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Fundamental and Computational Sciences Directorate

Staff information

Malak Tfaily

Biogeochemical Transform
Joint Appointment
Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352

PNNL Publications


  • Baalousha M., M. Sikder, B.A. Poulin, M.M. Tfaily, and N.J. Hess. 2022. "Natural organic matter composition and nanomaterial surface coating determine the nature of platinum nanomaterial-natural organic matter corona." Science of the Total Environment 806, no. Part 1:Article No. 150477. PNNL-SA-167226. doi:10.1016/j.scitotenv.2021.150477
  • Colleary C., S. O'Reilly, A. Dolocan, J.G. Toyoda, R.K. Chu, M.M. Tfaily, and M.F. Hochella, et al. 2022. "Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments." Biology 11, no. 9:Art. No. 1304. PNNL-SA-178797. doi:10.3390/biology11091304
  • Dohnalkova A., M.M. Tfaily, R.K. Chu, P. Smith, C.J. Brislawn, T. Varga, and A.R. Crump, et al. 2022. "Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-scale Approach." Frontiers in Earth Science 10. PNNL-SA-167716. doi:10.3389/feart.2022.799694
  • Honeker L.K., G. Hildebrand, J.D. Fudyma, E. Daber, D.W. Hoyt, S.E. Flowers, and J. Gil Loaiza, et al. 2022. "Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques." Environmental Science & Technology 56, no. 3:2021-2032. PNNL-SA-163445. doi:10.1021/acs.est.1c06772
  • Zhao Q., A.M. Thompson, S.J. Callister, M.M. Tfaily, S.L. Bell, S. Hobbie, and K.S. Hofmockel. 2022. "Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils." Science of the Total Environment 806, no. Part 1:Article No. 150514. PNNL-SA-166164. doi:10.1016/j.scitotenv.2021.150514


  • Fudyma J.D., J.G. Toyoda, R.K. Chu, K.K. Weitz, H.M. Heyman, E. Eder, and D.W. Hoyt, et al. 2021. "Sequential abiotic-biotic processes drive organic carbon transformation in peat bogs." Journal of Geophysical Research: Biogeosciences 126, no. 2:e2020JG006079. PNNL-SA-160453. doi:10.1029/2020JG006079
  • Lin Y., A.N. Campbell, A. Bhattacharyya, N. DiDonato, A.M. Thompson, M. Tfaily, and P.S. Nico, et al. 2021. "Differential effects of redox conditions on the decomposition of litter and soil organic matter." Biogeochemistry 154, no. 1:1-15. PNNL-SA-151491. doi:10.1007/s10533-021-00790-y
  • McGivern B.B., M. Tfaily, M. Borton, S. Kosina, R. Daly, C.D. Nicora, and S.O. Purvine, et al. 2021. "Decrypting bacterial polyphenol metabolism in an anoxic wetland soil." Nature Communications 12, no. 1:2466. PNNL-SA-155819. doi:10.1038/s41467-021-22765-1
  • Neurath R., J. Pett-Ridge, I. Jacoby, D. Herman, T. Whitman, P.S. Nico, and A.S. Lipton, et al. 2021. "Root carbon interation with soil minerals is dynamic, leaving a legacy of microbially derived residues." Environmental Science & Technology 55, no. 19:13345-13355. PNNL-SA-158887. doi:10.1021/acs.est.1c00300
  • Raczka N., J. Piņeiro, M. Tfaily, R.K. Chu, M.S. Lipton, L. Pasa-Tolic, and E. Morrissey, et al. 2021. "Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil." Scientific Reports 11. PNNL-SA-159823. doi:10.1038/s41598-021-97942-9
  • Waldo N., M. Tfaily, C.R. Anderton, and R.B. Neumann. 2021. "The Importance of Nutrients for Microbial Priming in a Bog Rhizosphere." Biogeochemistry 152, no. 2-3:271-290. PNNL-SA-159934. doi:10.1007/s10533-021-00754-2


