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.     

Iron oxide solubilization by organic matter and its effect on iron availability

The solubility of Fe in soils is largely controlled by Fe oxides; ferrihydrite, amorphous ferric hydroxide, and soil-Fe are generally believed to exert the major control. Fe(III) hydrolysis species constitute the major Fe species in solution. Other inorganic Fe complexes are present, but their concentrations are much less than the hydrolysis species. Organic complexes of Fe including those of organic acids like citrate, oxalate, and malate contribute slightly to increased Fe solubility in acid soils, but not in alkaline soils.The most important influence that organic matter has on the solubilization of Fe is through reduction. Respiration of organic matter creates reduction microsites in soil where Fe²⁺ concentrations increase above those of the Fe(III) hydrolysis species. Fluctuating redox conditions in these microsites are conducive to the formation of a mixed valency ferrosic hydroxide. This metastable precipitate maintains an elevated level of soluble inorganic Fe for prolonged periods and increases Fe availability to plants. The release of reducing agents and acids next to roots, as well as the production of siderophores by microorganisms within the rhizosphere, contribute to the solubilization and increased availability of Fe to plants.     

Oxalate Extraction of Pb and Zn from Polluted Soils: Solubility Limitations

Oxalate (Ox) was used to extract Pb and Zn from industrially contaminated soils. Although Ox effectively releases metals bound by hydrous oxide soil components, it forms insoluble salts with some heavy metals unlike conventional extractants (e.g., EDTA). The insolubility of PbOx(s) (K_sp=2.74 × 10^?11) precluded the use of Ox as a single-step extractant even for soils mildly contaminated with Pb. The usefulness of Ox as a Zn extractant, however, depends on the level of soil contamination. A Zn solubility model, based on published equilibrium constants, was developed to assess Ox suitability as a function of system conditions. Precipitation of ZnOx(s) hindered Zn recovery under acidic conditions where formation of soluble oxalato complexes was small. For pH<3, the presence of 1?M Ox actually reduced Zn release compared to simple acid washing. Although Ox displaces oxide-bound metals and thus is potentially useful in soil washing, solubility limitations must be defined for effective remediation of metal-laden soils.     

Combined effects of waterlogging and salinity on electrochemistry, water-soluble cations and water dispersible clay in soils with various salinity levels

The combination effects of waterlogging and salinity on redox potential (Eh), pH, electric conductivity (EC), water-soluble cations (NH₄ ⁺, K⁺, Na⁺, Ca²⁺, Mg²⁺, Fe²⁺, and Mn²⁺) and water-dispersible clay (WDC) were studied in six soils collected near salt lakes in western Australia. The soils with various salinity levels were incubated under a waterlogged condition at 30 °C for 12 weeks. The Eh, pH, EC, and cations of soil solutions were monitored over the waterlogged period. The Eh values generally dropped to the lowest point within 12 days of waterlogging, then increased slightly, and reached equilibrium after 4 weeks of waterlogging. Increasing salinity levels increased soil Eh. While waterlogging increased soil pH in the first 3–4 weeks, increasing salinity level decreased soil pH during the entire waterlogging period. Waterlogging increased the EC values in the first 2 weeks, partly due to dissolution of insoluble salts. The concentrations of water-soluble NH₄ ⁺ were significantly increased with salinity level and waterlogging, and reached maximum values at week 2, and then declined to the initial level. Waterlogging and salinity increased the concentrations of water-soluble K⁺, Ca²⁺, Mg²⁺, Fe²⁺, and Mn²⁺ ions, but the magnitudes of changes were greatly affected by soil properties. Increases in water-soluble K⁺, Ca²⁺ and Mg²⁺ were attributed to increased solubility of insoluble salts, and increased competition for the adsorption sites of the soil exchange complex due to elevated concentrations of Na⁺, Fe²⁺ and Mn²⁺. Increases in water-soluble Fe²⁺ and Mn²⁺ induced by waterlogging were attributed to the dissolution of Fe and Mn oxides under reduced conditions. Waterlogging increased, but salinity decreased, the amounts of water-dispersible clay in the soils of low EC value. The higher salinity level can counteract the adverse effect of waterlogging on clay flocculation.     

