Abstract Microbes have a dramatic impact on the mineralogy of the environment as a result of their metabolic processes. Microorganisms can control both acidity and redox chemistry as a result of respiration, photosynthesis, chemoautotrophy or anaerobic respiration. The net impact of these biogeochemical reactions can result in formation of minerals that have distinctive ‘bulk’ and surface chemical characteristics, morphology and trace element or isotopic composition that is distinct from those produced abiotically. This chapter describes several examples of both direct and indirect biomineralization including the role of neutrophilic and acidophilic iron oxidizers on the biogeochemistry of Fe minerals in two mine sites, the role of microbial metabolic processes on mineral weathering and nutrient cycling, and the enhanced mobility and enrichment of economically important trace elements such as zinc, gold and the rare earth elements. The purpose of this chapter is to provide some insight into how microorganisms affect the chemistry, mineralogy and physical characteristics of their surroundings. This chapter is not intended to be an exhaustive review, though some basic concepts are summarized and specific examples to illustrate in more detail the intimate connections between biological and mineralogical processes are given. It is critical that studies of environmental mineralogy and geochemistry include analysis of the types of microorganism present and the ways in which they influence reaction kinetics in natural systems. Consequently, this paper concludes with a brief summary of microbiological methods that find special relevance to environmental mineralogy and a discussion of the importance of recent breaks through in genome analysis for Earth Sciences.

Abstract The purpose of this chapter is to provide some insight into how microorganisms affect the chemistry and physical characteristics of their surroundings. It is not intended to be an exhaustive review. Rather, we will summarise some basic concepts and draw upon some specific examples to illustrate in more detail the intimate connections between biological and mineralogical processes. It is critical that studies of environmental mineralogy and geochemistry include analysis of the types of microorganism present and the ways in which they influence reaction kinetics in natural systems. Consequently, this paper concludes with a brief summary of microbiological methods that find special relevance to environmental mineralogy and a discussion of the importance of recent breakthroughs in genome analysis for Earth Sciences. Microorganisms are single celled life forms that are found in great abundance in a wide variety of environments near the Earth’s surface. They are subdivided into three groups, or domains: Eukaryotes, Bacteria, and Archaea ( Woese et al ., 1990 ; Winkler & Woese, 1991 ). Of these, the prokaryotes (Bacteria and Archaea) have the most ancient origins, probably extending back over at least 3.48 Ga ( Schopf, 1993 ; Schopf & Packer, 1987 ) and possibly 3.8 Ga ( Mojzsis et al ., 1996 ) of Earth history. Prokaryotes have extremely diverse metabolic capabilities. They can utilise a large range of inorganic and organic compounds as energy sources and terminal electron acceptors, and can occupy niches that are not colonised by higher life forms. Microbial metabolisms can be subdivided into several groups. Heterotrophs (many eukaryotes and prokaryotes) utilise fixed organic carbon as energy sources.