Talk by Zhen Li, Postdoctoral Researcher, Lawrence Livermore National Lab: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry

Hosted by the Ecosystem Genomics GIDP

Alaska Arctic Wetlands


noon to 1 p.m., April 10, 2024

Harvill 107

Seminar Format 

Available in-person and via Zoom webinar. Contact the department to subscribe to the email list (zoom link provided in announcement).


Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, and mechanistic ecosystem models has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and demonstrated its application at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides the first example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.


Zhen (Jen) Li is currently a post-doctoral researcher in Lawrence Livermore National Laboratory (LLNL). She received a Ph.D. in Civil and Environmental Engineering from Colorado School of Mines. Prior joining LLNL, she was a post-doctoral associate at the University of Arizona/Lawrence Berkeley National Laboratory working with Dr. Bill Riley. Her expertise lies in terrestrial ecosystem modeling, permafrost carbon dynamics, soil physics and vadose zone hydrology. Her interest in multidisciplinary research and upscaling drives her to collaborate with experts from different fields, including microbiologist, biogeochemist and ecologists. She strives to characterize and enhance process-based terrestrial ecosystem models at the site-scale, with the goal of improving earth system models.

Zhen Li Email | Website | Google Scholar


Scott Saleska, Host