The Interaction of Geology and Microbiology within Biofilms

Bacteria and other microorganisms represent the oldest and most successful life forms on Earth. Unlike higher organisms, prokaryotes (Bacteria and Archaea) survive and sometimes thrive under extreme conditions of temperature, pH, Eh, and other harsh chemical conditions. Direct observations of microorganisms in nature, reveals that surface attachment and biofilm formation are a common mode of growth. In contrast to their unattached (planktonic) counterparts, biofilm organisms are much more resistant to many adverse environmental conditions. Although traditional culture techniques are still important for bacterial identification; culture-independent approaches such as DNA or RNA isolation and genetic approaches are becoming much more common. Bacterial cell surface components including membranes, cell wall components, and extracellular polymers (slime) are an integral part of biofilms. DNA and nano-sized membrane vesicles have also been described in the extracellular matrix. Most bacterial cell surface components are anionic and thus can interact with metal and other ions in their environment; in some cases resulting in mineral formation and in other cases contributing to microbial-induced corrosion. Microorganisms are metabolically active. Within biofilms, bacterial metabolism, interactions between microbial species, and diffusion gradients can generate chemical microenvironments. These microenvironments can differ markedly in terms of Eh, pH, etc from the bulk environment. Several examples of biofilm-induced mineral formation will be presented. These include a potential role for biofilms during leaf fossilization and biofilm-mediated stone formation in the urinary tract (kidney stones).