Analytical Chemist
Analytical Chemist


Dr. John Cliff is an analytical chemist with the Ecosystem Interfaces team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. He leads the nanoscale secondary ion mass spectrometry capability for biology and biogeochemistry. When not helping EMSL users with their research, he 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 learn about the factors controlling greenhouse gas emissions. 

Research Interest

  • Microbial and nuclear forensics and biogeochemistry 

  • Developing capabilities to analyze and understand our world at micron length scales  

  • Collaborating with researchers studying early life on our planet  

  • Understanding sulfur metabolizing microorganisms from the Archean Eon to today 


  • PhD in Soil Science, minor in Environmental Engineering, Oregon State University, 2001 

  • MS in Environmental Microbiology, West Virginia University, 1996  

  • BS in Biology with honors, minor in Chemistry, Shepherd University, 1989 

Awards and Recognitions

  • Technical leader for the first International Atomic Energy Network Laboratory to be housed in a university 

  • Outstanding Achievement Award, Subgroup on Safeguards Technical Support and International Safeguards Project Office (2008) 

  • Outstanding Achievement Award, National Security Division, United States Department of Energy (2005) 



Boiteau, R. M., R. Kukkadapu, J. B. Cliff, C. R. Smallwood, L. Kovarik, M. G. Wirth, M. H. Engelhard, T. Varga, A. Dohnalkova, D. E. Perea, T. Wietsma, J. J. Moran, and K. S. Hofmockel. 2020. “Calcareous Organic Matter Coatings Sequester Siderophores in Alkaline Soils.” Science of the Total Environment 724.

Bone, S. E., J. Cliff, K. Weaver, C. J. Takacs, S. Roycroft, S. Fendorf, and J. R. Bargar. 2020. “Complexation by Organic Matter Controls Uranium Mobility in Anoxic Sediments.” Environmental Science and Technology 54 (3): 1493-1502.

Reilly, D. D., C. L. Beck, E. C. Buck, J. B. Cliff, A. M. Duffin, T. G. Lach, M. Liezers, K. W. Springer, S. J. Tedrow, and M. M. Zimmer. 2020. “Focused Ion Beam for Improved Spatially-Resolved Mass Spectrometry and Analysis of Radioactive Materials for Uranium Isotopic Analysis.” Talanta 211.


Brislawn, C. J., E. B. Graham, K. Dana, P. Ihardt, S. J. Fansler, W. B. Chrisler, J. B. Cliff, J. C. Stegen, J. J. Moran, and H. C. Bernstein. 2019. “Forfeiting the Priority Effect: Turnover Defines Biofilm Community Succession.” ISME Journal 13 (7): 1865-1877.

Gregory, D., I. Mukherjee, S. L. Olson, R. R. Large, L. V. Danyushevsky, A. S. Stepanov, J. N. Avila, J. Cliff, T. R. Ireland, R. Raiswell, P. H. Olin, V. V. Maslennikov, and T. W. Lyons. 2019. “The Formation Mechanisms of Sedimentary Pyrite Nodules Determined by Trace Element and Sulfur Isotope Microanalysis.” Geochimica et Cosmochimica Acta 259: 53-68.

Mulcahy, J. R., S. He, D. S. Jin, W. Guo, S. Arteta, J. B. Cliff, Z. Zhu, and W. D. Wei. 2019. “Experimental Insights into the Growth of Single Truncated Anatase Bipyramids.” Chemistry - A European Journal 25 (4): 993-996.

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 (8): 2429-2440.

Vasdekis, A. E., H. Alanazi, A. M. Silverman, C. J. Williams, A. J. Canul, J. B. Cliff, A. C. Dohnalkova, and G. Stephanopoulos. 2019. “Eliciting the Impacts of Cellular Noise on Metabolic Trade-Offs by Quantitative Mass Imaging.” Nature Communications 10 (1).