  • Aminitabrizi R., R.M. Wilson, J.D. Fudyma, S. Hodgkins, H.M. Heyman, V. Rich, and S. Saleska, et al. 2020. "Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas Emissions Across a Permafrost Thaw Gradient in Northern Sweden." Frontiers in Earth Science 8. PNNL-SA-156978. doi:10.3389/feart.2020.557961
  • Xu J., S. Roley, M. Tfaily, R.K. Chu, and J.M. Tiedje. 2020. "Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales." Soil Biology and Biochemistry 150. PNNL-SA-155812. doi:10.1016/j.soilbio.2020.107986
  • Zhao Q., S.J. Callister, A.M. Thompson, R.K. Kukkadapu, M. Tfaily, L.M. Bramer, and N. Qafoku, et al. 2020. "Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites." Science of the Total Environment 736. PNNL-SA-144529. doi:10.1016/j.scitotenv.2020.137839


  • Clair G., S.M. Reehl, K.G. Stratton, M.E. Monroe, M. Tfaily, C.K. Ansong, and J.E. Kyle. 2019. "Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data." Bioinformatics 35, no. 21:4507-4508. PNNL-SA-142630. doi:10.1093/bioinformatics/btz250
  • Fudyma J.D., J.E. Lyon, R. Aminitabrizi, H. Gieschen, R.K. Chu, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites." Plant Direct 3, no. 11:Article No. e00179. PNNL-SA-146621. doi:10.1002/pld3.179
  • Garcia Arredondo M., C.R. Lawrence, M.S. Schulz, M.M. Tfaily, R.K. Kukkadapu, M.E. Jones, and K.E. Boye, et al. 2019. "Root-driven weathering impacts on mineral-organic associations in deep soils over pedogenic time scales." Geochimica et Cosmochimica Acta 263. PNNL-SA-137958. doi:10.1016/j.gca.2019.07.030
  • Hopple A.M., L. Pfeifer-Meister, C.A. Zalman, J.K. Keller, M. Tfaily, R.M. Wilson, and J. Chanton, et al. 2019. "Does dissolved organic matter or solid peat fuel anaerobic respiration in peatlands?." Geoderma 349. PNNL-SA-145430. doi:10.1016/j.geoderma.2019.04.040
  • Nunez J., S.M. Colby, D.G. Thomas, M. Tfaily, N. Tolic, E. Ulrich, and J.R. Sobus, et al. 2019. "Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples." Journal of Chemical Information and Modeling 59, no. 9:4052-4060. PNNL-SA-148332. doi:10.1021/acs.jcim.9b00444
  • Rivas-Ubach A., Y. Liu, A.L. Steiner, J. Sardans, M.M. Tfaily, G.R. Kulkarni, and Y. Kim, et al. 2019. "Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research." Environmental Monitoring and Assessment 191, no. 2:Article No. 78. PNNL-SA-118888. doi:10.1007/s10661-019-7205-x
  • Saup C.M., S. Bryant, A.R. Nelson, K.D. Harris, A.H. Sawyer, J.N. Christensen, and M. Tfaily, et al. 2019. "Hyporheic zone microbiome assembly is linked to dynamic water mixing patterns in snowmelt-dominated headwater catchments." Journal of Geophysical Research: Biogeosciences 124, no. 11:3269-3280. PNNL-SA-152884. doi:10.1029/2019JG005189
  • Shen Y., R. Zhao, N. Tolic, M. Tfaily, E.W. Robinson, R.M. Boiteau, and L. Pasa Tolic, et al. 2019. "Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter." Faraday Discussions 218. PNNL-SA-141115. doi:10.1039/C9FD00011A
  • Tfaily M., R.M. Wilson, H.M. Brewer, R.K. Chu, H.M. Heyman, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Single-throughput complementary high-resolution analytical techniques for characterizing complex natural organic matter mixtures." Journal of Visualized Experiments. PNNL-SA-138197. doi:10.3791/59035


