Jennifer Pett-Ridge

Portrait of Jennifer Pett-Ridge

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  • Title
    Group Leader, Environmental Isotope Systems
  • Email
    pettridge2@llnl.gov
  • Phone
    (925) 424-2882
  • Organization
    Not Available

Research Interests

Jennifer Pett-Ridge is a senior staff scientist and group leader at LLNL who uses the tools of systems biology and biogeochemistry to link, identity, and function in environmental microbial communities. Recently awarded a DOE Early Career award to work on responses of tropical soil microbes to climate change, she has also pioneered the use of NanoSIMS isotopic imaging in the fields of microbial biology and soil biogeochemistry. As lead scientist of the LLNL Genomic Science Biofuels Scientific Focus Area (SFA) from 2009–2018 and more recently the LLNL Soil Microbiome SFA (2018-present), she helps to coordinate multi-disciplinary teams that integrate biogeochemistry, stable isotope probing, NanoSIMS imaging, molecular microbial ecology, and computational modeling to understand biotic interactions and energy flow in microbial communities critical to soil nutrient cycling and sustainable biofuel production. She is the group lead for the Environmental Isotope Systems group in the Nuclear and Chemical Sciences division and manages a portfolio of over $25 million in DOE, NSF, NASA, and other funding. She helps to mentor a group of staff scientists, postdocs, and graduate students working on terrestrial and marine carbon cycling, plant-soil interactions, and development of novel isotope tracing methods (El-FISH, Chip-SIP, STXM-SIMS) and collaborates frequently with scientists at academic institutions and other national labs. Pett-Ridge has published over 110 peer-review articles, including a patent ROI for the "ChipSIP" approach linking microbial identity and function using NanoSIMS analysis of microarrays.

Background

  • 2018-present, Adjunct Full Professor, Life & Environmental Sciences Dept., UC Merced
  • 2020-present, Senior Editor, ISME Communications
  • 2018, Visiting Scholar, University of San Francisco de Quito, Ecuador (sabbatical leave)
  • 2017-present, Group Leader, Environmental Isotope Systems Group, LLNL
  • 2018–2020, Associate Editor, Soil Systems
  • 2018–present, Subject Editor, Soil Biology & Biochemistry
  • 2017–present, Carbon Uptake Pillar Lead, LLNL 'Carbon Initiative'
  • 2017–present, Group Leader, Environmental Isotope Systems Group
  • 2017–present, Science Lead, DOE Genomic Sciences Soil Microbiome SFA
  • 2016–present, Guest appointment, UC Berkeley, Environmental Science Policy and Management Dept.
  • 2015–present, Senior staff scientist, LLNL
  • 2015–present, Editorial Board, BMC Microbiology
  • 2015–present, Editorial Board, Environmental Microbiology
  • 2014–present, ISME Ambassador
  • 2013–2017, EMSL User Executive Committee
  • 2012–2018, Adjunct Faculty, Crop and Soil Science, Oregon State University
  • 2012–present, Editorial Board, Applied and Environmental Microbiology
  • 2011–present, Associate Editor, Frontiers in Microbiological Chemistry
  • 2011–present, Guest Scientist, Lawrence Berkeley National Lab
  • 2010–2017, Deputy Group Leader, Isotopic Signatures Group, Livermore, CA
  • 2010–present, Review Editor for Frontiers in Terrestrial Microbiology
  • 2009–2018, Science Lead, DOE Genomic Sciences Biofuels SFA
  • 2009–present, Career Staff Scientist, Lawrence Livermore National Laboratory
  • 2007, Stanford University, Hopkins Microbiology Course
  • 2006–2009, Vice Chair, Soil Ecology Section, Ecological Society of America
  • 2005–2008, Postdoctoral Fellow, Lawrence Livermore National Lab
  • 2000–2004, Graduate Fellow, DOE Global Change Education Program, UC Berkeley
  • 2000, University of Utah, Salt Lake City, UT, Stable Isotope Ecology summer course

Mentions in Popular Press

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

Sokol, N.W., Slessarev, E., Marschmann, G., Nicolas, A., Blazewicz, S., Brodie, E, Firestone, M., Foley, M., Hungate, B., Hestrin, R., Koch, B. Stone, B., Sullivan, M., Zablocki, O., Pett-Ridge, J. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. (in review)

Craig R. See, Adrienne B. Keller, Sarah E. Hobbie, Peter G. Kennedy, Jennifer Pett-Ridge. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. (in review)

Bhattacharyya, A., A. N. Campbell, Y. Lin, P. K. Weber, W. L. Silver, P. S. Nico and J. Pett-Ridge. Redox sensitivity to and soil organic matter decomposition and organomineral associations in a humid tropical forest soil. (in review)

Sieradzki, E.T., E. Nuccio, J. Pett-Ridge, M. Firestone. Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass. bioRxiv https://doi.org/10.1101/2020.12.14.422732 (in review)

