Staff information

Allan Konopka

Deputy Division Director
Laboratory Fellow, TL
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/371-6950

Biography

Allan Konopka is a microbial ecologist who serves as Director of Microbiology in PNNL's Biological Sciences Division.

He came to PNNL after 30 years as a Professor of Biological Sciences at Purdue University. His research has focused on diverse microbial habitats, including aquatic, surface and subsurface soils, and upon the ecology of both photoautotrophic and chemoheterophic microorganisms. He has investigated the role of microbes upon the fate and transport of both organic xenobiotic compounds and inorganic metals. These studies have had scopes ranging from analysis of microbial community composition and activity in natural samples to physiological and molecular analyses of microbes isolated from natural habitats. At PNNL, he is leading efforts on analysis of microbial communities and the development of novel technologies to develop a mechanistic understanding of microbial community ecology.

This area of research requires cross-disciplinary cooperation, and Konopka has performed collaborative research with limnologists, hydrologists, environmental chemists, soil physicists, geologists, envrionmental engineers and chemical engineers. Experimental analyses have been carried out on field sites (such as freshwater aquatic ecosystems and subsurface sediments), in laboratory microcosms, and upon pure cultures of microbes.

Konopka has authored or co-authored approximately 100 peer-reviewed publications in journals for microbiology and microbial ecology. He has also published several materials related to undergraduate education in microbiology, including software used to simulate laboratory exercises in microbiology.

Research Interests

  • Physiological ecology of microbes in natural and engineered ecosystems
  • Microbial community ecology
  • Continuous culture of microorganisms.
  • Subsurface microbiology
  • Mathematical modeling of microbial processes

Education and Credentials

  • Ph.D., Microbiology, University of Washington, 1975
  • M.S., Microbiology, University of Washington, 1973
  • B.S., Microbiology, University of Illinois, 1971

Affiliations and Professional Service

  • American Society for Microbiology
  • Sigma Xi
  • International Society for Microbial Ecology
  • Serves on editorial boards for Applied and Environmental Microbiology and Microbial Ecology.

Awards and Recognitions

  • Fulbright Scholar
  • Fogarty International Senior Fellow
  • Erskine Fellow
  • Elected to the American Academy of Microbiology

PNNL Publications

2014

  • Sadler NC, MR Melnicki, MH Serres, ED Merkley, WB Chrisler, EA Hill, MF Romine, S Kim, EM Zink, S Datta, RD Smith, AS Beliaev, A Konopka, and AT Wright. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9(1):291-300.  doi:10.1021/cb400769v

2013

  • Fu N, D Su, JR Cort, B Chen, Y Xiong, W Qian, A Konopka, DJ Bigelow, and TC Squier. 2013. "Synthesis and Application of an Environmentally Insensitive Cy3-Based Arsenical Fluorescent Probe to Identify Adaptive Microbial Responses Involving Proximal Dithiol Oxidation." Journal of the American Chemical Society 135(9):3567-3575.  doi:10.1021/ja3117284
  • Stegen JC, X Lin, JK Fredrickson, X Chen, DW Kennedy, CJ Murray, ML Rockhold, and A Konopka. 2013. "Quantifying Community Assembly Processes and Identifying Features that Impose Them." The ISME Journal 7:2069-2079.  doi:10.1038/ismej.2013.93
  • Bailey VL, LA McCue, SJ Fansler, MI Boyanov, F DeCarlo, KM Kemner, and A Konopka. 2013. "Micrometer-Scale Physical Structure and Microbial Composition of Soil Macroaggregates." Soil Biology and Biochemistry 65:60-68.  doi:10.1016/j.soilbio.2013.02.005
  • Lanekoff IT, OV Geydebrekht, GE Pinchuk, A Konopka, and J Laskin. 2013. "Spatially-Resolved Analysis of Glycolipids and Metabolites in Living Synechococcus sp. PCC7002 Using Nanospray Desorption Electrospray Ionization." Analyst 138(7):1971-1978.  doi:10.1039/C3AN36716A
  • Melnicki MR, GE Pinchuk, EA Hill, LA Kucek, S Stolyar, JK Fredrickson, A Konopka, and AS Beliaev. 2013. "Feedback-Controlled LED Photobioreactor for Photophysiological Studies of Cyanobacteria." Bioresource Technology 134:127-133.  doi:10.1016/j.biortech.2013.01.079
  • Song HS, D Ramkrishna, GE Pinchuk, AS Beliaev, A Konopka, and JK Fredrickson. 2013. "Dynamic Modeling of Aerobic Growth of Shewanella oneidensis. Predicting Triauxic Growth, Flux Distributions and Energy Requirement for Growth." Metabolic Engineering 15:25-33.  doi:10.1016/j.ymben.2012.08.004
  • Vu T, EA Hill, LA Kucek, A Konopka, AS Beliaev, and JL Reed. 2013. "Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production." Biotechnology Journal 8(5):619-630.  doi:10.1002/biot.201200315
  • Zachara JM, PE Long, J Bargar, JA Davis, PM Fox, JK Fredrickson, MD Freshley, A Konopka, C Liu, JP McKinley, ML Rockhold, KH Williams, and SB Yabusaki. 2013. "Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater-river interaction zone." Journal of Contaminant Hydrology 147:45-72.  doi:10.1016/j.jconhyd.2013.02.001