  • Bhattacharyya A., A. Campbell, M.M. Tfaily, Y. Lin, R.K. Kukkadapu, W. Silver, and P.S. Nico, et al. 2018. "Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils." Environmental Science & Technology 52, no. 24:14129-14139. PNNL-SA-135734. doi:10.1021/acs.est.8b03408
  • Bottos E.M., D.W. Kennedy, E.B. Romero, S.J. Fansler, J.M. Brown, L.M. Bramer, and R.K. Chu, et al. 2018. "Dispersal Limitation and Thermodynamic Constraints Govern Spatial Structure of Permafrost Microbial Communities." FEMS Microbiology Ecology 94, no. 8:fiy110. PNNL-SA-130968. doi:10.1093/femsec/fiy110
  • Boye K.E., A.M. Herrmann, M.V. Schaefer, M.M. Tfaily, and S. Fendorf. 2018. "Discerning Microbially Mediated Processes During Redox Transitions in Flooded Soils Using Carbon and Energy Balances." Frontiers in Environmental Science 6. PNNL-SA-134588. doi:10.3389/fenvs.2018.00015
  • Graham E.B., A.R. Crump, D.W. Kennedy, E.V. Arntzen, S.J. Fansler, S.O. Purvine, and C.D. Nicora, et al. 2018. "Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone." Science of the Total Environment 642. PNNL-SA-133671. doi:10.1016/j.scitotenv.2018.05.256
  • Orton D.J., M.M. Tfaily, R.J. Moore, B.L. Lamarche, X. Zheng, T.L. Fillmore, and R.K. Chu, et al. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90, no. 1:737-744. PNNL-SA-128111. doi:10.1021/acs.analchem.7b02986
  • Pracht L., M.M. Tfaily, B. Ardissono, and R.B. Neumann. 2018. "Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization." Biogeosciences 15, no. 6:1733-1747. PNNL-SA-133552. doi:10.5194/bg-15-1733-2018
  • Reynolds L.L., K. Lajtha, R.D. Bowden, M.M. Tfaily, B.R. Johnson, and S.D. Bridgham. 2018. "The path from litter to soil: Insights into soil C cycling from long-term input manipulation and high-resolution mass spectrometry." Journal of Geophysical Research: Biogeosciences 123, no. 5:1486-1497. PNNL-SA-121067. doi:10.1002/2017JG004076
  • Tfaily M.M., N.J. Hess, A. Koyama, and R.D. Evans. 2018. "Elevated [CO2] changes soil organic matter composition and substrate diversity in an arid ecosystem." Geoderma 330. PNNL-SA-129666. doi:10.1016/j.geoderma.2018.05.025
  • Tfaily M.M., R.M. Wilson, W.T. Cooper, J.E. Kostka, P.J. Hanson, and J. Chanton. 2018. "Vertical Stratification of Peat Pore Water Dissolved Organic Matter composition in a peat bog in Northern Minnesota." Journal of Geophysical Research: Biogeosciences 123, no. 2:479-494. PNNL-SA-132063. doi:10.1002/2017JG004007
  • Wilson R.M., and M. Tfaily. 2018. "Advanced Molecular Techniques Provide New Rigorous Tools for Characterizing Organic Matter Quality in Complex Systems." Journal of Geophysical Research: Biogeosciences 123, no. 6:1790-1795. PNNL-SA-138120. doi:10.1029/2018JG004525
  • Wilson R.M., and M.M. Tfaily. 2018. "Advanced Molecular Techniques Provide New Rigorous Tools for Characterizing Organic Matter Quality in Complex Systems." Journal of Geophysical Research: Biogeosciences 123, no. 6:1790-1795. PNNL-SA-135802. doi:10.1029/2018JG004525
  • Yao Q., Z. Li, Y. Song, J. Wright, X. Guo, S.G. Tringe, and M.M. Tfaily, et al. 2018. "Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil." Nature Ecology & Evolution 2, no. 3:499-509. PNNL-SA-131384. doi:10.1038/s41559-017-0463-5


