Microbial Community Ecology
The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Defining what constitutes a community of interacting microbial populations is important for rigorous progress in the field.
Important elements of research in microbial community ecology include
- Analysis of functional pathways for nutrient resource and energy flows
- Mechanistic understanding of interactions between microbial populations and their environment
- Emergent properties of the complex community, including biological diversity, functional redundancy and, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome.
PNNL is leading research to explore this important field and its implications for carbon sequestration and management, bioenergy development, and controlling disease. This includes a Lab-level initiative began in October 2009, the Microbial Communities Initiative. The focus of the Initiative is on understanding microbial community interactions at the fundamental scale at which they occur—at the microscale (<100 microns).
Publications
A key feature of CSiTE is shared access to multiple field sites representing important managed and unmanaged ecosystems. A task-oriented experimental and modeling approach during the first three years has established the basis for the evolution in 2003 to a research approach that is site-focused and integrated across spatial scales. CSiTE is a distributed research consortium that is integrated across several collaborating institutions. Robin Graham (ORNL) and F. Blaine Metting (PNNL) coordinate CSiTE. Chief scientists are Julie Jastrow (ANL), Cesar Izaurralde (PNNL), and Mac Post (ORNL).
"What is Microbial Community Ecology" by Allan Konopka. A Perspective in The ISME Journal, advance online publication 6 August 2009; doi: 10.1038/ismej.2009.88
"Ecology, Microbial" by Allan Konopka in Encyclopedia of Microbiology 3rd Edition, pp. 91-106, Moselio Schaechter, Editor, Oxford: Elsevier.
Programs and Projects
Consortium for research on Enhancing Carbon Sequestration in Terrestrial Ecosystems (CSiTE) - The goal of this DOE consortium is to discover and characterize links among critical pathways and mechanisms for creating larger, longer-lasting carbon pools in terrestrial ecosystems.
Research is designed to establish the scientific basis for enhancing carbon capture and long-term terrestrial sequestration by developing 1) fundamental understanding of carbon sequestration mechanisms in terrestrial ecosystems across multiple scales from the molecular to the landscape levels, 2) conceptual and computational models for extrapolation of process understanding across spatial and temporal scales, 3) estimates of regional and national carbon sequestration potential, and 4) assessments of the environmental impacts and economic implications of approaches to enhance carbon sequestration.
Other Research Staff
Vanessa Bailey and Harvey Bolton, Jr.
Microbial Community Ecology Resources
PNNL has a wide range of instrumentation, laboratories, and capabilities that support our microbial community ecology research goals.
Microbial Cell Dynamics Laboratory. In our Microbial Cell Dynamics Laboratory, researchers not only develop and apply highly monitored and controlled cultivation technologies that provide quality samples for downstream analyses, but also design and conduct experiments to probe the molecular dynamics of microbes. This research is relevant to environmental remediation, alternative energy production and carbon sequestration. Light
PNNL microbiologists have developed a novel cutting-edge custom light enclosure for a photobioreactor that blocks ambient light from entering a bioreactor while providing red and blue light using energy-efficient LEDs. This photobioreactor will be used to optimize hydrogen and biofuel production from photosynthetic microbes. Its large volume and continuous culture capability enables mass-production of biomass for biofuels and alternative fuel research.
The MCDL allows careful control and manipulation of microbial growth conditions, including extreme temperature, pH, radiation, pressure and other unusual environmentally relevant conditions. The lab houses flexible experimental systems capable of making multiplexed measurements of cellular responses and processes under these conditions. Samples can be analyzed with a suite of state-of-the-art microscopic and spectroscopic instruments.
The MCDL's core capabilities support both single-organism and microbial community studies. These include:
- Dedicated co-located laboratories and analytical stations, including mobile culturing equipment and analytical instruments
- Small reactor-scale (1-50 liter) culturing of prokaryotic cells under equilibrium conditions for generating cell populations with a minimum level of biochemical variability
- Systems for growth and analysis of planktonic cells and cells associated with surfaces or residing in biofilms
- Systems for controlling cell-cell interaction distance and rates of substrate diffusion to probe cell-signaling events
- Rapid harvesting of cultures and processing and delivering cells and components to multiple analytical instruments with minimal composition alteration
- Real-time analysis of in situ biological, chemical and physical processes and parameters through automated liquid and headspace analysis
- Analysis of gene expression and signaling in individual cells and bulk populations.
- Highly instrumented cultivation equipment
- Homogeneous and reproducible samples for high resolution 'omics"
- Real time monitoring & control
- Mass balance, including automated gas headspace analysis
- Broad range of cultivation conditions—fermentation, photosynthesis, aerobic & anaerobic respiration
- Single organisms and mixed cultures
Real-Time Quantitative Analyses of Microbial Metabolism. We have designed and built a novel bioreactor that could shed light on how to convince microbes to convert or metabolize municipal garbage into biodiesel and other fuels. The bioreactor offers accurate, detailed data on chemicals produced by the microbes without sampling.
New technologies will have broad application to other biological systems (eukaryotic cells, tissues and organs)
Highlight
- New Technology Provides Accurate, Noninvasive Look at Microbial Metabolism
Publication
Majors PD, JS McLean, and JC Scholten. 2008. "NMR Bioreactor Development for Live In-Situ Microbial Functional Analysis." Journal of Magnetic Resonance 192(1):159-166. Artwork from this article was featured on the cover of the journal.