Naupaka Zimmerman


Biogeography, ecological function, and evolution of plant microbiomes.

Complete CV (updated September 2023)

Naupaka Zimmerman is currently an Associate Professor in the Biology Department at the University of San Francisco, where he teaches courses in Microbiology, Ecology, Urban Ecology, California Ecology, and Bioinformatics (among others). He is broadly interested in the intersection between microbial community and ecosystem ecology, and is currently examining it in the context of endophytic fungal communities via next-gen molecular methods (e.g. Zimmerman et al. 2014). While these communities are incredibly diverse, particularly in the tropics, we know very little about their functions in ecosystems. Using a combination of field surveys and greenhouse manipulations, he is currently engaged in a number of different projects trying to understand what these enigmatic organisms are up to.

Prior to USF, he was a postdoc at the University of Arizona as a Gordon and Betty Moore Fellow of the Life Sciences Research Foundation, working in the Arnold Lab. His work there focused on understanding the mechanisms of interaction between foliar endophytes and host (Huang, Zimmerman, and Arnold 2018) in black cottonwood (Populus trichocarpa), on the circumglobal biogeography of boreal endophytes (U’Ren et al. 2019), and the phylogenetic distinctness of endophytes in the Xylariaceae (U’Ren et al. 2016).

His PhD dissertation at Stanford (as part of the Vitousek Lab) focused primarily on the biogeography of communities of foliar fungal endophytes that inhabit the asymptomatic leaves of ʻōhiʻa (Metrosideros polymorpha), an endemic Hawaiian tree (Zimmerman and Vitousek 2012). He also worked on a number of collaborative projects examining the functional consequences of pathogen-endophyte-genotype interactions (Busby et al. 2013) in narrowleaf cottonwood (Populus angustifolia).

After graduating from college, he spent a year in the Schrag geochemical oceanography lab as a technician reconstructing past climatic trends from oxygen isotope records in marine sulfate (e.g. Turchyn et al. 2009) and in cores from long-lived tropical tree species (e.g. Anchukaitis et al. 2008). He also spent a year teaching in Seoul, South Korea before starting grad school.

His undergrad degree was in Environmental Science and Public Policy and Social Anthropology at Harvard University. His interdisciplinary honors thesis focused on understanding how differing environmental conceptions (scientific, indigenous, economic, etc) play out in the construction of public narrative and policy. His ecological research during that time was focused on lowland wet forest communities along a substrate age (successional) gradient in Hawaiʻi, with particular focus on how invasive species alter the successional trajectories of these forests (Zimmerman et al. 2008).


Anchukaitis, K. J., M. N. Evans, N. T. Wheelwright, and D. P. Schrag. 2008. “Stable Isotope Chronology and Climate Signal Calibration in Neotropical Montane Cloud Forest Trees.” Journal of Geophysical Research 113 (G3).
Busby, Posy E, Naupaka B. Zimmerman, David J Weston, Sara S Jawdy, Jos Houbraken, and George Newcombe. 2013. “Leaf Endophytes and Populus Genotype Affect Severity of Damage from the Necrotrophic Leaf Pathogen, Drepanopeziza Populi.” Ecosphere 4 (10): art125.
Huang, YL, NB Zimmerman, and AE Arnold. 2018. “Observations on the Early Establishment of Foliar Endophytic Fungi in Leaf Discs and Living Leaves of a Model Woody Angiosperm, Populus Trichocarpa (Salicaceae).” J Fungi (Basel) 4 (2).
Turchyn, Alexandra V., Daniel P. Schrag, Rodolfo Coccioni, and Alessandro Montanari. 2009. “Stable Isotope Analysis of the Cretaceous Sulfur Cycle.” Earth and Planetary Science Letters 285 (1-2): 115–23.
U’Ren, JM, F Lutzoni, J Miadlikowska, NB Zimmerman, I Carbone, G May, and AE Arnold. 2019. “Host Availability Drives Distributions of Fungal Endophytes in the Imperilled Boreal Realm.” Nat Ecol Evol 3 (10): 1430–37.
U’Ren, JM, J Miadlikowska, Naupaka B. Zimmerman, F Lutzoni, JE Stajich, and AE Arnold. 2016. “Contributions of North American Endophytes to the Phylogeny, Ecology, and Taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).” Molecular Phylogenetics and Evolution 98: 210–32.
Zimmerman, Naupaka B., R Flint Hughes, Susan Cordell, Patrick J Hart, Heather Kalei Chang, David Perez, Ryan Kaipoalohaakala Like, and Rebecca Ostertag. 2008. “Patterns of Primary Succession of Native and Introduced Plants in Lowland Wet Forests in Eastern Hawai’i.” Biotropica 40 (3): 277–84.
Zimmerman, Naupaka B., Jacques Izard, Christian Klatt, Jizhong Zhou, and Emma Aronson. 2014. “The Unseen World: Environmental Microbial Sequencing and Identification Methods for Ecologists.” Frontiers in Ecology and the Environment 12 (4): 224–31.
Zimmerman, Naupaka B., and Peter M Vitousek. 2012. “Fungal Endophyte Communities Reflect Environmental Structuring Across a Hawaiian Landscape.” Proceedings of the National Academy of Sciences 109 (32): 13022–27.