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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... more
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...
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A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater... more
A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera i...
Research Interests: Environmental Science, Arsenic, Groundwater, Ecology, China, and 15 moreEnvironmental Chemistry, Medicine, Multidisciplinary, Microbial Population Biology, Biological Sciences, Molecular typing, Pseudomonas, Enterobacteriaceae, PLoS one, AQUIFER, Acinetobacter, Inner Mongolia, Microbiota, Microbial Community Structure, and Arthrobacter
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Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate‐reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The... more
Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate‐reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu‐2, mixed‐layer illite‐smectite RAr‐1 and ISCz‐1, and illite IMt‐1) were exposed to D. vulgaris in a non‐growth medium with and without anthraquinone‐2,6‐disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absenc...
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Research Interests: Geology, Chemistry, Mössbauer Spectroscopy, Transmission Electron Microscopy, Nuclear Chemistry, and 14 moreIron, Dissolution, Soil sciences, High Performance Liquid Chromatography, Goethite, Jarosite, Surface Area, Mossbauer Spectroscopy, Reaction Kinetics, Electron Energy Loss Spectroscopy, Direct Current, Agricultural and Bioresource Engineering, Illite, and CN
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Research Interests: Environmental Engineering, Microbiology, Environmental Science, Geology, Geochemistry, and 15 moreOceanography, Geomicrobiology, Kinetics, China, Chemical Geology, Marine Science, Dolomite, Data Collection, Integrated Approach, Marine Sediment, Geomicrobilogy, Microstructures, Indexation, Cell Wall, and Alkalinity
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Previous work documented the general antibacterial mechanism of iron containing clays that involved hydroxyl radical (•OH) production from soluble Fe(2+), and attack of cell membrane and intracellular proteins. Here we explore the role of... more
Previous work documented the general antibacterial mechanism of iron containing clays that involved hydroxyl radical (•OH) production from soluble Fe(2+), and attack of cell membrane and intracellular proteins. Here we explore the role of clay structural Fe(II) in •OH production at near neutral pH and identify a lipid involved in the antibacterial process. Structural Fe(III) in nontronite NAu-2 was reduced (rNAu-2) and E. coli, a model bacterium, was exposed to rNAu-2 in oxic suspension. The antibacterial activity of rNAu-2 was dependent on pH and Fe(II) concentration, where E. coli were completely killed at pH 6, but survived at pH 7 and 8. In the presence of a •OH scavenger or in anaerobic atmosphere, E. coli survived better, suggesting that cell death may be caused by •OH generated from oxidation of structural Fe(II) in rNAu-2. In-situ imaging revealed damage of a membrane lipid, cardiolipin, in the polar region of E. coli cells, where reactive oxygen species and redox-active lab...
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A large number of rare earth element mining and application resulted in a series of problems of soil and water pollution. Environmental remediation of these REE-contaminated sites has become a top priority. This paper explores the use of... more
A large number of rare earth element mining and application resulted in a series of problems of soil and water pollution. Environmental remediation of these REE-contaminated sites has become a top priority. This paper explores the use of Bacillus licheniformis to adsorb lanthanum and subsequent mineralization process in contaminated water. The maximum adsorption capacity of lanthanum on bacteria was 113.98 mg/g (dry weight) biomass. X-ray diffraction (XRD) and transmission electron microscopy (TEM) data indicated that adsorbed lanthanum on bacterial cell surface occurred in an amorphous form at the initial stage. Scanning electron microscopy with X-ray energy-dispersive spectroscopy (SEM/EDS) results indicated that lanthanum adsorption was correlated with phosphate. The amorphous material was converted into scorpion-like monazite (LaPO4 nanoparticles) in a month. The above results provide a method of using bacterial surface as adsorption and nucleation sites to treat REE-contaminate...