  • Bailey V.L., A.P. Smith, M.M. Tfaily, S.J. Fansler, and B. Bond-Lamberty. 2017. "Differences in Soluble Organic Carbon Chemistry in Pore Waters Sampled from Different Pore Size Domains." Soil Biology and Biochemistry 107. PNNL-SA-118268. doi:10.1016/j.soilbio.2016.11.025
  • Boye K.E., V. Noel, M.M. Tfaily, S.E. Bone, K.H. Williams, J. Bargar, and S. Fendorf. 2017. "Thermodynamically controlled preservation of organic carbon in floodplains." Nature Geoscience 10. PNNL-SA-126035. doi:10.1038/NGEO2940
  • Dalcin Martins P., D.W. Hoyt, S. Bansal, C. Mills, M.M. Tfaily, B.A. Tangen, and R.G. Fincchiaro, et al. 2017. "Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands." Global Change Biology 23, no. 8:3107-3120. PNNL-SA-120033. doi:10.1111/gcb.13633
  • Dohnalkova A., M.M. Tfaily, A.P. Smith, R.K. Chu, A.R. Crump, C.J. Brislawn, and T. Varga, et al. 2017. "Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere." Soils 1, no. 1:Article No. 4. PNNL-SA-128886. doi:10.3390/soils1010004
  • Fox P.M., P.S. Nico, M.M. Tfaily, K. Heckman, and J.A. Davis. 2017. "Characterization of Natural Organic Matter in Low-Carbon Environments: Extraction and Analytical Approaches." Organic Geochemistry 114. PNNL-SA-123194. doi:10.1016/j.orggeochem.2017.08.009
  • Graham E.B., J.C. Stegen, A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, and D.W. Kennedy, et al. 2017. "Organic carbon thermodynamics elucidate spatiotemporal mechanisms governing hyporheic zone biogeochemical cycling." In Proceedings of the Subsurface Biogeochemical Research and Terrestrial Ecosystem Science Joint Meeting April 25-26, 2017, Potomac, Maryland. Washington, District Of Columbia:US Department of Energy, Office of Biological and Environmental Research. PNNL-SA-125130.
  • Graham E.B., M.M. Tfaily, A.R. Crump, A.E. Goldman, L.M. Bramer, E.V. Arntzen, and E.B. Romero, et al. 2017. "Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes." Journal of Geophysical Research: Biogeosciences 122, no. 12:3188-3205. PNNL-SA-125144. doi:10.1002/2017JG003967
  • Rue G., N. Rock, R.S. Gabor, J. Pitlick, M.M. Tfaily, and D.M. Mcknight. 2017. "Concentration-discharge relationships during the recession of an extreme flood in the Boulder Creek Watershed: stability of major base cation concentrations contrasts with decreases in concentration and changes in chemical quality of dissolved organic material." Water Resources Research 53, no. 7:5276-5297. PNNL-SA-120916. doi:10.1002/2016WR019708
  • Smith A.P., B. Bond-Lamberty, B.W. Benscoter, M.M. Tfaily, R. Hinkle, C. Liu, and V.L. Bailey. 2017. "Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought." Nature Communications 8. PNNL-SA-121121. doi:10.1038/s41467-017-01320-x
  • Staley C., A.P. Ferrieri, M.M. Tfaily, Y. Cui, R.K. Chu, P. Wang, and J.B. Shaw, et al. 2017. "Diurnal Cycling of Rhizosphere Bacterial Communities is Associated with Shifts in Carbon Metabolism." Microbiome 5. PNNL-SA-121718. doi:10.1186/s40168-017-0287-1
  • Tfaily M.M., R.K. Chu, J.G. Toyoda, N. Tolic, E.W. Robinson, L. Pasa Tolic, and N.J. Hess. 2017. "Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry." Analytica Chimica Acta 972. PNNL-SA-125053. doi:10.1016/j.aca.2017.03.031
  • Tolic N., Y. Liu, A.V. Liyu, Y. Shen, M.M. Tfaily, E.B. Kujawinski, and K. Longnecker, et al. 2017. "Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultra-High Resolution Mass Spectra." Analytical Chemistry 89, no. 23:12659-12665. PNNL-SA-128094. doi:10.1021/acs.analchem.7b03318
  • Truex M.J., B.D. Lee, C.D. Johnson, N. Qafoku, J.E. Szecsody, J.E. Kyle, and M.M. Tfaily, et al. 2017. Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site. PNNL-24709 Rev. 2. Richland, WA: Pacific Northwest National Laboratory. Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site
  • Walker L.R., M.M. Tfaily, J.B. Shaw, N.J. Hess, L. Pasa Tolic, and D.W. Koppenaal. 2017. "Unambiguous Identification & Discovery of Bacterial Siderophores by Direct Injection 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Metallomics 9, no. 1:82-92. PNNL-SA-121375. doi:10.1039/c6mt00201c
  • Wilson R.M., M.M. Tfaily, V. Rich, J.K. Keller, S.D. Bridgham, C. Medvedeff Zalman, and L. Meredith, et al. 2017. "Hydrogenation of Organic Matter as a Terminal Electron Sink Sustains High CO2:CH4 Production Ratios During Anaerobic Decomposition." Organic Geochemistry 112. PNNL-SA-127483. doi:10.1016/j.orggeochem.2017.06.011


