The Challenge
We face a series of critical problems related to the production and consumption of energy, as well as to the environmental consequences of those processes. For these problems, microbial processes are important elements of solutions such as sustainable bioenergy and bioprocessing, assessment of climate change impact and adaptation, and cost-effective cleanup technologies.
Microbial Communities are Complex Adaptive Systems
Microorganisms in natural or engineered ecosystems rarely live alone, but instead function as integrated units—or communities—that process energy and materials and thereby impact their environment. Despite their importance, we know little about microbial community function and behavior. As a result, we have little ability to predict changes in microbial community dynamics during either natural cycles of change or environmental perturbations—such as climate change or inputs of toxic pollutants.
The adaptive behavior of microbial communities occurs at three time scales that are relevant to natural processes
- Cellular regulation of gene expression and activity over minutes to hours
- Dynamic changes in community composition over days to months
- Genetic/evolutionary changes that occur over months to years.
Focus of the Microbial Communities Initiative
The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities.
The focus of the MCI is on understanding microbial community interactions at the fundamental scale at which they occur—at the microscale (<100 microns). Therefore, the science questions and associated capabilities and technologies are largely focused on making measurements at or near the scale of single cells. This focus requires significant technology development and its specific application to community-level ecological questions.
A predictive understanding of microbial communities requires:
- Analysis of the network of energy and resource flow through the ecosystem.
- Analysis of the "interaction milieu." Microbial community composition and function are dynamic in space and time. The abiotic and biotic forces of interaction driving these dynamics must be determined at the fundamental spatial scale at which they occur (the microenvironment).
- Analysis of emergent properties (diversity/stability-resistance-resiliency/collective genetic potential). In particular, properties that relate microbial functionality to ecosystem services are needed.
Seeing the World That Microbes See
In particular, the MCI will develop novel technologies that address fundamental questions in the field of microbial community ecology:
- "Seeing the world that microbes see," that is, at a spatial scale of microns
- Analyzing individual cell properties related to material and energy flux rates and environmental stress responses
- Applying genomic/proteomic technologies to questions in microbial community ecology.
Leveraging Recent Research Advances
We face significant technical challenges in developing these approaches, but they are logical extensions of recent advances in microfluidics, imaging, and sensor technology. These technologies can lead to quantitative analysis of resource fluxes, and identification of the interactions between community members.
Applying these tools at the microscale will facilitate making a functional connection between the seemingly infinite microbial diversity to environmentally relevant processes such as
- Greenhouse gas formation and consumption
- Plant polymer decomposition for creating biofuels and sequestering carbon
- Mineral formation and dissolution for remediating contaminants.
Within the Microbial Communities Initiative, experiments at the microcosm—or representative system—level will provide valuable data for developing models and technologies that will further understanding of microbial communities at the microscale.
Focus Areas
The Microbial Communities Initiative consists of three Focus Areas
- Microengineering and Microanalytics This focus area addresses the capacity to measure the chemical environment, distribution, and activity of microbes at the microscale, as well as coupling biogeochemical reaction rate analyses to specific identification of the microbes responsible for those biogeochemical transformations.
- Simulation Modeling This focus area aspires to develop novel simulation models that represent the biological diversity of microbial communities as well as the physical and chemical heterogeneities of natural environments at the microscale.
- Extending Genomics & Proteomics to Quantitative Functional Analyses This focus area will develop techniques to apply these technologies to address community ecology questions; in particular, the analysis of functional redundancy in microbial communities.
Outcome
At the completion of the MCI, we expect to have a set of integrated technologies that drive environmental science to a mechanistic understanding of microbial communities at the microscale.
Why PNNL?
PNNL is providing leadership in these areas, based on
- Our longstanding expertise in examining environmentally relevant microbes using a systems biology approach
- Our significant strengths in subsurface science including numerical simulation
- The capabilities within the Environmental Molecular Sciences Laboratory (EMSL), many of which can be applied and modified to address key scientific questions in microbial community ecology.