Lee, J., R. Hestrin, E.E. Nuccio, K.D. Morrison, C.E. Ramon, J. Pett-Ridge, S.S. Ly, T.A. Laurence, P.K. Weber. Label-free multiphoton imaging of microbes in root, mineral and soil matrices in optically opaque samples with time-gated coherent Raman and fluorescence lifetime imaging. (in review)

Bolduc, B., O. Zablocki, J. Guo, A.A. Zayed, D. Vik, P. Dehal, E.M. Wood-Charlson, A. Arkin, N. Merchant, J. Pett-Ridge, S. Roux, M. Vaughn, M.B. Sullivan. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. (in review)

Stone, B., S. Blazewicz, B. Koch, P. Dijkstra, M. Hayer, X.-J. A. Liu, R. Mau, J. Pett-Ridge, E. Schwartz, B. Hungate. Nutrients strengthen density dependence of per-capita growth and mortality rates across all major phyla of soil bacteria. (in review)

Li, J., B.W. Stone, P. Dijkstra, B. J. Koch, E. M Morrissey, S. Blazewicz, K. Hofmockel, X.-J. A. Liu, R.L. Mau, M. Hayer, J. Pett-Ridge, E. Schwartz and B.A. Hungate. Divergent microbial traits in regulating plant and microbial cell wall residue degradation. (in response to review)

Bhattacharyya, A., Kukkadapu, R.K., M.E. Bowden, J. Pett-Ridge, P.S. Nico. Incongruent removal of Al and Fe from Fe(III)- oxides is responsible for crystallinity changes in humid tropical soils. Soil Science Society of America Journal (in response to review)

McDaniel, M.D., J.A. Bird, J. Pett-Ridge, E. Marin-Spiotta, T.M. Schmidt, A.S. Grandy. Past agroecosystem diversity subtly alters retention of new carbon and nitrogen from crop residue. Ecological Applications (in response to review)

Fossum, C., K. Estera-Molina, M. Yuan, D. Herman, I. Chu-Jacoby, P. Nico, K. Morrison, J. Pett-Ridge, M. Firestone. Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil. bioRxiv https://biorxiv.org/cgi/content/short/2021.08.23.457405v1 (in response to review)

Kakouridis, A., J.A. Hagen, M.P. Kan, S. Mambelli, L. J. Feldman, D. J. Herman, J. Pett-Ridge, and M. K. Firestone. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants and identification of a hyphal transport pathway. bioRxiv https://doi.org/10.1101/2020.09.21.305409 (in response to review)

Button, E., D.R. Chadwick, D.V. Murphy, Y. Kuzyakov, J. Pett-Ridge, D.L. Jones. Deep-C storage: A critical evaluation of physical, chemical and biological strategies to enhance carbon stocks in agricultural subsoils. (in response to review)

Parada, A.E., X. Mayali, P.K. Weber, J. Wollard, A. Santoro, J.A. Fuhrman, J. Pett-Ridge and A.E. Dekas. Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota. (in response to review)

Slessarev, E.W., O.A. Chadwick, N. Sokol, E.E. Nuccio, J. Pett-Ridge. Weathering creates hotspots in soil carbon storage at a continental scale. Biogeochemistry Letters (in press)

Nuccio, E.E., N. Nguyen, U. Nunes da Rocha, J. Bougoure, P. Weber, E. Brodie, M.K. Firestone, J.Pett-Ridge. Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil. bioRxiv https://doi.org/10.1101/2021.01.12.426429. ISME Comms (in press)

Purcell, A.M., M. Hayer, B.J. Koch, R.L. Mau, S.J. Blazewicz, P. Dijkstra, M. C. Mack, J. C. Marks, E. M. Morrissey, J. Pett-Ridge, R. L. Rubin, E. Schwartz, N. C. van Gestel, and B. A. Hungate. Decreased growth of wild soil microbes after fifteen years of warming in a montane meadow. Global Change Biology (in press)

ter Horst, A.M., C. Santos-Medellín, J.W. Sorensen, L.A. Zinke, R.M. Wilson, E.R. Johnston, G.G. Trubl, J. Pett-Ridge, S.J. Blazewicz, P.J. Hanson, J.P. Chanton, C.W. Schadt, J.E. Kostka, J.B. Emerson. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. bioRxiv doi.org/10.1101/2020.12.15.422944 Microbiome (In press)

Trubl, G., J. A. Kimbrel1, J. Liquet-Gonzalez, E.E. Nuccio, P.K. Weber, J. Pett-Ridge, J.K. Jansson, M.P. Waldrop, S.J. Blazewicz. Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics. bioRxiv https://doi.org/10.1101/2021.01.25.428156. Microbiome (in press)

Neurath, R.A., Whitman, T., Chu-Jacoby, I.X., Thompson, A.M., Lipton, A., Tfaily, M.; Kyle, J., Bloodsworth, Kent J., Herman, D. J., Nico, P.S., Pett-Ridge, J., Firestone, M.K. 2021 Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues. ES&T. https://doi.org/10.1021/acs.est.1c00300

