Characterization and environmental applications of soil biofilms: a review

Abstract

Despite the major influence of soils on climate change, carbon sequestration, pollution remediation, and food security, soil remains a largely unexplored media with an extreme complexity of microbes, minerals, and dead organic matter, most of them being actually poorly known. In particular, soil biofilms have recently attracted attention because they strongly influence biogeochemical reactions and processes. Here we review biofilms with focus on their behavior, proliferation, distribution, characterization methods, and applications. Characterization methods include optical, electron, scanning probe, and X-ray microscopy; metagenomics, metatranscriptomics, metaproteomics, metabolomics; and tracking approaches. Applications comprise pollution remediation by metal immobilization or organics degradation; and methane oxidation, carbon dioxide reduction, and carbon sequestration. Advanced methods such as DNA-stable isotope probing and meta-omics have uncovered the multiple functions of soil biofilms and their underlying molecular mechanisms. Investigations have improved our understanding of inter- and intra-kingdom interactions, and of gene transfer. Extracellular materials such as polysaccharides enhance the transport of substances and electrons flow among microorganisms.