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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

EESA Scientists Investigate How Tropical Soil Microbes Might Respond to Future Droughts

March 14, 2023

As the most biologically diverse terrestrial ecosystems on Earth, tropical rainforests are just as critical to sustaining environmental and human systems as they are beautiful. Their unique climate with high temperatures, humidity, and precipitation promotes high primary productivity, which offsets high respiration, resulting in these ecosystems being one of the largest carbon sinks on Earth,…

Doubling Protected Lands for Biodiversity Could Require Tradeoffs With Other Land Uses, Study Finds

March 3, 2023

This article first appeared on lbl.gov. Scientists show how 30% protected land targets may not safeguard biodiversity hotspots and may negatively affect other sectors – and how data and analysis can support effective conservation and land use planning Although more than half the world’s countries have committed to protecting at least 30% of land and oceans…

A Q&A With Rachel Ward

February 13, 2023

After witnessing tropical deforestation in Honduras and collaborating with farmers impacted by the degradation in these forests, Ph.D. candidate Rachel Ward knew what she wanted to study next–tropical forest regeneration. Ward’s passion to study the impact of tropical forests on both communities and the global carbon cycle led her to pursuing a Ph.D. with the…

A Q&A With Jessica Needham

After being immersed in the Bornean rainforest and surrounded by Dipterocarp trees–large tropical trees with winged seeds–during a field trip in Borneo, Research Scientist Jessica Needham’s life was changed. Since then, her passion to study forests has only grown stronger–and has even led her to modeling tree growth patterns all over the world.  Question: What…

A Q&A With Barbara Bomfim

Growing up in Brasilia, Postdoctoral Research Fellow Barbara Bomfim experienced the transformation of the savannas and rainforests that surrounded her. Now studying wind disturbance and nutrient cycling on the NGEE-Tropics project, Bomfim is passionate about tropical forest response to disturbances in the hopes of advancing science necessary for well-informed and effective forest management.  Question: What…

A Q&A with Marcos Longo

As he conducted field work in the Amazon, Research Scientist Marcos Longo experienced the deforestation of Amazon forests and witnessed the thick clouds of smoke from these ecosystems as they were on fire. Since then, Longo has dedicated his career towards researching the impacts of climate change and disturbance on tropical ecosystems.  What led you…

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