Influence of Seasonal and Geochemical Changes on the Geomicrobiology of an Iron Carbonate Mineral Water Spring

Fuschna Spring in the Swiss Alps (Engadin region) is a bicarbonate iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(III) (oxyhydr)oxides in the flow channel. Gradients of O₂, dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seasonal changes influence mineral identity, crystallinity, and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. X-ray diffraction and Mössbauer spectroscopy revealed calcite (CaCO₃) and ferrihydrite [Fe(OH)₃] to be the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. Denaturing gradient gel electrophoresis banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between the flow channel and the flanking microbial mat. Microbial community analysis in combination with most-probable-number analyses and quantitative PCR (qPCR) showed that the mat was dominated by cyanobacteria and the channel was dominated by microaerophilic Fe(II) oxidizers (1.97 × 10⁷ ± 4.36 × 10⁶ 16S rRNA gene copies g⁻¹ using Gallionella-specific qPCR primers), while high numbers of Fe(III) reducers (10⁹ cells/g) were identified in both the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II) oxidizers were present as well, although in lower numbers (10³ to 10⁴ cells/g). In summary, our data suggest that mainly seasonal changes caused microbial community shifts, while geochemical gradients along the flow path influenced mineral crystallinity.     

Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbe-mineral interface: the application of STXM-XMCD

A combination of scanning transmission X‐ray microscopy and X‐ray magnetic circular dichroism was used to spatially resolve the distribution of different carbon and iron species associated with Shewanella oneidensis MR‐1 cells. S. oneidensis MR‐1 couples the reduction of Fe(III)‐oxyhydroxides to the oxidation of organic matter in order to conserve energy for growth. Several potential mechanisms may be used by S. oneidensis MR‐1 to facilitate Fe(III)‐reduction. These include direct contact between the cell and mineral surface, secretion of either exogenous electron shuttles or Fe‐chelating agents and the production of conductive ‘nanowires’. In this study, the protein/lipid signature of the bacterial cells was associated with areas of magnetite (Fe₃O₄), the product of dissimilatory Fe(III) reduction, which was oversaturated with Fe(II) (compared to stoichiometric magnetite). However, areas of the sample rich in polysaccharides, most likely associated with extracellular polymeric matrix and not in direct contact with the cell surface, were undersaturated with Fe(II), forming maghemite‐like (γ‐Fe₂O₃) phases compared to stoichiometric magnetite. The reduced form of magnetite will be much more effective in environmental remediation such as the immobilisation of toxic metals. These findings suggest a dominant role for surface contact‐mediated electron transfer in this study and also the inhomogeneity of magnetite species on the submicron scale present in microbial reactions. This study also illustrates the applicability of this new synchrotron‐based technique for high‐resolution characterisation of the microbe–mineral interface, which is pivotal in controlling the chemistry of the Earth’s critical zone.     

Biogeochemistry of oxalate in the antarctic cryptoendolithic lichen-dominated community

