Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization

Abstract

Soil is inhabited by a myriad of microorganisms, many of which can form supracellular structures, called biofilms, comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival. Biofilms enable intensive inter- and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins. Here, we first discuss organization, dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome. Social interactions among bacteria, such as cooperation and competition, are discussed. We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms. Microfluidic platforms, which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with high-throughput screening and novel measurements, are also highlighted. This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.