Genomics:GTL

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Laboratory Cultivation Techniques to Simulate Natural Community Structure

Microbes associating within a biofilm surface offer the opportunity for members of a discrete population and individual organisms representing different species to establish fixed spatial relationships over extended periods of time. Surfaces enable microorganisms to establish high cell densities in localized areas. For example, products of cell metabolism in a colony of one type of microorganism diffuse to adjacent surface areas, forming strong concentration gradients within the intercellular volume of a biofilm.

To identify the function of genes preferentially expressed by specific populations in the structured community, new cultivation techniques are being developed that incorporate surfaces for microbial colonization and RNA extraction. During the past decade, researchers have developed reactors in which biofilms can be imaged using confocal scanning laser microscopy (CSLM) and other light-microscopic techniques. When combined with fluorescent in situ hybridization (FISH) to distinguish populations of cells in multipopulation biofilms and fluorescent reporters (green fluorescent protein) of functional gene expression, CSLM has been used to demonstrate how gene expression by one population affects gene expression in another proximally located population.

The mobile pilot-plant fermentor shown here has a 90-L capacity and currently is used to generate large volumes of cells and cell products such as outer-membrane vesicles under highly controlled conditions.This fermentor allows the end user precise control of culture growth to produce high-quality samples. Future generations of fermentors will be more highly instrumented, possessing sophisticated imaging and other analytical devices developed to analyze interactions among cells in biofilms under an array of condition.