Waring, B., C. Averill, C. Creamer, D. Cusack, S.J. Hall, A. Jilling, K.M. Kemner, M. Kleber, X. Lin, J. Pett-Ridge, S.C. Reed, M. Schultz, A.P. Smith, and B. Sulman. 2021. Response to 'Connectivity and pore accessibility in models of soil carbon cycling.' Global Change Biology https://doi.org/10.1111/gcb.15850

Oerter, E., E. Slessarev, A. Visser, K. Min, M. Kan, K.J McFarlane, M. Saha, A.A. Berhe, J. Pett-Ridge, E. Nuccio. Hydraulic redistribution by deeply rooted grasses and its ecohydrologic implications in the Southern Great Plains of North America. Hydrological Processes https://doi.org/10.1002/hyp.14366

Starr, E.P., S. Shi, S.J. Blazewicz, B.J. Koch, A.J. Probst, B.A. Hungate, J. Pett-Ridge, M.K. Firestone*, J.F. Banfield*. Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil. mSystems https://journals.asm.org/doi/10.1128/mSphere.00085-21

Min, K., E. Slessarev, M. Kan, K. McFarlane, E. Oerter, J. Pett-Ridge, E. Nuccio, A.A Berhe. Soil depth gradients in microbial growth kinetics under deeply- vs. shallow-rooted plants. Soil Biology and Biochemistry 162: 108401 https://doi.org/10.1016/j.soilbio.2021.108401

Waring, B., C. Averill, C. Creamer, D. Cusack, S.J. Hall, A. Jilling, K.M. Kemner, M. Kleber, X. Lin, J. Pett-Ridge, S.C. Reed, M. Schultz, A.P. Smith, and B. Sulman. 2021. Response to 'Stochastic and deterministic interpretation of pool models.' Global Change Biology https://doi.org/10.1111/gcb.15580

Hestrin, R., P.K. Weber, J. Pett-Ridge, J. Lehmann. 2021. Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport. New Phytologist 231: 1746-1757 https://doi.org/10.1111/nph.17527.

Hungate, B.A., J.C. Marks, M.E. Power, E. Schwartz, K.J. van Groenigen, S.J. Blazewicz, P. Chuckran, P. Dijkstra, B.K. Finley, M.K. Firestone, M. Foley, A. Greenlon, K. Hofmockel, B.J. Koch, M.C. Mack, R.L. Mau, S.N. Miller, E.M. Morrissey, J.R. Propster, A.M. Purcell, E.P. Starr, B.W. Stone, C. Terrer, J. Pett-Ridge. The functional significance of bacterial predators in soil. mBio 12:e00466-21. https://doi.org/10.1128/mBio.00466-21

Zhalnina, K., C. Hawkes, A. Shade, M.K. Firestone, J. Pett-Ridge. 2021. Managing microbiomes for sustainable biofuel production. Phytobiomes 5:3-13 https://doi.org/10.1094/PBIOMES-12-20-0090-E.

Ceja-Navarro, J. A., Y. Wang, D. Ning, A. Arellano, L. Ramanculova, M. Yuan, A. Byer, K. Craven, M. Saha, E.L. Brodie, J. Pett-Ridge, M.K. Firestone. 2021. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome 9: 96 doi.org/10.1186/s40168-021-01042-9

Lin, Y., A. N. Campbell, A. Bhattacharyya, N. DiDonato, A. M. Thompson, M. M. Tfaily, P. S. Nico, W. L. Silver, and J. Pett-Ridge. Differential effects of redox conditions on the decomposition of litter and soil organic matter. Biogeochemistry Letters 154: 1-15 https://doi.org/10.1007/s10533-021-00790-y

Yuan, M.M., A. Kakouridis, E. Starr, N. Nguyen, S. Shi, J. Pett-Ridge, E. Nuccio, J. Banfield, J. Zhou, M. Firestone. 2021. Fungal-bacterial co-occurrence patterns differ between arbuscular mycorrhizal fungi and non-mycorrhizal fungi across soil niches. mBio 12: e03509-20. https://doi.org/10.1128/mBio.03509-20.

