Molecular simulations of metal adsorption to bacterial surfaces

The atomic-scale interactions that occur between cations and the metal-binding cell wall components common to many gram-positive bacteria were investigated using molecular simulations techniques. We examined the adsorption of Cd and Pb onto peptidoglycan and teichoic acid components of the bacterial cell wall using classical energy force field methods. Within the framework of molecular mechanics and the Cerius² modeling software, we used energy minimization, conformational analysis, and molecular dynamics to examine the different components of the cell wall and to determine relative binding energies and structural configurations of the cell wall components, both with and without the metals present. Electronic structure calculations of representative metal-organic complexes validate the more practical classical methods required in simulating the large number of atoms associated with the cell wall components. The classical force field simulations were conducted in both gas phase and solvated periodic cells. Force field-based simulation techniques can adequately describe the interactions of Cd with the cell wall, defining both metal ion coordinations and binding distances. However, the classical force field approach is inconsistent in describing the observed Pb-cell wall interactions due to possible limitations in the force field parameters, the propensity for Pb to form hydroxides at circumneutral pH, or the dominance of other adsorption mechanisms.     

Effect of cultivation and experimental conditions on the surface reactivity of the metal-resistant bacteria Cupriavidus metallidurans CH34 to protons,cadmium and zinc

The surface chemistry of the cell wall of the metal resistant bacterium Cupriavidus metallidurans CH34 was investigated through proton exchange and zinc and cadmium sorption experiments. The effect of organic and mineral nutrients availability, culture age and viability on cell wall reactivity to H⁺, Zn or Cd was specifically addressed. Parameter sensitivity studies allowed constraining the pH-validity domain of the titration experiments and defining experimental conditions that permit reproducible experiments with this bacterium. The results were satisfactorily fitted with a non-electrostatic model that allowed the determination of the stability constants of three discrete acid–base functional groups differing in acidity at bacterial cell surfaces. These results revealed that C. metallidurans CH34 did not particularly stand out in terms of its surface reactivity as compared to metal-sensitive bacteria. This may confirm a generic global reactivity of all bacteria towards non-redox sensitive metals. The same reactivity to zinc was observed for C. metallidurans CH34 cells grown in LB-rich or TSM-mineral media. Cell surface reactivity was found to be independent of organic substrates availability but strongly dependent on cell growth stage and cell viability. Zinc sorption by C. metallidurans CH34 was only slightly (15% decrease) affected by phosphate availability. This suggests the involvement of phosphorus sites in metal binding. Zn and Cd stability constants compared to those of strong chelating ligands but were higher than those of weak ligands, such as acetic acid or phosphoric acid. This indicates that bacterial cells strongly compete with small dissolved organic components that are potentially less reactive to metals than bacteria. This competition potentially affects metal mobility in soils.     

Metabolic patterning of biosilicification

Here we show a discernibly unique biosilicification pattern for live, metabolically active Synechococcus cyanobacterial cell surfaces compared to dead Synechococcus cells under identical experimental conditions. The live cell treatments showed signs of cell division and the growth of fimbriae indicating metabolic activity during the 5-day silicification experiment. Live treatment cells were also recultivable after the experiments confirming their continued viability. The metabolically active live cyanobacteria treatment bound twice the amount of colloidal SiO₂ and held it more tightly compared to the dead cell treatment. Further, biosilicification of the live, actively metabolizing bacteria was unipolar, leaving the core surface largely unencrusted. In contrast, biosilicification of the dead cells was heterogeneous, occurring across the entire cell surface with no observable localized pattern. The directed biosilicification localization of live cell surfaces is likely a bacterial strategy to protect the cell functionality against the potentially inhibitory effects of mineral encrustation. Localization of silica biominerals to the polar end of the cell is also consistent with reported bacteria regulated cell polarity, which, under the experimental pH of 3, would enable localized differential attraction between the charged colloidal silica (+) particles and the bacterial cell polar surface (−). Our results show a novel metabolically-linked distinct colloidal SiO₂ biomineralization fingerprint, suggesting a putative biomineralization signature.     

