Research Interests

Erin Nuccio is a soil microbial ecologist who studies how roots and their associated microbiome affect microbial processes in soil. She recently received a DOE Early Career award to study how tripartite plant-mycorrhizal-soil interactions impact terrestrial nutrient cycling and ecosystem sustainability. She co-leads the plant-microbial interactions thrust of LLNL’s Biofuels Scientific Focus Area (bio-sfa.llnl.gov), which studies microbial symbioses associated with bioenergy plants. She uses metagenomics, metatranscriptomics, isotope technologies (e.g., stable isotope probing, Chip-SIP, radiocarbon), and microscopy as tools to determine the mechanisms that underpin plant-microbial-soil interactions. She is particularly interested ecological factors that shape the microbial communities living on and around plant roots and hyphae—soil microhabitats known as the rhizosphere and hyphosphere—and near-surface carbon cycling (0-3m). She is currently the Vice Chair of the EMSL User Executive Committee.

Ph.D., Microbiology, University of California, Berkeley, 2013

MESM, Environmental Science and Management, University of California, Santa Barbara, 2006

B.S., Environmental Science, Santa Clara University, 2004

B.A., Religious Studies, Santa Clara University, 2004

Nuccio E.E., Blazewicz S.J., Lafler M., Campbell A.N., Kakouridis A., Kimbrel J.A., Wollard J., Vyshenska D., Riley R., Tomatsu A., Hestrin R., Malmstrom R.R., Firestone M.K., and J. Pett-Ridge. 2022. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 10: 199. https://doi.org/10.1186/s40168-022-01391-z Video Byte: https://youtu.be/6s-5G-_SZpQ

Slessarev, E.S., 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. 00: 1–9. https://doi.org/10.1111/gcb.16491

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

Greenlon A., Sieradzki E., Zablocki O., Koch B.J., Foley M.A., Kimbrel J.A., Hungate B.A., Blazewicz S.J., Nuccio E.E., Sun C.L., Chew A., Mancilla C.J., Sullivan M.B., Firestone M.K., Pett-Ridge J., 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. https://doi.org/10.1128/msystems.00417-22

Lee J., Hestrin R., Nuccio E.E., Morrison K.D., Ramon C.E., Samo T.J., Pett-Ridge J., Ly S.S., Laurence T.A., and P.K. Weber. 2022. Label-Free Multiphoton Imaging of Microbes in Root, Mineral, and Soil Matrices with Time-Gated Coherent Raman and Fluorescence Lifetime Imaging. Environmental Science & Technology. 56(3): 1994-2008. https://doi.org/10.1021/acs.est.1c05818

Slessarev E.W., Chadwick O.A., Sokol N.W., Nuccio E.E., and J. Pett-Ridge. 2022. Rock weathering enhances the potential for soil carbon storage at a continental scale. Biogeochemistry. 157: 1-13. https://doi.org/10.1007/s10533-021-00859-8

Nuccio E.E., Nguyen N.H., Nunes da Rocha U., Mayali X., Bougoure J., Weber P.K., Brodie E.L., Firestone M.K., and 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

Min K., Slessarev E., Kan M., McFarlane K.J., Oerter E., Pett-Ridge J., Nuccio E.E., and A. Asefaw 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

Oerter E., Slessarev E., Visser A., Min K., Kan M., McFarlane K.J., Saha M.C., Asefaw Berhe A., Pett-Ridge J., and E.E. Nuccio. 2021. Hydraulic Redistribution by Deeply Rooted Grasses and its Ecohydrologic Implications in the Southern Great Plains of North America. Hydrological Processes. 35(9): e14366. https://doi.org/10.1002/hyp.14366

Trubl, G., Kimbrel J.A., Liquet-Gonzalez J., Nuccio E.E., Weber P.K., Pett-Ridge J., Jansson J.K., Waldrop M.P., and S.J. Blazewicz. 2021. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome. 9(208). https://doi.org/10.1186/s40168-021-01154-2

Nicolas, A.M., Jaffe A.L., Nuccio E.E., Taga M.E., Firestone M.K., and J.F. Banfield. 2021. Soil CPR encode components of aerobic metabolism and co-occur with nanoarchaea in the rare biosphere of rhizosphere grassland communities. mSystems. 6(4): e01205-20. https://doi.org/10.1128/mSystems.01205-20

Yuan M., Kakouridis A., Starr E., Nguyen N., Shi S., Pett-Ridge J., Nuccio E.E., Zhou J., and M.K. Firestone. 2021. Fungal-bacterial co-occurrence patterns differ between AMF and non-mycorrhizal fungi across soil niches. mBio. 12(2): e03509-20. https://doi.org/10.1128/mBio.03509-20

