Lawrence Livermore National Laboratory



Jennifer Pett-Ridge

Deputy Lead for the Isotopic Signatures Group
Nuclear and Chemical Sciences Division


 +1 925-424-2882


DegreeDiscipline/InstitutionYear
Hopkins Microbiology Course
Stanford University
2007
Ph.D. Soil Microbial Ecology
University of California at Berkeley
2005
M.S. Forest Science
Yale School of Forestry & Environmental Studies
1996
B.A. Biology
Studies in Environment, Yale University
1994

Research Interests

Jennifer Pett-Ridge's research uses the tools of systems biology and biogeochemistry to link identity and function in microbial communities that are relevant to DOE's Office of Biological and Environmental Research. Recently awarded a DOE Early Career award to work on responses of tropical soils to climate change, she has pioneered the use of NanoSIMS isotopic imaging in microbial biology and soils research. As Lead Scientist of LLNL's Genomic Science Biofuels Scientific Focus Area (SFA), she is responsible for a multi-disciplinary team that integrates biogeochemistry, stable isotope probing, NanoSIMS imaging, molecular microbial ecology and computational modeling to understand biotic interactions and energy flow in microbial communities critical to nutrient cycling and biofuel production. She is Deputy Lead for the Isotopic Signatures group, and supervises a group of staff scientists, postdocs and graduate students working on terrestrial and marine carbon cycling, plant-soil interactions and development of new isotope tracing methods (El-FISH, Chip-SIP, STXM-SIMS). She has published over 35 peer-review articles and has a patent ROI for the "ChipSIP" approach linking microbial identity and function using NanoSIMS analysis of microarrays.

Awards

2014DOE Early Career Fellowship
2014Elected to EMSL User Executive Committee
2013AGU, Best Talk
2009International Society for Microbial Ecology, Journal Cover Contest
2007AEM Gordon Research Conference, Best Poster
2000-2004Graduate Fellowship, DOE Global Change Education Program, UC Berkeley

Publications

Shi, S., D.J. Herman, Z. He, J. Pett-Ridge, L. Wu, J. Zhou, and M.K. Firestone. Plant roots alter microbial functional capacity to mediate soil organic carbon decomposition. ISME Journal, in review.

Stuart, R.K., X. Mayali, J.Z. Lee, R.C. Everroad, M. Hwang, B. Bebout, P.K. Weber, J. Pett-Ridge, and M.P. Thelen. Cyanobacterial recycling of the extracellular matrix in microbial mats. ISME Journal, in review.

S. Shi, E. Nuccio, D.J. Herman, R. Rijkers, U.N. da Rocha, Z. He, J. Zhou, J. Pett-Ridge, E. Brodie, and M.K. Firestone. Succession of a soil microbiome associated with the common annual grass Avena fatua. mBio, in review.

Keiluweit, M., J.J. Bougoure, J. Pett-Ridge, P.K. Weber, P.S. Nico, M. Kleber. 2015. Root exudates counteract mineral control on soil carbon turnover. Nature Climate Change, DOI: 10.1038/NCLIMATE2580.

Hong-Hermesdorf, A.* M. Miethke,* S.D. Gallaher, J. Kropat, S.C. Dodani, D. Barupala, J. Chan, D.W. Domaille, D.I. Shirasaki, J.A. Loo, P.K. Weber, J. Pett-Ridge, T.L. Stemmler, C. J. Chang & Sabeeha S Merchant*. (2014) Selective sub-cellular visualization of trace metals identifies dynamic sites of Cu accumulation in Chlamydomonas. Nature Chemical Biology, 10: 1034–1042 *equal contrib.

Woebken, D., L.C. Burow, X. Mayali, E.D. Fleming, L. Prufert-Bebout, S.W. Singer, A.López Cortés, T.M. Hoehler, Je. Pett-Ridge, A.M. Spormann, P.K. Weber, B.M. Bebout. (2014) A functional single-cell approach to the N2 fixation activity in coastal microbial mats from Guerrero Negro, Mexico. ISME Journal 9: 485–496.

Lee, J.Z., L. Burow, D. Woebken, R.C. Everroad, M.D. Kubo, A. Spormann, P.K. Weber, J. Pett-Ridge, B.M. Bebout, T.M. Hoehler. (2014) Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats. Frontiers Microbial Physiology and Metabolism. 5:61. doi: 10.3389/fmicb.2014.00061.