China, S., S. M. Burrows, B. Wang, T. H. Harder, J. Weis, M. Tanarhte, L. V. Rizzo, J. Brito, G. G. Cirino, P. L. Ma, J. Cliff, P. Artaxo, M. K. Gilles, and A. Laskin. 2018. “Fungal Spores as a Source of Sodium Salt Particles in the Amazon Basin.” Nature Communications 9 (1).

Doubleday, Z. A., J. Cliff, C. Izzo, and B. M. Gillanders. 2018. “Untapping the Potential of Sulfur Isotope Analysis in Biominerals.” Marine Ecology Progress Series 598: 159-166.

LeTourneau, M. K., M. J. Marshall, J. B. Cliff, R. F. Bonsall, A. C. Dohnalkova, D. V. Mavrodi, S. I. Devi, O. V. Mavrodi, J. B. Harsh, D. M. Weller, and L. S. Thomashow. 2018. “Phenazine-1-Carboxylic Acid and Soil Moisture Influence Biofilm Development and Turnover of Rhizobacterial Biomass on Wheat Root Surfaces.” Environmental Microbiology 20 (6): 2178-2194.

Nuñez, J., R. Renslow, J. B. Cliff, and C. R. Anderton. 2018. “NanoSIMS for Biological Applications: Current Practices and Analyses.” Biointerphases 13 (3).

Proetto, M. T., C. E. Callmann, J. Cliff, C. J. Szymanski, D. Hu, S. B. Howell, J. E. Evans, G. Orr, and N. C. Gianneschi. 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 (11): 1477-1484.


Bone, S. E., J. J. Dynes, J. Cliff, and J. R. Bargar. 2017. “Uranium(Iv) Adsorption by Natural Organic Matter in Anoxic Sediments.” Proceedings of the National Academy of Sciences of the United States of America 114 (4): 711-716.

Fehrenbacher, J. S., A. D. Russell, C. V. Davis, A. C. Gagnon, H. J. Spero, J. B. Cliff, Z. Zhu, and P. Martin. 2017. “Link between Light-Triggered Mg-Banding and Chamber Formation in the Planktic Foraminifera Neogloboquadrina dutertrei.” Nature Communications 8.

Holmes, A. J., Y. V. Chew, F. Colakoglu, J. B. Cliff, E. Klaassens, M. N. Read, S. M. Solon-Biet, A. C. McMahon, V. C. Cogger, K. Ruohonen, D. Raubenheimer, D. G. Le Couteur, and S. J. Simpson. 2017. “Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints.” Cell Metabolism 25 (1): 140-151.

Johnson, S. P., F. J. Korhonen, C. L. Kirkland, J. B. Cliff, E. A. Belousova, and S. Sheppard. 2017. “An Isotopic Perspective on Growth and Differentiation of Proterozoic Orogenic Crust: From Subduction Magmatism to Cratonization.” Lithos 268-271: 76-86.

McGrail, B. P., H. T. Schaef, F. A. Spane, J. B. Cliff, O. Qafoku, J. A. Horner, C. J. Thompson, A. T. Owen, and C. E. Sullivan. 2017. “Field Validation of Supercritical CO2 Reactivity with Basalts.” Environmental Science and Technology Letters 4 (1): 6-10.

Roelofs, B., M. Barham, J. Cliff, M. Joachimski, L. Martin, and K. Trinajstic. 2017. “Assessing the Fidelity of Marine Vertebrate Microfossil δ18O Signatures and Their Potential for Palaeo-Ecological and -Climatic Reconstructions.” Palaeogeography, Palaeoclimatology, Palaeoecology 465: 79-92.

Spetsius, Z. V., J. Cliff, W. L. Griffin, and S. Y. O'Reilly. 2017. “Carbon Isotopes of Eclogite-Hosted Diamonds from the Nyurbinskaya Kimberlite Pipe, Yakutia: The Metasomatic Origin of Diamonds.” Chemical Geology 455: 131-147.