Acid-base activity of live bacteria: Implications for quantifying cell wall charge

To distinguish the buffering capacity associated with functional groups in the cell wall from that resulting from metabolic processes, base or acid consumption by live and dead cells of the Gram-negative bacterium Shewanella putrefaciens was measured in a pH stat system. Live cells exhibited fast consumption of acid (pH 4) or base (pH 7, 8, 9, and 10) during the first few minutes of the experiments. At pH 5.5, no acid or base was required to maintain the initial pH constant. The initial amounts of acid or base consumed by the live cells at pH 4, 8, and 10 were of comparable magnitudes as those neutralized at the same pHs by intact cells killed by exposure to gamma radiation or ethanol. Cells disrupted in a French press required higher amounts of acid or base, due to additional buffering by intracellular constituents. At pH 4, acid neutralization by suspensions of live cells stopped after 50 min, because of loss of viability. In contrast, under neutral and alkaline conditions, base consumption continued for the entire duration of the experiments (5 h). This long-term base neutralization was, at least partly, due to active respiration by the cells, as indicated by the build-up of succinate in solution. Qualitatively, the acid-base activity of live cells of the Gram-positive bacterium Bacillus subtilis resembled that of S. putrefaciens. The pH-dependent charging of ionizable functional groups in the cell walls of the live bacteria was estimated from the initial amounts of acid or base consumed in the pH stat experiments. From pH 4 to 10, the cell wall charge increased from near-zero values to about −4 × 10⁻¹⁶ mol cell⁻¹ and −6.5 × 10⁻¹⁶ mol cell⁻¹ for S. putrefaciens and B. subtilis, respectively. The similar cell wall charging of the two bacterial strains is consistent with the inferred low contribution of lipopolysaccharides to the buffering capacity of the Gram-negative cell wall (of the order of 10%).     

Potentiometric titrations of Bacillus subtilis cells to low pH and a comparison of modeling approaches

To provide constraints on the speciation of bacterial surface functional groups, we have conducted potentiometric titrations using the gram-positive aerobic species Bacillus subtilis, covering the pH range 2.1 to 9.8. Titration experiments were conducted using an auto-titrator assembly, with the bacteria suspended in fixed ionic strength (0.01 to 0.3 M) NaClO₄ solutions. We observed significant adsorption of protons over the entire pH range of this study, including to the lowest pH values examined, indicating that proton saturation of the cell wall did not occur under any of the conditions of the experiments. Ionic strength, over the range studied here, did not have a significant effect on the observed buffering behavior relative to experimental uncertainty. Electrophoretic mobility measurements indicate that the cell wall is negatively charged, even under the lowest pH conditions studied. These experimental results necessitate a definition of the zero proton condition such that the total proton concentration at the pH of suspension is offset to account for the negative bacterial surface charge that tends towards neutrality at pH <2.The buffering intensity of the bacterial suspensions reveals a wide spread of apparent pKa values. This spread was modeled using three significantly different approaches: a Non-Electrostatic Model, a Constant Capacitance Model, and a Langmuir-Freundlich Model. The approaches differ in the manner in which they treat the surface electric field effects, and in whether they treat the proton-active sites as discrete functional groups or as continuous distributions of related sites. Each type of model tested, however, provides an excellent fit to the experimental data, indicating that titration data alone are insufficient for characterizing the molecular-scale reactions that occur on the bacterial surface. Spectroscopic data on the molecular-scale properties of the bacterial surface are required to differentiate between the underlying mechanisms of proton adsorption inherent in these models. The applicability and underlying conceptual foundation of each model is discussed in the context of our current knowledge of the structure of bacterial cell walls.     

