Jennifer Pett-Ridge

Group Leader, Environmental Isotope Systems
Nuclear and Chemical Sciences Division
Email: pettridge2@llnl.gov
Phone: +19254242882

Education

  • 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 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, 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 newly-formed Environmental Isotope Systems group in the Nuclear and Chemical Sciences division and manages a portfolio of over $7 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 new 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 60 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, Crop and Soil Science, UC Merced, School of Natural Sciences
  • 2018–present, 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
  • 2008–2009, Flex-term Staff Scientist, Lawrence Livermore National Lab
  • 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

Awards

  • 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

Publications

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 (in review).

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, bioRxiv https://www.biorxiv.org/content/10.1101/2020.02.25.965764v1 mSystems in review

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. Biogeosciences Discussions (in review)

Hestrin, R. M.R. Lee2, B.K. Whitaker2, J. Pett-Ridge. The switchgrass microbiome: A review of structure, function, and taxonomic distribution. Phytobiomes (in review)

Aigle, Axel, Gubry-Rangin, Cecile, Thion, Cecile, Estera, Katerina, Richmond, Heather, Pett-Ridge, Jennifer, Firestone, Mary, Nicol, Graeme, Prosser, James. Experimental testing of hypotheses for temperature- and pH-based niche specialisation of ammonia oxidising archaea and bacteria. Environmental Microbiology and Environmental Microbiology Reports (in review)

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 and 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 

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. 

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 

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

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 DOI: 10.1128/mBio.01318-19 

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 and 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 phototroph-associated microbiome of a microbial mat. bioRxiv.

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 disjunctusISME 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