Zablocki, O., M. Michelsen, M. Burris, N. Solonenko, J. Warwick-Dugdale, R. Ghosh, J. Pett-Ridge, M.B. Sullivan, and B. Temperton. 2020. VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature. PeerJ 9: e11088 https://doi.org/10.7717/peerj.11088

Wang, C., R.L. Mau, M. Hayer, J. Piniero Nevado, M. Mack, J.C. Marks, S.L. Bell, S.N. Miller, E. Schwartz, P. Dijkstra, B.J. Koch, B.W. Stone, A.M. Purcell, S.J. Blazewicz, K. Hofmockel, J. Pett-Ridge, B.A. Hungate, and E.M. Morrissey. 2021. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME Journal https://doi.org/10.1038/s41396-021-00959-1

Stone, B.W., J. Li, B. J Koch, S. Blazewicz, P. Dijkstra, M. Hayer, K.S. Hofmockel, Xiao-Jun Allen Liu, R.L Mau, E. Morrissey, J. Pett-Ridge, E. Schwartz, B.A. Hungate. Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community. 2021. Nature Communications 12: 3381 https://doi.org/10.1038/s41467-021-23676-x

Bates, C., A. Escalas, J. Kuang, Jialiang, L. Hale, Y. Wang, D. Herman, E. Nuccio, X. Wang, Y. Fu, R. Tian, G. Wang, D. Ning, Y. Yang, L. Wu, J. Pett-Ridge, M. Saha, K. Craven, M. Firestone, J. Zhou. 2021. Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumption. ISME Journal https://doi.org/10.1038/s41396-021-00916-y

Lin, Y., A. N. Campbell, A. Bhattacharyya, N. DiDonato, A. M. Thompson, M. M. Tfaily, P. S. Nico, W. L. Silver, and J. Pett-Ridge. Differential effects of redox conditions on the decomposition of litter and soil organic matter. Biogeochemistry Letters 154: 1-15 https://doi.org/10.1007/s10533-021-00790-y

Terrer, C., R.P. Phillips, B.A. Hungate, J. Rosende, J. Pett-Ridge, M. Craig, K.J. van Groenigen, T.F. Keenan, B.N. Sulman, B.D. Stocker, P.B. Reich, A. F.A. Pellegrini, E. Pendall, H. Zhang, R.D. Evans, Y. Carrillo, J. B. Fisher, R.B. Jackson. A trade-off between plant and soil carbon storage under elevated CO2. 2021. Nature 591: 599–603. doi.org/10.1038/s41586-021-03306-8

Pett-Ridge, J. and P. Weber. NanoSIP: NanoSIMS applications for microbial biology, Microbial Systems Biology: Methods and Protocols, Second Edition. (Ali Navid, ed.), Methods in Molecular Biology pp. 91-136 https://doi.org/10.1007/978-1-0716-1585-0

Waring, B., C. Averill, C. Creamer, D. Cusack, S.J. Hall, A. Jilling, K.M. Kemner, M. Kleber, X. Lin, J. Pett-Ridge, S.C. Reed, M. Schultz, A.P. Smith, and B. Sulman. 2020. From pools to flow: the PROMISE framework provides new insights on soil carbon cycling in a changing world. Global Change Biology 26: 6631-6643 https://doi.org/10.1111/gcb.15365

Nayfach et al. 2021. A Genomic Catalogue of Earth's Microbiomes, (as part of IMG/M Data Consortium) Resource to Nature Biotechnology 39: 499–509 https://doi.org/10.1038/s41587-020-0718-6

Dove, N.C., K. Arogyaswamy, S.A. Billings, J.K. Bothoff, C.J. Carey, C. Cisco, J.L. DeForest, D. Fairbanks, N. Fierer, R.E. Gallery, J.P. Kaye, K.A. Lohse, M.R. Maltz, E. Mayora, J. Pett-Ridge, W.H. Yang, S.C. Hart, E.L. Aronson. 2020. Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity. Environmental Research Letters 15: 1040a1 https://doi.org/10.1088/1748-9326/abb0b3

Hestrin, R. M.R. Lee, B.K. Whitaker, J. Pett-Ridge. The switchgrass microbiome: A review of structure, function, and taxonomic distribution. Phytobiomes 231: 1746-1757 https://doi.org/10.1111/nph.17527

Pett-Ridge, J., J. Shi, K. Estera-Molina, E.E. Nuccio, M. Yuan, R. Rijkers, T. Swenson, K. Zhalnina, T. Northen, J. Zhou, M.K. Firestone. 2020. Rhizosphere carbon turnover from cradle to grave: the role of microbe-plant interactions, in Rhizosphere Biology: Interactions with plants, V. Gupta & A.K. Sharma, Eds. Springer Nature Press.

Aigle, A., Gubry-Rangin, C., Thion, C., Estera, K., Richmond, H., Pett-Ridge, J., Firestone, M., Nicol, G., Prosser, J.. Experimental testing of hypotheses for temperature- and pH-based niche specialisation of ammonia oxidising archaea and bacteria. Environmental Microbiology and Environmental Microbiology Reports 22: 4032-4045 https://doi.org/10.1111/1462-2920.15192

Slessarev, E.W., E.E. Nuccio, K.J. McFarlane, C. Ramon, M. Saha, M.K. Firestone, J. Pett-Ridge. 2020. Quantifying subsoil organic C accumulation under switchgrass (Panicum virgatum) across a soil texture gradient using natural abundance 14C. Global Change Biology Bioenergy 12: 834-847 https://doi.org/10.1111/gcbb.12729

