Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)
Barrow Environmental Observatory

Photo by:  Roy Kaltschmidt
The Barrow Environmental Observatory, 330 miles north of the Arctic Circle.

Environmental & Biological Systems Sciences Program Area

Research Mission is to...Develop a predictive understanding of microbial metabolic diversity that mediates biogeochemical processes in Earth systems and that can be harnessed to provide environmental solutions, such as biofuel pathway development


Physical, chemical, and biological soil and subsurface interactions are critically important for sustaining life. These interactions regulate the geochemical flux of life-critical elements, control the production of food, and purify water. Biologically based processes can also be used to extract or enhance natural energy resources. To ensure the sustainability of these critical terrestrial system services, it is imperative to develop a quantitative and predictive understanding of how abiotic and biotic components interact and can be harnessed to create new classes of green solutions.

A key characteristic of ESD’s Environmental & Biological Systems Sciences Program Area is its ability to interrogate and interpret small-scale biological processes within the context of larger Earth systems, including molecules in leaves as well as microbial communities in terrestrial environments, marine systems, and energy reservoirs. Scientists working in this Program Area strive to develop the understanding and capabilities to predict how living systems are organized and function, from molecular to watershed and reservoir scales. Scientists also develop cutting edge tools to facilitate such understanding, including the R&D 100 award winning PhyloChip and the ESD-led Berkeley Synchrotron Infrared Structural Biology (BSISB) program. ESD scientists working in this Program Area draw on extensive environmental science expertise in the Division, including a reputation for path-breaking work in molecular environmental microbiology, microbial physiology, shallow subsurface biogeochemistry, environmental geophysics, and multiscale mechanistic modeling of microbially mediated processes. Research in this Program Area is aligned with the LBNL Biosciences Area strategic direction, particularly contributing to the quantification of how microbial communities interact with and transform the functioning of dynamic and heterogeneous Earth Systems.

Research in this Program Area is also highly aligned with the Carbon and Climate Sciences Program Area, because quantifying the affect of climate change on biological systems (and vice versa) requires consideration of bedrock-through-atmospheric processes.

Deepwater Horizon Response

Program Area Leads

Susan S. Hubbard | | 510-486-5266

Eoin Brodie | | 510-486-6584


Bioenergy Program

Harry Beller | | 510-486-7321

Research projects in ESD’s Bioenergy Program apply synthetic biology and bioengineering for fuels production. Four key themes form the crux of the Bioenergy Program: (1) enhancing photosynthesis for food and fuels; (2) constructing biofuel pathways; (3) exploiting microbial diversity, and (4) enhancing microbial hydrocarbon recovery and mitigating hydrocarbon souring. Synthetic biology and metabolic and enzyme engineering are used to establish biochemical pathways for direct conversion of CO2 and CH4 to advanced fuels, including three ARPA-E projects that focus on establishing tobacco as a platform for foliar production of advanced biofuels; development of Microbial Electrocatalytic Biofuel Production; and engineering enzymes for direct methane conversion. ESD scientists lead the JBEI Biofuels Pathways and Microbial Communities Departments, which focus, respectively, on developing new biofuel enzyme candidates and novel pathways in heterotrophic microorganisms, and exploiting microbial communities for the discovery and application of novel biochemistry in lignocellulosic deconstruction. The Petroleum Microbiology Project focuses on integrating reservoir ecogenomics, rates, and mechanisms with monitoring and modeling to develop microbially enhanced hydrocarbon recovery approaches, as well as approaches to remediate reservoir souring.

Key sponsors of the Bioenergy Program include DOE ARPA-E, DOE Genomics Science (JBEI) and the Energy Bioscience Institute. Industry sponsorship of projects in this program is significant and growing, as is the emphasis on establishing biotechnology-to-market plans.


Ecosystems Biology Program

Eoin Brodie | | 510-486-6584

The Ecosystems Biology Program focuses on discovering and understanding the molecular basis of microbial interactions, including specific gene functions, species interactions, and community dynamics under a variety of environmental conditions—ranging from groundwater, soil, and sediments to human and invertebrate guts. The Program also develops technology that enables such understanding. A prime example of advanced technology is the DOE-supported Berkeley Synchrotron Infrared Structural Biology program at the Advanced Light Source, which enables live cell chemical imaging and single-cell metabolic phenotyping of living cells by SF-FTIR spectromicroscopy.

A hallmark characteristic of research in this program is the ability to combine high throughput sequencing and other “omics” technologies (metagenomics, metatranscriptomics, metaproteomics, metabolomics) to determine the microbial community composition, functional gene content, and gene expression in different ecosystems and under different environmental conditions. Research projects in this program include the use of omics tools to explore the impact of climate change (altered precipitation patterns, climate warming, etc.) on microbial survival and processing of soil carbon in a variety of ecosystems that are vulnerable to climate change. Such ecosystems include California grasslands, desert crusts, the Great Prairie of the U.S., and Arctic and tropical soils. The datasets from these ecosystems represent the most extensive molecular characterizations of soil ecosystems in the world.

Research in this program also focuses on advancing multi-omics approaches to gain an understanding of the function of another biome: the human microbiome. Like the Earth system, understanding the role of microbes and microbial community within a human body is challenging and subject to environmental pressures. ESD health-biome research includes investigation of the impact of diet and disease on the gut microbiome. Ongoing multi-omic research directions include exploration of Crohn’s disease and the human gut microbiome, the impact of carbohydrate and resistant starch diets on the human gut microbiome, and assessments of the foregut microbiome at various stages of reflux disorder developing toward esophageal adenocarcinoma.

The lack of environmental isolates impedes physiological investigation of most of the microorganisms driving the cycling of nutrients in ecosystems. To predict “who is where, with whom and doing what” requires linkage of structure and function—from individual microbes to complex communities. An active area of research in this program is focused in unearthing the “dark matter,” the vast majority of isolates hitherto uncultivated from myriad environments through combining meta-‘omics’ with physiological information obtained through isolation and meticulous characterization of Earth’s diverse microbes.

Key sponsors in this program are DOE-Biological and Environmental Research (BER), NIH, and industry.

Environmental Remediation and Water Resources

Kenneth Hurst Williams | | 510-701-1089

Projects in the ESD Environmental Remediation and Water Resources Program contribute to the predictive understanding of coupled hydro-biogeochemical processes and their role in water resources, environmental contaminants, and related terrestrial environment biogeochemical cycling: from the scale of the pore to that of the regional catchment. This research relies heavily on linking controlled laboratory experiments with field observations at sites of relevance to DOE, particularly those expected to be at elevated risk due to the impacts of global climate change or persistent contamination. The ESD Sustainable Systems Science Focus Area 2.0 is emblematic of this research focus. It seeks to develop the process understanding and genome-enabled capabilities required to simulate microbe-catalyzed biogeochemical processes, particularly those relevant for terrestrial environmental feedbacks to climate, contaminant mobility, and agricultural sustainability. Tied with this project, Berkeley Lab leads perhaps the most used subsurface community biogeochemical field observatory in the world: the Rifle, CO, site.

The collection of projects in this program is overwhelmingly multidisciplinary and multi-institutional, involving close collaboration with other National Laboratories, universities, and industry partners. Financial support is provided by DOE-BER as well as DOE Environmental Management and Legacy Management, DOD SERDP, the Bureau of Land Management, various California Water Agencies, and DOE’s Small Business Innovative Research program.

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