The effect of thiosulfate-oxidizing bacteria on the stability of the gold-thiosulfate complex

An Acidithiobacillus thiooxidans spp., isolated from the Driefontein Consolidated Gold Mine, Witwatersrand Basin, Republic of South Africa was able to precipitate gold from Au(S₂O₃)₂³⁻ in the presence of up to 0.26 mM gold. In chemical control experiments and with the presence of dead bacteria, gold was not precipitated under similar experimental conditions and duration. During growth, the pH of the culture medium decreased from pH 5.4 to 1.9, while the Eh increased from 0.3 to between 0.5 to 0.6 V within a period of 75 days. In the active (live) bacterial culture systems, acid production enhanced thiosulfate disproportionation, after which the elemental sulfur and any other intermediate sulfur species were oxidized completely to sulfate. The gold, Au(S₂O₃)₂³⁻, was stable in the bacterial systems until sulfur oxidation was complete; then the bacteria precipitated gold from Au(S₂O₃)₂³⁻. The bacterial systems (0.02-0.26 mM gold) precipitated 87 to 100% of the gold under diurnal light exposure, while only 11 to 69% of the gold was precipitated in the dark. The presence of gold (≥0.08 mM) reduced bacterial growth, disrupted cell division causing cell elongation, and was ultimately toxic to this bacterium, killing the cultures. The gold was precipitated inside the bacterial cells as fine-grained colloids ranging between 5 and 10 nm in diameter and in the bulk fluid phase as crystalline micrometer-scale gold. Observations using transmission electron microscopy revealed that the gold was deposited throughout the cell; however, it was concentrated in the cell envelope, especially along the cytoplasmic membrane, suggesting that gold precipitation was likely enhanced via electron transport processes associated with energy generation. Seven months after population growth had stopped, the gold had formed coiled or wire gold, irregular and rounded structures with an approximate size ranging from 0.5 to 5 μm, and crystalline octahedral gold.     

The effects of non-metabolizing bacterial cells on the precipitation of U, Pb and Ca phosphates

In this study, we test the potential for passive cell wall biomineralization by determining the effects of non-metabolizing bacteria on the precipitation of uranyl, lead, and calcium phosphates from a range of over-saturated conditions. Experiments were performed using Gram-positive Bacillus subtilis and Gram-negative Shewanella oneidensis MR-1. After equilibration, the aqueous phases were sampled and the remaining metal and P concentrations were analyzed using inductively coupled plasma-optical emission spectroscopy (ICP-OES); the solid phases were collected and analyzed using X-ray diffractometry (XRD), transmission electron microscopy (TEM), and X-ray absorption spectroscopy (XAS).At the lower degrees of over-saturation studied, bacterial cells exerted no discernable effect on the mode of precipitation of the metal phosphates, with homogeneous precipitation occurring exclusively. However, at higher saturation states in the U system, we observed heterogeneous mineralization and extensive nucleation of hydrogen uranyl phosphate (HUP) mineralization throughout the fabric of the bacterial cell walls. This mineral nucleation effect was observed in both B. subtilis and S. oneidensis cells. In both cases, the biogenic mineral precipitates formed under the higher saturation state conditions were significantly smaller than those that formed in the abiotic controls.The cell wall nucleation effects that occurred in some of the U systems were not observed under any of the saturation state conditions studied in the Pb or Ca systems. The presence of B. subtilis significantly decreased the extent of precipitation in the U system, but had little effect in the Pb and Ca systems. At least part of this effect is due to higher solubility of the nanoscale HUP precipitate relative to macroscopic HUP. This study documents several effects of non-metabolizing bacterial cells on the nature and extent of metal phosphate precipitation. Each of these effects likely contributes to higher metal mobilities in geologic media, but the effects are not universal, and occur only with some elements and only under a subset of the conditions studied.     

Competitive interference during the biodegradation of cresols

Phenol and its methylated derivatives, cresol isomers, are hazardous pollutants that are commonly present in various industrial effluents and known to have detrimental effect on aquatic life as well as human health, due to their toxic and carcinogenic nature. It is essential, therefore, to reduce the concentration of these contaminants in industrial effluent to acceptable levels prior to being discharged into the environment. Bacterial cells of the strain Pseudomonas putida, with excellent biodegradation capabilities and high tolerance of cresols, were extracted and immobilized in polyvinyl alcohol (PVA) gel for cresols biodegradation. The biodegradation was carried out at different operating conditions, in both batch and continuous modes, using a cylindrical spouted bed bioreactor. Factors affecting o-cresol and m-cresol degradation were studied in batch experiments, and the results showed that the immobilized bacteria could tolerate cresols concentration up to 200 mg/l. Moreover, the experiments indicated that the biodegradation rate was highly affected by the operating parameters such as pH and temperature, with optimum ranges of 6–8 for pH and 30–35 °C for temperature. However, the optimum conditions were different for each cresol isomer. The potential of P. putida in degrading binary and ternary mixtures of cresols was also examined in the continuous process and compared with single component biodegradation. The experimental results revealed that the biodegradation of o-cresol was highly inhibited by the presence of p-cresol and m-cresol.     