Cryptoendolithic (hidden in rock) lichen-dominated microbial communities from the Ross Desert of Antarctica were shown to produce oxalate (oxalic acid). Oxalate increased mineral dissolution, which provides nutrients, creates characteristic weathering patterns, and may ultimately influence the biological residence time of the community. Oxalate was the only organic acid detectable by HPLC, and its presence was verified by GC/MS. Community photosynthetic metabolism was involved in oxalate production since rates of ¹⁴C-oxalate production from ¹⁴C0₂ were higher in light than in dark incubations. Flaking of the sandstone at the level of the lichen-dominated zone a few millimeters beneath the rock surface can be explained by dissolution of the sandstone cement, which was enhanced by Si, Fe, and Al oxalate complex formation. Added oxalate was observed to increase the solubility of Si, Fe, Al, P, and K. Oxalate's ability to form soluble trivalent metal-oxalate complexes correlated with the observed order of metal oxide depletion from the lichen-dominated zone (Mn > Fe > Al). Thermodynamic calculations predict that Fe oxalate complex formation mobilizes amorphous Fe oxides (ferrihydrite) in the lichen-dominated zone, and where oxalate is depleted, ferrihydrite should precipitate. Hematite, a more crystalline Fe oxide, should remain solid at in situ oxalate concentrations. Oxalate was not a carbon source for the indigenous heterotrophs, but the microbiota were involved in oxalate mineralization to CO₂, since oxalate mineralization was reduced in poisoned incubations. Photooxidation of oxalate to C02 coupled with photoreduction of Fe(Ill) may be responsible for oxalate removal in situ, since rates of ¹⁴C-oxalate mineralization in dark incubations were at least 50% lower than those in the light. Removal of oxalate from Si, Fe, and Al complexes should allow free dissolved Si, Fe, and Al to precipitate as amorphous silicates and metal oxides. This may explain increased siliceous crust (rock varnish or desert varnish) formation near the surface of colonized rocks were light intensity is greatest.Offprint requests to: C.G. Johnston.     

Modes of Biomineralization of Magnetite by Microbes

Biomineralization processes have traditionally been grouped into two distinct modes; biologically induced mineralization (BIM) and biologically controlled mineralization (BCM). In BIM, microbes cause mineral formation by sorbing solutes onto their cell surfaces or extruded organic polymers and/or releasing reactive metabolites which alter the saturation state of the solution proximal to the cell or polymer surface. Such mineral products appear to have no specific recognized functions. On the other hand, in BCM microbes exert a great degree of chemical and genetic control over the nucleation and growth of mineral particles, presumably because the biominerals produced serve some physiological function. Interestingly, there are examples where the same biomineral is produced by both modes in the same sedimentary environment. For example, the magnetic mineral magnetite (Fe ₃ O ₄ ) is generated extracellularly in the bulk pore waters of sediments by various Fe(III)-reducing bacteria under anaerobic conditions, while some other anaerobic and microaerophilic bacteria and possibly protists form magnetite intracellularly within preformed vesicles. Differences in precipitation mechanisms might be caused by enzymatic activity at specific sites on the surface of the cell. Whereas one type of microbe might facilitate the transport of dissolved Fe(III) into the cell, another type will express its reductive enzymes and cause the reduction of Fe(III) external to the cell. Still other microbes might induce magnetite formation indirectly through the oxidation of Fe(II), followed by the reaction of dissolved Fe(II) with hydrolyzed Fe(III). The biomineralization of magnetite has significant effect on environmental iron cycling, the magnetization of sediments and thus the geologic record, and on the use of biomarkers as microbial fossils.     

微生物介导硝酸盐还原耦合亚铁氧化过程的动力学及其影响因素

【目的】探究不同菌浓度和亚铁浓度条件下,Acidovorax sp. strain BoFeN1介导的厌氧亚铁氧化耦合硝酸盐还原过程的动力学和次生矿物。【方法】构建包含菌BoFeN1、硝酸盐、亚铁的厌氧培养体系,测试硝酸根、亚硝酸根、乙酸根、亚铁等浓度,并收集次生矿物,采用XRD、SEM进行矿物种类和形貌表征。【结果】在微生物介导硝酸盐还原耦合亚铁氧化的体系中,高菌浓度促进硝酸盐还原,对亚铁氧化也有一定促进作用;高浓度亚铁在低菌浓度下氧化反应速率和程度降低,但是在高菌浓度下无明显影响;亚铁浓度越高次生矿物结晶度越高,但对硝酸盐还原具有一定抑制作用。在微生物介导亚硝酸盐还原耦合亚铁氧化的体系中,高的菌浓度和亚铁浓度都会促进亚硝酸盐还原,但亚铁氧化的次生矿物会对亚硝酸盐的微生物还原产生较强的抑制作用,次生矿物的种类和结晶度主要受亚铁浓度影响。【结论】硝酸盐还原主要是生物反硝化作用,亚硝酸盐还原包含生物反硝化和化学反硝化两部分,在硝酸盐体系中亚铁氧化与次生矿物生成是受生物和化学反硝化作用的共同影响,但亚硝酸盐体系中亚铁氧化与次生矿物生成主要是受化学反硝化作用影响。该研究可为深入理解厌氧微生物介导铁氮耦合反应机制提供基础数据和理论支撑。     

