Mineral–microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral–microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral–microbe interactions for the benefit of humankind.

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10⁸cells/g at the water-sediment interface to 10⁷cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with theBacteroideteswere the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to theHalobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.

Clays and clay minerals are common components in soils, sediments, and sedimentary rocks, and they play an important role in many environmental processes. Iron is ubiquitous in clays and clay minerals and its oxidation state, in part, controls the physical and chemical properties of these fine-grained minerals. The structural ferric iron in clay minerals can be reduced either chemically or biologically. Biological reductants include mesophilic and thermophilic microorganisms from diverse environments such as soils, sediments, sedimentary rocks, and hydrothermal hot springs. Multiple clay minerals have been used for microbial reduction studies, including dioctahedral smectiteillite series, palygorskite, chlorite, and their various mixtures in natural soils and sediments. All of these clay minerals are reducible by microorganisms under various conditions with smectite (nontronite) being the most reducible and illite the least. The rate and extent of bioreduction depends on many experimental factors, such as the type of microorganisms and clay minerals, solution chemistry, and temperature. Despite significant efforts, current understanding of the mechanisms of microbial reduction of ferric iron in clay minerals is still limited. Whereas some studies have presented evidence for a solid-state reduction mechanism, others argue that the clay mineral structure partially dissolves when the extent of reduction is high. This inconsistency may be related to several experimental conditions, and their specific effects are discussed in this paper. Whereas past experiments have been largely conducted in well-controlled laboratory systems, recent efforts have attempted to transfer knowledge to the field to improve our understanding of more complex soil systems for better agricultural practices. Biologically reduced clay minerals are also important agents in remediating inorganic and organic contaminants in soil and groundwater systems. This paper reviews the most recent developments and suggests some directions for future research.

Summary: Previous investigations of the salinity effects on the microbial community composition have largely been limited to dynamic estuaries and coastal solar salterns. In this study, the effects of salinity and mineralogy on microbial community composition was studied by using a 900‐cm sediment core collected from a stable, inland hypersaline lake, Lake Chaka, on the Tibetan Plateau, north‐western China. This core, spanning a time of 17 000 years, was unique in that it possessed an entire range of salinity from freshwater clays and silty sands at the bottom to gypsum and glauberite in the middle, to halite at the top. Bacterial and archaeal communities were studied along the length of this core using an integrated approach combining mineralogy and geochemistry, molecular microbiology (16S rRNA gene analysis and quantitative polymerase chain reaction), cultivation and lipid biomarker analyses. Systematic changes in microbial community composition were correlated with the salinity gradient, but not with mineralogy. Bacterial community was dominated by the Firmicutes ‐related environmental sequences and known species (including sulfate‐reducing bacteria) in the freshwater sediments at the bottom, but by halophilic and halotolerant Betaproteobacteria and Bacteroidetes in the hypersaline sediments at the top. Succession of proteobacterial groups along the salinity gradient, typically observed in free‐living bacterial communities, was not observed in the sediment‐associated community. Among Archaea , the Crenarchaeota were predominant in the bottom freshwater sediments, but the halophilic Halobacteriales of the Euryarchaeota was the most important group in the hypersaline sediments. Multiple isolates were obtained along the whole length of the core, and their salinity tolerance was consistent with the geochemical conditions. Iron‐reducing bacteria were isolated in the freshwater sediments, which were capable of reducing structural Fe(III) in the Fe(III)‐rich clay minerals predominant in the source sediment. These data have important implications for understanding how microorganisms respond to increased salinity in stable, inland water bodies.