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An anaerobic nitrate-reducing Fe(II)-oxidizing bacterium, Pseudogulbenkiania sp. strain 2002, was used to investigate As immobilization by biogenic Fe oxyhydroxides under different initial molar ratios of Fe/As in solutions. Results... more
An anaerobic nitrate-reducing Fe(II)-oxidizing bacterium, Pseudogulbenkiania sp. strain 2002, was used to investigate As immobilization by biogenic Fe oxyhydroxides under different initial molar ratios of Fe/As in solutions. Results showed that Fe(II) was effectively oxidized, mainly forming lepidocrocite, which immobilized more As(III) than As(V) without changing the redox state of As. When the initial Fe/As ratios were kept constant, higher initial Fe(II) concentrations immobilized more As with higher Asimmobilized/Feprecipitated in biogenic lepidocrocite. EXAFS analysis showed that variations of initial Fe(II) concentrations did not change the As-Fe complexes (bidentate binuclear complexes ((2)C)) with a fixed As(III) or As(V) initial concentration of 13.3 μM. On the other hand, variations in initial As concentrations but fixed Fe(II) initial concentration induced the co-occurrence of bidentate binuclear and bidentate mononuclear complexes ((2)E) and bidentate binuclear and monod...
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Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving... more
Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at...
Research Interests: Chemistry, Environmental Remediation, Arsenic, Groundwater, X ray absorption spectroscopy, and 15 moreEnvironmental Chemistry, Medicine, Multidisciplinary, Adsorption, Nitrates, Nitrate, Ferrihydrite, Sulfate, X ray diffraction, Solutions, Magnetite, Ferrous, Geologic Sediments, Ferric Compounds, and Microcosm
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We investigate the distribution of archaeal lipids in a 5.8-m-long sedimentary core recovered from Lake Qinghai to extract regional hydroclimate and temperature signals since the last deglaciation for this important region. The... more
We investigate the distribution of archaeal lipids in a 5.8-m-long sedimentary core recovered from Lake Qinghai to extract regional hydroclimate and temperature signals since the last deglaciation for this important region. The paleohydrology was reconstructed from the relative abundance of thaumarchaeol (%thaum) and the archaeol and caldarchaeol ecometric (ACE) index. The %thaum-inferred lake-level record was extended to deglaciation, showing three periods (11.9–13.0, 14.1–14.7 and 15.1–17.2 cal ka BP) with relatively higher lake levels than those during the early Holocene. The ACE record demonstrates three periods (10.6–11.2, 13.2–13.4 and 17.4–17.6 cal ka BP) of elevated salinity when the lake was shallow. Filtered TEX86 record based on archaeal lipid distributions corresponded to relatively higher lake levels, implying that a certain lake size is required for using the TEX86 paleothermometer. At 1–4 cal ka BP, the reconstructed temperature fluctuated significantly and correlated...
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Biological redox cycling of structural Fe in phyllosilicates is an important but poorly understood process. The objective of this research was to study microbially catalyzed redox cycles of Fe in nontronite (NAu-2). During the reduction... more
Biological redox cycling of structural Fe in phyllosilicates is an important but poorly understood process. The objective of this research was to study microbially catalyzed redox cycles of Fe in nontronite (NAu-2). During the reduction phase, structural Fe(III) in NAu-2 served as electron acceptor, lactate as electron donor, AQDS as electron shuttle, and dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens CN32 as mediator in bicarbonate- and PIPES-buffered media. During the oxidation phase, biogenic Fe(II) served as electron donor and nitrate as electron acceptor. Nitrate-dependent Fe(II)-oxidizing bacterium Pseudogulbenkiania sp. strain 2002 was added as mediator in the same media. For all three cycles, structural Fe in NAu-2 was able to reversibly undergo three redox cycles without significant dissolution. Fe(II) in bio-reduced samples occurred in two distinct environments, at edges and in the interior of the NAu-2 structure. Nitrate reduction to nitrogen gas was cou...
