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Environmental & Biological Systems Science

Ecosystems Biology Program

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.

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

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.

Primary Sponsors