Jennifer Pett-Ridge

Portrait of Jennifer Pett-Ridge
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  • Title
    Distinguished Member of Technical Staff, Physical and Life Sciences Directorate
  • Email
    pettridge2@llnl.gov
  • Phone
    (925) 424-2882
  • Organization
    Not Available

Research Interests

Dr. Jennifer Pett-Ridge is a Distinguished Member of Technical Staff at LLNL, Adjunct Professor at UC Merced and a principal investigator at the UC Berkeley Innovative Genomics Institute. She uses the tools of systems biology and biogeochemistry (stable isotope probing, NanoSIMS imaging, molecular microbial ecology, computational modeling) to study how earth system changes affect microbiome interactions and ecosystem processes. Much of her current work focuses on soil carbon persistence and sustainable agriculture. She leads the Carbon Initiative at LLNL, as well as team projects for the US Department of Energy, including the Microbes Persist Soil Microbiome Scientific Focus Area and Terraforming Soils Energy Earthshot Research Center. In 2023, she led a team of over 70 scientists on Roads to Removal, an assessment of carbon dioxide removal options in the USA. Dr. Pett-Ridge has co-authored over 170 peer-reviewed publications that have collectively received over 16,000 total citations. Pett-Ridge is a Fellow of AAAS and the Ecological Society of America, recipient of a DOE Early Career award (2014), Geochemical Society Endowed Biogeochemistry Medal (2019), Secretary of Energy Achievement Award (2021), and the DOE Office of Science Ernest Orlando Lawrence Award (2022).

Professional Appointments

  • 2025-present, DOE Biological and Environmental Research Advisory Committee (BERAC)
  • 2023-present, Lead Scientist, LLNL Carbon Initiative
  • 2022-present, Distinguished Member of Technical Staff, LLNL
  • 2022-present, Investigator, Innovative Genomics Institute, UC Berkeley
  • 2018-present, Adjunct Full Professor, Life & Environmental Sciences Department, UC Merced
  • 2018, Visiting Scholar, University of San Francisco de Quito, Ecuador (sabbatical leave)
  • 2017-2023, Group Leader, Environmental Isotope Systems Group, LLNL
  • 2015-present, Senior Staff Scientist, LLNL
  • 2016-present, Guest Affiliate, UC Berkeley, Environmental Science Policy and Management
  • 2012-2017, Adjunct Faculty, Crop and Soil Science, Oregon State University
  • 2010-2017, Deputy Group Leader, Isotopic Signatures Group, LLNL
  • 2009- 2015, Career Staff Scientist, LLNL
  • 2008-2009, Flex-term Staff Scientist, LLNL
  • 2005-2008, Postdoctoral Fellow, LLNL
  • 2000-2005, DOE Global Change Education Program graduate student fellow
  • 1998-2000, Graduate Student Researcher, UC Berkeley
  • 1996-1998, Project Manager and Research Technician, USDA Forest Service, Hubbard Brook Experimental Forest, NH
  • 1996, Research Technician, Yale School of Forestry and Environmental Studies
  • 1995-1996, Project Manager and Research Technician, USDA Forest Service, International Institute of Tropical Forestry, Puerto Rico
  • 1994-1996, Teaching Assistant, Yale School of Forestry and Environmental Studies

Mentions in Popular Press

Ph.D., Soil Microbial Ecology, University of California Berkeley, 2005

M.S., Forest Science, Yale School of Forestry & Environmental Studies, 1996

B.A., Biology, Studies in Environment, Yale University, 1994

In Review  

  1. Terrer, C.*, E.C. Fricke*, S. Bell, R. Jia, S. Cook-Patton, S. Ren, M.E. Macfarlane, J. Sanderman, A.F.A. Pellegrini, C.J. Nolan, R.B. Jackson, J. Pett-Ridge, J.B. Yu, S. Cerasoli, Y. Zou, P. Ciais, Y. Xu, H. Yin, W. Jiao, A. Rosel, C. Folberth, C. Schillaci, P. Dutt, C. Barriocana, D. Gol, C. Cruz, A.C. Koberle. Soils match biomass carbon gains across restored farmlands. Nature (in review)
  2. Calabrese, S., S. Sadik Tulip, S. Perez Castro, A. Thompson, J. Pett-Ridge, Z. Nikolov. Fluxes vs. pools: connecting temperature dependence and sensitivity of soil carbon dynamics across timescales Journal of Geophysical Research – Biogeosciences (in review)
  3. Slessarev, E., J. Pett-Ridge, K. Min, A.A. Berhe, S. Das, R.D. Jackson, J.D. Jastrow, M. Kan, S. Kumar, T. Longbottom, K.J. McFarlane, E. Oerter, B.K. Richards, G.P. Robertson, G. Sanford, E.E. Nuccio. Tracing the effects of a deeply rooted grass, Panicum virgatum, on soil organic carbon cycling in a range of environments across the USA. bioRxiv https://doi.org/10.1101/2025.08.01.668182  Earth Futures (in review)
  4. Trubl, G., S. Roux, M. Kellom, D. Vyshenska, A. Tomatsu , K. Singh, J. A. Kimbrel, E. Eloe-Fadrosh, R. R. Malmstrom, J. Pett-Ridge, S.J. Blazewicz. Tracking persistence and dynamics of active soil viruses with SIP-Viromics. bioRxiv. https://doi.org/10.1101/2025.05.25.655894 mSystems (in review)
  5. Sokol, N.W., M.M. Foley, S.J. Blazewicz, N. DiDonato, K. Estera-Molina, M. Firestone, A. Greenlon, B.A. Hungate, W. Kew, L. Paša-Tolić, E. Slessarev, J. Pett-Ridge. Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a semi-arid grassland soil. bioRxiv https://doi.org/10.1101/2025.05.23.655838  Global Change Biology (in review)
  6. Schwartz, E., M. Hayer, R.L. Mau, K. Nantz, B.A. Hungate, S. Blazewicz, G.Allen, E. Morrisey, B. Tripathi, J. Pett-Ridge. Internal DNA standards for isopycnic centrifugation of environmental DNA in quantitative stable isotope probing. bioRxiv https://doi.org/10.1101/2025.06.27.661829, Applied and Environmental Microbiology (in review)
  7. Hedlund, B.P, T. Alvarado, T.R. Murphy, A. Torres, A.M. Blocker, C.O. Seymour, D. Lai, X. Mayali, A. Muok, R. Xiao, E. Levon, J.T. Phoenix, K. Mazdra, T. Sons, J. Ledesma, J. Jiries, A. Manriquez, A. Vamvakas, A. Rivera Martinez, A. Camacho, Z. Owerkowicz, J. Lacy, P.K. Weber, A. Briegel, D.P. Moser, J. Pett-Ridge, J.A. Dodsworth, and S.D. Hamilton-Brehm. Folate auxotrophy in Atribacterota reveals pervasive microbial cultivation problem. Nature Microbiology (in review)
  8. Ye, Z., Y. Yang, J. Kuang, C.T. Bates, A. Escalas, D. Ning, L. Wu, S. Liu, S. Deng, J. Lei, X. Chen, J. Pett-Ridge, M. Saha, K. Craven, M. Firestone, and J. Zhou. Bioenergy cropping reduces spatiotemporal scaling of soil bacterial biodiversity. PNAS (in review)
  9. Fitzpatrick, R., B. Hungate, M. Power, M. Foley, T. Samo, E. Schwarz, M. Hayer, P.K. Weber, J. Pett-Ridge, J. Marks. Composition, growth, succession, and function in the Cladophora microbiome: insights from quantitative Stable Isotope Probing (qSIP) and NanoSIMS imaging. bioRxiv doi: https://doi.org/10.1101/2025.05.12.652736  Environmental Microbiology (in review)
  10. Lai*, D., D. Mosier, M. Palmer, X. Mayali, J. Johnston, W. Saldivar, J.K. Covington, J.-Y. Jiao, R. Murali, C.O. Seymour, L. Liu, Z.-S. Hua, W.-J. Li, P.K. Weber, J. Pett-Ridge, D.R. Colman, E.S. Boyd, T. Nunoura, J.A. Dodsworth* and B.P. Hedlund. Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. Nature Communications (in review)
  11. Penev, P.I., K. Estera-Molina, G.M. Allen, R. Sachdeva, S. Lei, K.K. Law, J. Hoff, S.J. Blazewicz, J. Pett-Ridge, J.F. Banfield. The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts bioRxiv  https://doi.org/10.1101/2024.12.19.629468 (in review)
  12. Trubl, Gareth, Ikaia Leleiwi, Ashley Campbell, Jeffrey A. Kimbrel, Amrita Bhattacharyya, Robert Riley, Rex Malstrom, Steven J. Blazewicz, Jennifer Pett-Ridge.  Soil redox conditions drive virus-host community dynamics and plant biomass degradation in tropical rainforest soils. bioRxiv https://doi.org/10.1101/2024.09.13.612973. Microbiome (in review)
  13. Foley, M., N. Sokol, B. Stone, S. Blazewicz, K. Estera-Molina, A. Greenlon, M. Hayer, J. Kimbrel, J. Pett-Ridge, B. Hungate. Specialist-generalist trade-offs in microbial growth rates across soil habitats. bioRxiv. https://doi.org/10.1101/2025.05.20.655198 mBio (in response to review)
  14. Mayer, A., J. Dumortier, Z. Hausfather, J. Pett-Ridge, E. Slessarev. Cost of cooling: The value of reversible carbon storage in a zero-emissions world. CDRxiv.  https://doi.org/10.70212/cdrxiv.2025348.v1.  Environmental Science & Technology Manuscript ID: es-2025-05767s (in response to review) 
  15. Chuckran, P. F., S. J. Blazewicz, J. Ceja-Navarro, J. Pett-Ridge, E. Schwartz, P. Dijkstra. Unique relationships between gene traits and transcriptional response under growth, starvation, and extreme heat in an agricultural soil. PeerJ (in response to review).
  16. Ceja-Navarro, J.A., P. Kosina, D. Patel, G. Genco, A. Byer, N. Xiao, D. Ning, K.H. Wang, S.E. Celniker, J. Zhou, P. Dijkstra, B.A. Hungate, J. Pett-Ridge, E.L. Brodie. Cross-domain microbial network resilience increases in response to ecosystem retrogression Microbiological Research (in response to review)