Sieradzki, E. T., B.J. Koch, A. Greenlon, R. Sachdeva, R.R. Malmstrom, R.L. Mau, S.J. Blazewicz, M.K. Firestone, K. Hofmockel, E. Schwartz, B.A. Hungate, J. Pett-Ridge. Measurement error and resolution in quantitative stable 1 isotope probing: implications for experimental design, mSystems 5:e00151-20. https://doi.org/10.1128/mSystems.00151-20

Sher, Y., N. R. Baker, D.J. Herman, C. Fossum, L. Hale, X.-X. Zhang, E. E. Nuccio, M. C. Saha, J. Zhou, J. Pett-Ridge, M. K. Firestone. 2020. Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential. Soil Biology & Biochemistry 143: 107742 doi.org/10.1016/j.soilbio.2020.107742

Blazewicz, S.J., E.E. Nuccio, B.J. Koch, B.A. Hungate, E. Morrissey, E.L. Brodie, E. Schwartz, J. Pett-Ridge, M.K. Firestone. Taxon-specific growth and mortality rates of bacteria in soil following the rewetting of a seasonally dried grassland. ISME Journal doi.org/10.1038/s41396-020-0617-3

Starr, E.P., E.E. Nuccio, J. Pett-Ridge, J.F. Banfield* and M.K. Firestone*. 2019. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in the rhizosphere, detritosphere and bulk soil. PNAS doi.org/10.1073/pnas.1908291116

Nuccio, E.E., E. Starr, U. Karaoz, E.L. Brodie, J. Zhou, S. Tringe, R.R. Malmstrom, T. Woyke, J. Banfield, M.K. Firestone and J. Pett-Ridge. 2020. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME Journal doi.org/10.1038/s41396-019-0582-x

Dekas, A.E., A. Parada, X. Mayali, J.A. Fuhrman, J. Wollard, P. Weber, J. Pett-Ridge. Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope nanoSIP. 2019. Frontiers in Microbiology doi.org/10.3389/fmicb.2019.02682

Tsednee, M., M. Castruita, P. A. Salomé, A. Sharma, B. Elizabeth Lewis, S. R. Schmollinger, D. Strenkert, K. Holbrook, M.S. Otegui, K. Khatua, S. Das, A. Datta, S. Chen, C. Ramon, M. Ralle, P. K. Weber, T. L. Stemmler, J. Pett-Ridge, B. M. Hoffman and S. S. Merchant. 2019. Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions. Journal of Biological Chemistry 294: 17626-17641. doi/10.1074/jbc.RA119.009130.

Gross, A.#, Y. Lin#, P.K. Weber, J. Pett-Ridge, and W. L. Silver. 2019. The role of soil redox conditions in microbial phosphorus cycling in humid tropical forests. Ecology 101: e02928 https://doi.org/10.1002/ecy.2928 #co-first authors

Brewer, T.E., E. Aronson, K. Arogyaswamy, S.A. Billings, J.K. Bothoff, A.N. Campbell, N.C. Dove, D. Fairbanks, R.E. Gallery, S.C. Hart, J. Kaye, G. King, K.A. Lohse, M.R. Maltz, C. O'Neill, S.M. Owens, A. Packman, J. Pett-Ridge, A.F. Plante, D.D. Richter, W.L. Silver, W.H. Yang, N. Fierer. 2019. Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons. mBio 10: mBio01318-19

Sevim, V., J. Lee, R. Egan, A. Clum, H. Tice, J. Lee, R.C. Everroad, A.M. Detweiler, B.M. Bebout, J. Pett-Ridge, M. Göker, A. Murray, S.R. Lindemann, H.-P. Klenk, R. O'Malley, M. Zane, J.-F. Cheng, A. Copeland, C. Daum, E. Singer, and T. Woyke. 2019. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Scientific Data 6:285 doi.org/10.1038/s41597-019-0287-z

Mayali, X. P. K. Weber, E. Nuccio, J. Lietard, M. Somoza, S. J. Blazewicz, and J. Pett-Ridge (2019) Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS. In Marc G. Dumont and Marcela Hernández García (eds.), Stable Isotope Probing: Methods and Protocols, Methods in Molecular Biology, vol. 2046 https://doi.org/10.1007/978-1-4939-9721-3_6

Morrissey, E.M. R.L. Mau, M. Hayer, X.J.A. Liu, E. Schwartz, P. Dijkstra, B.J. Koch, K. Allen, S.J. Blazewicz, K. Hofmockel, J. Pett-Ridge, B.A. Hungate. 2019. Evolutionary history constrains microbial traits across environmental variation. Nature Ecology and Evolution 3: 1064–1069 doi.org/10.1038/s41559-019-0918-y