Fougerouse, D., S. Micklethwaite, A. Halfpenny, S. M. Reddy, J. B. Cliff, L. A. J. Martin, M. Kilburn, P. Guagliardo, and S. Ulrich. 2016. “The Golden Ark: Arsenopyrite Crystal Plasticity and the Retention of Gold through High Strain and Metamorphism.” Terra Nova 28 (3): 181-187.


Kaiser, C., M. R. Kilburn, P. L. Clode, L. Fuchslueger, M. Koranda, J. B. Cliff, Z. M. Solaiman, and D. V. Murphy. 2015. “Exploring the Transfer of Recent Plant Photosynthates to Soil Microbes: Mycorrhizal Pathway vs Direct Root Exudation.” New Phytologist 205 (4): 1537-1551.

Ribeiro, Y., R. C. Figueiredo e Silva, L. M. Lobato, L. C. Lima, F. J. Rios, S. G. Hagemann, and J. Cliff. 2015. “Fluid Inclusion and Sulfur and Oxygen Isotope Studies on Quartz-Carbonate-Sulfide Veins of the Carvoaria Velha Deposit, Córrego Do Sítio Gold Lineament, Quadrilátero Ferrífero, Minas Gerais, Brazil.” Ore Geology Reviews 67: 11-33.

Smithies, R. H., C. L. Kirkland, J. B. Cliff, H. M. Howard, and R. Quentin de Gromard. 2015. “Syn-Volcanic Cannibalisation of Juvenile Felsic Crust: Superimposed Giant 18O-Depleted Rhyolite Systems in the Hot and Thinned Crust of Mesoproterozoic Central Australia.” Earth and Planetary Science Letters 424: 15-25.

Van Kranendonk, M. J., C. L. Kirkland, and J. Cliff. 2015. “Oxygen Isotopes in Pilbara Craton Zircons Support a Global Increase in Crustal Recycling at 3.2ga.” Lithos 228-229: 90-98.

Wacey, D., M. R. Kilburn, M. Saunders, J. B. Cliff, C. Kong, A. G. Liu, J. J. Matthews, and M. D. Brasier. 2015. “Uncovering Framboidal Pyrite Biogenicity Using Nano-Scale CNorg Mapping.” Geology 43 (1): 27-30.

Wacey, D., N. Noffke, J. Cliff, M. E. Barley, and J. Farquhar. 2015. “Micro-Scale Quadruple Sulfur Isotope Analysis of Pyrite from the ~3480ma Dresser Formation: New Insights into Sulfur Cycling on the Early Earth.” Precambrian Research 258: 24-35.

Yang, J., F. Meng, X. Xu, P. T. Robinson, Y. Dilek, A. B. Makeyev, R. Wirth, M. Wiedenbeck, and J. Cliff. 2015. “Diamonds, Native Elements and Metal Alloys from Chromitites of the Ray-Iz Ophiolite of the Polar Urals.” Gondwana Research 27 (2): 459-485.


Bougoure, J., M. Ludwig, M. Brundrett, J. Cliff, P. Clode, M. Kilburn, and P. Grierson. 2014. “High-Resolution Secondary Ion Mass Spectrometry Analysis of Carbon Dynamics in Mycorrhizas Formed by an Obligately Myco-Heterotrophic Orchid.” Plant, Cell and Environment 37 (5): 1223-1230.

Chew, Y. V., A. J. Holmes, and J. B. Cliff. 2014. “Visualization of Metabolic Properties of Bacterial Cells Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS).” Methods in Molecular Biology 1096: 133-146. 

Evans, K. A., A. G. Tomkins, J. Cliff, and M. L. Fiorentini. 2014. “Insights into Subduction Zone Sulfur Recycling from Isotopic Analysis of Eclogite-Hosted Sulfides.” Chemical Geology 365: 1-19.

Fu, B., J. Cliff, and R. E. Zartman. 2014. “Zircon Oxygen Isotopic Constraints from Plutonic Rocks on the Magmatic and Crustal Evolution of the Northern Appalachians in Southern New England, USA.” Canadian Journal of Earth Sciences 51 (5): 485-499.