 

Peer Reviewed

177. Kelliher, J., Mirzayi, C., Bordenstein, S., Oliver, A., Kellogg, C., Hatcher, E., Berg, M., Baldrian, P., Aljumaah, M., Miller, C., Mungall, C., Novak, V., Palucki, A., Smith, E., Tabassum, N., Bonito, G., Brister, J., Chain, P., Dundore-Arias, J., Emerson, J., Fernandes, V., Flores, R., Gonzalez, A., Hansen, Z., Jackson, S., Mongodin, E., Moustafa, A., Northen, T., Pariente, N., Pett-Ridge, J., Record, S., Reji, L., Reysenbach, A., Rich, V., Richardson, L., Roux, S., Schriml, L., Shabman, R., Sierra, M., Sullivan, M., Sundaramurthy, P., Thibault, K., Thompson, L., Tighe, S., Vereen, E., STREAMS Consortium, & Eloe-Fadrosh, E. A. (2025) The standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. Nature Microbiology (in press). 

176. Szabo, G., J. Pett-Ridge, E. Eloe-Fadrosh and T. Woyke. (2025) A genomic view of Earth's biomes. Nature Reviews Genetics https://doi.org/10.1038/s41576-025-00888-1

175. Plante, A., and J. Pett-Ridge. (2025) Advances in understanding the role of soil microbiomes in carbon cycling in soil. pp 231-254. In: K. Dunfield (ed) Understanding and utilising soil microbiomes for a more sustainable agriculture. Burleigh Dodds Science Publishing, Cambridge, UK. https://ingram-indiepubsuk.myshopify.com/basket/add?isbn=9781801464741&publisher= burleigh-dodds-science-publishing

174. Marks, J.C., M. Zampini, R. Fitzpatrick, S.H. Kariunga, T, Samo, P. Weber, S. Thomas, B.A. Hungate, C. Ramon, M. Wulf, V.O. Leshyk, E. Schwartz, J. Pett-Ridge, M.E. Power. (2025) Ecosystem consequences of a nitrogen-fixing proto-organelle. PNAS 122: e2503108122. www.pnas.org/doi/10.1073/pnas.2503108122

173. Dai, T., N.C. Ellebracht, E. Hunter-Sellars, A. Aui, H.M. Goldstein, W. Li, C.M. Hellwinckel, L. Price, A.A. Wong, P. Nico, B. Basso, G.P. Roberton, J. Pett-Ridge, M. Langholtz, S.E. Baker, S.H. Pang, C.D. Scown. (2025) Land-based resources for engineered carbon dioxide removal in the United States exceed the expected needs. One Earth 8: 101349. https://doi.org/10.1016/j.oneear.2025.101349

172. Narayanan, A., F. Maillard, B. Beatty, J. Novak, J. Gardner, J. Schilling, J. Pett-Ridge, P. Kennedy. (2025) Bacterial and fungal growth on microbial necromass and its diverse components: shared profiles and divergent constraints revealed by high-throughput phenotyping. Functional Ecology 39: 2268-2283. http://doi.org/10.1111/1365-2435.70128 

171. Kelliher, J., M. Aljumaah, S.R. Bordenstein, J.R. Brister, P. Chain, J.P. Dundore-Arias, J.B. Emerson, V.M.C. Fernandes, R. Flores, A. Gonzalez, Z.A. Hansen, E.L. Hatcher, S.A. Jackson, C.A. Kellogg, R. Madupu, C.M.L. Miller, C. Mirzayi, A.M. Moustafa, C. Mungall, A. Oliver, N. Pariente, J. Pett-Ridge, S. Record, L. Reji, A.L. Reysenbach, V.I. Rich, L. Richardson, L.M. Schriml, R.S. Shabman, M.B. Sullivan, P.I. Sundaramurthy, K.M. Thibault, L.R. Thompson, S. Tighe, E. Vereen, E.A. Eloe-Fadrosh. (2025) Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024. Environmental Microbiome 20: 40 https://doi.org/10.1186/s40793-025-00702-9

170. Clauser, N., C. D. Scown, J. Pett-Ridge, W. J. Sagues. (2025) A techno-economic assessment of carbon dioxide removal pathways via biochemical conversion of lignocellulose to biofuels and bioplastics. Renewable and Sustainable Energy Reviews. 216: 115714. https://doi.org/10.1016/j.rser.2025.115714  

169. Slanzon, G. S., M. Yuan, K. Estera-Molina, A. Chew, J. Pett-Ridge, M. K. Firestone, S. J. Blazewicz, G. M. Allen, N. H. Nguyen. (2025) Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere. Microbiome 13: 109. https://doi.org/10.1186/s40168-025-02100-2

168. Sieradzki, E.T., G. M. Allen, J. A. Kimbrel, G. Nicol, C. Hazard, E. Nuccio, S. J. Blazewicz, J. Pett-Ridge, and G. Trubl. (2025) Phosphate amendment drives bloom of RNA viruses after soil wet-up. Soil Biology and Biochemistry. 205: 109791. https://doi.org/10.1016/j.soilbio.2025.109791

167. Hazard, C., K. Anantharaman, L. S. Hillary, U. Neri, G. W. Nicol, J. Pett-Ridge, S. Roux, G. Trubl, K. Williamson, J. B. Emerson. (2025) Beneath the surface: Unsolved questions in soil virus ecology. Soil Biology and Biochemistry. 205: 109780. https://doi.org/10.1016/j.soilbio.2025.109780

166. Barcellos, D., S. P. Castro, A. Campbell, J, Kimbrel, S. J. Blazewicz, J. Pett-Ridge, A. Thompson. (2025) Duration of O2 exposure determines dominance of FeII vs CH4 production in tropical forest soils. ES&T. 59: 4469-4481. https://pubs.acs.org/doi/full/10.1021/acs.est.4c12329.