Prediction of reducible soil iron content from iron extraction data

Soils contain various iron compounds that differ in solubility, reducibility and extractability. Moreover, the contribution of the various iron compounds to total iron (Fe) and total Fe concentrations differs highly among soils. As a result, the total reducible Fe content can also differ among soils, and so does the dynamics of iron reduction. These factors complicate the prediction of reducible Fe based on Fe extraction data and hamper the application of process-based models for reduced or waterlogged soils where redox processes play a key-role. This paper presents a theoretical analysis relating reducible to extractable Fe reported in the literature. Predictions made from this theoretical analysis were evaluated in soil incubations using 18 rice paddy soils from all over the world. The incubation studies and the literature study both show that reducible Fe can be related to Fe from some selected, but not all, iron extractions. The combination of measurements for labile Fe(III)oxides (derived from oxalate-extractable Fe) and stabile Fe(III)oxides (derived from dithionite-citrate-extractable Fe) shows highly significant correlations with reducible Fe with high coefficients of determination (r² = 0.92–0.95 depending on the definition of stabile Fe(III)oxides). Given the high diversity in rice soils used for the incubations, these regression equations will have general applicability. Application of these regression equations in combination with soil database information may improve the predictive ability of process-based models where soil redox processes are important, such as CH₄ emission models derived for rice paddies or wetlands.     

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.     

Efficient Reduction of Iron Oxides by Paenibacillus spp. Strains Isolated from Tropical Soils

The genus Paenibacillus was hardly described as a Fe(III)-reducing agent, only limited to reduce soluble forms or Fe inserted in poorly crystallized structures. In this study, three Paenibacillus strains capable of reducing manganese oxides in addition to iron oxides were isolated from Cameroonian and Brazilian soils. These strains reduced iron minerals from poorly crystallized 2-line ferrihydrite to well-crystallized Al-substituted and pure goethite with a significant production of soluble ferrous iron. These Paenibacillus strains, inhabitants from ferralitic temporarily waterlogged soils, could play an important role in the bioweathering of minerals and metal mobility in soils.     

Fe3O4 precipitation in magnetotactic bacteria

Using Mössbauer resonance spectroscopy of ⁵⁷Fe, we have determined the nature and distribution of major iron compounds in the magnetotactic bacterium Aquaspirillum magnetotacticum. In addition to magnetite (Fe₃O₄), cells contained a low-density hydrous ferric oxide, a high-density hydrous ferric oxide (ferrihydrite), and ferrous iron. Analysis at different temperatures of whole cells harvested early and late in growth, of mutant cells unable to synthesize magnetite, and of cell fractions enriched in ⁵⁷Fe indicated that Fe₃O₄ precipitation resulted from partial reduction of the high-density hydrous ferric oxide precursor.     

Reductive Reactivity of Iron(III) Oxides in the East China Sea Sediments: Characterization by Selective Extraction and Kinetic Dissolution

Reactive Fe(III) oxides in gravity-core sediments collected from the East China Sea inner shelf were quantified by using three selective extractions (acidic hydroxylamine, acidic oxalate, bicarbonate-citrate buffered sodium dithionite). Also the reactivity of Fe(III) oxides in the sediments was characterized by kinetic dissolution using ascorbic acid as reductant at pH 3.0 and 7.5 in combination with the reactive continuum model. Three parameters derived from the kinetic method: m ₀ (theoretical initial amount of ascorbate-reducible Fe(III) oxides), k′ (rate constant) and γ (heterogeneity of reactivity), enable a quantitative characterization of Fe(III) oxide reactivity in a standardized way. Amorphous Fe(III) oxides quantified by acidic hydroxylamine extraction were quickly consumed in the uppermost layer during early diagenesis but were not depleted over the upper 100 cm depth. The total amounts of amorphous and poorly crystalline Fe(III) oxides are highly available for efficient buffering of dissolved sulfide. As indicated by the m ₀, k′ and γ, the surface sediments always have the maximum content, reactivity and heterogeneity of reactive Fe(III) oxides, while the three parameters simultaneously downcore decrease, much more quickly in the upper layer than at depth. Albeit being within a small range (within one order of magnitude) of the initial rates among sediments at different depths, incongruent dissolution could result in huge discrepancies of the later dissolution rates due to differentiating heterogeneity, which cannot be revealed by selective extraction. A strong linear correlation of the m ₀ at pH 3.0 with the dithionite-extractable Fe(III) suggests that the m ₀ may represent Fe(III) oxide assemblages spanning amorphous and crystalline Fe(III) oxides. Maximum microbially available Fe(III) predicted by the m ₀ at pH 7.5 may include both amorphous and a fraction of other less reactive Fe(III) phases.     