Navid, A., Jiao, Y., Wong, S.E. and J. Pett-Ridge. 2019. System-level analysis of metabolic trade-offs during anaerobic phototrophic growth in Rhodopseudomonas palustris. BMC Bioinformatics 20:233 doi.org/10.1186/s12859-019-2844-z

Li, J., R.L. Mau, P. Dijkstra, B.J. Koch, E. Schwartz, A.M. Purcell, Xi. Liu, E.M. Morrissey, S.J. Blazewicz, J. Pett-Ridge, B.W. Stone, M. Hayer, B.A. Hungate. 2019. Predictive genomic traits for bacterial growth in culture versus actual growth in soil. ISME Journal (Nature) doi: 10.1038/s41396-019-0422-z

Zengler, K., K. Hofmockel, N.S. Baliga, S.W. Behie, H.C. Bernstein, J.B. Brown, J.R. Dinneny, S.A. Floge, S.P. Forry, M.Hess, S.A. Jackson, C. Jansson, S.R. Lindemann, J. Pett-Ridge, C. Maranas, E.A. Shank, O.S. Venturelli, M.D. Wallenstein, and T.R. Northen. 2019. EcoFAB: Advancing microbiome science through standardized fabricated ecosystems. Nature Methods 16: 567–571

Ceja-Navarro, J., U. Karaoz, M. Bill, Z. Hao, R.A. White III, A. Arellano, L. Ramanculova, T.R. Filley, T. Berry, M.E. Conrad, M. Blackwell, C.D. Nicora, Y.M. Kim, P.N. Reardon, M.S. Lipton, J.N. Adkins, J. Pett-Ridge, and E.L. Brodie. 2019. Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle. Nature Microbiology 4: 864–875

Gross, A., J. Pett-Ridge and W. L. Silver. 2018. Soil oxygen limits microbial phosphorus utilization in humid tropical forest soils, Soil Systems 2:65 doi:10.3390/soilsystems2040065

Bhattacharyya, A., A.N. Campbell, M.M. Tfaily, Y. Lin, R.K. Kukkadapu, W.L. Silver, P.S. Nico, J. Pett-Ridge. (2018) Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils. Environmental Science & Technology, 52: 14129-14139. doi/10.1021/acs.est.8b03408

Shi, S., D.J. Herman, Z. He, J. Pett-Ridge, L. Wu, J. Zhou and M.K. Firestone. (2018) Plant roots alter microbial functional genes supporting root litter decomposition. Soil Biology and Biochemistry 127: 90-99 doi.org/10.1016/j.soilbio.2018.09.013

Lin, L., A. Bhattacharyya, A. N. Campbell, P. S. Nico, J. Pett-Ridge#, and W. L. Silver#. (2018) Phosphorus fractionation responds to dynamic redox conditions in a humid rainforest soil. JGR-Biogeosciences 123: 3016-3027 doi.org/10.1029/2018JG004420 #co-corresponding authors

Whitman, T., R. Neurath, A. Perera, D. Ning, J. Zhou, P. Nico, J. Pett-Ridge, M. Firestone. (2018) Microbial community assembly differs across minerals in a rhizosphere microcosm. Environmental Microbiology 20:4444-4460. doi.org/10.1111/1462-2920.14366

Lee, J.Z., R.C. Everroad, U. Karaoz, A.M. Detweiler, J. Pett-Ridge, P.K. Weber, L. Prufert-Bebout, B.M. Bebout. (2018) Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PlosOne 13: e0202792. https://doi.org/10.1371/journal.pone.0202792

Samo T.J., J.A. Kimbrel, D.J. Nilson, J. Pett-Ridge, P.K. Weber, X. Mayali. (2018) Attachment between heterotrophic bacteria and microalgae influences mutualistic microscale interactions. Environmental Microbiology 20: 4385-4400. https://doi.org/10.1111/1462-2920.14357

Pett-Ridge, J. 2018. Mary K. Firestone: Groundbreaking Journey of a Microbial Matriarch. Women in Microbiology Ed. Rachel J. Whitaker, Hazel A. Barton, ASM Press. doi:10.1128/9781555819545.ch31.

Ackerman, C.; P. Weber, T. Xiao, B. Thai, T. Kuo, E. Zhang, J. Pett-Ridge, C. Chang. 2018. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 10: 474-485.

Koch, B.J., T.A. McHugh, M. Hayer, E. Schwartz, S.J. Blazewicz, P. Dijkstra, N. van Gestel, J.C. Marks, R.L. Mau, E.M. Morrissey, J. Pett-Ridge, B.A. Hungate. 2018. Estimating taxon-specific population dynamics in intact microbial communities. Ecosphere doi: 10.1002/ecs2.2090.

Souza, I. F., L.F.J. Almeida, G.L. Jesus, J. Pett-Ridge, P.S. Nico, M. Kleber, I.R. Silva. 2017. Carbon sink strength of subsurface horizons in Brazilian Oxisols. Soil Science Society of America Journal doi:10.2136/sssaj2017.05.0143.