165. Min, K., E. Nuccio, E. Slessarev, M. Kan, K. J. McFarlane, E. Oerter, A. Jurusik, G. Sanford, K. D. Thelen, J. Pett-Ridge, A. A. Berhe. (2025) Deep-rooted plants alter microbial availability and chemical composition of carbon in density fractions along soil depth profiles. Geoderma. 455: 117202. https://doi.org/10.1016/j.geoderma.2025.117202

164. Chuckran, P. F., K. Estera-Molina, A. M. Nicolas, E. T. Sieradzki, P. Dijkstra, M. K. Firestone, J. Pett-Ridge, S. J. Blazewicz. (2025) Codon bias, nucleotide selection, and genome size predict in situ bacterial growth and expression in rewetted soil. Proceedings of the National Academy of Sciences. 122: e2413032122. https://doi.org/10.1073/pnas.2413032122

163. Weber, P. K., M. Debliqui, C. Defouilloy, X. Mayali, M. C. Liu, R. Hestrin, J. Pett-Ridge, R. Stuart, M. Morris, C. Ramon, D. M. Jorgens, R. Zalpuri, L. Arnoldi, J. Farcy, N. Saquet, Sarah Vitcher Fichou, L. Renaud, A. Thomen. (2024) The NanoSIMS-HR: the next generation of high spatial resolution dynamic SIMS. Analytical Chemistry. 96: 19321-19329. https://doi.org/10.1021/acs.analchem.4c03091. Cover Article.

162. McMurtry, A., C. S. Kasmerchak, E. A. Vaughan, M. Dolui, L. M. Phillips, C. W. Mueller, J. Pett-Ridge, A. A. Berhe, J. A. Mason, E. Marin-Spiotta, M. A. de Graaff. (2024) Getting to the root of the problem: Soil carbon and microbial responses to root inputs within a buried paleosol along an eroding hillslope in southwestern Nebraska, USA. Soil Biology and Biochemistry. 198: 109549. https://doi.org/10.1016/j.soilbio.2024.109549

161. Nou, N. O., J. K. Covington, D. Lai, X. Mayali, C. O. Seymour, J. Johnston, J. Y. Jiao, S. Buessecker, D. Mosier, A. R. Muok, N. Torosian, A. M. Cook, A. Briegel, T. Woyke, E. Eloe-Fadrosh, N. Shapiro, S. G. Bryan, S. Sleezer, J. Dimapilis, C. Gonzalez, L. Gonzalez, M. Noriega, M. Hess, R. Carlson, L. Liu, M. M. Li, Z. H. Lian, S. Zhu, F. Liu, X. Sun, B. Gao, R. Mewalal, M. Harmon-Smith, I. K. Blaby, J. F. Chen, P. K. Weber, W. J. Li, A. E. Dekas, J. Pett-Ridge, J. A. Dodsworth, M. Palmer, B. P. Hedlund. (2024) Genome-guided isolation and ecophysiology of polysaccharide-degrading Fervidibacter sacchari and universal polysaccharide metabolism in the Armatimonadota. Nature Communications. 15: 9534. https://doi.org/10.1038/s41467-024-53784-3

160. Anthony, W., S. D. Allison, C. M. Broderick, L. C. Rodriguez, A. Clum, H. Cross, E. Eloe-Fadrosh, S. Evans, D. Fairbanks, R. Gallery, J. B. Gontijo, J. Jones, J. McDermott, J. Pett-Ridge, S. Record, J. L. M. Rodrigues, W. Rodriguez-Reillo, K. L. Shek, T. Takacs-Vesbach, J. L. Blanchard. (2024)  From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. Environmental Microbiome. 19: 56. https://doi.org/10.1186/s40793-024-00599-w

159. Foley, M. M., B.W.G. Stone, T. Caro, N.W. Sokol, B.J. Koch, S.J. Blazewicz, P. Dijkstra, M. Hayer, K. Hofmockel, B. K. Finley, M. Mack, J. Marks, R. Mau, V. Monsaint-Queeney, E. Morrissey, J. Propster, A. Purcell, E. Schwartz, J. Pett-Ridge, N. Fierer, B. A. Hungate. (2024) Growth rate as a link between microbial diversity and soil biogeochemistry. Nature Ecology and Evolution. https://doi.org/10.1038/s41559-024-02520-7  

158. Grant, K. E., M. N. Repasch, K. M. Finstad, J. D. Kerr, M. Marple, C. J. Larson, T.A.B. Broek, J. Pett-Ridge, and K. J. McFarlane. (2024) Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil. Biogeochemistry. https://doi.org/10.5194/bg-21-4395-2024

157. Sokol, N. W., J. Sohng, K. Moreland, E. Slessarev, H. Goertzen, R. Schmidt, S. Samaddar, I. Holzer, M. Almaraz, E. Geoghegan, B. Houlton, I. Montañez, J. Pett-Ridge, K. Scow. (2024) Reduced accrual of mineral-associated organic matter after two years of enhanced rock weathering in cropland soils, though no net losses of soil organic carbon. Biogeochemistry.  https://doi.org/10.1007/s10533-024-01160-0

156. Hallberg, Z. F., A. M. Nicolas, Z. I. Alvarez-Aponte, K. C. Mok, E. T. Sieradzki, J. Pett-Ridge, J. F. Banfield, H. K. Carlson, M. K. Firestone, and M. E. Taga. (2024) Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B 12. ISME J. https://doi.org/10.1093/ismejo/wrae094

155. Baker N. R., K. Zhalnina, M. Yuan, D. Herman, L. Wu, C. Fossum, A. Chew, Y. Fu, E. Nuccio, M. Saha, T. Northen, J. Zhou, J. Pett-Ridge, M. Firestone. (2024) Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. PNAS. https://doi.org/10.1073/pnas.2303439121

154. DiDonato, N., A. Rivas-Ubach, W. Kew, N. Sokol, C. Clendinen, J. E. Kyle, C. E. Martínez, M. Foley, N. Tolić, J. Pett-Ridge, L. Paša-Tolić. (2024) Improved characterization of soil organic matter by integrating FT-ICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions. Analytical Chemistry https://doi.org/10.1021/acs.analchem.4c00184

153. Fudyma, J. D., A. M. ter Horst, C. Santos-Medellín, J. Sorensen, G. Gogul, L. Hillary, S. Geonczy, J. Pett-Ridge, J. B. Emerson. (2024) Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities. Soil Biology and Biochemistry https://doi.org/10.1016/j.soilbio.2024.109419

152. Chuckran, P. F., K. Estera-Molina, M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, S. Mukherjee, T. B. K. Reddy, C. Daum, A. Copeland, I. M. A. Chen, N. N. Ivanova, N. C. Kyrpides, C. Pennacchio, E. A. Eloe-Fadrosh, S. J. Blazewicz, J. Pett-Ridge. (2024) Metatranscriptomes of Mediterranean-grassland soil microbial communities during rewetting.  Microbiology Resource Announcements https://doi.org/10.1128/mra.00322-24

151. Sokol, N., M. Foley, S. Blazewicz, A. Bhattacharyya, N. DiDonato, K. Estera-Molina, M. Firestone, A. Greenlon, B. Hungate, J. Kimbrel, J. Liquet, M. Lafler, M. Marple, P. Nico, L. Paša-Tolić, E. Slessarev, J. Pett-Ridge. (2024) The path from root input to mineral-associated soil carbon is dictated by habitat-specific microbial traits and soil moisture. Soil Biology and Biochemistry. 193: 109367 https://doi.org/10.1016/j.soilbio.2024.109367