2012

  • Lee JH, JK Fredrickson, RK Kukkadapu, MI Boyanov, KM Kemner, X Lin, DW Kennedy, BN Bjornstad, A Konopka, DA Moore, CT Resch, and JL Phillips. 2012. "Microbial Reductive Transformation of Phyllosilicate Fe(III) and U(VI) in Fluvial Subsurface Sediments." Environmental Science & Technology 46(7):3721-3730.  doi:10.1021/es204528m
  • Lin X, DW Kennedy, AD Peacock, JP McKinley, CT Resch, JK Fredrickson, and A Konopka. 2012. "Distribution of microbial biomass and the potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment." Applied and Environmental Microbiology 78(3):759-767. 
  • Lin X, DW Kennedy, JK Fredrickson, BN Bjornstad, and A Konopka. 2012. "Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site." Environmental Microbiology 14(2):414-425.  doi:10.1111/j.1462-2920.2011.02659.x
  • Lin X, JP McKinley, CT Resch, RM Kaluzny, C Lauber, JK Fredrickson, RC Knight, and A Konopka. 2012. "Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer." The ISME Journal 5:1665-1676.  doi:10.1038/ismej.2012.26
  • Stegen JC, X Lin, A Konopka, and JK Fredrickson. 2012. "Stochastic and Deterministic Assembly Processes in Subsurface Microbial Communities." The ISME Journal 6(9):1653-1664.  doi:10.1038/ismej.2012.22
  • Bailey VL, CL Bilskis, SJ Fansler, LA McCue, JL Smith, and A Konopka. 2012. "Measurements of Microbial Community Activities in Individual Soil Macroaggregates." Soil Biology and Biochemistry 48:192-195.  doi:10.1016/j.soilbio.2012.01.004
  • Konopka A, and MJ Wilkins. 2012. "Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state." Frontiers in Microbiology 3:Article No. 184.  doi:10.3389/fmicb.2012.00184
  • Melnicki MR, GE Pinchuk, EA Hill, LA Kucek, JK Fredrickson, A Konopka, and AS Beliaev. 2012. "Sustained H2 Production Driven by Photosynthetic Water Splitting in a Unicellular Cyanobacterium." mBio 3(4):Article No. e00197-12.  doi:10.1128/mBio.00197-12
  • Resat H, VL Bailey, LA McCue, and A Konopka. 2012. "Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources." Microbial Ecology 63(4):883-897.  doi:10.1007/s00248-011-9965-x
  • Vu T, S Stolyar, GE Pinchuk, EA Hill, LA Kucek, RN Brown, MS Lipton, AL Osterman, JK Fredrickson, A Konopka, AS Beliaev, and JL Reed. 2012. "Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):E1002460.  doi:10.1371/journal.pcbi.1002460
  • Vu T, S Stolyar, GE Pinchuk, EA Hill, LA Kucek, RN Brown, MS Lipton, AL Osterman, JK Fredrickson, A Konopka, AS Beliaev, and JL Reed. 2012. "Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):e1002460.  doi:10.1371/journal.pcbi.1002460
  • Work VH, AS Beliaev, A Konopka, and MC Posewitz. 2012. "Microbial hydrocarbons: back to the future." Biofuels 3(2):103-105.  doi:10.4155/bfs.12.3
  • Zachara JM, BN Bjornstad, JN Christensen, MS Conrad, JK Fredrickson, MD Freshley, R Haggerty, GE Hammond, DB Kent, A Konopka, PC Lichtner, C Liu, JP McKinley, CJ Murray, ML Rockhold, Y Rubin, VR Vermeul, RJ Versteeg, and C Zheng. 2012. Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFRC Focused on Hanford's 300 Area Uranium Plume January 2011 to January 2012PNNL-21169, Pacific Northwest National Laboratory, Richland, WA. 