The Influence of Oyster Farming on Sediment Bacterial Communities

Aquaculture currently provides half of all fish for human consumption, and this proportion is expected to increase to meet the growing global demand for protein. As aquaculture, including oyster farming, expands, it is increasingly important to understand effects on coastal ecosystems. The broad-scale ecological effects of oyster aquaculture are well documented; however, less is known regarding the influence of oyster aquaculture on sediment bacterial communities. To better understand this relationship, we compared three different oyster farming practices that varied in oyster biomass and proximity of oysters to the sediment. We used high-throughput sequencing and quantitative polymerase chain reaction to examine the effect of oyster farming on sediment bacterial communities. We examined the entire bacterial community and looked specifically at bacteria that support essential estuarine ecosystem services (denitrifiers), as well as bacteria that can be detrimental to human health (members of the Vibrio genus). We found that oyster biomass increased Vibrio richness and sediment carbon content, which influenced bacterial community composition. When compared to reference sites, the overall abundance of bacteria was increased by the bottom planting method, but the associated increases in denitrifiers and Vibrio were not significant. We were unable to detect V. parahaemolyticus, V. vulnificus, or V. cholera, the three most common Vibrio pathogens, in any sample, suggesting that oyster farming did not enhance these potential human pathogens in sediments at the time of sampling. These results highlight how differences in oyster farming practice can affect sediment bacterial communities, and the ecosystem services they provide.     

Hydrous ferric oxide precipitation in the presence of nonmetabolizing bacteria: Constraints on the mechanism of a biotic effect

We have used room temperature and cryogenic ⁵⁷Fe Mössbauer spectroscopy, powder X-ray diffraction (pXRD), mineral magnetometry, and transmission electron microscopy (TEM), to study the synthetic precipitation of hydrous ferric oxides (HFOs) prepared either in the absence (abiotic, a-HFO) or presence (biotic, b-HFO) of nonmetabolizing bacterial cells (Bacillus subtilis or Bacillus licheniformis, ∼10⁸ cells/mL) and under otherwise identical chemical conditions, starting from Fe(II) (10⁻², 10⁻³, or 10⁻⁴ mol/L) under open oxic conditions and at different pH (6-9). We have also performed the first Mössbauer spectroscopy measurements of bacterial cell wall (Bacillus subtilis) surface complexed Fe, where Fe(III) (10^−3.5-10^−4.5 mol/L) was added to a fixed concentration of cells (∼10⁸ cells/mL) under open oxic conditions and at various pH (2.5-4.3). We find that non-metabolic bacterial cell wall surface complexation of Fe is not passive in that it affects Fe speciation in at least two ways: (1) it can reduce Fe(III) to sorbed-Fe²⁺ by a proposed steric and charge transfer effect and (2) it stabilizes Fe(II) as sorbed-Fe²⁺ against ambient oxidation. The cell wall sorption of Fe occurs in a manner that is not compatible with incorporation into the HFO structure (different coordination environment and stabilization of the ferrous state) and the cell wall-sorbed Fe is not chemically bonded to the HFO particle when they coexist (the sorbed Fe is not magnetically polarized by the HFO particle in its magnetically ordered state). This invalidates the concept that sorption is the first step in a heterogeneous nucleation of HFO onto bacterial cell walls. Both the a-HFOs and the b-HFOs are predominantly varieties of ferrihydrite (Fh), often containing admixtures of nanophase lepidocrocite (nLp), yet they show significant abiotic/biotic differences: Biotic Fh has less intraparticle (including surface region) atomic order (Mössbauer quadrupole splitting), smaller primary particle size (magnetometry blocking temperature), weaker Fe to particle bond strength (Mössbauer center shift), and no six-line Fh (6L-Fh) admixture (pXRD, magnetometry). Contrary to current belief, we find that 6L-Fh appears to be precipitated directly, under a-HFO conditions, from either Fe(II) or Fe(III), and depending on Fe concentration and pH, whereas the presence of bacteria disables all such 6L-Fh precipitation and produces two-line Fh (2L-Fh)-like biotic coprecipitates. Given the nature of the differences between a-HFO and b-HFO and their synthesis condition dependences, several biotic precipitation mechanisms (template effect, near-cell environment effect, catalyzed nucleation and/or growth effect, and substrate-based coprecipitation) are ruled out. The prevailing present view of a template or heterogeneous nucleation barrier reduction effect, in particular, is shown not to be the cause of the large observed biotic effects on the resulting HFOs. The only proposed mechanism (relevant to Fh) that is consistent with all our observations is coprecipitation with and possible surface poisoning by ancillary bacteriagenic compounds. That bacterial cell wall functional groups are redox active and the characteristics of biotic (i.e., natural) HFOs compared to those of abiotic (i.e., synthetic) HFOs have several possible biogeochemical implications regarding Fe cycling, in the photic zones of water columns in particular.     

