Aindrila Mukhopadhyay, a dark-haired person wearing a white jacket, poses for a headshot in the lab.

Soil-plant-microbe interactions

Studying how genomics shape microbial and plant function and microbial communities influence plant growth using various technologies to transform our ability to seamlessly quantify and predict soil-microbe-plant interactions.

Microbiomes or microbial communities

Studying how microbes drive geochemical cycles, environmental dynamics shape microbial communities, and ecosystems affect energy, water and nutrient cycles, and fundamental processes.


Gaining insight from large data sets and developing new simulation tools for ecosystem science using high-performance computing and machine learning.


Using fabricated ecosystems of different scales to bridge the gap between lab and field research and make ecosystem experiments reproducible.

Artistic rendering of the exterior of the BioEPIC facility after construction.

BioEPIC focuses on understanding how microbes interact with soils and plants to influence the environment.

Scientist and two students in a bioscience lab with glass bioreactors.

ENIGMA researchers collaborate to create a predictive model of microbial communities’ effects on critical processes within an ecosystem.

Scientist holding a glass square container with a plant sample.

A project that aims to understand and control the microscopic organisms that live on plant roots to support sustainable bioenergy.

A color sculpture of helix DNA in front of a dusk-bathed building.

Advances genomics in support of U.S. Department of Energy missions related to clean energy generation and environmental characterization and cleanup.

Four people gathered around a computer desk smiling

KBase enables users to analyze, share, and collaborate using data and tools designed to help build increasingly realistic models for biological function.

Green field in front of blue, cloud-filled sky.

Empowers the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.

Field at sunset.

Replicate important ecosystem dynamics to streamline microbe study and make research reproducible.

Scientist makes adjustments on the SmartSoils testbed.

This testbed will help usher in breakthroughs in our ability to understand and predict soil-microbe-plant interactions and their regulation of ecosystem functioning under changing, real-world conditions from laboratory to testbed to field, and from hours to decades.

Scientist works in an orange lit laboratory.

Develops and deploys novel sensing tools and associated analytical and telemetry capabilities to quantify interactions between key environmental factors and biological functioning within ecosystems across scales.

Two scientists looking at computer models.

An advanced simulation framework for the realistic portrayal of plant-soil-microbe interactions across scales.

Gloved hands collect sample from soil.

Aims to pilot “twin” ecosystems in the laboratory and field that use sensors and autonomous controls to study changes in root secretions during drought stress to see if they select for beneficial microbes.

Birdseye view of green algal bloom.

As part of this multi-institutional effort, Berkeley Lab scientists are studying and modeling the exchanges of carbon, nutrients, and elements across coastal terrestrial-aquatic interfaces.

Scientist holding a petri dish.

The ExaBiome project aims to provide scalable tools for three core computational problems in metagenomics: metagenome assembly, protein clustering and annotation, and signature-based approaches.

Person with medium-length black hair wearing glasses and a black cardigan over a blue top, photographed against a dark gray background.

Romy Chakraborty is head of the Ecology Department in the Earth and Environmental Sciences Area. Chakraborty has pioneered discovery of unique microbes catalyzing key biogeochemical processes in diverse ecosystems to enable translational solutions for improving environmental health and sustainable agriculture.

Eoin Brodie, a person with short gray hair wearing a black Patagonia vest over a blue and white checkered collared shirt, photographed outdoors.

Eoin Brodie is the deputy director of the Earth and Environmental Sciences Area's Climate and Ecosystem Sciences Division, using technologies to reverse-engineer complex microbiomes in natural and managed ecosystems. He is also the Laboratory Research Manager of the Watershed Function Science Focus Area, a science co-lead for BioEPIC, and co-directs the Joint Berkeley Initiative for Microbiome Sciences (JBIMS).

Jonelle Basso, a person with long dark braided hair wearing a black blazer over a white printed top.

Jonelle Tamara Basso is a research scientist at the DOE Joint Genome Institute focusing on plant-microbe interactions. Her research investigates the quantitative impact of phage genes on root colonization and the molecular underpinnings of a presumptive plant-bacterial-phage interaction.

A computer screen floating in front of a supercomputing facility with a virus and bacteria coming out of the top. A large root system connects the computer with dirt floor full of soil organisms. A person with medium-length brown hair wearing a black top, photographed against a large tree.

A team of scientists led by Berkeley Lab has developed a new model that incorporates genetic information from microbes. This new model enables the scientists to better understand how certain soil microbes efficiently store carbon supplied by plant roots, and could inform agricultural strategies to preserve carbon in the soil in support of plant growth and climate change mitigation.

Diatoms do so much for us already – they’re the base of the oceans’ food chains and take up 20% of the planet’s carbon dioxide through photosynthesis. But biologist Setsuko Wakao thinks they’d be great at another job too: acting as tiny sponges to store toxic or useful metals using the molecule structure of their gorgeous shells.

Microscope illustration shining a light on proteins. Construction on the BioEPIC building. A vial containing brightly colored shapes representing molecules sits on a beige surface next to empty blue vials Charlie Koven conducting fieldwork outdoors. Closeup shot of sorghum with a bee nearby. View of Earth from space.