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Interrogation of Microbial Biofilm Activity and Behavior

Margie Romine, Principal Investigator

Most bacteria in natural ecosystems exist in complex assemblages consisting of one or more species. Biofilms, an example of such an assemblage, are complex communities of microorganisms that adhere to surfaces. Pacific Northwest National Laboratory's (PNNL) Interrogation of Microbial Biofilm Activity and Behavior team is developing capabilities for studying cell behavior in biofilms primarily using Shewanella oneidensis MR-1 as a model system. These efforts address a major challenge in microbiology, and they complement a major objective of the U.S Department of Energy's (DOE) Genomics: Genomes to Life (GTL) program to obtain a functional understanding of multi-species microbial communities.

What are Biofilms?

Biofilms are composed of highly structured polysaccharide matrix-enclosed communities separated by a network of open water channels. This architecture is an optimal environment for cell-cell interactions, including the intercellular exchange of genetic material, communication signals, and metabolites, which enables diffusion of necessary nutrients to the biofilm community. The advantages provided by this surface-attached lifestyle, as well as the unsurpassed metabolic versatility and phenotypic plasticity of microbes, likely explain how bacteria are able to persist in so many different types of environments, including those that are inhospitable to higher forms of life. By forming organized communities with other microbes, they can even further extend their ability to adapt and thrive in even the most hostile environments.

Why Study Biofilms?

It is widely recognized that the majority of bacteria in natural, clinical, and industrial settings persist in association with living or abiotic surfaces. Bacterial communities in nature play an important role in the synthesis and degradation of organic matter; the degradation of environmental pollutants; and the cycling of nitrogen, sulfur, and metals. These metabolic processes are complex and typically can only be conducted through the concerted effort of multiple, metabolically distinct microbes. With regard to human health, biofilms account for more than 80% of all microbial infections of the human body. The protective nature of the biofilm structure makes the bacteria embedded within it remarkably difficult to treat with antimicrobials and highly resistant to both immunological and non-specific defense mechanisms of the body. In industrial settings, biofilms are important in processing sewage, treatment of petroleum-contaminated groundwater, and nitrification.

Why Use Shewanella oneidensis MR-1 as a Model System?

Shewanella oneidensis MR-1 forms complex biofilms that are biologically and chemically heterogeneous, has a known genome sequence, and is amenable to genetic manipulation. It is a motile, facultative bacterium with remarkable metabolic versatility for electron acceptor use; it can use oxygen, nitrate, trimethylamine-N-oxide, sulfur compounds, fumarate, and oxidized metals as terminal electron acceptors during respiration. Its ability to reduce polyvalent metals and radionuclides makes it of interest for a potential role in biogeochemical cycling and the bioremediation of contaminant metals and radionuclides. Hence, Shewanella oneidensis MR-1 is relevant to DOE's environmental cleanup and stewardship mission area.

How Will We Study Biofilms?

The current focus of modern microbiology research is primarily on pure culture, planktonic (free-swimming) bacteria. While extremely useful for deconvoluting the functional components and the regulatory networks of a single cell, this research tells us very little about community behavior. Unlike planktonic cell studies, measurements of the three-dimensional distribution of cells and chemical substances are necessary for understanding biofilm properties and behavior. Consequently, desirable technologies are those that are nondestructive, quantitative, and capable of producing spatially resolved temporal measurements.

Interrogation of Microbial Biofilm Activity and Behavior Supports Five Complementary Projects

Systems Biology at PNNL

Research & Capabilities


BSI Scientific Areas

Biofilm Projects

Biomolecular Systems Initiative, image