微生物在石油生成中的作用(一)--降解和去含氧基团

近20~30年来,高温微生物学研究取得了迅猛发展,已发现高温菌（大于50℃~60℃）约70个属140种。最适合生长的温度普遍在60℃或80℃以上,最高生长温度可达110℃~113℃。在沉积物的浅层至深层,由低温至高温都广泛分布着厌氧微生物群体。它们分布在深层水中或岩石表面,包括各种分解菌、产氢菌、产甲烷菌等。这些菌种生存的温度同石油生成的主要温度段（60℃~100℃）大体相同。微生物是单细胞生物,个体小,结构简单。当环境变化时,每个细胞能直接感受到环境的刺激,更易发生适应作用,发生遗传上的变异。高温、高压、高盐环境成为嗜热菌生存的良好环境。嗜热菌的大量发现为认识生命起源、油气藏的形成提供了坚实的理论基础。沉积物中有机质转化成石油是由大分子有机质（分子量可达数万至数十万）降解成中、低分子化合物的过程,由有机质富含含氧基团、杂原子变成基本不含含氧基团的过程。这些功能主要是由微生物作用完成的。碳是构成生命的核心原子,微生物需要从有机质中吸取碳源组成细胞壁、细胞膜、细胞质、细胞核等细胞物质。大分子有机质需逐步分解成简单的有机质才能被微生物吸收,如蛋白质分解成二肽,碳水化合物水解成单糖便可被微生物利用。厌氧微生物不断获取碳使有机质逐步变成简单化合物。微生物的厌氧呼吸使有机质中的含氧化合物减少,形成一些较原来基质更为还原的化合物。在沉积物的厌氧呼吸中,作为最终电子受体的物质是有机物结构上的羟基、羧基等官能团,除去含氧基团便形成了烃类。     

Fatty acids of bacterial origin in contemporary marine sediments

Contributions by bacteria to recent sediments have been recognized as one important source of input for the extractable lipids. It has, however, proved difficult so far to conclusively relate the components identified to the contributing bacteria. This fact is primarily related to the lack of information on both the lipid chemistry of marine bacteria, and of detailed structures of the sedimentary lipids. In this paper a study of the fatty acids from a tropical marine sediment selected because of its high biomass content is reported, and relationships between the sedimentary extracts of the surface layer to fatty acid components of bacteria cultured from the sediment sample are detailed. By selecting specific structural features, a group of fatty acids have been identified as valid markers for bacteria in this environment: these include iso- and anteiso-branched chain acids; 10-methylpalmitic acid; cyclopropyl 17:0 and 19:0 acids of which ▽19:0 (11,12) is unique to bacteria; cis-vaccenic acid; and the 15:1, 17:1 ω6 and ω8 isomers especially when these occur in pairs; iso Δ7–15: 1 and iso Δ9–17:1 are branched unsaturated acids apparently unique to bacteria. Trans-monoene fatty acids are likely to be a direct bacterial input, and the hydroxy acids identified are probably of bacterial cell wall origin. This study, whilst emphasizing the necessity for detailed structural information on fatty acids in order to use them validly as biological markers, considerably extends the range of fatty acids as markers of bacterial input to contemporary sediments.     