Vertical distribution of biological and geochemical phosphorus subcycles in two southern Appalachian forest soils

We measured Al, Fe, and P fractions by horizon in two southern Appalachian forest soil profiles, and compared solution PO₄ ^–1 removal in chloroform-sterilized and non-sterilized soils, to determine whether biological and geochemical P subcycles were vertically stratified in these soils. Because organic matter can inhibit Al and Fe oxide crystallization, we hypothesized that concentrations of non-crystalline (oxalate-extractable) Al (Al₀) and Fe (Fe₀), and concomitantly P sorption, would be greatest in near-surface mineral (A) horizons of these soils.Al₀ and Fe₀ reached maximum concentrations in forest floor and near-surface mineral horizons, declined significantly with depth in the mineral soil, and were highly correlated with P sorption capacity. Small pools of readily acid-soluble (AF-extractable) and readily-desorbable P suggested that PO₄ ^3– was tightly bound to Al and Fe hydroxide surfaces. P sorption in CHCl₃-sterilized mineral soils did not differ significantly from P sorption in non-sterilized soils, but CHCl₃ sterilization reduced P sorption 40–80% in the forest floor. CHCl₃ labile (microbial) P also reached maximum concentrations in forest floor and near-surface mineral horizons, comprising 31–35% of forest floor organic P. Combined with previous estimates of plant root distributions, data suggest that biological and geochemical P subcycles are not distinctly vertically stratified in these soils. Plant roots, soil microorganisms, and P sorbing minerals all reach maximum relative concentrations in near-surface mineral horizons, where they are likely to compete strongly for PO₄ ^3– available in solution.     

Precipitation of iron,silica, and sulfate on bacterial cell surfaces

The present study documents the precipitation of Fe(III), silica, and sulfate in the presence of 3 different bacteria (Bacillus subtilus, Bacillus licheniformis, and Pseudomonas aeruginosa), under different total Fe(III) concentrations (10^?2 M, 10^?3 M, 10^?4 M) at constant pH (4.0). Morphology and chemical composition of the precipitates were compared with those formed in abiotic control systems, while chemical composition and precipitation of the precipitates were modeled according to solution chemistry data. Transmission electron microscopy (TEM) observations showed morphological differences between the biotic and abiotic systems. All systems contained small grains (diam. 2–50 nm), but amorphous material (i.e., material without any specific morphology) and nodules were present only in the cell systems. This is because bacterial surfaces and exopolymers provided numerous binding sites for metal and anion sorption and promoted heterogeneous nucleation of hydrous ferric oxides (HFO). The initial Fe/Si and Fe/SO₄ molar ratios of the solutions dictated the type of precipitates in most systems, since abiotic control systems were saturated to oversaturated with respect to amorphous silica, siliceous ferrihydrite, schwertmannite, ferrihydrite, goethite, or combinations of these. Of the three strains studied, B. licheniformis appeared to have the greatest influence on the chemical composition of the precipitates, especially in the presence of Si. B. licheniformis (a gram‐positive bacterium with a large capsule) favored the precipitation of HFO containing less Si than the predicted solids, because Si rather than Fe oxides was preferentially sorted to extracellular polymers (capsule). On the other hand, the formation of SO₄‐rich HFO (similar to schwertmannite) did not seem to be affected by the presence of bacteria.     

