Soil Microbiology at the University of California, Berkeley
Firestone Lab


Google Scholar


Sieradzki, Ella T, BJ Koch, A Greenlon, R Sachdeva, RR Malmstrom, RL Mau, SJ Blazewicz, MK Firestone, K Hofmockel, E Schwartz, BA Hungate, J Pett-Ridge. 2020. Measurement error and resolution in quantitative stable isotope probing: implications for experimental design. mSystems 5:e00151-20 https.//

Slessarev, Eric W,  EE Nuccio,  KJ McFarlane,  C Ramon,  M Saha, MK Firestone, Jennifer Pett-Ridge. 2020.  Quantifying the effects of switchgrass (Panicum virgatum) on deep organic C stocks using natural abundance 14C in three marginal soils. GCB Bioenergy. doi:

Daliang Ning, Mengting Yuan, Linwei Wu, Ya Zhang, Xue Guo, Xishu Zhou, Yunfeng Yang, Adam Arkin, Mary Firestone, and Jizhong Zhou. 2020.  A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming.  Nature Comm. (In press)

Pett-Ridge, Jennifer, S Shi, K Estera-Molina, E Nuccio, R Rijkers, K Zhalnina, T Northen, J Zhou, MK Firestone. 2021. Rhizosphere Carbon Turnover from Cradle to Grave: the Role of Microbe-Plant Interactions.  In: Gupta, V and Sharma, A (eds)  Rhizosphere Biology: Interactions Between Microbes and Plants.  Springer, Singapore. .1007/978-981-15-6125-2_2 

Chenchao Xu, K Zhang, W Zhu, J Xiao, C Zhu, N Zhang, F Yu, Shuyao Li, C Zhu, Q Tu, Xin Chen, J Zhu, S Hu, RT. Koide, MK Firestone & Lei Cheng. 2020.  Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO2.  Science Advances.

Aigle, Axel, C Gubry-Rangin, C Thion, K Estera, H Richmond, J Pett-Ridge, MK Fire

stone, G Nicol, J Prosser, (2020). Experimental testing of hypotheses for temperature- and pH-based niche specialisation of ammonia oxidising archaea and bacteria. Environmental Microbiology and Environmental Microbiology Reports

Barnard, R.L., Blazewicz, S.J. & Firestone M.K. (2020) Rewetting of soil: Revisiting the origin of soil CO2 emissions. Soil biology and Biogeochemistry.

Nuccio, E.E., Star, E.P., Karaoz, U., Brodie, E.L., Zhou, J., Tringe, S.G., Malmstrom, R.R., Woyke, T., Banfield, J.F., Firestone, M.K. & Pett-Ridge, J. (2020). Niche differentiation is spatially and temporally regulated in the rhizosphere. The ISME Journal DOI: 10.1038/s41396-019-0582-x

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

Blazewicz, S.J., Hungate, B.A., Koch, B.J., Nuccio, E.E., Morrissey, E., Brodie, E.L., Schwartz, E., Pett-Ridge, J & Firestone, M.K. (2020) Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J 14, 1520–1532 .

Bates, C. T., Escalas, A., Kuang, J. Hale, L., Wang, Y., Herman, D., Nuccio, E.E., Wang, X., Ning, D., Yang, Y., Wu, L. Pett-Ridge, J., Saha, M., Craven, K., Firestone, M.K. & Zhou, J. (2020). Conversion of marginal land into switchgrass conditionally accrues soil carbon and reduces methane consumption. bioRxiv 2020.03.18.997304 (2020) DOI:10.1101/2020.03.18.997304.

Sieradzki, E. T., Koch, B.J., Greenlon, A., Sachdeva, R., Malmstrom, R.R., Mau, R.L., Blazewicz, S.J. (2020). “Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.” BioRxiv:

Ning, D., Yuan, M., Wu, L., Zhang, Y., Guo, X, Zhou, X. Yang, Y., Arkin, A.P., Firestone, M.K. & Zhou, J. (2020). A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming. BioRxiv DOI:


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. PNAS 116 (51): 25900-25908 DOI: 10.1073/pnas.1908291116


Starr, E.P., Shi, S., Blazewicz, S.J., Probst, A.J., Herman, D.J., Firestone, M.K. & Banfield, J.F. (2018). Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. Microbiome 6(1) DOI: 10.1186/s40168-018-0499-z

Zhalnina, Kate, K.B. Louie, Z. Hao, N. Mansoori, U. Nunes da Rocha, S. Shi, H. Cho, U. Karaoz, D. Loqué, B.P. Bowen, M.K. Firestone, T.R. Northen, and E.L. Brodie. 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature Microbiology 3:470-480.

Whitman, Thea, R. Neurath, A. Perera, D. Ning, J. Zhou, P. Nico, J. Pett-Ridge, and M. Firestone. 2018. Microbial community assembly differs across minerals in a rhizosphere microcosm.   Environ Microbiol. 20:  4444-4460. DOI: 10.1111/1462-2920.14366

Gao, J., Sasse, J., Lewald, K.M., Zhalnina, K., Cornmesser, L.T., Duncombe, T.A., Yoshikuni, Y., Vogel, J.P., Firestone, M.K., Northen, T.R.  2018. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. J. Vis. Exp. (134), e57170, doi:10.3791/57170.Shi, Shengjing, D.J. Herman, Z. He, J Pett-Ridge, L. Wu, J. Zhou, M.K. Firestone.  2018. Plant roots alter microbial functional genes supporting root litter decomposition. Soil Biol. Biochem. 97:90-99.