Alison Berry

image of Alison Berry

Professor of Plant Sciences


Plant Sciences, College of Agricultural and Environmental Sciences

Offices and Labs

Room 2228, Plant and Environmental Sciences Building (PES)
(530) 752-7683


1983 PhD Botany University of Massachusetts
1978 MS Botany University of Massachusetts
1970 BA Anthropology Harvard University

Research Contribution

1. Nitrogen is the nutrient most often limiting in forest and agroecosystems. Biological nitrogen fixation contributes net N without using petroleum-based resources. One focus of my work explores the molecular bases of root nodule development and nitrogen assimilation. 2. Microbial communities contribute to plant biomass turnover and feedstock deconstruction for biofuels crops; and to soil carbon and nutrient cycling, especially in the rhizosphere. Projects in my program have elucidated genomic and biochemical aspects of biomass degradation. 3. My program is also concerned with human impacts on natural systems, specifically a) the impact of transportation infrastructure on plant communities and habitat; and b) modeling interactions between tree root systems and levee infrastructure. 4. A current project is investigating microbiomes in soil profiles, using next-gen sequencing together with an array of markers for biogeochemical processes.

Research Interests

Biological nitrogen fixation; root and rhizosphere plant-microbe associations, and applications in agroecology; soil microbial ecology; microbial genomics; tree root architecture; plant nutrition and ecophysiology; microbial deconstruction of cellulosic biomass and microbial biofuels.


2010: Honorary Doctorate, Faculty of Science, Stockholm University, Sweden
2008-present: Visiting Professor, Department of Botany, Stockholm University, Sweden
1997 (Fall): Visiting professor, Stockholm University, Department of Botany
1996 (Spring): Visiting professor, University of Lyon (France), Department of Soil Microbial Ecology
1966-1970: National Merit Scholarship

Department and Center Affiliations

Director, UC Davis Road Ecology Center


American Society for Microbiology
American Society of Plant Biologists
Ecological Society of America

Specialties / Focus

Plant Biology
  • Molecular Biology, Biochemistry and Genomics
  • Environmental and Integrative Biology

Graduate Groups not Housed in CBS

Ecology Graduate Group
Horticulture and Agronomy Graduate Group


11/16/2011 8:54:17 AM
  • Berry, AM, Mendoza-Herrera A, Guo Y-Y, Hayashi J, Persson T, Barabote R, Demchenko K, Zhang S, and Pawlowski K. 2011. New perspectives on nodule nitrogen assimilation in actinorhizal symbioses. Functional Plant Biology 38: 645-652.
  • Pawlowski K, Bogusz D, Ribeiro A, and Berry AM. 2011. Progress in research on actinorhizal plants. Functional Plant Biology 38: 633-638.
  • Rezaei F, Joh LD, Berry AM, VanderGheynst JS. 2011. Xylanase and cellulase production by Acidothermus cellulolyticus grown on switchgrass in solid-state fermentation. Biofuels 2 (1): 21-32.
  • Barabote R, Parales J, Parales R, and AM Berry. 2010. Characterization of a thermostable family 10 endo-xylanase (Xyl-1) from Acidothermus cellulolyticus 11B. Appl. & Env. Microbiology.
  • Joh LD, Rezaei F, Barabote RD, Parales JV, Parales RE, Berry AM, VanderGheynst JS. 2010. Effects of Phenolic Monomers on Growth of Acidothermus cellulolyticus . Biotechnology Progress.
  • VanderGheynst J, Rezaei F, Dooley TM and AM Berry. 2010. Switchgrass leaching requirements for solid-state fermentation by Acidothermus cellulolyticus. Biotechnology Progress,26 (3): 622-626.
  • Holmes, K.A., K.E. Veblen, A.M. Berry & T.P. Young. 2010. Effects of prescribed fires on planted valley oak saplings at a research restoration site in the Sacramento Valley. Restoration Ecology.
  • Li T, Shilling F, Thorne J, Li F, Schott H, Boynton R, Berry AM. 2010. Fragmentation of China’s landscape by roads and urban areas. Landscape Ecology.
  • Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Medigue C, Adney WS, Xu XC, Lapidus A, Detter JC, Pujic P, Parales R, Bruce D, Lavire C, Challacombe JF, Brettin TS, and AM Berry. 2009. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Research 19(6): 1033-1043.
  • Adney WS, van der Lelie N, Berry A, and ME Himmel. 2008. Understanding the biomass decay community: Biomass recalcitrance. IN: M. Himmel, ed., Deconstructing the Plant Cell Wall for Bioenergy. Oxford, UK: Blackwell Publishing pp. 454-479.
  • Girvetz EH, Thorne JH, Berry AM, and JAG Jaeger. 2008. Integration of landscape fragmentation analysis into regional planning: A statewide multi-scale case study from California, USA. Landscape & Urban Planning 86: 205-218
  • Solomeshch A.I., S.N. Long, M.G. Barbour, and A.M. Berry. 2009. Floristic Composition of Roadside Grasslands, Yolo County, California. IN: IN: Espinosa-García F, Hubbard T, Van Devender TR, Harper-Lore B, editors. Invasive Plants on the Move. Controlling them in North America. Proceedings, Weeds Across Borders 2006, Hermosillo, Mexico. Arizona-Sonora Desert Museum Press, Tucson, AZ.
  • Normand P. , Lapierre P., Tisa L.S., J.P., Alloisio N., Bassi C.A., Berry A.M., Bickhart D.M., Choisne N., Couloux A., Cournoyer B, Cruveiller S., Daubin V., Demange N., Pilar Francino M., Goltsman E., Huang Y., Kopp O., Labarre L., Lapidus A., Lavire C., Marechal J., Martinez M., E. Mastronunzio J.E., Mullin B., Niemann J., Pujic P., Rawnsley T., Rouy Z., Schenowitz C., Sellstedt A., Tavares F., Tomkins J.P., Vallenet D., Valverde C., Wall L., Wang Y., Medigue C. & Benson D.R.. 2007. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Research 17(1): 7-15.
  • Pawlowski K., K.R. Jacobsen, N. Alloisio, R.F. Denison, M. Klein, J.D. Tjepkema, T. Winzer, A. Sirrenberg, C. Guan, A.M. Berry. 2007. Truncated hemoglobins in actinorhizal nodules of Datisca glomerata. Plant Biol. 9, 776-785.
  • Alloisio N, Maréchal J, Brian Vanden Heuvel B, Normand P, Berry AM. Characterization of a gene locus containing squalene-hopene cyclase (shc) in Frankia ACN14a and an shc homolog in Acidothermus cellulolyticus . 2005. Symbiosis 39: 83-90.
  • King AP and AM Berry. 2005. Vineyard 15N, nitrogen and water status in perennial clover and bunch grass cover crop systems of California’s Central Valley. Agriculture Ecosystems & Environment 109 (3-4): 262-272.
  • Berry AM, Murphy TM, Okubara PA, Jacobsen KR, Swensen SM, and K Pawlowski. 2004. Novel expression pattern of cytosolic glutamine synthetase in nitrogen-fixing root nodules of the actinorhizal host, Datisca glomerata Plant Physiology 135: 1849-1862.