After spending many months working with all types of biofilms and biomat samples from around San Diego and speaking with scientists all over the world, we understand the difficulty in determining the microbial diversity in these sample types.
In many ways, biofilms are similar to soils in that they are mixed microbial communities, with varying degrees of cell densities, moisture content, chemical composition and inhibitors. Much like soils they can contain humic substances, metals, and salts, not to mention the polysaccharides, all of which can impact isolation and purification of nucleic acids. However, the basic structural components of soils and biofilms are vastly different and require different approaches for optimized recovery of DNA and RNA.
Here (at the source link) we describe some of the things to consider when working with biofilms. Let us know your tips and tricks for collecting biofilms and where you've collected your most unusual samples.