150. Georgiou, K., C. D. Koven, W. R. Wieder, J. Pett-Ridge, N. J. Bouskill, W. J. Riley, R. Z. Abramoff, A. Ahlström, M. D. Hartman, A. F. A. Pellegrini, D. Pierson, E. Slessarev, B. N. Sulman, Q. Zhu, R. B. Jackson. (2024) Emergent temperature sensitivity of soil organic carbon driven by mineral associations. Nature Geoscience https://doi.org/10.1038/s41561-024-01384-7

149. Kakouridis, A., M. Yuan, E. E. Nuccio, J. A. Hagen, C. A. Fossum, M. L. Moore, K. Y. Estera-Molina, P. S. Nico, P. K. Weber, J. Pett-Ridge, and M. K. Firestone. (2024) Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. New Phytologist https://doi.org/10.1111/nph.19560  

148. Marschmann, G., J. Tang, K. Zhalnina, U. Karaoz, H. Cho, B. Le, J. Pett-Ridge, and E. Brodie. (2024) Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nature Microbiology. 9: 421-433. https://doi.org/10.1038/s41564-023-01582-w  

147. Finstad, K., E. Nuccio, K. Grant, T. Broek, J. Pett-Ridge, K. McFarlane. (2023) Radiocarbon analysis of soil microbial biomass via direct chloroform extraction. Radiocarbon. 1-9. https://doi.org/10.1017/RDC.2023.80.

146. Pavlopoulos, G. A., F. A. Baltoumas, S. Liu, O. Selvitopi, A. P. Camargo, S. Nayfach, A. Azad, S. Roux, L. Call, N. N. Ivanova, I. M. Chen, D. Paez-Espino, E. Karatzas, Novel Metagenome Protein Families Consortium, I. Iliopoulos, K. Konstantinidis, J. M. Tiedje, J. Pett-Ridge, D. Baker, A. Visel, C. A. Ouzounis, S. Ovchinnikov, A. Buluç, N. C. Kyrpides. (2023) Unraveling the functional dark matter through global metagenomics. Nature. 622: 594-602. https://doi.org/10.1038/s41586-023-06583-7

145. Santos-Medellín, C. S. J. Blazewicz, J. Pett-Ridge, J. B. Emerson. (2023) Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nature Ecology and Evolution. 7:1809-1822. https://doi.org/10.1038/s41559-023-02207-5

144. Sieradzki, E. T, E .E. Nuccio, J. Pett-Ridge, M. K. Firestone. (2023) Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development. mSystems. 8:e00315-23. https://doi.org/10.1128/msystems.00315-23.

143. Nicolas, A. M., E. T. Sieradzki, J. Pett-Ridge, J. F. Banfield, M. E. Taga, M. K. Firestone, S. J. Blazewicz. (2023) A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil. Nature Communications.14: 5835. https://doi.org/10.1038/s41467-023-40835-4.

142. Hicks Pries, C., R. Ryals, B. Zhu, K. Min, A. Cooper, S. Goldsmith, J. Pett-Ridge, M. Torn, A. A. Berhe. (2023) The deep soil organic carbon response to global change. Annual Review of Ecology, Evolution, and Systematics. 54: 375-401. https://doi.org/10.1146/annurev-ecolsys-102320-085332. 

141. Walkup, J., C. Dang, R. L. Mau, M. Hayer, E. Schwartz, B. W. Stone, K. S. Hofmockel, B. J. Koch, A. M. Purcell, J. Pett-Ridge, C. Wang, B. A. Hungate, E. Morrissey. (2023) The predictive power of phylogeny on growth rates in soil bacterial communities. ISME Communications. 3:73. https://doi.org/10.1038/s43705-023-00281-1.

140. Riley, R., R. Bowers, A. Camargo, A. Campbell, R. Egan, E. Eloe-Fadrosh, B. Foster, S. Hofmeyr, M. Huntemann, M. Kellom, J. Kimbrel, L. Oliker, K. Yelick, J. Pett-Ridge, A. Salamov, N. Varghese, A. Clum. (2023) Terabase-scale coassembly of a tropical soil microbiome. Microbiology Spectrum. e00200-23. https://doi.org/10.1128/spectrum.00200-23.

139. Maillard, F., T. J. Michaud, C. R. See, L. C. DeLancey, S. J. Blazewicz, J. A. Kimbrel, J. Pett-Ridge, P. G. Kennedy. (2023) Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems. e00390-23 https://doi.org/10.1128/msystems.00390-23.

138. Vyshenska, D., P. Sampara, K. Singh, A. Tomatsu, W. B. Kauffman, E. E. Nuccio, S. J. Blazewicz, J. Pett-Ridge, N. Varghese, M. Kellom, A. Clum, R. Riley, S. Roux, E. A. Eloe-Fadrosh, R. M. Ziels, R. R. Malmstrom. (2023) A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems 8: e01280-22 https://doi.org/10.1128/msystems.01280-22.

137. Palmer, M., J. K. Covington, E. M. Zhou, S. C. Thomas, N. Habib, C. O. Seymour, D. Lai, J. Johnston, A. Hashimi, J. Y. Jiao, A. R. Muok, L. Liu, W. D. Xian, X. Y. Zhi, M. M. Li, L. P. Silva, B. P. Bowen, K. Louie, A. Briegel, J. Pett-Ridge, P. K. Weber, E. I. Tocheva, T. Woyke, T. R. Northen, X. Mayali, W. J. Li, B. P. Hedlund. (2023) Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. ISME Journa.l 17: 952–966 https://doi.org/10.1038/s41396-023-01405-0.

136. Blanc-Betes E., N. Gomez-Casanovas, W. Yang, J. Chandrasoma, T. Clark, E. De Lucia, C. Hyde, A. Kent, J. Pett-Ridge, J. Rabinowitz, S. Raglin, J. Schwender, Y. Shen, R. Van Allen, A. von Haden. (2023) Accelerating the development of a sustainable bioenergy portfolio through stable isotopes. Global Change Biology, Bioenergy. 15: 840-866. http://doi.org/10.1111/gcbb.13056.

135. Sieradzki, E. T., E. Nuccio, J. Pett-Ridge, M. Firestone. (2023) Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass. ISME Journal. 17: 967-975  https://doi.org/10.1038/s41396-023-01402-3.

134. Trubl, G., K. M. Stedman, P. J. Boston, K. F. Bywaters, E. E. Matula, P. Sommers, S. Roux, N. Merino, J. Yin, J. T. Kaelber, A. Avail-Herrera, P. A. Johnson, S. B. Johnson, P. K. Weber, J. Pett-Ridge. (2023) Astrovirology: how viruses enhance our understanding of life in the Universe. Invited review-- International Journal of Astrobiology. 22: 247-271. https://doi.org/10.1017/S1473550423000058.

133. Lang, A. K., J. Pett-Ridge, K. J. McFarlane, R. P. Phillips. (2023) Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests. Journal of Ecology. 111: 1254-1269. https://doi.org/10.1111/1365-2745.14094.

