The studies of mineral-microbe interactions lie at the heart of the emerging field of Geomicrobiology, as minerals and rocks are the most fundamental earth materials with which microbes interact at all scales. Microbes have been found in a number of the Earth’s extreme environments and beyond. In spite of the diverse geological environments in which microbes are found and diverse approaches taken to study them, a common thread, mineral-microbe interactions, connects all these environments and experimental approaches under the same umbrella, i.e., Geomicrobiology. Minerals and rocks provide microbes with nutrients and living habitats, and microbes impact rock and mineral weathering and diagenesis rates through their effects on mineral solubility and speciation. Given a rapid growth of research in this area in the last two decades, it is not possible to provide a comprehensive review on the topic. This review paper focuses on three area, i.e., microbial dissolution of minerals, microbial formation of minerals, and certain techniques to study mineral-microbe interactions. Under the first area, three subjects are reviewed; they include siderophores as important agents in promoting mineral dissolution, microbial oxidation of reduced minerals (acid mine drainage and microbial leaching of ores), and microbial reduction of oxidized minerals. Under the second topic, both biologically controlled and induced mineralizations are reviewed with a special focus on microbially induced mineralization (microbial surface mediated mineral precipitation and microbial precipitation of carbonates). Under the topic of characterization, the focus is on transmission electron microscopy (TEM) and electron energy loss spectroscopy. It is the author’s hope that this review will promote more focused research on mineral-microbe interactions and encourage more collaboration between microbiologists and mineralogists.

A heterotrophic Bacillus sp. strain (5C-1) was isolated from Heshang cave, an oligotrophic karst cave in the middle reaches of Yangtze River, and identified by BIOLOG and 16S rDNA sequencing. Bacterially induced formation of calcium carbonate by 5C-1 was investigated in several comparative experimental sets with or without the cell and extracellular enzymes. The temporal variations of both the amount of the precipitates and the pH values of the solution were measured by a spectrophotometer and a pH meter, respectively. The morphological characteristics of the calcium carbonate precipitates were observed with environmental scanning electronic microscopy (ESEM). The growth of 5C-1 was found to greatly promote the pH value of the liquid medium in the first 2 days, which favors the formation of calcium carbonate. No precipitates were formed with the pH value lower than 8.6, though the pH value was demonstrated to be not the only factor controlling the formation of the calcium carbonate. The accumulation of extracellular polysaccharide substance was observed to favor the precipitate formation. Only when both factors reached a threshold did the precipitates form with the addition of CaCl₂. Cells and extracellular enzymes were not the factors that limit the precipitate formation in our microbial systems. The precipitates of a variety of morphological features including dumb bells, peanuts, irregular and spherical and rhombic forms were mainly observed in our microbial systems but not in the chemical control system. Interestingly, imprints of bacterial cells and spores were observed to be present on the surface of the precipitates of a peanut or a dumb bell form, probably indicative of the microbial escaping mechanism during the mineralization of calcium carbonate.

This study focused on the ferric sulfate precipitates formed during the culture of Acidithiobacillus ferrooxidans (A. ferrooxidans) in a modified 9K medium by applying a potential control on the electrode. X-ray diffraction (XRD), environmental scanning electron microscope (ESEM), Raman spectroscopy (Raman) and Fourier Transform Infrared spectroscopy (FTIR) were carried out to characterize and identify the precipitates which were formed, respectively, in the electrochemical cultivation with a fixed cathode potential (bias-experiment) and in the conventional batch cultivation without cathode potential control (no-bias-experiment). The results indicated that K-jarosite presented in both experiments while NH₄-jarosite and schwertmannite were only found in the no-bias-experiment. The formation of different precipitates could be attributed to the different growth statuses and rates of A. ferrooxidans and the different concentrations of Fe³⁺. In the bias-experiment, external electrons reproduced Fe²⁺ and promoted the growth of A. ferrooxidans, thus resulting in the low Fe³⁺ concentration and the rapid depletion of NH₄⁺ as the nitrogen source, in which K-jarosite was preferentially formed. In the no-bias- experiment, the lower concentration of A. ferrooxidans was observed, which was due to the continuous consumption of Fe²⁺ by bacteria, thus resulting in the relatively higher Fe³⁺ and the NH₄⁺ concentration in culture. The high concentration of Fe³⁺ favored the precipitation of the solid solution of K-NH₄-H₃O jarosite, and led to the formation of schwertmannite after K⁺ and NH₄⁺ were depleted.

