Erin Elaine Nuccio

Staff Scientist
Nuclear and Chemical Sciences Division
Phone: +19254239983


  • 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

Research Interests

Nuccio’s research focuses on how roots and mycorrhizae affect key microbial processes in soil, such as the decomposition of plant residues and turnover of soil organic matter. She uses metagenomics, metatranscriptomics, and isotope technologies (e.g., stable isotope probing, Chip-SIP, radiocarbon) as tools to understand the molecular underpinnings that drive these processes in soil. She is particularly interested in near-surface carbon cycling (0-3m) and the ecological factors that shape the microbial communities living on and around plant roots and hyphae—soil microhabitats known as the rhizosphere and hyphosphere.


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.

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. 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 (in press).

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.

Liang, Y., Xiao X., Nuccio E.E., Yuan M., Zhang N., Xue K., Cohan F., Zhou J., and B. Sun. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Environmental Microbiology (in press).

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, 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. (in press)

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.

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

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. *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

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.

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. 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.

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.

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.