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Staff information


John Cliff

Isotope & Chemical Analysis
Earth Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-93
Richland, WA 99352


Dr. Cliff leads the NanoSIMS capability for biology and biogeochemistry at EMSL. When not helping EMSL users with their research, Dr. Cliff is busy developing techniques that help us understand nutrient fluxes at small spatial scales in terrestrial ecosystems, guard against nuclear proliferation and other weapons of mass destruction, and understand the factors that control greenhouse gas emissions. Ongoing projects include developing mass tags for antibodies and nucleic acid probes for imaging mass spectrometry and developing isotope ratio methods for determining reactor fuel burn up.

Research Interests

  • Dr. Cliff has a wide variety of research interests. He has a strong background in microbial and nuclear forensics, and biogeochemistry. Dr. Cliff has a strong interest in developing capabilities to analyze and understand our world at micron length scales. Dr. Cliff also has a strong record of collaboration with researchers studying early life on our planet and is strongly attracted to understanding sulfur metabolizing microorganisms from the Archean Eon to today.

Education and Credentials

  • Ph.D. Soil Science, Minor in Environmental Engineering, June 2001, Oregon State University, Corvallis, Oregon
  • M.S. Environmental Microbiology, December 1996, West Virginia University, Morgantown, West Virginia
  • B.S. Biology, with honors, minor in chemistry, May 1989, Shepherd College, Shepherdstown, West Virginia

Awards and Recognitions

  • Technical leader for the first International Atomic Energy Network Laboratory to be housed in a University
  • Outstanding Achievement Award 2008. Subgroup on Safeguards Technical Support and International Safeguards Project Office
  • Outstanding Achievement Award 2005. National Security Division, United States Department of Energy

PNNL Publications


  • Boiteau R.M., R.K. Kukkadapu, J.B. Cliff, C.R. Smallwood, L. Kovarik, M.G. Wirth, and M.H. Engelhard, et al. 2020. "Calcareous organic matter coatings sequester siderophores in alkaline soils." Science of the Total Environment 724. PNNL-SA-147851. doi:10.1016/j.scitotenv.2020.138250
  • Bone S.E., J.B. Cliff, K. Weaver, C.J. Takacs, S.J. Roycroft, S. Fendorf, and J.R. Bargar, et al. 2020. "Complexation by Organic Matter Controls Uranium Mobility in Anoxic Sediments." Environmental Science & Technology 54, no. 3:1493-1502. PNNL-SA-142857. doi:10.1021/acs.est.9b04741
  • Reilly D.D., C.L. Beck, E.C. Buck, J.B. Cliff, A.M. Duffin, T.G. Lach, and M. Liezers, et al. 2020. "Focused Ion Beam for Improved Spatially-Resolved Mass Spectrometry and Analysis of Radioactive Materials for Uranium Isotopic Analysis." Talanta 211. PNNL-SA-144768. doi:10.1016/j.talanta.2020.120720


  • Brislawn C.J., E.B. Graham, K.L. Dana, P.D. Ilhardt, S.J. Fansler, W.B. Chrisler, and J.B. Cliff, et al. 2019. "Forfeiting the priority effect: turnover defines biofilm community succession." The ISME Journal 13, no. 7:1865-1877. PNNL-SA-133067. doi:10.1038/s41396-019-0396-x
  • Mulcahy J.R., S. He, D.S. Jin, W. Guo, S. Arteta, J.B. Cliff, and Z. Zhu, et al. 2019. "Experimental Insights into the Growth of Single Truncated Anatase Bipyramids." Chemistry - A European Journal 25, no. 4:993-996. PNNL-SA-140103. doi:10.1002/chem.201805773
  • Taylor S.D., L. Kovarik, J.B. Cliff, and K.M. Rosso. 2019. "Facet-Selective Adsorption of Fe(II) on Hematite Visualized by Nanoscale Secondary Ion Mass Spectrometry." Environmental Science Nano 6, no. 8:2429-2440. PNNL-SA-144858. doi:10.1039/C9EN00562E
  • Vasdekis A.E., H. Alanazi, A.M. Silverman, C.J. Williams, A.J. Canul, J.B. Cliff, and A. Dohnalkova, et al. 2019. "Eliciting the Impacts of Cellular Noise on Metabolic Trade-offs by Quantitative Mass Imaging." Nature Communications 10, no. 1:Article No. 848. PNNL-SA-141117. doi:10.1038/s41467-019-08717-w