132. Stone, B., S. Blazewicz, B. Koch, P. Dijkstra, M. Hayer, K.S. Hofmockel, X.-J. A. Liu, R. Mau, J. Pett-Ridge, E. Schwartz, B. Hungate. (2023) Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community, Oecologica 201: 771-782 https://doi.org/10.1007/s00442-023-05322-z

131. Stone, B. W. G., P. Dijkstra, B. Finley, R. Fitzpatrick, M. Foley, M. Hayer, K. Hofmockel, B.J. Koch, J. Li, X. J. A. Liu, A. Martinez, R.L. Mau, J. Marks, V. Monsaint-Queeney, E.M. Morrissey, J. Propster, J. Pett-Ridge, A. Purcell, E. Schwartz, B.A. Hungate. (2023) Life history strategies among soil bacteria - dichotomy for few, continuum for many. ISME Journal 17: 611-619 https://doi.org/10.1038/s41396-022-01354-0  

130. Parada, A.E., X. Mayali, P.K. Weber, J. Wollard, A. Santoro, J.A. Fuhrman, J. Pett-Ridge and A.E. Dekas. (2023) Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota. Environmental Microbiology 25: 689-704 http://doi.org/10.1111/1462-2920.16299

129. Chuckran, P.F., C. Flagg, J. Propster, W.A. Rutherford, E. Sieradzki, S. Blazewicz, B. Hungate, J. Pett-Ridge, E. Schwartz, P. Dijkstra. (2023) Edaphic controls on genome size and GC content of bacteria in soil microbial communities. Soil Biology and Biochemistry 178: 108935 https://doi.org/10.1016/j.soilbio.2022.108935

128. McDaniel, M.D., J.A. Bird, J. Pett-Ridge, E. Marin-Spiotta, T.M. Schmidt, A.S. Grandy. (2023) Diversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residues Ecological Applications 33: e2784 https://doi.org/10.1002/eap.2784

127. Foley, M.M., S. J. Blazewicz, K. J. McFarlane, A. Greenlon, M. Hayer, J. A. Kimbrel, B. J. Koch, V. Monsaint-Queeney, K. Morrison, E. Morrissey, B. A. Hungate, J. Pett-Ridge. (2023) Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands Soil Biology and Biochemistry 177: 108886 https://doi.org/10.1016/j.soilbio.2022.108886

126. Slessarev, E.W., A. Mayer, C. Kelly, K. Georgiou, J. Pett-Ridge, E.E. Nuccio. (2022) Initial soil organic carbon stocks govern changes in soil carbon: reality or artifact? Global Change Biology 29: 1239–11247 https://doi.org/10.1111/gcb.16491

125. Santos-Medellín, C., K. Estera-Molina, M. Yuan, J. Pett-Ridge, M.K. Firestone, J.B. Emerson. (2022) Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands, PNAS 119: e2209132119 https://www.pnas.org/doi/10.1073/pnas.2209132119.

124. Nuccio, E., S. Blazewicz, M. Lafler, A. Campbell, A. Kakouridis, J.A. Kimbrel, J. Wollard, D. Vyshenska, R. Riley, A. Tomatsu,  R. Hestrin, R.R. Malmstrom, M. Firestone, J. Pett-Ridge. (2022) HT-SIP: A semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 10: 199 https://doi.org/10.1186/s40168-022-01391-z  

123. Greenlon, A., E. Sieradzki, O. Zablocki, B.J. Koch, M.M. Foley, J.A. Kimbrel, B.A. Hungate, S.J. Blazewicz, E.E. Nuccio, C.L. Sun, A. Chew, C.-J. Mancilla, M.B. Sullivan, M. Firestone, J. Pett-Ridge, and J.F. Banfield. (2022) Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems 7: e00417-22 https://doi.org/10.1128/msystems.00417-22 

122. Fremin BJ, A.S. Bhatt, N.C. Kyrpides, and (J. Pett-Ridge as part of Global Phage Small Open Reading Frame (GP-SmORF) Consortium). (2022) Thousands of small, novel genes predicted in global phage genomes. Cell Reports. 39:110984. DOI: 10.1016/j.celrep.2022.110984  

121. Hestrin, R., M. Kan, M. Lafler, J. Wollard, J.A. Kimbrel, P. Ray, S. Blazewicz, R. Stuart, K. Craven, M. Firestone, E. Nuccio, J. Pett-Ridge. (2022) Plant-associated fungi support bacterial resilience following water limitation. The ISME Journal 16: 2752-2762 https://doi.org/10.1038/s41396-022-01308-6

120. Buessecker, S. M. Palmer, D. Lai, J. Dimapilis, X. Mayali, D. Mosier, J.Y. Jiao, D. R. Colman, L. Keller, E. St. John, M. Miranda, C. Gonzalez, L. Gonzalez, C. Sam, C. Villa, M. Zhuo, N. Bodman, F. Robles, E. Boyd, A. D. Cox, B. St. Clair, Z.S. Hua, W.J. Li, A.L. Reysenbach, M. B. Stott, P. K. Weber, J. Pett-Ridge, B. P. Hedlund, A. E. Dekas, J. A. Dodsworth. (2022) An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nature Communications 13: 3773 https://doi.org/10.1038/s41467-022-31452-8

119. Kakouridis, A., J.A. Hagen, M.P. Kan, S. Mambelli, L.J. Feldman, D.J. Herman, P.K. Weber, J. Pett-Ridge, and M.K. Firestone. (2022) Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants and identification of a hyphal transport pathway. New Phytologist 236: 210-221 https://doi.org/10.1111/nph.18281

118. Button, E., D.R. Chadwick, D.V. Murphy, Y. Kuzyakov, J. Pett-Ridge, D.L. Jones. (2022) Deep-C storage: Biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoils Soil Biology and Biochemistry 170: 108697 https://doi.org/10.1016/j.soilbio.2022.108697

117. Sokol N., E. D. Whalen, A. Jilling, C. Kallenbach, J. Pett-Ridge, K. Georgiou. (2022) The global distribution of mineral-associated soil organic matter, and its formation and fate under a changing climate. Functional Ecology 36: 1411-1429 https://doi.org/10.1111/1365-2435.14040

116. Sokol, N.W., Slessarev, E., Marschmann, G., Nicolas, A., Blazewicz, S., Brodie, E, Firestone, M., Foley, M., Hestrin, R., Hungate, B., Koch, B. Stone, B., Sullivan, M., Zablocki, O., LLNL Soil Microbiome Consortium, Pett-Ridge, J. (2022) Life and death in the soil microbiome: how ecological processes influence biogeochemistry Nature Reviews Microbiology 20: 415-430 https://doi.org/10.1038/s41579-022-00695-z 

115. 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. (2022) 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. Environmental Science & Technology 56: 1994–2008 https://doi.org/10.1021/acs.est.1c05818

114. Kolton M, DJ Weston, X Mayali, PK Weber, K McFarlane, J Pett-Ridge, M Somoza, JB Glass, EA Lilleskov, AJ Shaw, S Tringe, PJ Hanson, JE Kostka. (2022) Defining the core Sphagnum microbiome and its role in ecosystem function in peatlands across the North American continent mBio 13: e03714-21  https://doi.org/10.1128/mbio.03714-21

113. Bhattacharyya, A., R.K. Kukkadapu, M.E. Bowden, J. Pett-Ridge, P.S. Nico. (2022) Fast redox switches lead to rapid transformation of goethite in humid tropical soils: A Mossbauer spectroscopy study. Soil Science Society of America Journal 86: 264-274 http://doi.org/10.1002/saj2.20382

112. See, C.R., A.B. Keller, S.E. Hobbie, P.G. Kennedy, P.K. Weber, J. Pett-Ridge. (2022) Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. Global Change Biology 28: 2527–2540. https://doi.org/10.1111/gcb.16073

111. Fossum, C., K. Estera-Molina, M. Yuan, D. Herman, I. Chu-Jacoby, P. Nico, K. Morrison, J. Pett-Ridge, M. Firestone. (2022) Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland. Soil Biology and Biochemistry 165: 108519 https://doi.org/10.1016/j.soilbio.2021.108519

110. Kopittke, P.K., A.A. Berhe, Y. Carrillo, T. R. Cavagnaro, D. Chen, Q.-L. Chen, M. Román Dobarco, F. A. Dijkstra, D. J. Field, M. J. Grundy, J.-Z.He, F. C. Hoyle, I. Kögel-Knabner, S. Kee Lam, P. Marschner, C. Martinez, A.B. McBratney, E. McDonald-Madden, N. W. Menzies, L. M. Mosley, C. W. Mueller, D.V. Murphy, U.N. Nielsen, A. G. O’Donnell, E. Pendall, J. Pett-Ridge, C. Rumpel, I. M. Young & B. Minasny. (2022) Ensuring planetary survival: the centrality of organic carbon in balancing the multifunctional nature of soils, Critical Reviews in Environmental Science and Technology 52: 4308-4324  https://doi.org/10.1080/10643389.2021.2024484