Mayali, X., P.K. Weber, S. Mabery, J. Pett-Ridge. (2014) Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay. PlosOne, 9(4):e95842.

Burow, L.C., D. Woebken, B. M. Bebout, I.P.G. Marshall, S.W. Singer, J. Pett-Ridge, L. Prufert-Bebout, A.M. Spormann, P. K. Weber and T.M. Hoehler. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiology, 12: 221-230.

Ceja-Navarro, J.A.*, N.H. Nguyen*, U. Karaoz, S. R Gross, D.J. Herman, G.L Andersen, T.D. Bruns, J. Pett-Ridge, M. Blackwell, E.L Brodie. (2014) Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. ISME Journal 8:6-18. *equal contribution.

K.J. Carpenter, P.K. Weber, J. Pett-Ridge, M.L. Davisson, M.I. Haverty, P.J. Keeling (2013) Correlated SEM, FIB-SEM, TEM, and NanoSIMS imaging of microbes from the hindgut of a lower termite: Methods for in-situ functional and ecological studies of uncultivable microbes. Microscopy and Microanalysis 19: 1490-1501.

Everroad, R.C.*, D. Woebken*, S.W. Singer, L.C. Burow, N. Kyrpides, T. Woyke, L. Goodwin, A. Detweiler, L. Prufert-Bebout, J. Pett-Ridge. (2013) Draft genome sequence of the cyanobacterium ESFC-1. Genome Announcements 4:e00527-13 *equal contribution

Pett-Ridge, J., D. G. Petersen, E. Nuccio and M. K. Firestone. (2013), Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil. FEMS Microb. Ecology. 85:179-194.

Mueller, C.W., P. K. Weber, M. R. Kilburn, C. Hoeschen, M. Kleber and J. Pett-Ridge. (2013) Advances in the Analysis of Biogeochemical Interfaces: NanoSIMS to Investigate Soil Microenvironments. Advances in Agronomy, Ed. D. Sparks, Vol 121, ISBN: 978-0-12-407685-3.

Nuccio E., A. Hodge, J. Pett-Ridge, D.J. Herman, P.K. Weber, M.K. Firestone. (2013) An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition. Environmental Microbiology 15:1870-81. Cover Image.

Mayali X, Weber P. K., Pett-Ridge J. (2013) Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. FEMS Microb. Ecology 83:402-412.

Burow, L.C.*, D. Woebken*, I.P.G. Marshall, E.A. Lindquist, B.M. Bebout, L. Prufert-Bebout, T.M. Hoehler, S.G. Tringe, J. Pett-Ridge, P.K. Weber, A.M. Spormann, S.W. Singer. (2013). Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS. *equal contribution, ISME Journal 7: 817-29. Top 10 most downloaded.

Keiluweit, M., J.J. Bougoure, L. Zeglin, D. Myrold, P. Weber, M. Kleber, P. Nico, J. Pett-Ridge. (2012) Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon. Geochim. et Cosmochim. Acta 95:213-226.

Jiao Y., A. Navid, B.J. Stewart, J.B. McKinlay, M. Thelen and J. Pett-Ridge. (2012). Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production. International Journal of Hydrogen Energy 37: 11719–11726.

Treseder, K. K. , T. C. Balser, M. A. Bradford, E. L. Brodie, E. A. Dubinsky, V. T. Eviner, K. S. Hofmockel, J. T. Lennon, U. Y. Levine, B. J. MacGregor, J. Pett-Ridge, and M. P. Waldrop. (2012). Integrating microbial ecology into ecosystem models: Challenges and priorities. Biogeochemistry 109: 7-18.

Woebken, D., L. Prufert-Bebout, L. Burow, B. Bebout, T. Hoehler, J. Pett-Ridge, A. M. Spormann, P.K. Weber, S.W. Singer. (2012). Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS. ISME Journal 6: 1427-1439. Top 10 most downloaded.

Mayali, X., P.K. Weber, E.L. Brodie, S. Mabery, P. D. Hoeprich, J. Pett-Ridge. (2012). High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME Journal 6: 1210-1221.