Microbially Available Phosphorus in Boreal Forests: Effects of Aluminum and Iron Accumulation in the Humus Layer

Soil microorganisms play an important role in the mobilization of phosphorus (P), and these activities may be beneficial for plant P utilization. We investigated the effects on microbial P availability of different combinations of aluminum and iron (Al + Fe) concentrations and different P pools in humus soils from boreal forest ecosystems. We measured respiration rates in laboratory incubations before and after additions of glucose plus (NH₄)₂SO₄ (Glu+N), with or without a small dose of KH₂PO₄. Glu+N was added in excess so that the availability of the inherent soil P would be growth-limiting for the microorganisms. The exponential increases observed in microbial growth after substrate additions (Glu+N) was slower for humus soils with high Al+Fe concentrations than for humus soils with low Al+Fe concentrations. Adding a small dose of KH₂PO₄ to humus soils with high Al+Fe concentrations did, however, increase the exponential growth, measured as the slope of the log-transformed respiration rates, by more than 200%. By contrast, the average increase in exponential growth was only 6% in humus soils with low Al+Fe concentrations. Almost eight times more carbon dioxide (CO₂) was evolved between the substrate additions and the point at which the respiration rate reached 1 mg CO₂ h^–1 for soils with high Al+Fe concentrations compared to humus soils with low Al+Fe concentrations. The amount of CO₂ evolved was positively related to the Al+Fe concentration of the humus soils (r ² = 0.86, P < 0.001), whereas the slope was negatively related to Al+Fe concentration (r ² = 0.70, P < 0.001). Easily available P forms were negatively related to the Al+Fe concentration, whereas organic P showed a strong positive relationship to Al+Fe (r ² = 0.85, P < 0.001), suggesting that other forms of P, as well as inorganic P, are affected by the increased sorption capacity. The results indicate that P mobilization by microorganisms is affected by the presence of sorption sites in the humus layer, and that this capacity for sorption may relate not only to phosphate but also to organic P compounds.     

Ancient microbial activity recorded in fracture fillings from granitic rocks (Äspö Hard Rock Laboratory, Sweden)

Fracture minerals within the 1.8‐Ga‐old Äspö Diorite (Sweden) were investigated for fossil traces of subterranean microbial activity. To track the potential organic and inorganic biosignatures, an approach combining complementary analytical techniques of high lateral resolution was applied to drill core material obtained at ?450 m depth in the Äspö Hard Rock Laboratory. This approach included polarization microscopy, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), confocal Raman microscopy, electron microprobe (EMP) and laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS). The fracture mineral succession, consisting of fluorite and low‐temperature calcite, showed a thin (20–100 μm), dark amorphous layer lining the boundary between the two phases. Microscopic investigations of the amorphous layer revealed corrosion marks and, in places, branched tubular structures within the fluorite. Geochemical analysis showed significant accumulations of Si, Al, Mg, Fe and the light rare earth elements (REE) in the amorphous layer. In the same area, ToF‐SIMS imaging revealed abundant, partly functionalized organic moieties, for example, C_xH_y⁺, C_xH_yN⁺, C_xH_yO⁺. The presence of such functionalized organic compounds was corroborated by Raman imaging showing bands characteristic of C‐C, C‐N and C‐O bonds. According to its organic nature and the abundance of relatively unstable N‐ and O‐ heterocompounds, the organic‐rich amorphous layer is interpreted to represent the remains of a microbial biofilm that established much later than the initial cooling of the Precambrian host rock. Indeed, δ¹³C, δ¹⁸O and ⁸⁷Sr/⁸⁶Sr isotope data of the fracture minerals and the host rock point to an association with a fracture reactivation event in the most recent geological past.     