109. 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. (2021) iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Communications 1: 77. https://doi.org/10.1038/s43705-021-00083-3 

108. Slessarev, E.W., O.A. Chadwick, N. Sokol, E.E. Nuccio, J. Pett-Ridge. (2021) Rock weathering controls the potential for soil carbon storage at a continental scale. Biogeochemistry Letters 157: 1-13 https://doi.org/10.1007/s10533-021-00859-8

107. Nuccio, E.E., N. Nguyen, U. Nunes da Rocha, J. Bougoure, P. Weber, E. Brodie, M.K. Firestone, J.Pett-Ridge. (2021) Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil. ISME Communications 1: 72  https://doi.org/10.1038/s43705-021-00059-3

106. Neurath, R.A., T. Whitman, I.X. Chu-Jacoby, A.M. Thompson, Lipton, M. Tfaily, J. Kyle, K.J. Bloodsworth, D.J. Herman, P.S. Nico, J. Pett-Ridge, M.K. Firestone. (2021) Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially derived residues. Environmental Science and Technology 55: 13345-13355  https://doi.org/10.1021/acs.est.1c00300

105. 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. (2021) Decreased growth of wild soil microbes after fifteen years of warming in a montane meadow. Global Change Biology 28: 128-139 https://doi.org/10.1111/gcb.15911

104. 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. (2021) Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 9: 1-18 https://doi.org/10.1186/s40168-021-01156-0

103. Trubl, G., J. A. Kimbrel, J. Liquet-Gonzalez, E.E. Nuccio, P.K. Weber, J. Pett-Ridge, J.K. Jansson, M.P. Waldrop, S.J. Blazewicz. (2021) Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9: 1-15 https://doi.org/10.1186/s40168-021-01154-2

102. 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 27:e15–e16. https://doi.org/10.1111/gcb.15850

101. Oerter, E., E. Slessarev, A. Visser, K. Min, M. Kan, K.J McFarlane, M. Saha, A.A. Berhe, J. Pett-Ridge, E. Nuccio. (2021) Hydraulic redistribution by deeply rooted grasses and its ecohydrologic implications in the Southern Great Plains of North America. Hydrological Processes 35: e14366. https://doi.org/10.1002/hyp.14366

100. 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*. (2021) Stable-isotope-informed, genome-resolved metagenomics uncovers potential cross-kingdom interactions in rhizosphere soil. mSystems 6: e00085-21 https://journals.asm.org/doi/10.1128/mSphere.00085-21

99. Min, K., E. Slessarev, M. Kan, K. McFarlane, E. Oerter, J. Pett-Ridge, E. Nuccio, A.A Berhe. (2021) Active microbial biomass decreases, but microbial growth potential remains similar across soil depth profiles under deeply-vs. shallow-rooted plants. Soil Biology and Biochemistry 162: 108401 https://doi.org/10.1016/j.soilbio.2021.108401

98. 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 27: e11–e12. https://doi.org/10.1111/gcb.15580

97. 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.

96. 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. (2021) The functional significance of bacterial predators. mBio 12: e00466-21. https://doi.org/10.1128/mBio.00466-21 

95. 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.

94. 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

93. 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. (2021) 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

92. 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.

91. Zablocki, O., M. Michelsen, M. Burris, N. Solonenko, J. Warwick-Dugdale, R. Ghosh, J. Pett-Ridge, M.B. Sullivan, and B. Temperton. (2021) 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

90. 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 15: 2738-2747 https://doi.org/10.1038/s41396-021-00959-1

89. 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. (2021) 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 

88. 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 16: 10-25 https://doi.org/10.1038/s41396-021-00916-y 

87. 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. (2021) A trade-off between plant and soil carbon storage under elevated CO2. Nature 591: 599–603. doi.org/10.1038/s41586-021-03306-8

86. Pett-Ridge, J. and P. Weber. (2021) NanoSIP: NanoSIMS applications for microbial biology”, Microbial Systems Biology: Methods and Protocols, Second Edition. (Ali Navid, ed.), Methods in Molecular Biology 2349: 91-136 https://doi.org/10.1007/978-1-0716-1585-0

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

84. 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

83. 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

82. Hestrin, R. M.R. Lee, B.K. Whitaker, J. Pett-Ridge. (2021) The switchgrass microbiome: A review of structure, function, and taxonomic distribution. Phytobiomes 5:14-28. https://doi.org/10.1094/PBIOMES-04-20-0029-FI 

81. 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. (2021) Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions. In: Gupta V., Sharma A. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-6125-2_2

80. Aigle, Axel, Gubry-Rangin, Cecile, Thion, Cecile, Estera, Katerina, Richmond, Heather, Pett-Ridge, Jennifer, Firestone, Mary, Nicol, Graeme, Prosser, James. (2020) Experimental testing of hypotheses for temperature- and pH-based niche specialisation of ammonia oxidising archaea and bacteria. Environmental Microbiology 22: 4032-4045 https://doi.org/10.1111/1462-2920.15192

79. 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

78. 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. (2020) Measurement error and resolution in quantitative stable isotope probing: implications for experimental design, mSystems 5: e00151-20. https://doi.org/10.1128/mSystems.00151-20.

77. 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

76. 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. (2020) Taxon-specific growth and mortality rates of bacteria in soil following the rewetting of a seasonally dried grassland. ISME Journal 14:1520–1532 doi.org/10.1038/s41396-020-0617-3 

75. 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 14: 999-1014 doi.org/10.1038/s41396-019-0582-x 

74. 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 116: 25900-25908 doi.org/10.1073/pnas.1908291116 

73. Dekas, A.E., A. Parada, X. Mayali, J.A. Fuhrman, J. Wollard, P. Weber, J. Pett-Ridge. (2019) Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope nanoSIP. Frontiers in Microbiology 10: 2682 doi.org/10.3389/fmicb.2019.02682 

72. 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. 

71. 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

70. 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  

69. 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         

68. 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) 

67. 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  

66.  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  

65. 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) 13: 2162–2172 doi: 10.1038/s41396-019-0422-z 

64. 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 

63. 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 https://doi.org/10.1038/s41564-019-0384-y

62. 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 https://doi.org/10.3390/soilsystems2040065 

61. 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. https://doi.org/10.1021/acs.est.8b03408  

60. 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

59. Lin, Y., 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 https://doi.org/10.1029/2018JG004420  #co-corresponding authors

58. 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

57. 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

56. 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

55. Pett-Ridge, J. Mary K. Firestone: Groundbreaking Journey of a Microbial Matriarch. (2018) Women in Microbiology Ed. Rachel J. Whitaker, Hazel A. Barton, ASM Press. Washington DC pp 87-97. doi:10.1128/9781555819545.ch31

54. Ackerman, C.; Weber, P.; Xiao, T.; Thai, B.; Kuo, T.; Zhang, E.; Pett-Ridge, J.; Chang, C. (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

53. 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 9:e02090. https://doi.org/10.1002/ecs2.2090

52. Souza, I. F., L.F.J. Almeida, G.L. Jesus, J. Pett-Ridge, P.S. Nico, M. Kleber, I.R. Silva. (2018) Carbon sink strength of subsurface horizons in Brazilian Oxisols. Soil Science Society of America Journal 82:76-86. https://doi.org/10.2136/sssaj2017.05.0143

51.   D’haeseleer, P.#, J.Z. Lee#, L. Prufert-Bebout, L.C. Burow, A. Detweiler , P.K. Weber , U. Karaoz, E.L. Brodie, T. Glavina del Rio, S. Tringe, 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 12: 67 DOI: 10.1186/s40793-017-0279-6. #co-first authors

50.   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 11: 2781-2792.