The effects of goethite on the anaerobic bio-decomposition of sulfate minerals were investigated by using the beef extract as a carbon source and the activated sludge as the source of mixed bacteria. Solution pH, sulfate concentration, total iron ion concentration and the solid products of four different batch tests were monitored and analyzed. Experimental results showed that the presence of iron oxide can improve the alkalinity of the reaction system which results in the increase of pH value. Moreover, the added goethite consumed a large amount of H₂S generated from the sulfate minerals by SRB, thereby significantly enhancing the decomposition of gypsum and anhydrite compared with the control batch tests. In addition, the SEM observation and the EDS spectra showed that there were some rod-shaped microorganisms and new generated minerals, such as iron sulfide, calcium carbonate crystals, and elemental sulfur. Both of the proliferation of new minerals (iron sulfide and calcium carbonate crystals) and the complete disappearance of sulfate minerals indicated that iron oxide can play the role in fixing the S element through the metabolism of SRB and hence improve the bio-decomposition of sulfate minerals.

Bio-related techniques have been proved to be efficient and specific in eliminating impure minerals such as goethite, hematite and kaolinite from aluminum hydroxides in bauxite processing. In this study, the bacterium Paenibacillus polymyxa (P. polymyxa) mediated dissolution and flotation of bauxite were experimentally investigated. To disclose the contribution of adhered bacteria to these two processes, comparative experiments were designed, with one (and the other not) being dialyzed to prevent cells from contacting with bauxite. The results show that all the release rates of Al, Fe and Si are accelerated by the involvement of bacteria during 11 experimental days. More Al, Si and especially Fe are leached out in contact trial than in dialysis trial, and simultaneously, a large amount of Si-enriched flocs are formed. Further analysis indicates that with the adhesion of P. polymyxa and high molecular weight metabolites, Fe minerals are much more dissolvable than kaolinite. However, kaolinite can be floated easily with the mediation of adhered bacteria and metabolites. This study suggests that in bauxite biobeneficiation, sufficient contact between microbes and bauxite can facilitate the elimination of impurities such as iron and silicon.

The interpretation of the pollen records from lake sediments is always hampered by a lack of information relating to different pollen production, transportation, deposition, and preservation. It is important to understand the modern process of pollen sedimentation and its climatic implications. This paper presents results from a palynological study on 61 surface sediments samples from Bosten Lake, the largest inland freshwater lake in China. Our results suggest that Chenopodiaceae and Artemisia dominate the modern pollen assemblages and have stable percentages at most sites of the lake basin except for the estuary area. Pollen Artemisia/Chenopodiaceae ratio is about 0.5, indicating the dry climate of the region. Principle Components Analysis (PCA) of pollen data can identify the pollen samples as several ecological groups from different parts of the lake. Pollen transportation dynamics and the mixing effect of lake currents and waves on pollen deposition have affected the pollen assemblages. The distribution of Typha pollen seems to be affected by the location where the parent plants grow. Picea pollen has higher percentages at estuary area, suggesting fluvial transport. Pollen concentration has high values at the central part of the lake basin due to the sedimentation focusing process effect. Our results suggest that the pollen assemblages of the sediment core from the central part of the lake can potentially record the regional vegetation history.

Located in the central Eurasian continent and far from oceans, northwestern China is characterized as an extremely dry environment with much higher evaporation than the available precipitation. This area is one of the most severe, unique and typical arid regions in the world. Therefore, this area is not only sensitive to regional climate changes, but may also be closely linked to global change. Climate studies of this region are representative and have a typical significance. However, it is hard to get a comprehensive understanding of the regional climate change because of the lack of meteorological records. Because of its accuracy, continuity, high-resolution, variable measurement accuracy, sensitivity to climatic factors, wide distribution, easy sampling and ease of obtaining a large volume of copies, dendro-science may be the perfect high-resolution climate index. Currently, dendrochronology is widely used in various fields of past environment change. A lot of researches have been developed around the Tianshan and Qilian Mountains. Dendroclimatology, dendroecology and dendrohydrology are applied in these areas. With ring width and density, as well as isotope data, we can reconstruct past environment changes. Long-term chronologies that developed from the middle Qilian Mountains and Qaidam Basin are important for learning paleo-climate change. Through the dendro-science achievements in northwest China as the text introduced, we can see that dendro-science still has a long way to go. This paper summarizes the tree-ring related studies since the early part of the last century in northwest China, which may help give an overview of the dendrochronology studies in this area.

