Cultivation of Environmental Bacterial Communities as Multispecies Biofilms

Abstract

Microbes play an important role in the biogeochemistry of hydrocarbons and are frequently studied for potential applications in hydrocarbon biotechnologies. The empirical study of microbes often requires their cultivation, a problematic proposition as approximately only 1% of bacteria may be cultured by traditional methods. One promising strategy to grow the “unculturables” is to grow environmental microbes directly as mixed species biofilms – surface-bound, slime-encapsulated microbial communities. Mixed species biofilms can mimic natural environmental conditions and support microbial growth through beneficial social interactions between microbes, along with the inclusion of cell-cell signaling. Here, we describe a simple, flexible method for growing environmental mixed species biofilms in vitro using the Calgary Biofilm Device (CBD). Additionally, we describe a battery of assays for biofilm characterization. Using our approach, we have successfully grown mixed-species biofilms from a variety of hydrocarbon-contaminated environments, while demonstrating high retention of the original microbial diversity and the metabolic potential for biotechnology applications.