Quantifying Biofilm Structure: Facts and Fiction

Abstract

There is no doubt among biofilm researchers that biofilm structure is important to many biofilm processes, such as the transport of nutrients to deeper layers of the biofilm. However, biofilm structure is an elusive term understood only qualitatively, and as such it cannot be directly correlated with any measurable parameters characterizing biofilm performance. To correlate biofilm structure with the parameters characterizing biofilm performance, such as the rate of nutrient transport within the space occupied by the biofilms, biofilm structure must first be quantified and expressed numerically on an appropriate scale. The task of extracting numerical parameters quantifying biofilm structure relies on using biofilm imaging and image analysis. Although defining parameters characterizing biofilm structure is relatively straightforward, and multiple parameters have been described in the computer science literature, interpreting the results of such analyses is not trivial. Existing computer software developed by several research groups, including ours, for the sole purpose of analyzing biofilm images helps quantify parameters from biofilm images but does nothing to help interpret the results of such analyses. Although computing structural parameters from biofilm images permits correlating biofilm structure with other biofilm processes, the meaning of the results is not obvious. The first step to understanding the quantification of biofilm structure, developing image analysis, methods to quantify information from biofilm images, has been made by several research groups. The next step is to explain the meaning of these analyses. This presentation explains the meanings of several parameters commonly used to characterize biofilm structure. It also reviews the authors' research and experience in quantifying biofilm structure and their attempts to quantitatively relate biofilm structure to fundamental biofilm processes.

Keywords:

• biofilms
• biofilm structure
• biofilm modeling
• image analysis

Acknowledgements

The work was supported by grant N-00014-02-1-0567 from the US Office of Naval Research, grants DE-FG03-01ER63270 and DE-FG03-98ER62630/A001 from the Natural and Accelerated Bioremediation Research (NABIR) program, and by Biological and Environmental Research (BER) and the US Department of Energy.