D'haeseleer, P.*, J.Z. Lee*, , R.C. Everroad, L. Prufert-Bebout, L.C. Burow, A. Detweiler , P.K. Weber , U. Karaoz, E.L. Brodie, S. Tringe, T. Glavina del Rio, B. Bebout, J. Pett-Ridge. 2017. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Standards in Genomic Sciences doi: 10.1186/s40793-017-0279-6.

Lee, J.Z., R.C. Everroad, U. Karaoz, A.M. Detweiler, J. Pett-Ridge, P.K. Weber, L. Prufert-Bebout, B.M. Bebout. 2017. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PlosOne 13: e0202792. https://doi.org/10.1371/journal.pone.0202792

Bryson, S., Z. Li, F. Chavez, P. K. Weber, J. Pett-Ridge, R.L. Hettich, C. Pan, X. Mayali, R. S. Mueller. 2017. Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME Journal, doi: 10.1038/ismej.2017.128.

Warren, M., X. Lin, J. Gaby, C. Kretz, P. Morton, J. Pett-Ridge, D. Weston, C. Schadt, J. Kostka, and J. Glass. 2017. Diazotrophy in a Sphagnum-dominated peat bog. Applied and Environmental Microbiology doi: 10.1128/AEM.01174-1.

Pett-Ridge, J. and M. K. Firestone. (2017) Using stable isotopes to explore root-microbe-mineral interactions in soil. Rhizosphere 3: 244-253.

Stuart, R. X. Mayali, M. P. Thelen, J. Pett-Ridge and P.K. Weber. 2017. Measuring cyanobacterial metabolism in biofilms with NanoSIMS isotope imaging and scanning electron microscopy (SEM). Bio-protocol 7:e2263. doi: 10.21769/BioProtoc.2263.

Musat, N., F. Musat, P.K. Weber, and J. Pett-Ridge (2016) Tracking microbial interactions with NanoSIMS. Current Opinion in Biotechnology, 41: 114-121. doi.org/10.1016/j.copbio.2016.06.007.

Everroad, R.C., R. K Stuart, B.M Bebout, A. M Detweiler, J. Z Lee, D. Woebken, L. Prufert-Bebout, J. Pett-Ridge. (2016) Permanent draft genome of strain ESFC-1: Ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. Standards in Genomic Sciences 11: 53. doi: 10.1186/s40793-016-0174-6.

Stuart, R. K., X. Mayali, A. Boaro, M. Lipton, J. Z. Lee, R. C. Everroad, B. M. Bebout, P. K. Weber, J. Pett-Ridge, and M. P. Thelen. (2016) Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm. mBio vol. 7: e00650-16. doi: 10.1128/mBio.00650-16.

Bryson, S., Z. Li, J. Pett-Ridge, R. Hettich, X. Mayali, C. Pan, and R.Mueller. (2016) Proteomic-based stable isotope probing reveals taxonomically distinct patterns in amino acid assimilation by coastal marine bacterioplankton. mSystems, 1: e00027-15 doi: 10.1128/mSystems.00027-15.

Nuccio, E.E., J. Anderson-Furgeson, K. Y. Estera, J. Pett-Ridge, P. de Valpine, E. L. Brodie, M. K. Firestone. (2016) Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass. Ecology, 97: 1307-1318.

Moyes, A.B., L. M. Kueppers, J. Pett-Ridge, D. Carper, N. Vandehey, J. O'Neil, A. C. Frank. (2016). Evidence for foliar endophytic nitrogen-fixation in a widely distributed subalpine conifer. New Phytologist, 210:657-668.

Eloe-Fadrosh, E. A., D. Paez-Espino, J. Jarett, P. F. Dunfield, B. P. Hedlund, A. E. Dekas, S. E. Grasby, A. L. Brady, H. Dong, B. R. Briggs, W.Li, D. Goudeau, R. Malmstrom, A. Pati, J. Pett-Ridge, E. M. Rubin, T. Woyke, N. C. Kyrpides, N. N. Ivanova. (2016). Global metagenomic survey reveals taxonomic "blind spots" in geothermal springs. Nature Communications, 7: 10476.

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. (2015) Cyanobacterial reuse of extracellular organic carbon in microbial mats. ISME Journal (Nature), 10:1240-1251.

Keiluweit, M. S. Nico, M. Harmon, J. Mao, J. Pett-Ridge, and M. Kleber. (2015) Long-term litter decomposition controlled by manganese redox cycling, Proceedings of the National Academy of Sciences, 112: E5253–E5260.

Shi, S., E. Nuccio, D.J. Herman, R. Rijkers, U.N. da Rocha, Z. He, J. Zhou, J. Pett-Ridge, E. Brodie, and M.K. Firestone. (2015) Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 01/2015; 6(4). doi: 10.1128/mBio.00746-15.

