[1] Methods for studying bacterial biofilms associated with plants

Plant surfaces are not the same as the inert substrates often used in laboratory studies of biofilm formation. The surface may be subject to alteration or digestion by the microorganisms. In addition, the extracellular matrix that surrounds the bacteria and fungi in a biofilm may be provided, in part, by the plant. The root tip produces a layer of mucigel that may be incorporated into the biofilm. In addition, the root secretes substances including sugars, amino acids, and dicarboxylic acids that support microbial growth. Other parts of the plant also supply chemical substrates that support bacterial growth, although these are usually secreted in smaller amounts than the concentrations typically found surrounding roots. The plant may respond actively to the presence of microorganisms growing in its vicinity or on its surface. Biofilms on plant surfaces as on other surfaces are fragile, and disturbing them to make observations or measurements may give a misleading picture of the biofilm in the absence of disturbance. Therefore, it is important to attempt to confirm any observations made by techniques that disturb the biofilm with additional observations of undisturbed material. Mutational analysis of biofilms provides information on those genes essential for biofilm formation. However, there is broader group of genes that are differentially regulated by conditions within the biofilm. Included among these are some of the genes essential for biofilm formation, but also genes that may have important, yet nonessential functions.