The bacterial respiratory quinones and membrane phospholipid fatty acids (PLFA) were measured to test the biochemical responses to the redox conditions after the respiration of diverse electron acceptors by microorganisms. Shewanella putrefaciens strain CN32 was examined for its growth with O₂, nitrate, ferrihydrite, ferric citrate, and sulfite as electron acceptors. The same parameters were also measured for Desulfovibrio desulfuricans strain G-20, Geobacter metallireducens strain GS-15, Thioploca spp., two strains of magnetotactic bacteria (Magneteospirilum magnetotactium marine vibrioid strain MV-1 and M. sp. strain AMB-1), and environmental sediments. Microorganisms with aerobic respiratory of oxygen (MV-1 and AMB-1) have high ratios of monounsaturated to saturated straight chain PLFA and ubiquinone to menaquinone ratios; while those that conduct strict anaerobic respirations (G-20 with sulfate and GS-15 with ferric iron) have low ratios of monounsaturated to saturated straight chain PLFA and uniquinone to menaquinone ratios. The facultative respiratory of nitrate (Thioploca) has these parameters in the middle. The ratios of menaquinones to ubiquinones in CN32 cells systematically increase according to the increase of redox potential and bioavalibility of electron acceptors. The correlation between SUQ-n/SMK-n ratios and redox conditions indicates the structure of respiratory quinone responses sensitively to the microbial ecophysiological conditions.

This paper presents an integrated effort of a long-term risk analysis for the emergency response of nuclear power plants in complex terrains. Use of coupled source term, fate and transport, and exposure assessment models associated with eight synoptic weather patterns successfully provides timely and reasonably accurate long-range prognostic wind fields to simulate the possible exposure episodes and risk potential. The seamless integration of multi-scale simulation models in accordance with different release scenarios of process source term in the nuclear power plants permits the simulation of pollutant fate, transport, and deposition processes in multiple dimensions of atmospheric environment. With the aid of spatial analysis, the assessment of potential detrimental impacts for the accidental release of various nuclides from nuclear power plants becomes achievable. The practical implementation of this integrated modeling system was assessed by case studies at one existing nuclear power plant in southern Taiwan, China. Two- and three-dimensional fly-through visualization technologies make risk assessment practical and credible based on the differing weather patterns identified at the continental scale in advance.

In this paper, we introduced a clear object-oriented framework to implement the complicated adaptive procedure with C++ programming language. In this framework, it consisted of the unstructured mesh generation, a-posterior error estimating, adaptive strategy, and the postprocessing. Unlike the procedure-oriented framework, whichis commonly used in DC resistivity modeling with FORTRAN language, the object-oriented one, which is famous for its characteristic of encapsulation, could be used for a class of problems that would be executed by only making some changes on the user interface. To validate its flexibility, two synthetic DC examples were tested here.

Long-term climate data records (CDR) are often constructed using observations made by multiple Earth observing sensors over a broad range of spectra and a large scale in both time and space. These sensors can be of the same or different types operated on the same or different platforms. They can be developed and built with different technologies and are likely operated over different time spans. It has been known that the uncertainty of climate models and data records depends not only on the calibration quality (accuracy and stability) of individual sensors, but also on their calibration consistency across instruments and platforms. Therefore, sensor calibration inter-comparison and validation have become increasingly demanding and will continue to play an important role for a better understanding of the science product quality. This paper provides an overview of different methodologies, which have been successfully applied for sensor calibration inter-comparison. Specific examples using different sensors, including MODIS, AVHRR, and ETM+, are presented to illustrate the implementation of these methodologies.