Taxonomy and distribution of surface microlayer bacteria from two estuarine sites

The surface microlayer population of two estuarine sites was sampled to determine the numbers of bacteria present. Random isolates from one site were examined taxonomically, with subsurface and sediment samples taken for comparison. There were 130 to 5000 times more bacterial cells per ml in the surface microlayer as compared to the subsurface water, agreeing with the observations of other investigators. The surface population was found to be different taxonomically from the subsurface and sediment isolates. Pseudomonads predominated among the surface isolates while ca. onethird of the subsurface isolates werePseudomonas species.Alcaligenes species were found only in the subsurface population and comprised nearly one-half of these isolates. The majority of the surface and subsurface bacteria required no salts for growth, whereas most of the sediment bacterial isolates required either Na⁺ or Mg⁺⁺.     

Carbonate biomineralization induced by soil bacterium Bacillus megaterium

Biogenic carbonates spawned from microbial activities are common occurrences in soils. Here, we investigate the carbonate biomineralization mediated by the bacterium Bacillus megaterium, a dominant strain separated from a loess profile in China. Upon completing bacterial cultivation, the ensuring products are centrifuged, and the resultant supernatant and the concentrated bacterial sludge as well as the un-separated culture are added separately into a Ca-CO₃ containing solution for crystallization experiments. Results of XRD and SEM analysis indicate that calcite is the dominant mineral phase formed when the bacteria are present. When the supernatant alone is used, however, a significant portion of vaterite is also precipitated. Experimental results further reveal that the bacteria have a strong tendency to colonize the center area of the calcite {1 0  4} faces. Observed crystal morphology suggests that the bacterial colony may promote the growth normal to each individual {1 0  4} face of calcite when the cell concentration is high, but may retard it or even cause dissolution of the immediate substrate surfaces when the concentration is low. SEM images taken at earlier stages of the crystallization experiments demonstrate the nucleation of calcite on the bacterial cell walls but do not show obvious morphological changes on the nanometer- to submicron-sized nuclei. δ¹³C measurements unveil that the crystals grown in the presence of bacteria are further enriched in the heavy carbon isotope, implying that the bacterial metabolism may not be the carbon sources for the mineralization. Based upon these findings, we propose a mechanism for the B. megaterium mediated calcite mineralization and conclude that the whole process involves epi- and inter-cellular growth in the local microenvironments whose conditions may be controlled by cell sequestration and proton pumping during bacterial respiration.     

Microbial response to surface microtopography: the role of metabolism in localized mineral dissolution

We examine the role of microtopographical surface features on sulfide minerals in localizing and aligning bacterial adhesion. Experimental data shows strong correlation between bacterial cell alignment and principal crystallographic axes of pyrite (100 and 110). While bacteria often adhere to visible surface imperfections such as scratches, in many cases no associated surface features are visible. Additionally, the size of the surface imperfection does not unambiguously determine its effect in localizing and aligning bacterial cells. We theoretically model bacterial adhesion. We find that the depth of a surface feature such as a scratch is less important than its cross-sectional shape. Surface features that conform to the bacterial shape can strongly alter local bacterial adhesion energies, even with heights of only 10 nm. Hence, small local surface alterations due to bacterial metabolism could strongly affect local adhesion parameters, and may account for the observed bacterial distributions on mineral surfaces.     