49.   Warren, M., X. Lin, J. Gaby, C. Kretz, M. Kolton, P. Morton, J. Pett-Ridge, D. Weston, C. Schadt, J. Kostka, and J. Glass. (2017) Molybdenum-based diazotrophy in a Sphagnum peatland in northern Minnesota. Applied and Environmental Microbiology 83: e01174-17 doi: 10.1128/AEM.01174-17.

48.   Pett-Ridge, J. and M. K. Firestone. (2017) Using stable isotopes to explore root-microbe-mineral interactions in soil. Rhizosphere 3: 244-253. https://doi.org/10.1016/j.rhisph.2017.0  4.016

47.   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: https://doi.org/10.21769/BioProtoc.2263.

46.   Musat, N., F. Musat, P.K. Weber, and J. Pett-Ridge (2016) Tracking microbial interactions with NanoSIMS. Current Opinion in Biotechnology 41: 114-121.

45.   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.

44.   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 7: e00650-16. doi: 10.1128/mBio.00650-16.

43.   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.

42.   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.

41.   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. https://doi.org/10.1111/nph.13850

40.   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.

39. 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, 10:1240-1251.

38. Keiluweit, M. S. Nico, M. Harmon, J. Mao, J. Pett-Ridge, and M. Kleber. (2015) Long-term litter decomposition controlled by manganese redox cycling, PNAS, 112: E5253–E5260.

37.   Shi, S., E. Nuccio, D.J. Herman, R. Rijkers, K. Estera, J. Li, U.N. da Rocha, Z. He, J. Pett-Ridge, E. Brodie, J. Zhou and M.K. Firestone. (2015) Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6: e00746-15, https://doi.org/10.1128/mbio.00746-15

36.   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.

35.   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 exudates.  Nature Climate Change 5: 588–595. https://doi.org/10.1038/nclimate2580

34.   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.

33.   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 contribution.

32.   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.

31.   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.

30.   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.

29.   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. 

28.   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.

27.   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 doi.org/10.1128/genomeA.00527-13 *equal contribution

26.   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.

25.   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. https://doi.org/10.1016/B978-0-12-407685-3.00001-3

24.   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.

23.   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.

22.   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. 

21.   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. https://doi.org/10.1016/j.gca.2012.07.001

20.   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. https://doi.org/10.1016/j.ijhydene.2012.05.100

19.   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. https://doi.org/10.1007/s10533-011-9636-5

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.

17.   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. https://doi.org/10.1038/ismej.2011.175

16.   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 photo.

15.   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.

14.   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.  DOI: 10.1126/science.1202098

13.   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.

12.   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.

11.   Finzi, J.A.#, Pett-Ridge J. #, 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). Proceedings of the National Academy of Sciences. 106: 6345-6350. https://doi.org/10.1073/pnas.081054710 #co-first author

10.   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 photo.

9.     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 Microbiology 74:3143-3150. #co-first author. https://doi.org/10.1128/AEM.00191-08

8.     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.

7.     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 photo. https://doi.org/10.1016/j.soilbio.2007.03.011

6.     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. https://doi.org/10.1016/j.foreco.2007.06.047

5.     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. https://doi.org/10.1007/s10533-006-9032-8

4.     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.  3211488.

3.     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. https://doi.org/10.1128/AEM.71.11.6998-7007.2005

2.     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. https://doi.org/10.1002/hyp.5576 

1.     Pett-Ridge, J., and W. Silver.  (2002). Survival, growth, and ecosystem dynamics of displaced bromeliads in a montane tropical forest.  Biotropica 32: 211-224. https://doi.org/10.1111/j.1744-7429.2002.tb00532.x

 

White Papers and Technical Reports

  1. Pett-Ridge, Jennifer, Hamed Ziad Ammar, Alvina Aui, Mark Ashton, Sarah E. Baker, Bruno Basso, Mark Bradford, Alexander P. Bump, Ingrid Busch, Edna Rodriguez Calzado, Jackson W. Chirigotis, Nicolas Clauser, Sinéad Crotty, Nicholas Dahl, Tao Dai, Mark Ducey, Jerome Dumortier, Nathan C. Ellebracht, Ramon Gil Egui, Ames Fowler, Katerina Georgiou, Diamantoula Giannopoulos, Hannah Goldstein, Thomas Harris. Dermot Hayes, Chad Hellwinckel, Alina Ho, Mu Hong, Susan Hovorka, Elwin Hunter-Sellars, Whitney Kirkendall, Sara Kuebbing, Matthew Langholtz, Mark Layer, Ian Lee, Reid Lewis, Wenqin Li, Weier Liu, Jimena Terrazas Lozano, Abby Lunstrum, Allegra C. Mayer, Kimberley K. Mayfield, Wilson McNeil, Peter Nico, Anastasia O’Rourke, Simon H. Pang, Keith Paustian, George Peridas, Helene Pilorge, Maxwell Pisciotta, Lydia Price, Peter Psarras, G. Philip Robertson, William Joe Sagues, Daniel L. Sanchez, Corinne D. Scown, Briana Mordick Schmidt, Eric W. Slessarev, Noah Sokol, Alexander J. Stanley, Amy Swan, Crystal Toureene, Andrew A. Wong,  Mark Mba Wright, Yuan Yao, Bingquan Zhang, Yao Zhang, and Roger D. Aines.  Roads to Removal: Options for Carbon Dioxide Removal in the United States, Lawrence Livermore National Laboratory, Dec 2023, https://doi.org/10.2172/2301853
  2. (multi-author) Soil Biodiversity in California Agriculture: Framework and Indicators for Soil Health Assessment, Prepared by the Belowground Biodiversity Advisory Committee (BBAC) For the California Department of Food and Agriculture (CDFA), July 2023
  3. (multi-author) Microbes in Models: Integrating Microbes into Earth System Models for Understanding Climate Change: Report on an American Academy of Microbiology Virtual Colloquium held on Dec. 6 and 8, 2022. Washington (DC): American Society for Microbiology; 2023.  https://asm.org/Reports/Microbes-in-Models-Integrating-Microbes-into-Earth
  4. (multi-author) BERAC. 2022. U.S. Scientific Leadership Addressing Energy, Ecosystems, Climate, and Sustainable Prosperity: Report from the BERAC Subcommittee on International Benchmarking, DOE/SC-0208. M. McCann and P. Reed, eds. Biological and Environmental Research Advisory Committee. DOI:10.2172/1895129.
  5. Pett-Ridge, J., M. Ashton, S. E. Baker, B. Basso, M. Bradford, H. Breunig, A. Bump, I. Busch, E. Rodriguez Calzado, J. W. Chirigotis, M. Ducey, J. Dumortier, N. C. Ellebracht, R. Gil Egui, A. Fowler, K. Georgiou, H. Goldstein, D. Hayes, C. Hellwinckel, S. Hovorka, E. Hunter-Sellars, W. Kirkendall, S. Kuebbing, P. Lamers, M. Langholtz, M. Layer, R. Lewis, W. Li, A. Mayer, K. K. Mayfield, P. Nico, S. H. Pang, K. Paustian, G. Peridas, H. Pilorge, S. Ponomareva, L. Price, P. Psarras, G. P. Robertson, J. W. Sagues, D. Sanchez, C. Scown, B. M. Schmidt, E. W. Slessarev, A. J. Stanley, A. Swan, C. Toureene, A. A. Wong, E. Woods, M. Mba Wright, Y. Zhang, R. D. Aines, Initial Considerations for Large-Scale Carbon Removal in the United States: Description of Methods, Feedstocks, and Constraints, March, 2022, Lawrence Livermore National Laboratory
  6. Schmidt, B., J. Stolaroff, S. Baker, N. Ellebracht, W. Kirkendall, A. Simon, G. Peridas, E. Slessarev, J. Pett-Ridge, S. Pang, M. Langholtz and R. Aines, Carbon Negative by 2030: CO2 removal options for an early corporate buyer February, 2022, Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States).
  7. 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 https://doi.org/10.2172/1597217
  8. 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.
  9. (multi-author) Building a New Carbon Economy: An Innovation Plan, September 2018. Carbon 180 (formerly Center for Carbon Removal)
  10. (multi-author) Grand Challenges Workshop Report, March 2017 U.S. Department of Energy Office of Science, Biological and Environmental Research Advisory Committee (BERAC)
  11. (multi-contributor) “Microbes and Climate Change,” April, 2017, American Society for Microbiology (ASM) and American Geophysical Union (AGU)
  12. (multi-author) Technologies for Characterizing Molecules to Mesoscale Workshop Report, Sept 2016 U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
  13. (multi-author) Microbes and Climate Change, report on an American Academy of Microbiology and American Geophysical Union Colloquium held in Washington, DC, March 2016
  14. Groffman, P.M., AB Box, PJ Bohlen, L. Pardo, J. Pett-Ridge et al. 2015. Long-term measurements of microbial biomass and activity at the Hubbard Brook Experimental Forest, 1994 – present. Hubbard Brook Ecosystem Study
  15. Robertson, G.P, J. Pett-Ridge, M. Udvardi. 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