Giacometti, F., K. A. Evans, G. Rebay, J. Cliff, A. G. Tomkins, P. Rossetti, G. Vaggelli, and D. T. Adams. 2014. “Sulfur Isotope Evolution in Sulfide Ores from Western Alps: Assessing the Influence of Subduction-Related Metamorphism.” Geochemistry, Geophysics, Geosystems 15 (10): 3808-3829.

Ingham, E. S., N. J. Cook, J. Cliff, C. L. Ciobanu, and A. Huddleston. 2014. “A Combined Chemical, Isotopic and Microstructural Study of Pyrite from Roll-Front Uranium Deposits, Lake Eyre Basin, South Australia.” Geochimica et Cosmochimica Acta 125: 440-465.

Martyniuk, M., D. Baldwin, R. Jeffery, K. K. M. B. D. Silva, R. C. Woodward, J. Cliff, R. N. Krishnan, J. M. Dell, and L. Faraone. 2014. “Characterization of Mechanical, Optical and Structural Properties of Bismuth Oxide Thin Films as a Write-Once Medium for Blue Laser Recording.” Journal of British Studies 1633 (3).

Wacey, D., M. Saunders, J. Cliff, M. R. Kilburn, C. Kong, M. E. Barley, and M. D. Brasier. 2014. “Geochemistry and Nano-Structure of a Putative ~3240 Million-Year-Old Black Smoker Biota, Sulphur Springs Group, Western Australia.” Precambrian Research 249: 1-12.

Zhelezinskaia, I., A. J. Kaufman, J. Farquhar, and J. Cliff. 2014. “Large Sulfur Isotope Fractionations Associated with Neoarchean Microbial Sulfate Reduction.” Science 346 (6210): 742-744.


Ceh, J., M. R. Kilburn, J. B. Cliff, J. B. Raina, M. Van Keulen, and D. G. Bourne. 2013. “Nutrient Cycling in Early Coral Life Stages: Pocillopora damicornis Larvae Provide Their Algal Symbiont (Symbiodinium) with Nitrogen Acquired from Bacterial Associates.” Ecology and Evolution 3 (8): 2393-2400.

Farquhar, J., J. Cliff, A. L. Zerkle, A. Kamyshny, S. W. Poulton, M. Claire, D. Adams, and B. Harms. 2013. “Pathways for Neoarchean Pyrite Formation Constrained by Mass-Independent Sulfur Isotopes.” Proceedings of the National Academy of Sciences of the United States of America 110 (44): 17638-17643.

Fu, B., N. T. Kita, S. A. Wilde, X. Liu, J. Cliff, and A. Greig. 2013. “Origin of the Tongbai-Dabie-Sulu Neoproterozoic Low-δ 18O Igneous Province, East-Central China.” Contributions to Mineralogy and Petrology 165 (4): 641-662.

Huang, J. X., W. L. Griffin, Y. Gréau, N. J. Pearson, S. Y. O'Reilly, J. Cliff, and L. Martin. 2013. “Unmasking Xenolithic Eclogites: Progressive Metasomatism of a Key Roberts Victor Sample.” Chemical Geology 364: 56-65.

Kirkland, C. L., S. P. Johnson, R. H. Smithies, J. A. Hollis, M. T. D. Wingate, I. M. Tyler, A. H. Hickman, J. B. Cliff, S. Tessalina, E. A. Belousova, and R. C. Murphy. 2013. “Not-So-Suspect Terrane: Constraints on the Crustal Evolution of the Rudall Province.” Precambrian Research 235: 131-149.

Kirkland, C. L., R. H. Smithies, A. J. Woodhouse, H. M. Howard, M. T. D. Wingate, E. A. Belousova, J. B. Cliff, R. C. Murphy, and C. V. Spaggiari. 2013. “Constraints and Deception in the Isotopic Record; the Crustal Evolution of the West Musgrave Province, Central Australia.” Gondwana Research 23 (2): 759-781.