Soil organic sulfur dynamics in a coniferous forest

Sulfate microbial immobilization and the mineralization of organic S were measured in vitro in soil horizons (LFH, Ae, Bhf, Bf and C) of the Lake Laflamme watershed (47°17 N, 71°14 O) using ³⁵SO₄. LFH samples immobilized from 23 to 77% of the added ³⁵SO₄ within 2 to 11 days. The ³⁵SO₄ microbial immobilization increased with temperature and reached an asymptote after a few days. The mineral soil generally immobilized less than 20% of the added ³⁵SO₄, and an asymptote was reached after 2 days. An isotopic equilibrium was rapidly reached in mineral horizons. A two-compartment (SO₄ and organic S) model adequately described ³⁵SO₄ microbial immobilization kinetics. The active organic reservoir in the whole soil profile represented less than 1% of the total organic S. The average concentrations of dissolved organic S (DOS) in the soil solutions leaving the LFH, Bhf and Bf horizons were respectively 334, 282 and 143 µgL^–1. Assuming that the DOS decrease with soil depth corresponded to the quantities adsorbed in the B horizons, we estimated that 12 800 kgha^–1 of organic S could have been formed since the last glaciation, which is about 13 times the size of the actual B horizons reservoirs. Our results suggest that the organic S reservoirs present in mineral forest soils are mostly formed by the DOS adsorption resulting from incomplete litter decomposition in the humus layer. The capability of these horizons to immobilize SO₄ from the soil solution would be restricted to a 1% active fraction composed of microorganisms. Despite their refractory nature, these reservoirs can, however, be slowly decomposed by microorganisms and contribute to the S-SO₄ export from the watershed in the long term.     

In Situ Cultivation of Subsurface Microorganisms in a Deep Mafic Sill: Implications for SLiMEs

An in situ culturing device was incubated within a flowing borehole in a mafic sill at 1.474 km depth in Evander Au mine, South Africa. The device was designed to enrich methanogenic, Fe^{3 +}-reducing and SO₄ ^{2 ?}-reducing microorganisms using acetate, formate, methanol, Fe^{3 +}-citrate and SO₄ ^{2 ?} enriched agar and sand cartridges. At the end of the 33 day incubation geochemical analyses detected elevated H₂, acetate, CH₄ and Fe concentrations and depleted SO₄ ^{2 ?} concentrations. 16S rDNA sequences and PLFA analyses revealed that the microbial community composition of the substrate-bearing cartridges were distinct from that of the original borehole water and the non-substrate-bearing control cartridge. 16S rDNA and dissimilatory sulfite reductase, dsrAB, gene sequences indicated the device successfully targeted SO₄ ^{2 ?} reducing bacteria (SRB), which were not detected in the original borehole water. 16S rDNA sequences also revealed a shift in the microbial community from one relying on H₂ based methanogenesis to one suggestive of H₂ based acetogenesis supporting aceticlastic methanogenesis and SO₄ ^{2 ?} reduction compatible with the subsurface lithoautotrophic hypothesis.     

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle

Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO₄²⁻), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.     

Limited reduction of ferrihydrite encrusted by goethite in freshwater sediment

Many physical and chemical processes control the extent of Fe(III) oxyhydroxide reduction by dissimilatory Fe(III)‐reducing bacteria. The surface precipitation of secondary Fe minerals on Fe(III) oxyhydroxides limits the extent of microbial Fe(III) reduction, but this phenomenon has not yet been observed in nature. This paper reports the observation of secondary Fe‐mineral (goethite) encrustation on ferrihydrite surface within freshwater sediment up to 10 cm deep. The sediment surface was characterized by the predominance of ferrihydrites with biogenic stalks and sheaths. An Fe(II)‐oxidizing bacterium (Gallionellaceae) was detected by 16S rRNA gene analysis at sediment depths of 1 and 2 cm. Fe²⁺ concentration in the sediment pore water was relatively higher at 2–4 cm depths. The 16S rRNA genes affiliated with dissimilatory Fe(III)‐reducing bacteria were detected at 1, 2, and 4 cm depths. The results of the Fe K‐edge extended X‐ray absorption fine structure (EXAFS) analysis suggested the presence of goethite and siderite at depths below 3 cm. However, the change in the Fe‐mineral composition was restricted to sediment depths between 3 and 4 cm, despite the presence of abundant ferrihydrite at depths below 4 cm. An increase in CH₄ concentration was observed at deeper than 6 cm. Stable isotopic analysis of CH₄ in the pore water indicated that acetoclastic CH₄ occurred at depths below 7 cm. Transmission electron microscope observations suggested the presence of goethite and siderite on stalks and sheaths at depths below 3 cm. Results from conversion electron yield EXAFS analysis suggested that goethite dominated at 10 cm depth, thereby indicating that ferrihydrite was encrusted by goethite at this depth. Moreover, the incomplete reduction of ferrihydrite below depths of 4 cm was not due to the lack of organic carbon, but was possibly due to the surface encrustation of goethite on ferrihydrite.     

Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from Desulfovibrio gigas

The crystal structures of two active forms of dissimilatory sulphite reductase (Dsr) from Desulfovibrio gigas, Dsr‐I and Dsr‐II, are compared at 1.76 and 2.05 Å resolution respectively. The dimeric α₂β₂γ₂ structure of Dsr‐I contains eight [4Fe–4S] clusters, two saddle‐shaped sirohaems and two flat sirohydrochlorins. In Dsr‐II, the [4Fe–4S] cluster associated with the sirohaem in Dsr‐I is replaced by a [3Fe–4S] cluster. Electron paramagnetic resonance (EPR) of the active Dsr‐I and Dsr‐II confirm the co‐factor structures, whereas EPR of a third but inactive form, Dsr‐III, suggests that the sirohaem has been demetallated in addition to its associated [4Fe–4S] cluster replaced by a [3Fe–4S] centre. In Dsr‐I and Dsr‐II, the sirohydrochlorin is located in a putative substrate channel connected to the sirohaem. The γ‐subunit C‐terminus is inserted into a positively charged channel formed between the α‐ and β‐subunits, with its conserved terminal Cysγ104 side‐chain covalently linked to the CHA atom of the sirohaem in Dsr‐I. In Dsr‐II, the thioether bond is broken, and the Cysγ104 side‐chain moves closer to the bound sulphite at the sirohaem pocket. These different forms of Dsr offer structural insights into a mechanism of sulphite reduction that can lead to S₃O₆^2?, S₂O₃^2? and S^2?.     

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO₃⁻, Mn(IV), Fe(III), U(VI), and SO₄²⁻ significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO₃⁻, Mn(II), Fe(II), U(VI), and SO₄²⁻. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.     

Microbial production of isotopically light iron(II) in a modern chemically precipitated sediment and implications for isotopic variations in ancient rocks

The inventories and Fe isotope composition of aqueous Fe(II) and solid‐phase Fe compounds were quantified in neutral‐pH, chemically precipitated sediments downstream of the Iron Mountain acid mine drainage site in northern California, USA. The sediments contain high concentrations of amorphous Fe(III) oxyhydroxides [Fe(III)_am] that allow dissimilatory iron reduction (DIR) to predominate over Fe–S interactions in Fe redox transformation, as indicated by the very low abundance of Cr(II)‐extractable reduced inorganic sulfur compared with dilute HCl‐extractable Fe. δ⁵⁶Fe values for bulk HCl‐ and HF‐extractable Fe were ≈ 0. These near‐zero bulk δ⁵⁶Fe values, together with the very low abundance of dissolved Fe in the overlying water column, suggest that the pyrite Fe source had near‐zero δ⁵⁶Fe values, and that complete oxidation of Fe(II) took place prior to deposition of the Fe(III) oxide‐rich sediment. Sediment core analyses and incubation experiments demonstrated the production of millimolar quantities of isotopically light (δ⁵⁶Fe ≈ ?1.5 to ?0.5‰) aqueous Fe(II) coupled to partial reduction of Fe(III)_am by DIR. Trends in the Fe isotope composition of solid‐associated Fe(II) and residual Fe(III)_am are consistent with experiments with synthetic Fe(III) oxides, and collectively suggest an equilibrium Fe isotope fractionation between aqueous Fe(II) and Fe(III)_am of approximately ?2‰. These Fe(III) oxide‐rich sediments provide a model for early diagenetic processes that are likely to have taken place in Archean and Paleoproterozoic marine sediments that served as precursors for banded iron formations. Our results suggest pathways whereby DIR could have led to the formation of large quantities of low‐δ⁵⁶Fe minerals during BIF genesis.     