Pett-Ridge, J. and P. Weber. (2012) "NanoSIP: NanoSIMS applications for microbial biology", Microbial Systems Biology: Methods and Protocols. (Ali Navid, ed.), Methods in Molecular biology series, Vol. 881. Humana press. Cover Image.

Burow, L.C., D. Woebken, B. M. Bebout, P. J. McMurdie, S.W. Singer, J.Pett-Ridge, L.Prufert-Bebout, A.M. Spormann, P. K. Weber and T.M. Hoehler. (2012). Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME Journal, 6, 863–874.

Wolfe-Simon, F., J.S.Blum, T.R. Kulp, G. W. Gordon, S.E. Hoeft, J. Pett-Ridge, J.F. Stolz, S.M. Webb, P. K. Weber, P.C.W. Davies, A. D. Anbar and R.S. Oremland (2011). Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus" Science 332:1149.

Wolfe-Simon, F., J.S.Blum, T.R. Kulp, G. W. Gordon, S.E. Hoeft, J. Pett-Ridge, J.F. Stolz, S.M. Webb, P. K. Weber, P.C.W. Davies, A. D. Anbar and R.S. Oremland (2011). A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-6.

Myrold, D.D., J. Pett-Ridge, and P.J. Bottomley. (2011). Nitrogen mineralization and assimilation at millimeter scales. p. 91-114. Research on Nitrification and Related Processes, Part B (M.G. Klotz and L.Y. Stein, eds.) Methods in Enzymology, Vol. 496. Elsevier, Inc., Academic Press, Burlington.

Pett-Ridge, J., Hoeprich, P., Brodie, E., and Weber, P. (2011). PATENT #US20110195862. "Devices, Methods and Systems for Target Detection", US Patent and Trademark Office, Lawrence Livermore National Security, USA.

Finzi, J.A.*, J. Pett-Ridge*, P. Weber, R. Popa, S. J. Fallon, T. Gunderson, I. Hutcheon, K.Nealson, D.G. Capone. (2009). Fixation and fate of carbon and nitrogen in Trichodesmium IMS101 using nanometer resolution secondary ion mass spectrometry (NanoSIMS). *equal contribution. PNAS 106: 6345-6350

Templer, P.H., W. Silver, J. Pett-Ridge, K. DeAngelis and M.K. Firestone. (2008). Plant and microbial controls on nitrogen retention and loss in a humid tropical forest. Ecology, 89:3030-3040. (cover photograph).

Behrens, S.*, T. Loesekann*, J. Pett-Ridge, P.K. Weber, J. W.-O. Ng, B.S. Stevenson, I.D. Hutcheon, D.A. Relman, A.M. Spormann. (2008). Linking phylogeny with metabolic activity of single microbial cells using FISH-NanoSIMS. Applied and Environmental Biology, 74:3143-3150. *equal contribution.

Popa, R., P. Weber, J. Finzi, S. Fallon, J. Pett-Ridge, I.D. Hutcheon, K.H. Nealson and D.G. Capone. (2007). Carbon and nitrogen fixation and mobilization in and between individual cells of Anabaena oscillarioides. ISME Journal, 1: 354-360.

Herrmann, A.M., K. Ritz, N. Nunan, P.L. Clode, J. Pett-Ridge, M.R. Kilburn, D.V. Murphy, A.G. O'Donnell, E.A. Stockdale. (2007). Nano-scale secondary ion mass spectrometry - A new analytical tool in biogeochemistry and soil ecology. Soil Biology and Biochemistry, 39: 1835-1850. (cover photograph).

Pardo, L., H. Hemond, J. Montoya and J. Pett-Ridge. (2007). Natural abundance of 15N in soil and litter across a nitrate-output gradient in New Hampshire. Forest Ecology and Management, 251: 217-230.

Pett-Ridge, J., W. Silver and M.K. Firestone. (2006). Redox fluctuations in a humid tropical forest soil impact N-cycling rates by framing the composition of the soil microbial community. Biogeochemistry, 81: 95-110.

Pett-Ridge, J. (2006). Probing Sub-cellular Bacterial Metabolism with Isotopic Tracers. Chemistry and Materials Science Directorate Annual Report, LLNL, CA.

