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Environmental & Biological Systems Science

Ecosystems Biology Program

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Highlights
Projects
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Coffee bean borer on coffee bean; caffeine chain upper left; bacteria image from beetle gut right. Crop 16:9.
Coffee bean borer on its food, a coffee bean. Gut bacteria break down caffeine. Caffeine molecule. Credit: Berkeley Lab.

The Ecosystems Biology Program focuses on discovering and understanding the molecular basis of plant, microbial and metazoan interactions, including specific gene functions, species interactions, and community dynamics under a variety of environmental conditions—and developing the advanced technology that enables such understanding.

Highlights

This farm in Arkansas may soon be the most scientifically advanced farm in the world. (Credit: Jay McEntire)
Project

AR1K: Sustainable, Profitable Agriculture through Research

A part of the AR1K team, Berkeley Lab, the University of Arkansas, and Glennoe Farms are bringing together molecular biology, biogeochemistry, environmental sensing technologies, and machine learning, to revolutionize agriculture and create sustainable farming practices that benefit both the environment and farms.

Project

Mapping Soil Carbon from Cradle to Grave

In this EESA project, scientists seek to define a molecular blueprint for how organic carbon decomposition and stabilization processes in soil are impacted by the interactions between plant roots, the soil microbial community (bacteria, archaea, fungi, microfauna) and the soil matrix.

Microbe images imposed on Earth. Credit Berkeley Lab
Project

Microbes to Biomes (M2B): Harnessing the Soil Microbome for Food and Fuel Security

Microbes-to-Biomes (M2B) is a Berkeley Lab-wide initiative designed to reveal, decode, and harness microbes—the most abundant and diverse life form on Earth—in ways that protect our fuel and food supplies, environmental security, and personal health. It was launched in early 2015, featuring five projects funded through the LDRD program.

Project

Berkeley Synchrotron Infrared Structural Biology Imaging Project

The Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging Program develops and offers state-of-the-art instrumentation for characterizing and imaging interactions among plants, microbes and their environments.

Program Overview

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 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 (BSISB) imaging 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 tools of modern molecular biology and biochemistry with biogeochemical and isotopic analyses, and mathematical modeling to determine the relationships between microbial composition, metabolic potential and critical biogeochemical processes across Earth’s ecosystems. Research projects in this program include the study of soil carbon transformation and sequestration, microbial nutrient mobilization for plant productivity and the sustainable cultivation of bioenergy relevant crops, each within the context of ecosystems that are subject to climate or land-use change. As a founding group in the Microbes-to-Biomes initiative, our research spans molecules to ecosystems, with specific emphases on soil-plant-microbe interactions, interactions between microbes and metazoans (from humans to insects and soil fauna), and understanding the origin and fate of water borne microbial contaminants.

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

Featured Projects

Project

Berkeley Synchrotron Infrared Structural Biology Imaging Project

The Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging Program develops and offers state-of-the-art instrumentation for characterizing and imaging interactions among plants, microbes and their environments.

ENIGMA image
Project

ENIGMA

ENIGMA— Ecosystems and Networks Integrated with Genes and Molecular Assemblies—seeks to advance understanding of microbial biology and the impact of microbial communities on their ecosystems. Team members collaborate closely to generate detailed quantitative understanding across scales—from molecular to cellular and community levels. Scientists within ENIGMA have the technological and scientific skills and experience to link environmental microbiological field-studies to both highly advanced field and laboratory meta-functional genomic and genetics tools.

Project

Mapping Soil Carbon from Cradle to Grave

In this EESA project, scientists seek to define a molecular blueprint for how organic carbon decomposition and stabilization processes in soil are impacted by the interactions between plant roots, the soil microbial community (bacteria, archaea, fungi, microfauna) and the soil matrix.

Microbe images imposed on Earth. Credit Berkeley Lab
Project

Microbes to Biomes (M2B): Harnessing the Soil Microbome for Food and Fuel Security

Microbes-to-Biomes (M2B) is a Berkeley Lab-wide initiative designed to reveal, decode, and harness microbes—the most abundant and diverse life form on Earth—in ways that protect our fuel and food supplies, environmental security, and personal health. It was launched in early 2015, featuring five projects funded through the LDRD program.

Primary Sponsors

Program Contacts

Eoin Brodie
Deputy Director, Climate & Ecosystem Sciences Division;
Lead, Environmental & Biological Systems Sciences Program Domain

Jacob Gimbel
Program Operations Analyst

News & Events

Study Sheds Light on Microbial Communities in Earth’s Subsurface

August 16, 2023

  From the tops of tree canopies to the bottom of groundwater reservoirs, a vast amount of living organisms interact with nonliving components such as rock, water, and soil to shape this area of Earth known as the “critical zone.” Over half of Earth’s microbes are located in the subsurface critical zone, which ranges from…

DOE Funds Projects to Advance Forest Carbon Dioxide Removal Efforts and Agricultural Soil Carbon Conservation

August 1, 2023

The DOE Office of Fossil Energy and Carbon Management (FECM) and Office of Technology Transitions (OTT) recently announced $5 million in funding for four projects–two from Berkeley Lab with EESA leadership. The projects selected offer “promising solutions” to the nation’s climate change challenges by helping to reduce greenhouse gas emissions and will “accelerate their deployment…

Quantifying the strength of the land carbon sink

July 26, 2023

This article first appeared at nature.berkeley.edu/news. The world’s forests, grasslands, and other terrestrial ecosystems have played a substantial role in offsetting human carbon emissions—a capability that UC Berkeley researchers say would be threatened by continued global change. The assessment, published today as a new review paper in Nature Reviews Earth & Environment, presents a comprehensive analysis of…

EESA Scientists Close Rhizosphere Microbiome Knowledge Gaps

July 20, 2023

The rhizosphere–the region of soil surrounding plant roots in which soil and microbes closely interact–plays an important role in soil carbon cycling. The rhizosphere is only about 1-2% of Earth’s soil volume but can store up to 30-40% of Earth’s total soil organic matter. Plants secrete organic compounds such as amino acids or enzymes known…

A Q&A with Kripa Jagannathan

April 26, 2023

After interacting with coastal farming communities who experienced sea level rise and other direct impacts of climate change, Research Scientist Kripa Jagannathan recognized that environmental problems are livelihood issues for many communities around the world. This led her to EESA working as a social scientist, helping to facilitate the co-production of knowledge–a type of research…

New Look at Climate Data Shows Substantially Wetter Rain and Snow Days Ahead

April 24, 2023

Research shows that by the end of the century the biggest rain and snow days will be 20 to 30% wetter than they are today

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