Bates C.T., Escalas A., Kuang J., Hale L., Wang Y., Herman D.J., Nuccio E.E., Wan X.­­, Bhattacharyya A., Fu Y., Tian R., Wang G., Ning D., Yang Y., Wu L., Brodie E.L., Pett-Ridge J., Saha M., Craven K., Firestone M.K., and 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

Sieradzki E.T., Nuccio E.E., Pett-Ridge J., and M.K. Firestone. Transcription of macromolecular N degrading genes provides a window into organic nitrogen decomposition in soil. bioRxiv. https://doi.org/10.1101/2020.12.14.422732

Pett-Ridge, J., Shi S., Estera-Molina K., Nuccio E.E., Yuan M., Rijkers R., Swenson T., Zhalnina K., Northen T., Zhou J., and 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

Nuccio, E.E., Starr E., Karaoz U., Brodie E.L., Zhou J., Tringe S., Malmstrom R.R., Woyke T., Banfield J., Firestone M.K., and J. Pett-Ridge. 2020. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME Journal. 269(9): 1–16. https://doi.org/10.1038/s41396-019-0582-x

Blazewicz S.J., Hungate B.A., Koch B.J., Nuccio E.E., Morrissey E., Brodie E.L., Schwartz E., Pett-Ridge J., and M.K. Firestone. 2020. Taxon-specific growth and mortality rates of bacteria reveal temporal population responses in soil following perturbation from the rewetting of a seasonally dried grassland. ISME Journal. 14(6):1520-1532. https://doi.org/10.1038/s41396-020-0617-3

Sher, Y., Baker N.R., Herman D.J., Fossum C., Hale L., Zhang X., Nuccio E.E., Saha M., Zhou J., Pett-Ridge J., and 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. https://doi.org/10.1016/j.soilbio.2020.107742

Liang, Y., Xiao X., Nuccio E.E., Yuan M., Zhang N., Xue K., Cohan F., Zhou J., and B. Sun. 2020. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Environmental Microbiology. 22: 1327-1340. https://doi.org/10.1111/1462-2920.14945

Slessarev, E., Nuccio, E.E., McFarlane, K. J., Ramon, C., Saha, M., Firestone, M. K. & Pett-Ridge, J 2020. Quantifying the effects of switchgrass (Panicum virgatum) on deep organic C stocks using natural abundance 14C in three marginal soils. GCB Bioenergy. 12: 834–847. https://doi.org/10.1111/gcbb.12729

Starr, E. P., Nuccio, E.E., Pett-Ridge, J., Banfield, J. F., & Firestone, M. K. 2019. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proceedings of the National Academy of Sciences. 116(51): 25900–25908. https://doi.org/10.1073/pnas.1908291116

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

Shi, S.,* Nuccio E.E.,* Shi S., He Z., Zhou J., and M.K. Firestone. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecology Letters. 19(8): 926-936. https://doi.org/10.1111/ele.12630 *equal contribution

Nuccio, E.E., Anderson-Furgeson J., Estera K.Y., Pett-Ridge J., de Valpine P., Brodie E.L., and M. K. Firestone. 2016. Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass. Ecology, 97: 1307-1318. https://doi.org/10.1890/15-0882.1

Shi, S., Nuccio E.E., Herman D.J., Rijkers R., Estera K.Y., Li J., da Rocha U.N., He Z., Pett-Ridge J., Brodie E., Zhou J., 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

Nuccio E.E., Hodge A., Pett-Ridge J., Herman D.J., Weber P.K., and 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. https://doi.org/10.1111/1462-2920.12081 Cover Image

Pett-Ridge, J., Petersen D.G., Nuccio E.E., 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. https://doi.org/10.1111/1574-6941.12111

Nuccio, E.E. (2013). Deconstructing the soil microbiome: elucidating the influence of roots and arbuscular mycorrhizae on soil microbial communities. PhD dissertation. University of California, Berkeley.

Herman, D., Firestone M.K., Nuccio E.E., and A. Hodge. 2012. Interactions between an arbuscular mycorrhizal fungus and a soil microbial community mediating litter decomposition. FEMS Microbiology Ecology. 80:236-247. https://doi.org/10.1111/j.1574-6941.2011.01292.x

Watts, S.W., Uhl M.M., Maurano S.P., and E.E. Nuccio. 2010. Using small-scale studies to prioritize threats and guide recovery of a rare hemiparasitic plant: Cordylanthus rigidus ssp littoralis. PLoS ONE 5(1): e8892. https://doi.org/10.1371/journal.pone.0008892

• 2020 DOE Early Career Research Program Award