Element zoning trends in olivine phenocrysts from a supposed primary high-magnesian andesite: an electron- and ion-microprobe study

Electron and ion-probe microanalysis have been used to obtain zoning profiles for major and trace elements in olivine phenocrysts from a high-magnesian andesite from Shodo-Shima island, southwest Japan. This rock was previously thought to represent undifferentiated, primary magma. Some crystals have unzoned cores, while others show cores which are reversely zoned with respect to Mg/ (Mg+Fe), Ni, Mn and Cr. In addition, some Ni profiles show a normally zoned hump at the most central portions of the reversely zoned crystals. All crystals show normally zoned rims. The Li concentrations are constant throughout the cores of all crystals studied, but rise sharply, by a factor of up to at least six, in the rims. The Ca and Co concentrations are essentially constant throughout all the crystals. Mechanisms for producing the observed zoning profiles are discussed, and it is concluded that the reverse zoning was produced by the introduction of crystals into a less differentiated magma than that in which they grew. The reversely zoned crystals could therefore represent xenocrysts which were introduced into an undifferentiated magma, or phenocrysts introduced into a more primitive magma by a magma mixing process. The Ni profiles are used to estimate the residence time of these crystals in the more primitive magma. The following trace element partition co-efficients have been estimated for the olivine-groundmass system in this rock: D ^Ni=16; D ^Mn=1.1; D ^Co=4.2; D ^Ca =0.02; D ^Ti=0.005; D ^V=0.05; D ^Sc=0.2; D ^Na=0.0002. Studies of trace element zoning will become increasingly important as the new generation of trace element microprobes become available but a larger database of experimentally determined values for trace element partition coefficients and diffusion coefficients in crystals and magmas, and a better understanding of other disequilibrium processes are required to fully exploit the new data.     

Melt Inclusions in Primitive Olivine Phenocrysts: the Role of Localized Reaction Processes in the Origin of Anomalous Compositions

Melt inclusions are small portions of liquid trapped by growingcrystals during magma evolution. Recent studies of melt inclusionshave revealed a large range of unusual major and trace elementcompositions in phenocrysts from primitive mantle-derived magmaticrocks [e.g. in high-Fo olivine (Fo > 85 mol %), spinel, high-Anplagioclase]. Inclusions in phenocrysts crystallized from moreevolved magmas (e.g. olivine Fo < 85 mol %), are usuallycompositionally similar to the host lavas. This paper reviewsthe chemistry of melt inclusions in high-Fo olivine phenocrystsfocusing on those with anomalous major and trace element contentsfrom mid-ocean ridge and subduction-related basalts. We suggestthat a significant portion of the anomalous inclusion compositionsreflects localized, grain-scale dissolution–reaction–mixing(DRM) processes within the magmatic plumbing system. The DRMprocesses occur at the margins of primitive magma bodies, wheremagma is in contact with cooler wall rocks and/or pre-existingsemi-solidified crystal mush zones (depending on the specificenvironment). Injection of hotter, more primitive magma causespartial dissolution (incongruent melting) of the mush-zone phases,which are not in equilibrium with the primitive melt, and mixingof the reaction products with the primitive magma. Localizedrapid crystallization of high-Fo olivines from the primitivemagma may lead to entrapment of numerous large melt inclusions,which record the DRM processes in progress. In some magmaticsuites melt inclusions in primitive phenocrysts may be naturallybiased towards the anomalous compositions. The occurrence ofmelt inclusions with unusual compositions does not necessarilyimply the existence of new geologically significant magma typesand/or melt-generation processes, and caution should be exercisedin their interpretation. KEY WORDS: melt inclusions; olivine; geochemistry; mush zones; MORB; subduction-related magmas     

Bacteria,fungi and biokarst in Lechuguilla Cave,Carlsbad Caverns National Park,New Mexico