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Research Interests: Environmental Engineering, Civil Engineering, Marine Biology, Microbiology, Environmental Science, and 15 moreGeology, Hydrogeology, Soil Science, Hydrology, Geomicrobiology, Groundwater, Applied Economics, Hydraulic conductivity, Field Experiment, Water resource management, Grain size, AQUIFER, Plume, Field Data, and Lognormal Distribution
Temperature, pressure, and time have been thought to control the smectite-to-illite (S-I) reaction, an important diagenetic process used for petroleum exploration. We demonstrated that microorganisms can promote the S-I reaction by... more
Temperature, pressure, and time have been thought to control the smectite-to-illite (S-I) reaction, an important diagenetic process used for petroleum exploration. We demonstrated that microorganisms can promote the S-I reaction by dissolving smectite through reduction of structural Fe(III) at room temperature and 1atmosphere within 14 days. This reaction typically requires conditions of 300° to 350°C, 100 megapascals, and 4 to 5 months in the absence of microbial activity. These results challenge the conventional concept of the S-I reaction and of reaction kinetic models.
Research Interests: Geology, Chemistry, Kinetics, Minerals, Crystallization, and 15 moreDiagenesis, Clay Minerals, Medicine, Multidisciplinary, Atmospheres, Dissolution, Chemical Reactions, Microorganisms, Pressure, Room Temperature, Microbial Activity, Reaction Kinetics, Ferric Compounds, Petroleum Products, and Illite
Although microbial treatments of heavy metal ions in wastewater have been studied, the removal of these metals through incorporation into carbonate minerals has rarely been reported. To investigate the removal of Fe3+ and Pb2+, two... more
Although microbial treatments of heavy metal ions in wastewater have been studied, the removal of these metals through incorporation into carbonate minerals has rarely been reported. To investigate the removal of Fe3+ and Pb2+, two representative metals in wastewater, through the precipitation of carbonate minerals by a microbial flocculant (MBF) produced by Bacillus mucilaginosus. MBF was added to synthetic wastewater containing different Fe3+ and Pb2+ concentrations, and the extent of flocculation was analyzed. CO2 was bubbled into the mixture of MBF and Fe3+/Pb2+ to initiate the reaction. The solid substrates were analyzed via X-ray diffraction, transmission electron microscopy and energy dispersive spectroscopy. The results showed that the removal efficiency decreased and the MBF adsorption capacity for metals increased with increasing heavy metal concentration. In the system containing MBF, metals (Fe3+ and Pb2+), and CO2, the concentrated metals adsorbed onto the MBF combined with the dissolved CO2, resulting in oversaturation of metal carbonate minerals to form iron carbonate and lead carbonates. These results may be used in designing a method in which microbes can be utilized to combine CO2 with wastewater heavy metals to form carbonates, with the aim of mitigating environmental problems.
Research Interests: Earth Sciences, Chemistry, Carbon Dioxide, Adsorption, Desalination, and 15 moreCarbonates, Environmental Sciences, Drinking Water Treatment, Carbonate, Flocculation, Bacillus, Chlorination, Carbon Dioxide Fixation, Effluent Treatment, CHEMICAL SCIENCES, Chemical Precipitation, Activated Sludge Process, Carbon Fixation, Desalinization, and dessalement
Twenty-eight bacterial and Br transport experiments were performed in the field to determine the effects of physical and chemical heterogeneity of the aquifer sediment. The experiments were performed using groundwater from two field... more
Twenty-eight bacterial and Br transport experiments were performed in the field to determine the effects of physical and chemical heterogeneity of the aquifer sediment. The experiments were performed using groundwater from two field locations to examine the effects of groundwater chemistry on transport. Groundwater was extracted from multilevel samplers and pumped through 7-cm-long columns of intact sediment or repacked sieved and coated or uncoated sediment from the underlying aquifer. Two bacterial strains, Comamonas sp. DA001 and Paenibacillus polymyxa FER-02, were injected along with Br into the influent end of columns to examine the effect of cell morphology and cell surface properties on bacterial transport. The effects of column sediment grain size and mineral coatings coupled with groundwater geochemistry were also investigated. Significant irreversible attachment of DA001 was observed in the Fe oxyhydroxide-coated columns, but only in the suboxic groundwater where the concentrations of dissolved organic carbon (DOC) were ca. 1 ppm. In the oxic groundwater where DOC was ca. 8 ppm, little attachment of DA001 to the Fe oxyhydroxide-coated columns was observed. This indicates that DOC can significantly reduce bacterial attachment due electrostatic interactions. The larger and more negatively charged FER-02 displayed increasing attachment with decreasing grain size regardless of DOC concentration, and modeling of FER-02 attachment revealed that the presence of Fe and Al coatings on the sediment also promoted attachment. Finally, the presence of Al coatings and Al containing minerals appeared to significantly retard the Br tracer regardless of the concentration of DOC. These findings suggest that DOC in shallow oxic groundwater aquifers can significantly enhance the transport of bacteria by reducing attachment to Fe, Mn and Al oxyhydroxides. This effect appears to be profound for weakly and strongly charged hydrophilic bacteria and may contribute to differences in observations between laboratory experiments versus field-scale investigations particularly if the groundwater pH remains subneutral and Fe oxyhydroxide phases exist. These observation validate the novel approach taken in the experiments outlined here of performing laboratory-scale experiments on site to facilitate the use of fresh groundwater and thus be more representative of in situ groundwater conditions.