  • Hodgkins S., M.M. Tfaily, D.C. Podgorski, C. McCalley, S. Saleska, P.M. Crill, and V. Rich, et al. 2016. "Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland." Geochimica et Cosmochimica Acta 187. PNNL-SA-115139. doi:10.1016/j.gca.2016.05.015
  • Stegen J.C., A.H. Hurlbert, B. Bond-Lamberty, X. Chen, C.G. Anderson, R.K. Chu, and F. Dini-Andreote, et al. 2016. "Aligning the Measurement of Microbial Diversity with Macroecological Theory." Frontiers in Microbiology 7. PNNL-SA-122085. doi:10.3389/fmicb.2016.01487
  • Stegen J.C., J.K. Fredrickson, M.J. Wilkins, A. Konopka, W.C. Nelson, E.V. Arntzen, and W.B. Chrisler, et al. 2016. "Groundwater-Surface Water Mixing Shifts Ecological Assembly Processes and Stimulates Organic Carbon Turnover." Nature Communications 7. PNNL-SA-111962. doi:10.1038/ncomms11237
  • Tolic N., M.M. Tfaily, Y. Shen, R.K. Chu, T.L. Fillmore, R. Zhao, and K.J. Bloodsworth, et al. 2016. "Soil Organic Matter (SOM): Mass Spectrometry Data Analysis." In Encyclopedia of Soil Science, Third Edition, edited by R Lal. Boca Raton, Florida:CRC Press. PNNL-SA-117244. doi:10.1081/E-ESS3-120053757
  • Wilson R.M., A.M. Hopple, M.M. Tfaily, S. Sebestyen, C.W. Schadt, L. Pfeifer-Meister, and C. Medvedeff, et al. 2016. "Stability of a peatland carbon to rising temperatures." Nature Communications 7. PNNL-SA-118747. doi:10.1038/ncomms13723


  • Tfaily M.M., R.K. Chu, N. Tolic, K.M. Roscioli, C.R. Anderton, L. Pasa-Tolic, and E.W. Robinson, et al. 2015. "Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry." Analytical Chemistry 87, no. 10:5206-5215. PNNL-SA-107718. doi:10.1021/acs.analchem.5b00116

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