Lechuguilla Cave is a deep, extensive, gypsumand sulfur-bearing hypogenic cave in Carlsbad Caverns National Park, New Mexico, most of which (>90%) lies more than 300 m beneath the entrance. Located in the arid Guadalupe Mountains, Lechuguilla's remarkable state of preservation is partially due to the locally continuous Yates Formation siltstone that has effectively diverted most vadose water away from the cave. Allocthonous organic input to the cave is therefore very limited, but bacterial and fungal colonization is relatively extensive: (1)Aspergillus sp. fungi and unidentified bacteria are associated with iron-, manganese-, and sulfur-rich encrustations on calcitic folia near the suspected water table 466 m below the entrance; (2) 92 species of fungi in 19 genera have been identified throughout the cave in oligotrophic (nutrient-poor) soils and pools; (3) cave-air condensate contains unidentified microbes; (4) indigenous chemoheterotrophicSeliberius andCaulobacter bacteria are known from remote pool sites; and (5) at least four genera of heterotrophic bacteria with population densities near 5×10⁵ colony-forming units (CFU) per gram are present in ceiling-bound deposits of supposedly abiogenic condensation-corrosion residues. Various lines of evidence suggest that autotrophic bacteria are present in the ceiling-bound residues and could act as primary producers in a unique subterranean microbial food chain. The suspected autotrophic bacteria are probably chemolithoautotrophic (CLA), utilizing trace iron, manganese, or sulfur in the limestone and dolomitic bedrock to mechanically (and possibly biochemically) erode the substrate to produce residual floor deposits. Because other major sources of organic matter have not been detected, we suggest that these CLA bacteria are providing requisite organic matter to the known heterotrophic bacteria and fungi in the residues. The cavewide bacterial and fungal distribution, the large volumes of corrosion residues, and the presence of ancient bacterial filaments in unusual calcite speleothems (biothems) attest to the apparent longevity of microbial occupation in this cave.     

Microbial fossilization in carbonate sediments: a result of the bacterial surface involvement in dolomite precipitation

ABSTRACT Recent dolomitic sediment samples from Lagoa Vermelha, Brazil, were examined microscopically to study the process of bacterial fossilization in carbonate sediments. Bacteria‐like bodies were intimately associated with carbonate mineral surfaces, and coatings on the former demonstrate the calcification of single bacterial cells. The bacterial fossilization process in Lagoa Vermelha sediments was simulated in the laboratory by cultivation of mixed and pure cultures of sulphate‐reducing bacteria, which were isolated from the Lagoa Vermelha sediments. These cultures produced carbonate minerals that were studied to provide insight into the initiation of the fossilization process. In mixed culture experiments, bacterial colonies became calcified, whereas in pure culture experiments, single bacterial cells were associated with dolomite surfaces. Dolomite nucleated exclusively in bacterial colonies, intimately associated with extracellular organic matter and bacterial cells. Electrophoretic mobility measurements of the bacterial cells in electrolyte solutions demonstrated the specific adsorption of Ca²⁺ and Mg²⁺ onto the cell surfaces, indicating the role of the bacterial surface in carbonate nucleation and bacterial fossilization. The affinity of the cells for Mg²⁺ was related to the capability of the strains to mediate dolomite formation. Combined with sulphate uptake, which dissociates the [MgSO₄]⁰ ion pair and increases the Mg²⁺ availability, the concentration of Mg²⁺ ions in the microenvironment around the cells, where the conditions are favourable for dolomite precipitation, may be the key to overcome the kinetic barrier to dolomite formation. These results demonstrate that bacterial fossilization is a consequence of the cell surface involvement in carbonate precipitation, implying that fossilized bacterial bodies can be used as a tool to recognize microbially mediated carbonates.     

砾间接触氧化反应器中填料表面细菌多样性及其主要功能

采用分子生物学手段,通过构建16S rDNA基因文库,对新型剩余污泥减量化处理系统—生物砾间接触氧化反应器 (GCOR) 中载体表面附着细菌多样性进行了系统发育分析,并讨论了多种细菌共存对剩余污泥减量化的贡献。结果表明,附着细菌可分为好氧呼吸菌群、兼性厌氧菌群、厌氧水解发酵菌群和生长缓慢菌群等4大类。其中,优势菌群分别是以兼具呼吸/发酵代谢方式的β变形菌、嗜水气单胞菌及以发酵为主要代谢方式的拟杆菌属。此外,好氧菌群中还发育有假单胞菌属、硝化螺菌属细菌和黄杆菌属细菌等。慢速生长菌群包括Caldimonas taiwanensis strain On 1和Ideonella sp.。填料表面生物膜微生态环境复杂,微生物多样性较高,好氧、厌氧菌群以及慢速生长菌群等多种细菌共同作用,为在降解污水有机物的同时,达到剩余污泥减量化做出巨大贡献。结果分析表明,细菌的主要功能可归纳为：能量解偶联、共代谢作用、生物溶胞作用和慢性生长种群的影响。