Microbially enhanced dissolution of HgS in an acid mine drainage system in the California Coast Range

Mercury sulfides (cinnabar and metacinnabar) are the main ores of Hg and are relatively stable under oxic conditions (K_sp = 10^?54 and 10^?52, respectively). However, until now their stability in the presence of micro‐organisms inhabiting acid mine drainage (AMD) systems was unknown. We tested the effects of the AMD microbial community from the inoperative Hg mine at New Idria, CA, present in sediments of an AMD settling pond adjacent to the main waste pile and in a microbial biofilm on the surface of this pond, on the solubility of crystalline HgS. A 16S rRNA gene clone library revealed that the AMD microbial community was dominated by Fe‐oxidizing (orders Ferritrophicales and Gallionellas) and S‐oxidizing bacteria (Thiomonas sp.), with smaller amounts (≤6%) being comprised of the orders Xanthomondales and Rhodospirillales. Though the order Ferritrophicales dominate the 16S rRNA clones (>60%), qPCR results of the microbial community indicate that the Thiomonas sp. represents ~55% of the total micro‐organisms in the top 1 cm of the AMD microbial community. Although supersaturated with respect to cinnabar and metacinnabar, microcosms inoculated with the AMD microbial community were capable of releasing significantly more Hg into solution compared to inactivated or abiotic controls. Four different Hg‐containing materials were tested for bacterially enhanced HgS dissolution: pure cinnabar, pure metacinnabar, mine tailings, and calcine material (processed ore). In the microcosm with metacinnabar, the presence of the AMD microbial community resulted in an increase of dissolved Hg concentrations up to 500 μg L^‐1 during the first 30 days of incubation. In abiotic control microcosms, dissolved Hg concentrations did not increase above 100 ng L^?1. When Hg concentrations were below 50 μg L^‐1, the Fe‐oxidizing bacteria in the AMD microbial community were still capable of oxidizing Fe(II) to Fe(III) in the AMD solution, whereas concentrations above 50 μg L^?1 resulted in inhibition of microbial iron oxidation. Our experiments show that the AMD microbial community contributes to the dissolution of mercury sulfide minerals. These findings have major implications for risk assessment and future management of inoperative Hg mines worldwide.     

In situ analysis of oxygen consumption and diffusive transport in high‐temperature acidic iron‐oxide microbial mats

The role of dissolved oxygen as a principal electron acceptor for microbial metabolism was investigated within Fe(III)‐oxide microbial mats that form in acidic geothermal springs of Yellowstone National Park (USA). Specific goals of the study were to measure and model dissolved oxygen profiles within high‐temperature (65–75°C) acidic (pH = 2.7–3.8) Fe(III)‐oxide microbial mats, and correlate the abundance of aerobic, iron‐oxidizing Metallosphaera yellowstonensis organisms and mRNA gene expression levels to Fe(II)‐oxidizing habitats shown to consume oxygen. In situ oxygen microprofiles were obtained perpendicular to the direction of convective flow across the aqueous phase/Fe(III)‐oxide microbial mat interface using oxygen microsensors. Dissolved oxygen concentrations dropped from ～ 50–60 μM in the bulk‐fluid/mat surface to below detection (< 0.3 μM) at a depth of ～ 700 μm (～ 10% of the total mat depth). Net areal oxygen fluxes into the microbial mats were estimated to range from 1.4–1.6 × 10^?4 μmol cm^?2 s^?1. Dimensionless parameters were used to model dissolved oxygen profiles and establish that mass transfer rates limit the oxygen consumption. A zone of higher dissolved oxygen at the mat surface promotes Fe(III)‐oxide biomineralization, which was supported using molecular analysis of Metallosphaera yellowstonensis 16S rRNA gene copy numbers and mRNA expression of haem Cu oxidases (FoxA) associated with Fe(II)‐oxidation.     