Pett-Ridge, J. (2005). Rapidly Fluctuating Redox Regimes Frame the Ecology of Microbial Communities and Their Biogeochemical Function in a Humid Tropical Soil. Ph.D. Thesis. University of California, Berkeley.

Pett-Ridge J., and M. K. Firestone. (2005). Redox fluctuation structures microbial communities in a wet tropical soil. Applied and Environmental Microbiology 71: 6998-7007.

Pardo, L. H., C. Kendall, J. Pett-Ridge, and C. C. Y. Chang. (2004). Evaluating the source of streamwater nitrate using δ15N and δ18O in nitrate in two N.H. watersheds. Hydrologic Processes. 18: 2699-2712.

Pett-Ridge, J., and W. Silver. (2002). Survival, growth, and ecosystem dynamics of displaced bromeliads in a montane tropical forest. Biotropica 32: 211-224.

Synergistic Activities

  1. Invited Workshops: Radcliffe Institute "Peering into the Lives of Microbes" (March, 2015); co-chair DOE-OBER Sustainable Biofuel Plant Research (Oct, 2013); NGEE Tropics workshop (2012, 2014); DOE OBER Genomics:GtL "C cycling and Biosequestration" (2008); NSF Microscale Approaches to Macroscale Issues in Ecology" (2007).
  2. Session convener: "Drought Effects in Tropical Forests" Society for Tropical Ecology, Zurich, 2015; "Exploring Microbial Mat Communities: Functions, Interaction, and Signatures" AGU, San Francisco (2014); "Small-Talk: Mapping the Geochemistry of Microbe-Mineral Interactions and Microbe-Microbe Elemental Trafficking" Goldschmidt Conference, Sacramento CA (2014); "Surface Microscopy and Microanalysis in Materials and Biological Systems", Microscopy and Microanalysis Meeting, Portland OR (2010); "Linking microbial identity and activity with NanoSIMS", International Society of Microbial Ecology Meeting, Cairns, Australia (2008).
  3. Positions: Environmental Microbiology editorial board (2015-); ISME Ambassador (2014-); EMSL User Executive Committee (2013-); AEM Editorial Board (2012-); Review Editor for Frontiers in Terrestrial Microbiology (2010-); Associate Editor for Frontiers in Microbiological Chemistry (2011-); LLNL Lawrence Fellow committee (20012-2014); LLNL PLS AD hiring committee (2013); Vice Chair, Soil Ecology Section, Ecological Society of America (2006-2009).
  4. Invited Reviewer: NSF Ecosystems Panel (2014); LLNL Lawrence Fellowship Committee (2012-pres.); DOE Terrestrial Ecosystem Science Review Panel (2013); USDA-NIFA review panel (2013); DOE OBER Early Career Program, Microbial Environmental Processes Panel (2011) and (2012); Joint Genome Institute Community Sequencing Program review panel (April 2012, July 2012, July 2013, Jan 2014); Earth science expert for NSF advisory board for SRI Teacher Professional Continuum program (2005-2006); Yale University Alumni Schools Committee (2003-pres); UK BBSRC, NSF Ecosystems and Microbial Observatories programs; Ad hoc reviewer for AEM, Biogeochemistry, Ecology, Ecosystems, Env.Microbiology, Env. Science and Technology, Ecosphere, Ecosystems, Ecological Bulletin, ISME Journal, Nature Chemical Biology, New Phytologist, Organic Geochemistry, PLOS ONE, Soil Biol. and Biochemistry, Oecologia.

Graduate/Postdoctoral Advisors: Whendee Silver (UC Berkeley, M.S.), Mary Firestone (UC Berkeley, PhD), Ian Hutcheon (LLNL, Postdoc).

Postdoctoral Advisees: Xavier Mayali (2009-2012), Dagmar Woebken (@ NASA Ames, 2008-2011), Luke Burow (@ NASA Ames, 2008-2012), Kevin Carpenter (2009-2012), Jeremy Bougoure (2010-2012), Amy Englebrecht (2011-2013), Anne Dekas (2012-pres.), Erin Nuccio (2013-pres.), Steve Blazewicz (2014-pres.), Ashley Campbell (starting July 2015--).

PhD students: Co-Advisor: Marco Keiluweit (Oregon State University, 2010-2013), Rachel Neurath (UC Berkeley, 2013-pres).


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