Lu, Y. J., R. Kerrich, A. I. S. Kemp, T. C. McCuaig, Z. Q. Hou, C. J. R. Hart, Z. X. Li, P. A. Cawood, L. Bagas, Z. M. Yang, J. Cliff, E. A. Belousova, F. Jourdan, and N. J. Evans. 2013. “Intracontinental Eocene-Oligocene Porphyry Cu Mineral Systems of Yunnan, Western Yangtze Craton, China: Compositional Characteristics, Sources, and Implications for Continental Collision Metallogeny.” Economic Geology 108 (7): 1541-1576.

Lu, Y. J., R. Kerrich, T. C. McCuaig, Z. X. Li, C. J. R. Hart, P. A. Cawood, Z. Q. Hou, L. Bagas, J. Cliff, E. A. Belousova, and S. H. Tang. 2013. “Geochemical, Sr-Nd-Pb, and Zircon Hf-O Isotopic Compositions of Eocene-Oligocene Shoshonitic and Potassic Adakite-Like Felsic Intrusions in Western Yunnan, SW China: Petrogenesis and Tectonic Implications.” Journal of Petrology 54 (7): 1309-1348.

Peres, P., P. M. L. Hedberg, S. Walton, N. Montgomery, J. B. Cliff, F. Rabemananjara, and M. Schuhmacher. 2013. “Nuclear Safeguards Applications Using LG-SIMS with Automated Screening Capabilities.” Surface and Interface Analysis 45 (1): 561-565.

Pidgeon, R. T., A. A. Nemchin, and J. Cliff. 2013. “Interaction of Weathering Solutions with Oxygen and U-Pb Isotopic Systems of Radiation-Damaged Zircon from an Archean Granite, Darling Range Batholith, Western Australia.” Contributions to Mineralogy and Petrology 166 (2): 511-523.

Raimondo, T., C. Clark, M. Hand, J. Cliff, and R. Anczkiewicz. 2013. “A Simple Mechanism for Mid-Crustal Shear Zones to Record Surface-Derived Fluid Signatures.” Geology 41 (6): 711-714.

Wacey, D., N. McLoughlin, M. R. Kilburn, M. Saunders, J. B. Cliff, C. Kong, M. E. Barley, and M. D. Brasier. 2013. “Nanoscale Analysis of Pyritized Microfossils Reveals Differential Heterotrophic Consumption in the ̃1.9-Ga Gunflint Chert.” Proceedings of the National Academy of Sciences of the United States of America 110 (20): 8020-8024.


Fu, B., B. Paul, J. Cliff, M. Bröcker, and F. Bulle. 2012. “O-Hf Isotope Constraints on the Origin of Zircon in High-Pressure Mélange Blocks and Associated Matrix Rocks from Tinos and Syros, Greece.” European Journal of Mineralogy 24 (2): 277-287.

Raimondo, T., C. Clark, M. Hand, J. Cliff, and C. Harris. 2012. “High-Resolution Geochemical Record of Fluid-Rock Interaction in a Mid-Crustal Shear Zone: A Comparative Study of Major Element and Oxygen Isotope Transport in Garnet.” Journal of Metamorphic Geology 30 (3): 255-280.


Hedberg, P. M. L., P. Peres, J. B. Cliff, F. Rabemananjara, S. Littmann, H. Thiele, C. Vincent, and N. Albert. 2011. “Improved Particle Location and Isotopic Screening Measurements of Sub-Micron Sized Particles by Secondary Ion Mass Spectrometry.” Journal of Analytical Atomic Spectrometry 26 (2): 406-413.

Wacey, D., M. R. Kilburn, M. Saunders, J. Cliff, and M. D. Brasier. 2011. “Microfossils of Sulphur-Metabolizing Cells in 3.4-Billion-Year-Old Rocks of Western Australia.” Nature Geoscience 4 (10): 698-702.