Dissolved silica affects the bulk iron redox state and recrystallization of minerals generated by photoferrotrophy in a simulated Archean ocean

Chemical sedimentary deposits called Banded Iron Formations (BIFs) are one of the best surviving records of ancient marine (bio)geochemistry. Many BIF precursor sediments precipitated from ferruginous, silica-rich waters prior to the Great Oxidation Event at ~2.43 Ga. Reconstructing the mineralogy of BIF precursor phases is key to understanding the coevolution of seawater chemistry and early life. Many models of BIF deposition invoke the activity of Fe(II)-oxidizing photoautotrophic bacteria as a mechanism for precipitating mixed-valence Fe(II,III) and/or fully oxidized Fe(III) minerals in the absence of molecular oxygen. Although the identity of phases produced by ancient photoferrotrophs remains debated, laboratory experiments provide a means to explore what their mineral byproducts might have been. Few studies have thoroughly characterized precipitates produced by photoferrotrophs in settings representative of Archean oceans, including investigating how residual Fe(II)_aq can affect the mineralogy of expected solid phases. The concentration of dissolved silica (Si) is also an important variable to consider, as silicate species may influence the identity and reactivity of Fe(III)-bearing phases. To address these uncertainties, we cultured Rhodopseudomonas palustris TIE-1 as a photoferrotroph in synthetic Archean seawater with an initial [Fe(II)_aq] of 1 mM and [Si] spanning 0–1.5 mM. Ferrihydrite was the dominant precipitate across all Si concentrations, even with substantial Fe(II) remaining in solution. Consistent with other studies of microbial iron oxidation, no Fe-silicates were observed across the silica gradient, although Si coprecipitated with ferrihydrite via surface adsorption. More crystalline phases such as lepidocrocite and goethite were only detected at low [Si] and are likely products of Fe(II)-catalyzed ferrihydrite transformation. Finally, we observed a substantial fraction of Fe(II) in precipitates, with the proportion of Fe(II) increasing as a function of [Si]. These experimental results suggest that photoferrotrophy in a Fe(II)-buffered ocean may have exported Fe(II,III)-oxide/silica admixtures to BIF sediments, providing a more chemically diverse substrate than previously hypothesized.     

Analytical studies on the incorporation of aluminium in the cell walls of the marine diatom Stephanopyxis turris

The eukaryotic diatoms are unicellular algae. They are well known for their filigree micro- and nanostructured cell walls which mainly consist of amorphous silica as well as various organic compounds. However, diatoms are also known to incorporate certain amounts of aluminium into their cell walls. Unexpectedly, enhanced Al concentrations in the Southern Yellow Sea were found to be correlated with a diatom spring bloom. Therefore, we have analyzed the influence of strongly enhanced Al concentrations in the culture medium upon the growth behaviour of the diatom Stephanopyxis turris (S. turris). The uptake and incorporation of Al into the cell walls was monitored. It turned out that S. turris survives aluminium concentrations up to 105.5 μM (2.85 mg/l) in the culture medium. Under the applied conditions, this corresponds to an Al/Si ratio of 1:1. These large amounts of Al had to be offered in the form of bis–tris-chelates in order to prevent uncontrolled precipitation. Under these conditions, the Al/Si ratio in the cell walls could be increased up to about 1:15 as determined by ICP-OES, the highest amount of aluminium found in diatom cell walls yet. Structural characterization of the biosilica by ATR-FTIR and solid-state ²⁷Al NMR spectroscopy revealed that an amorphous aluminosilicate phase is formed where the aluminium exists as four- and sixfold-coordinated species.