  • China S., S.M. Burrows, B. Wang, T. Harder, J. Weis, M. Tanarhte, and L.V. Rizzo, et al. 2018. "Fungal spores as a source of sodium salt particles in the Amazon basin." Nature Communications 9. PNNL-SA-130861. doi:10.1038/s41467-018-07066-4
  • LeTourneau M.K., M.J. Marshall, J.B. Cliff, R.F. Bonsall, A. Dohnalkova, D.V. Mavrodi, and I. Devi, et al. 2018. "Phenazine-1-carboxylic acid and soil moisture influence biofilm development and turnover of rhizobacterial biomass on wheat root surfaces." Environmental Microbiology 20, no. 6:2178-2194. PNNL-SA-134049. doi:10.1111/1462-2920.14244
  • Proetto M.T., C.E. Callmann, J.B. Cliff, C.J. Szymanski, D. Hu, S.B. Howell, and J.E. Evans, et al. 2018. "Tumor Retention of Enzyme-Responsive Pt(II) Drug-Loaded Nanoparticles Imaged by Nanoscale Secondary Ion Mass Spectrometry and Fluorescence Microscopy." ACS Central Science 4, no. 11:1477-1484. PNNL-SA-138579. doi:10.1021/acscentsci.8b00444


  • Fehrenbacher J.S., A.D. Russell, C.V. Davis, A.C. Gagnon, H.J. Spero, J.B. Cliff, and Z. Zhu, et al. 2017. "Link between light-triggered Mg-banding and chamber formation in the planktic foraminifera Neogloboquadrina dutertrei." Nature Communications 8. PNNL-SA-123433. doi:10.1038/ncomms15441
  • Johnson S.P., F. Korhonen, C. Kirkland, J.B. Cliff, E. Belousova, and S. Sheppard. 2017. "An isotopic perspective on growth and differentiation of Proterozoic orogenic crust: from subduction magmatism to cratonization." Lithos 268-271. PNNL-SA-119918. doi:10.1016/j.lithos.2016.11.003
  • McGrail B.P., H.T. Schaef, F.A. Spane, J.A. Horner, A.T. Owen, J.B. Cliff, and O. Qafoku, et al. 2017. "Wallula Basalt Pilot Demonstration Project: Post-Injection Results and Conclusions." Energy Procedia 114. PNNL-SA-121381. doi:10.1016/j.egypro.2017.03.1716
  • Roelofs B., M. Barham, J.B. Cliff, M. Joachimski, L. Martin, and K. Trinajstic. 2017. "Assessing the fidelity of fossil marine microvertebrate d18O signatures and their potential for palaeo-ecological and -climatic reconstructions." Palaeogeography, Palaeoclimatology, Palaeoecology 465, no. A:79-92. PNNL-SA-117637. doi:10.1016/j.palaeo.2016.10.018


  • Cliff J.B., H.W. Kreuzer, C.J. Ehrhardt, and D.S. Wunschel. 2012. Chemical and Physical Signatures for Microbial Forensics. New York, New York:Humana Press. PNNL-SA-62125.


  • Cliff J.B., D.P. Frank, D.C. Gerlach, C.J. Gesh, W.W. Little, B.D. Reid, and G.V. Tsiklauri, et al. 2010. "Independent Verification of Research Reactor Operation (Analysis of the Georgian IRT-M Reactor by the Isotope Ratio Method)." In Proceedings of the 51st Annual Meeting of the Institute of Nuclear Materials Management, July 11-15, 2010, Baltimore, Maryland. Deerfield, Illinois:INMM. PNNL-SA-70908.
  • Gaspar D.J., and J.B. Cliff. 2010. "Secondary Ion Mass Spectrometry of Environmental Aerosols." In Encyclopedia of Mass Spectrometry. 506-514. Oxford:Elsevier. PNNL-SA-66813.