Patents

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.

Micklin, E.C., W. Moestopo, J. Pett-Ridge, A. Parakh. (2025). “System And Method for Biodegradable Soil Temperature Sensors” Case # LL-2025-180-0 I, initial patent filed. US Patent and Trademark Office, Lawrence Livermore National Security, USA.

  • 2025, Elected Fellow of American Association for the Advancement of Science (AAAS)
  • 2025, Elected to Alameda County Women’s Hall of Fame
  • 2024, LLNL Global Security Gold Award for “Roads to Removal” report
  • 2024, Elected Fellow of Ecological Society of America
  • 2023, Deborah A. Neher Career Award Soil Ecology Section-Ecological Society of America
  • 2023, Elected Member at Large, Soil Ecology Society
  • 2022, Promoted to Distinguished Member of the Technical Staff
  • 2022, DOE Office of Science Ernest Orlando Lawrence Award
  • 2021, DOE Secretary of Energy Achievement 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/Mid-Career Recognition Award
  • 2015, LLNL Director’s Science and Technology Award
  • 2014, DOE Early Career Research Program Fellowship
  • 2014, Elected to Environmental & Molecular Sciences Laboratory User Executive Committee
  • 2013, Best Talk, Biogeosciences Section, AGU Annual Meeting
  • 2009, International Society for Microbial Ecology, Journal Cover Contest
  • 2000-2004, Graduate Fellowship, DOE Global Change Education Program

Service

  1. Session Convener and Conference Organizer
  • Science Committee, 2022 Goldschmidt Conference (2021-2022)
  • Organizer, Switchgrass Microbiome meeting, UC Berkeley (April, 2019)
  • “Plants-microbes-minerals: interactions that drive soil organic matter cycling”, AGU Fall Meeting, San Francisco (Dec, 2019)
  • “How Spatial and Temporal Redox Dynamics Shape Biogeochemistry in Soils and Sediments Across Scales” Goldschmidt, Paris (July, 2017)
  • “Linking Microbial Identity and Activity with NanoSIMS”, International Society of Microbial Ecology Meeting, Cairns, Australia (Aug, 2008)
  1. Journal Editor and Leadership Positions:
  • Advisory Board, CDRXIV (2024-present)
  • Editor, American Society for Microbiology, Microbiology and Molecular Biology Reviews “MMBR” (2022-present)
  • Special Topic Editor, Soil Biology & Biochemistry “Soil virus ecology: how viral infection shapes microbial communities and biogeochemical processes” (2023-present)
  • Senior Editor, ISME Communications (2020-2024)
  1. Leadership Positions:
  • Guest Editor, Soil Biology and Biochemistry special issue on “Soil Viruses”
  • Scientific Advisory Board, Andes Bio (2024-present)
  • Scientific Advisory Committee (SAC), Joint Genome Institute (2022-present)
  • Scientific Advisory Board, Salk Institute Harnessing Plant Initiative (2022-present)
  • Chair: External Advisory Board, NSF Science & Technology Center, Center for Chemical Currencies of a Microbial Planet (C-CoMP). (2022-present)
  • Belowground Biodiversity Advisory Committee (BBAC), (2022-2023)
  • USA Senior Ambassador, International Society for Microbial Ecology (2019-present)
  • Committee Member, Goldschmidt Biogeochemistry Medal award committee (2020-2022)
  • Committee Member, AGU Biogeosciences Section Fellows committee (2018-2020)
  • Chair, SLAC Biosciences Division Scientific Advisory Committee (2015)
  1. Elected Service
  • At Large Member, Soil Ecology Society (2023-2025)
  • Secretary, Biogeosciences Section, American Geophysical Union (2018-2021)
  • User Executive Committee, Environmental and Molecular Sciences Lab, (2013-2017)
  • Vice Chair, Soil Ecology Section, Ecological Society of America (2006-2009)

Professional Affiliations

  • Ecological Society of America (Vice Chair for the Soil Ecology section 2006-2009)
  • American Geophysical Union (Secretary for Biogeosciences Section, 2018-2020)
  • International Society of Microbial Ecology (currently Senior Ambassador for USA)
  • American Society of Microbiology
  • Geochemical Society
  • AAAS
  • Soil Ecology Society (Member at Large, 2023-present)
  • European Association of Geochemistry
  • Applied Microbiology International
  • Earth Science Women’s Network
  • 500 Women Scientists

 

Ten Most Important Scientific Talks

  1. Closing Plenary: Rhizosphere 6 Meeting. The Future of Rhizosphere Research. Edinburgh, UK, June 19, 2025
  2. National Center for Soil Ecology Symposium on Climate-Friendly Agricultural Soils, “Farming Carbon: Harnessing Plant Roots, Microbial Ecophysiology, and Soil Minerals to Accelerate Soil-Based Carbon Drawdown”, Amsterdam, Netherlands, March 10, 2025
  3. International Microbiome Symposium, IIT, “Pursuing Wild Microbes: Microbiome Interactions and Ecophysiological Traits that Shape the Persistence of Soil Carbon”, Chennai India, Feb 19, 2025
  4. UC Berkeley Hans Jenny Memorial Lecture in Soil Science, “The Music of Soil: Environmental drivers, ecophysiological traits and microbiome interactions that shape the persistence of soil carbon” Berkeley, CA, Nov 7, 2024
  5. Plenary talk: Science Summit for Energy Earthshot Innovation, Roads to Removal: A Comprehensive Assessment of Carbon Dioxide Removal Options in the United States, Washington DC, Sept 2024
  6. Distinguished Karling Lecture: Mycological Society of America. Fungi and Friends: An Expanded View of Fungal-Bacterial Interactions and Biogeochemical Effects in the Mycorrhizal Hyphosphere. Flagstaff, AZ, July 2023
  7. Invited Lecture: NanoSIMS Workshop, National Physical Laboratory. Analyses on the edge of our comfort zone: NanoSIMS studies of soil organic matter, microbial interactions and viruses 2022 Teddington, UK, Oct 2022
  8. Keynote lecture: Joint Annual Meeting of the Soil Science Societies of Germany and Switzerland. How Phage and Fauna Shape the Movement of Root Carbon Through Microbial Pathways, Bern Switzerland, 8/19
  9. Endowed Biogeochemistry Lecture, Goldschmidt Meeting. Impacts of Dynamic Soil Redox on Biogeochemical Transformations and Soil Microbiomes, Barcelona, Spain, August 2019
  10. Invited talk: Kirkham Meeting. Carbon Transformations in The Rhizosphere: The Critical Role of Microbial Functional Capacity, Israel, April 2016