2011

  • Lin X, DW Kennedy, JK Fredrickson, BN Bjornstad, and A Konopka. 2011. "Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site." Environmental Microbiology 14(2):414-425.  doi:10.1111/j.1462-2920.2011.02659.x
  • Pinchuk GE, OV Geydebrekht, EA Hill, JL Reed, A Konopka, AS Beliaev, and JK Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77(23):8234-8240.  doi:10.1128/AEM.05382-11
  • Pinchuk GE, OV Geydebrekht, EA Hill, JL Reed, A Konopka, AS Beliaev, and JK Fredrickson. 2011. "Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions." Applied and Environmental Microbiology 77(23):8234-8240.  doi:10.1128/AEM.05382-11
  • Henne KL, JE Turse, CH Nakatsu, and A Konopka. 2011. "Protein Expression Profile of an Environmentally Important Bacterial Strain: the Chromate Response of Arthrobacter Species Strain FB24 ." Chapter 70 in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, ed. FJ de Bruijn, p. 663-674.  John Wiley & Sons, Inc., Hoboken, NJ. 
  • Kourtev PS, KA Hill, PB Shepson, and A Konopka. 2011. "Atmospheric cloud water contains a diverse bacterial community." Atmospheric Environment 45(30):5399-5405.  doi:10.1016/j.atmosenv.2011.06.041
  • Zachara JM, BN Bjornstad, JN Christensen, MS Conrad, JK Fredrickson, MD Freshley, R Haggerty, GE Hammond, DB Kent, A Konopka, PC Lichtner, C Liu, JP McKinley, CJ Murray, ML Rockhold, Y Rubin, VR Vermeul, RJ Versteeg, AL Ward, and C Zheng. 2011. Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFRC Focused on Hanford's 300 Area Uranium Plume January 2010 to January 2011PNNL-20257, Pacific Northwest National Laboratory, Richland, WA. 

2010

  • Pinchuk GE, EA Hill, OV Geydebrekht, J De Ingeniis, X Zhang, A Osterman, JH Scott, SB Reed, MF Romine, A Konopka, AS Beliaev, JK Fredrickson, and JL Reed. 2010. "Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: a Tool for Data Analysis and Hypothesis Generation." PLoS Computational Biology 6(6):Art. No. e1000822.  doi:10.1371/journal.pcbi.1000822
  • Zachara JM, BN Bjornstad, JN Christensen, ME Conrad, JK Fredrickson, MD Freshley, R Haggerty, G Hammon, DB Kent, A Konopka, PC Lichtner, C Liu, JP McKinley, CJ Murray, ML Rockhold, Y Rubin, VR Vermeul, RJ Versteeg, AL Ward, and C Zheng. 2010. Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFRC Focused on Hanford's 300 Area Uranium PlumePNNL-19209, Pacific Northwest National Laboratory, Richland, WA. 