  • Jarman K.H., H.W. Kreuzer-Martin, D.S. Wunschel, N.B. Valentine, J.B. Cliff, C.E. Petersen, and H.A. Colburn, et al. 2008. "Bayesian Integrated Microbial Forensics." Applied and Environmental Microbiology 74, no. 11:3573-3582. PNNL-SA-59675. doi:10.1128/AEM.02526-07


  • Bliss M., D.C. Gerlach, J.B. Cliff, M.B. Toloczko, D.S. Barnett, G. Ciampi, and K.A. Jones, et al. 2007. "Pb Quantification of CdZnTe microheterogeneities complimented by SEM, IR microscopy, EDX, and TOF-SIMS." In Proceedings of the 11th Symposium on Radiation Measurements and Applications, published in Nuclear Instruments and Methods in Physics Research, Part A, 579, 138-140. Amsterdam:Elsevier. PNNL-SA-50517. doi:10.1016/j.nima.2007.04.018
  • Heasler P.G., D.C. Gerlach, J.B. Cliff, and S.L. Petersen. 2007. GUM Analysis for TIMS and SIMS Isotopic Ratios in Graphite. PNNL-17036. Richland, WA: Pacific Northwest National Laboratory. GUM Analysis for TIMS and SIMS Isotopic Ratios in Graphite


  • Cliff J.B., P.J. Bottomley, D.J. Gaspar, and D.D. Myrold. 2006. "Nitrogen Mineralization and Assimilation at Millimeter Scales." Soil Biology and Biochemistry 39, no. 3:823-826. PNNL-SA-48741. doi:10.1016/j.soilbio.2006.10.005
  • Gerlach D.C., J.B. Cliff, D.E. Hurley, B.D. Reid, W.W. Little, G.H. Meriwether, and A.J. Wickham, et al. 2006. "Secondary Ionization Mass Spectrometric Analysis of Impurity Element Isotope Ratios in Nuclear Reactor Materials." In SIMS XV 2005, 15th International Conference on Secondary Ion Mass Spectrometry 12-16 September 2005 Manchester, UK. Published in Applied Surface Science, 252, 7041-7044. Amsterdam:Elsevier Science BV. PNNL-SA-46080.


  • Cliff J.B., K.H. Jarman, N.B. Valentine, S. Golledge, D.J. Gaspar, D.S. Wunschel, and K.L. Wahl. 2005. "Differentiation of Spores of Bacillus Subtilis Grown in Different Media by Elemental Characterization using Time-of-Flight Secondary Ion Mass Spectrometry." Applied and Environmental Microbiology 71, no. 11:6524-6530. PNNL-SA-44084.


  • Cliff J.B., D.J. Gaspar, P.J. Bottomley, and D.D. Myrold. 2004. "Peak Fitting to Resolve CN- isotope Ratios in Biological and Environmental Samples Using TOF-SIMS." In SIMS XIV, proceedings of the fourteenth international conference on secondary ion mass spectrometry and related topics, San Diego, CA, edited by Alfred Benninghoven, 912-916. Amsterdam:Elsevier Science BV. PNNL-SA-39184.
  • Cliff J.B., D.J. Gaspar, P.J. Bottomley, and D.D. Myrold. 2004. "Peak Fitting to Resolve CN-Isotope Ratios in Biological and Environmental Samples using TOF-SIMS." Applied Surface Science 231-232, no. Sp. Iss. SI:912-916. PNNL-SA-42830.


  • Cliff J.B., D.J. Gaspar, P.J. Bottomley, and D.D. Myrold. 2002. "Exploration of Inorganic C and N Assimilation by Soil Microbes with Time-of-Flight Secondary Ion Mass Spectrometry." Applied and Environmental Microbiology 68, no. 8:4067-4073. PNNL-SA-35798.

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