Mueller, R.S., S. Bryson, B. Kieft, Z. Li, J. Pett-Ridge, F. Chavez, R. L Hettich, C. Pan, X. Mayali. (2015) Metagenome sequencing of a coastal marine microbial community from Monterey Bay, California. Genome Announcements 3(2): doi: 10.1128/genomeA.00341-15.

Keiluweit, M., J.J. Bougoure, P.S. Nico, J. Pett-Ridge, P.K. Weber, M. Kleber. (2015). Mineral protection of soil carbon counteracted by root exudate. Nature Climate Change 5: 588–595.

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, F. Behnam, X. Mayali, A. Schintlmeister, E.D. Fleming, L. Prufert-Bebout, S.W. Singer, A. López Cortés, T.M. Hoehler, J. Pett-Ridge, A.M. Spormann, M. Wagner, P.K. Weber, B.M. Bebout. (2015) Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. 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. (2014) 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 (Nature) 8:6-18. *equal contribution.

Carpenter, K.J., 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 Microbiology 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 Microbiology 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 (Nature) 7: 817-29. Top 10 most downloaded.

Keiluweit, M., J.J. Bougoure, L. Zeglin, D. Myrold, P. Weber, J. Pett-Ridge M. Kleber, P. Nico. (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 (Nature) 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 (Nature) 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 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 (Nature) 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, W.O. Ng, B.S. Stevenson, I.D. Hutcheon, D.A. Relman, A.M. Spormann. (2008). Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and 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 (Nature) 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 d15N and d18O 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.

White Papers and Technical Reports

  1. Sarah E. Baker, Joshuah K. Stolaroff, George Peridas, Simon H. Pang, Hannah M. Goldstein, Felicia R. Lucci, Wenqin Li, Eric W. Slessarev, Jennifer Pett-Ridge, Frederick J. Ryerson, Jeff L. Wagoner, Whitney Kirkendall, Roger D. Aines, Daniel L. Sanchez, Bodie Cabiyo, Joffre Baker, Sean McCoy, Sam Uden, Ron Runnebaum, Jennifer Wilcox, Peter C. Psarras, Hélène Pilorgé, Noah McQueen, Daniel Maynard, Colin McCormick, Getting to Neutral: Options for Negative Carbon Emissions in California, January, 2020, Lawrence Livermore National Laboratory
  2. Pett-Ridge, J. (2018) Deeply rooted: evaluating plant rooting depth as a means for enhanced soil carbon sequestration. Conference paper: International Conference on Negative CO2 Emissions, Gothenburg, Sweden
  3. (multi-author) Building a New Carbon Economy: An Innovation Plan, September 2018. Carbon 180 (formerly Center for Carbon Removal)
  4. (multi-author) DOE BERAC Grand Challenges Workshop Report, March 2017
  5. (multi-author) DOE OBER Technologies for Characterizing Molecules to Mesoscale Workshop Report, Sept 2016
  6. (multi-author) Microbes and Climate Change, Report on an American Academy of Microbiology and American Geophysical Union Colloquium held in Washington, DC, March 2016
  7. (multi-author) U.S. DOE. 2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC-0167. U.S. Department of Energy Office of Science
  • 2021, DOE Secretary of Energy Achievement Award, for "Getting to Neutral" report
  • 2020, LLNL Director's Science and Technology Award, for "Getting to Neutral" report
  • 2019, Endowed Biogeochemistry Lecture, Geochemical Society, Goldschmidt conference
  • 2018, Elected Secretary, AGU Biogeosciences Section
  • 2017, Editor's Citation for Excellence in Refereeing, Geophysical Research Letters
  • 2015, LLNL Early and Mid-Career Recognition (EMCR) award
  • 2014, DOE Early Career Research Program Fellowship
  • 2014, Elected to EMSL User Executive Committee
  • 2012, Directorate Award, Physical and Life Sciences Directorate, LLNL
  • 2013, AGU, Best Talk, Biogeosciences Section
  • 2011, Publication Award, Chemical Sciences Division, LLNL
  • 2009, International Society for Microbial Ecology, Journal Cover Contest
  • 2007, AEM Gordon Research Conference, Best Poster
  • 2006, Institute for Complex Adaptive Matter award
  • 2000–2004, Graduate Fellowship, DOE Global Change Education Program, UC Berkeley
  • 2000, 2004, James P. Bennett Agriculture Fund Fellowship, U.C. Berkeley
  • 2000, 2001, 2002, 2003, 2004, U.C. Berkeley Graduate Division awards
  • 2003, Honorable mention for oral presentation, Soil Ecology Society
  • 2003, Student conference award, British Ecological Society
  • 2000, Carolyn Meek Memorial Scholarship, U.C. Berkeley
  • 1996, McLean Scholarship, Yale School of Forestry
  • 1995, Mellon Research Grant, Yale School of Forestry
  • 1995, Tropical Resource Institute Research Grant, Yale School of Forestry
  • 1994, Mellon Senior Research Grant, Yale College