Earth's Microbial Engines

Solving environmental challenges through Translational Ecology

Earth’s Microbial Engines (EME) aims to accurately predict how microbes impact terrestrial ecosystem function, and enable translational ecology approaches that develop solutions for enhancing ecosystem function and health based on integrating fundamental discovery and multi-scale sensing and simulation capabilities. Studying the mechanisms by which microbial communities modulate ecosystems and vice versa is necessary to develop a predictive understanding of the potential for naturally occurring microbes to improve the sustainable use of Earth’s resources. At the intersection of biology, ecology, biogeochemistry, and the environment, new theories about microbial metabolism and dynamics are leading us to many discoveries about the true impact and potential of microbes—the most diverse and abundant life form on Earth.

The ability to quantify, model, and predict microbial-ecosystem feedbacks to better understand our planet’s ecology and translate this knowledge into environmental strategies is critical to our understanding of these systems and how they will respond to rapid climate change, increasing environmental extremes, and other disturbances. This research is organized through four strategic research objectives:

1. Advance the fundamental understanding of in-situ microbial metabolic potential and coupled ecological and biogeochemical processes from bedrock to canopy

2. Develop multi-scale capabilities to accurately sense and simulate biological-environmental feedbacks

3. Document the impact of global change and other perturbations on microbial processes in soil and subsurface systems and the resulting impacts on ecosystem function

4. Translate ecological understanding into predictable solutions for environmental challenges

Photo Credit: Berkeley Lab

Recent science & program advances

  • $140M Biological and Environmental Program Integration Center (BioEPIC) gets green light from DOE
  • Established the most genomically characterized watershed in the world 
  • Documented that microtopography can predict subsurface microbial functional properties
  • Identified importance of soil and bedrock processes to riverine N exports
  • Identified metal constraints on organic P availability and microbial strategies to release P
  • Determined that plants can regulate rhizosphere microbiome by root exudate chemistry
  • Developed new approaches to improve microbial cultivation success
  • Developed new theories to scale microorganism kinetics across larger scales
  • Developed new approaches to non-invasively quantify rhizosphere distribution and dynamics

Relevant Projects


EESA benefits from rich partnerships with our collaborators and sponsors. See project & program links above for more information.

Publication Highlights

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater, bioRxiv preprint, 2020

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter, Frontiers in Microbiology, 2020

Microbial Communities across a Hillslope-Riparian Transect Shaped by Proximity to the Stream, Groundwater Table, and Weathered Bedrock, Ecology and Evolution, 2019

Depth- and Time- Resolved Distributions of Snowmelt-Driven Hillslope Subsurface Flow and Transport and Their Contributions to Surface Waters, Water Resources Research, 2019

Predicting Sedimentary Bedrock Subsurface Weathering Fronts and Weathering Rates, Scientific Reports, 2019

A Theory of Effective Microbial Substrate Affinity Parameters in Variably Saturated Soils and an Example Application to Aerobic Soil Heterotrophic Respiration, Journal of Geophysical Research: Biogeosciences, 2019

Comparison with Global Soil Radiocarbon Observations Indicates Needed Carbon Cycle Improvements in the E3SML and Model, Journal of Geophysical Research: Biogeosciences, 2019

Model Exploration of Interactions between Algal Functional Diversity and Productivity in Chemostats to Represent Open Ponds Systems across Climate Gradients, Ecological Modelling, 2019

Landscape Topography Structures the Soil Microbiomein Arctic Polygonal Tundra, Nature Communications, 2018

Dynamic Root Exudate Chemistry and Microbial Substrate Preferences Drive Patterns in Rhizosphere Microbial Community Assembly, Nature Microbiology, 2018

SUPECA Kinetics for Scaling Redox Reactions in Networks of Mixed Substrates and Consumers and an Example Application to Aerobic Soil Respiration, Geoscientific Model Development, 2017

A New View of the Tree of Life, Nature Microbiology, 2016

News Coverage

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