Wedlock, L. E., M. R. Kilburn, J. B. Cliff, L. Filgueira, M. Saunders, and S. J. Berners-Price. 2011. “Visualising Gold inside Tumour Cells Following Treatment with an Antitumour Gold(I) Complex.” Metallomics 3 (9): 917-925.


Kilburn, M. R., D. L. Jones, P. L. Clode, J. B. Cliff, E. A. Stockdale, A. M. Herrmann, and D. V. Murphy. 2010. “Application of Nanoscale Secondary Ion Mass Spectrometry to Plant Cell Research.” Plant Signaling and Behavior 5 (6): 760-762.

Williams, D. E., M. R. Kilburn, J. Cliff, and G. I. N. Waterhouse. 2010. “Composition Changes around Sulphide Inclusions in Stainless Steels, and Implications for the Initiation of Pitting Corrosion.” Corrosion Science 52 (11): 3702-3716.


Clode, P. L., M. R. Kilburn, D. L. Jones, E. A. Stockdale, J. B. Cliff, A. M. Herrmann, and D. V. Murphy. 2009. “In Situ Mapping of Nutrient Uptake in the Rhizosphere Using Nanoscale Secondary Ion Mass Spectrometry.” Plant Physiology 151 (4): 1751-1757.


Donohue, D., A. Ciurapinski, J. Cliff Iii, F. Rüdenauer, T. Kuno, and J. Poths. 2008. “Microscopic Studies of Spherical Particles for Nuclear Safeguards.” Applied Surface Science 255 (5 PART 2): 2561-2568.

Jarman, K. H., H. W. Kreuzer-Martin, D. S. Wunschel, N. B. Valentine, J. B. Cliff, C. E. Petersen, H. A. Colburn, and K. L. Wahl. 2008. “Bayesian-Integrated Microbial Forensics.” Applied and Environmental Microbiology 74 (11): 3573-3582.


Bliss, M., D. C. Gerlach, J. B. Cliff, M. B. Toloczko, D. S. Barnett, G. Ciampi, K. A. Jones, and K. G. Lynn. 2007. “Pb Quantification of CdZnTe Microheterogeneities Complimented by SEM, IR microscopy, EDX, and TOF-SIMS.” Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 579 (1): 138-140.

Cliff, J. B., P. J. Bottomley, D. J. Gaspar, and D. D. Myrold. 2007. “Nitrogen Mineralization and Assimilation at Millimeter Scales.” Soil Biology and Biochemistry 39 (3): 823-826.


Gerlach, D. C., J. B. Cliff, D. E. Hurley, B. D. Reid, W. W. Little, G. H. Meriwether, A. J. Wickham, and T. A. Simmons. 2006. “Secondary Ionization Mass Spectrometric Analysis of Impurity Element Isotope Ratios in Nuclear Reactor Materials.” Applied Surface Science 252 (19): 7041-7044.


Cliff, J. B., K. H. Jarman, N. B. Valentine, S. L. 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 (11): 6524-6530.


“Peak Fitting to Resolve CN- Isotope Ratios in Biological and Environmental Samples Using TOF-SIMS.” Applied Surface Science 231-232: 912-916.


“Erratum: Modeling the Effects of Diffusion Limitations on Nitrogen-15 Isotope Dilution Experiments with Soil Aggregates (Soil Science Society of America Journal (2002) 66 (1868-1877).” Soil Science Society of America Journal 67 (2): 677.


Cliff, J. B., P. J. Bottomley, R. Haggerty, and D. D. Myrold. 2002. “Modeling the Effects of Diffusion Limitations on Nitrogen-15 Isotope Dilution Experiments with Soil Aggregates.” Soil Science Society of America Journal 66 (6): 1868-1877.

Cliff, J. B., D. J. Gaspar, P. J. Bottomley, and D. D. Myrold. 2002. “Exploration of Inorganic C and N Assimilation by Soil Soil Microbes with Time-of-Flight Secondary Ion Mass Spectrometry.” Applied and environmental microbiology 68 (8): 4067-4073.