2009

  • Henne KL, JE Turse, CD Nicora, MS Lipton, SL Tollaksen, C Lindberg, G Babbnig, CS Giometti, CN Nakatsu, DK Thompson, and A Konopka. 2009. "Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24." Journal of Proteome Research 8(4)(Sp.Iss.SI):1704-16.  doi:10.1021/Pr800705f
  • Henne KL, CN Nakatsu, DK Thompson, and A Konopka. 2009. "High-Level Chromate Resistance in Arthrobacter sp. strain FB24 Requires Previously Uncharacterized Accessory Genes." BMC Microbiology 9:199-213.  doi:10.1186/1471-2180-9-199
  • Konopka A. 2009. "Ecology, Microbial." In Encyclopedia of Microbiology, Third Edition, ed. M Schaechter, pp. 91-106.  Elsevier, Oxford, United Kingdom. 
  • Konopka A. 2009. "Ecology, Microbial." In Encyclopedia of Microbiology, ed. Moselio Schaechter, pp. 91-106.  Elsevier, Amsterdam, Netherlands. 
  • Konopka A. 2009. "What is microbial community ecology?" The ISME Journal 3(11):1223-1230.  doi:10.1038/ismej.2009.88
  • Kourtev PS, CH Nakatsu, and A Konopka. 2009. "Inhibition of nitrate reduction by chromium (VI) in anaerobic soil microcosms." Applied and Environmental Microbiology 75(19):6249-6257.  doi:10.1128/AEM.00347-09

Selected Publications

2006

  • Konopka A. 2006. "Microbial Ecology: Searching for Principles." Microbe 1:175-179.
  • Becker JM, T Parkin, CH Nakatsu, JD Wilbur, and A Konopka. 2006. "Bacterial Activity, Community Structure, and Cm-Scale Spatial Heterogeneity in Contaminated Soil." Microbial Ecology 50:220-231.
  • Carrero-Colon M, CH Nakatsu, and A Konopka. 2006. "Microbial Community Dynamics in Nutrient-Pulsed Chemostats." FEMS Microbiology Ecology 57:1-8.
  • Carrero-Colon M, CH Nakatsu, and A Konopka. 2006. "The Effect of Nutrient Periodicity upon Microbial Community Dynamics." Applied Environmental Microbiology 72:3175-3183.
  • Kourtev PS, CH Nakatsu, and A Konopka. 2006. "Anaerobic Bacterial Community Responses to Organic C Addition in Chromium (VI) and Iron (III) Amended Microcosms."  Applied and Environmental Microbiology 72:628-637.
  • Staley JT, C Jenkins, and A Konopka. 2006. "Taxonomic Description of the Genus Ancylobacter" in Bergey's Manual of Systematic Bacteriology, 2nd Edition. Springer-Verlag, New York.

2005

  • Nakatsu CH, N Carmosini, B Baldwin, F Beasley, P Kourtev, and A Konopka. 2005. "Soil Microbial Community Responses to Additions of Organic Carbon Substrates and Heavy Metals (Pb and Cr)." Applied Environmental Microbiology 71:7679-7689.
  • Shi W, M Bischoff, RF Turco, and A Konopka. 2005. "Microbial Catabolic Diversity in Soils Contaminated with Hydrocarbons and Heavy Metals." Environmental Science and Technology 39:1974-1979.

2004

  • Konopka A. 2004. "Systems Biology - Not Brand New, But Different." American Society for Microbiology (ASM) News 70(4):163-168.

2002

  • Konopka A and T Zakharova. 2002. "Analysis of Bacterial Ecotoenzymes by Polyacrylamide gel Zymograms. Journal of Microbiolical Methods 51:273-282.
  • Konopka A, T Zakharova, and CN Nakatsu. 2002. "Effect of Starvation Length upon Lags in Substrate Degradation in a Biomass Recycle Reactor."  Journal of Industrial Microbiology and Biotechnology 29(5):286-291.
  • Curtis P, CH Nakatsu, and A Konopka. 2002. "Aciduric Proteobacteria Isolated from pH 3 Soil." Archives of Microbiology 178(1):65-70.
  • LaPara TM, T Zakharova, CH Nakatsu, and A Konopka. 2002. "Functional and Structural Adaptations of Bacterial Communities Growing on Particulate Substrates under Stringent Nutrient Limitation."  Microbial Ecology 44 (4):317-326.
  • Shi W, M Bischoff, R Turco, and A Konopka. 2002. "Long-Term Effects of Chromium and Lead upon the Activity of Soil Microbial Communities." Applied Soil Ecology 21:169-177.
  • Shi W, M Bischoff, R Turco, and A Konopka. 2002. "Association of Microbial Community Composition and Activity with Pb, Cr and Hydrocarbon Contamination." Applied Environmental Microbiology 68(8):3859-3866.

Biological Sciences

Seminar Series

Fundamental & Computational Sciences

Research Highlights

View All BSD Highlights

Contacts