Research Interests: Chemistry, Groundwater, Environmental Chemistry, Medicine, Multidisciplinary, and 15 moreAdsorption, Aluminum, Cell morphology, Contaminant hydrology, Bacillus, Laboratory experiment, Iron, Grain size, AQUIFER, Dissolved Organic Carbon, Cell Surface Markers, Geologic Sediments, Bromine, contaminant, and Electrostatic interaction
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Phylogenetic diversities of the endolithic bacterial communities in dolomite and limestone rocks from a karst canyon (Nanjiang Canyon), China, were analyzed based on the 16S rRNA gene analysis. In the dolomite endolithic bacterial... more
Phylogenetic diversities of the endolithic bacterial communities in dolomite and limestone rocks from a karst canyon (Nanjiang Canyon), China, were analyzed based on the 16S rRNA gene analysis. In the dolomite endolithic bacterial communities, members of Cyanobacteria were the most abundant followed in abundance by members of Alphaproteobacteria, Acidobacteria, and Actinobacteria. Members of Betaproteobacteria, Deltaproteobacteria, Bacteriodetes, Verrucomicrobia, and Chloroflexi were
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Research Interests: Earth Sciences, Geology, Climate Change, Climatology, Climate variability, and 13 moreMonsoon, Holocene, North Atlantic, Physical sciences, Late Holocene, Little Ice Age, East Asian Monsoon, Tibetan Plateau, Atmospheric Circulation, Asian monsoon, Total Organic Carbon, Medieval warm Period, and Solar Irradiance
ABSTRACT River-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended... more
ABSTRACT River-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended particles, yet factors that control particle aggregation and resulting sedimentation in these environments are poorly understood. This study was designed to investigate the role of microbial Fe(III) reduction and solution chemistry in aggregation of suspended particles in the Mississippi Delta. Three representative sites along the salinity gradient were selected and sediments were collected from the sediment-water interface. Based on quantitative mineralogical analyses 88–89 wt.% of all minerals in the sediments are clays, mainly smectite and illite. Consumption of SO42– and the formation of H2S and pyrite during microbial Fe(III) reduction of the non-sterile sediments by Shewanella putrefaciens CN32 in artificial pore water (APW) media suggest simultaneous sulfate and Fe(III) reduction activity. The pHPZNPC of the sediments was ≤3.5 and their zeta potentials at the sediment-water interface pH (6.9–7.3) varied from –35 to –45 mV, suggesting that both edges and faces of clay particles have negative surface charge. Therefore, high concentrations of cations in pore water are expected to be a predominant factor in particle aggregation consistent with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Experiments on aggregation of different types of sediments in the same APW composition revealed that the sediment with low zeta potential had a high rate of aggregation. Similarly, addition of external Fe(II) (i.e. not derived from sediments) was normally found to enhance particle aggregation and deposition in all sediments, probably resulting from a decrease in surface potential of particles due to specific Fe(II) sorption. Scanning and transmission electron microscopy (SEM, TEM) images showed predominant face-to-face clay aggregation in native sediments and composite mixtures of biopolymer, bacteria, and clay minerals in the bioreduced sediments. However, a clear need remains for additional information on the conditions, if any, that favor the development of anoxia in deep- and bottom-water bodies supporting Fe(III) reduction and resulting in particle aggregation and sedimentation.