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Environmental & Biological Systems Science

Ecosystems Biology Program

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  • Highlights
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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

Microbial Response to a Changing and Fire-Prone Arctic Ecosystem

April 27, 2022

Burning more than 1,000 square kilometers of tundra on Alaska’s North Slope, the 2007 Anaktuvuk river wildfire is one of the largest fires to occur within Arctic ecosystems. Berkeley Lab scientist Nick Bouskill led a study that used data from this disturbance event to predict ecosystem recovery as fires advance in a changing climate. (Credit:…

Study Evaluates Phosphorus Availability Underground using Plant Leaves as Biosensors

April 25, 2022

When envisioning renewable energy, sources that often come to mind are the sun, wind, batteries, and water. However, biofuel, a type of renewable energy that converts organic material from plants into liquid fuel, is an important part of a global effort to achieve net-zero emissions. Switchgrass, a deep-rooted native North American grass that grows in…

Researchers Investigate How Changes in Small-Scale Environmental Conditions Impact Microbial Structure and Function

  Just one teaspoon of soil or sediment can contain up to one billion microbes. These microorganisms in Earth’s subsurface, although invisible, largely influence the global carbon cycle through their ability to break down organic material, which releases carbon dioxide in the process. However, environmental conditions within Earth’s subsurface such as moisture, nutrient availability, and…

EESA Study Closes Knowledge Gaps of Drought Impacts on Microbial Activity

Climate change is leading to an increase in many vivid impacts, such as more frequent wildfires and floods. However, there are many effects of climate change that can’t be seen from miles away – or even seen at all. The intensity and frequency of drought is predicted to increase along with higher temperatures. Droughts can…

EESA Researchers Develop Open-Source Code for Modeling Soil Biogeochemistry

April 22, 2022

  Senior scientist William Riley and several EESA collaborators have published a chapter of a new book on soil biogeochemistry. Published in March, the book Multi-Scale Biogeochemical Processes in Soil Ecosystems: Critical Reactions and Resilience to Climate Changes was developed to provide a state-of-the-art overview of research in soil biogeochemical processes and strategies for greenhouse…

Berkeley Lab Team Hunts for Carbon in Soil Without Getting Their Hands Dirty

April 14, 2022

This article was published first at newscenter.lbl.gov.   Soil imaging with neutrons can give a quick, detailed look at the amount and distribution of carbon (and certain other important elements) in soil without disturbing the soil or plant roots Soil imaging with neutrons can give a quick, detailed look at the amount and distribution of…

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