Copper,Lead, Cadmium,and Zinc Sorption By Waterlogged and Air-Dry Soil

Competitive sorption of copper (Cu), lead (Pb), cadmium (Cd), and zinc (Zn) was studied in three soils of contrasting chemical and physical properties under air-dry and waterlogged conditions. Competitive sorption was determined using the standard batch technique using six solutions, each with Cu, Pb, Cd, and Zn concentrations of approximately 0, 2.5, 5, 10, 20, and 50?mg L^?1Waterlogged soils tended to sorb higher amounts of added Cu, Pb, Zn and Cd relative to soils in the air-dry condition; however, this increase in sorption was generally not statistically (p<0.05) significant. The magnitude of sorption under both waterlogged and air-dry conditions was affected by the type and amount of soil materials involved in metal sorption processes, and competition between other metals for the sorption sites. Metal sorption was closely correlated with soil properties such as cation exchange capacity, organic carbon, and Fe and Mn hydrous oxides. Exchangeable Al may have markedly reduced metal sorption due to its strong affinity for the sorption sites, while increases in exchangeable Mn may have enhanced Zn and Cd sorption. Heavy metal sorption was best described as a combination of both specific and nonspecific interactions. The extractability of Cu, Pb, Cd, and Zn under waterlogged and air-dry conditions was also studied. Three solutions containing these metals were mixed with each soil to achieve a final concentration of 0, 50, and 500?mg kg^?1. Each soil was extracted every 7 days using 1?M MgCl₂ (pH 7) to determine metal extractability. Metal extractability initially decreased then increased due to waterlogging. The increased extractability of added metals was closely related to increased solubility of Fe and Mn suggesting that dissolution of Fe and Mn, oxides under reducing conditions caused a release of previously sorbed Cu, Pb, Cd, and Zn.     

Adsorption Characteristics and the Effect of Dissolved Organic Matter on Mercury(II) Adsorption of Various Soils in China

To evaluate the adsorption characteristics and effects of dissolved organic matter (DOM) from wheat straw (DOM_W) and swine manure (DOM_S) on mercury [Hg(II)] adsorption by soils, a series of experiments was conducted on 26 soils with different soil properties.Results showed that the values of K_d (a solid–liquid partition coefficient) of soils varied within a range of 0.768–14.386 L g^?1. K_d values were mainly controlled by soil organic matter (SOM), cation exchange capacity (CEC), soil nitrogen (N), and soil sulfur (S). When DOM_W and DOM_S were added to the soil samples, the amount of Hg(II) adsorbed by the soils decreased significantly. Furthermore, based on the decreased percentage of adsorption of Hg(II) by soil upon adding DOM_W (P_DOMW) or DOM_S (P_DOMS), about 73.08% soils, the values of P_DOMS were smaller than those of P_DOMW. The P_DOMW values were related to SOM, pH, free Fe oxide content, and CEC, whereas P_DOMS values were related to soil free Fe/Al oxide contents. Therefore, we should pay more attention about mercury risk caused by the addition of exogenous organic matter in soils, especially for the soils with low or high pH, less SOM, low CEC, and less free Fe/Al oxide.     

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Reactive Fe(III) minerals can influence methane (CH₄) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH₄ oxidation. The balance between Fe(III) reduction, methanogenesis, and CH₄ oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH₄ fluxes to the atmosphere, thereby regulating the capacity for CH₄ to warm the early Earth under the Faint Young Sun. We studied CH₄ and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH₄ oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH₄ production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)‐dependent CH₄ oxidation, although some incubations displayed CH₄‐stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)‐reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH₄ as a greenhouse gas throughout the first half of Earth history.     

Phosphorus saturation and pH differentially regulate the efficiency of organic acid anion-mediated P solubilization mechanisms in soil

Exudation of organic acid anions by plants as well as root-induced changes in rhizosphere pH can potentially improve phosphate (P_i) availability in the rhizosphere and are frequently found to occur simultaneously. In non-calcareous soils, a major proportion of P_i is strongly sorbed to metal oxi(hydr)oxides of mainly iron (Fe) and aluminium (Al) and organic anions are known to compete with P_i for the same sorption sites (ligand exchange) or solubilize P_i via ligand-promoted mineral dissolution. Root-induced co-acidification may also further promote P_i release from soil. The relative efficiency of these different solubilization mechanisms, however, is poorly understood. The aims of this study were to gain a better mechanistic understanding of the solubilizing mechanisms of four carboxylates (citrate, malate, oxalate, malonate) in five soils with high and low P surface site saturation. Results indicate that at a lower P saturation of solid phase sorption sites, ligand-promoted mineral dissolution was the main P_i solubilization mechanism, while ligand exchange became more important at higher soil P concentrations. Co-acidification generally increased P_i solubility in the presence of carboxylates; however the relative solubilizing effect of carboxylates compared to the background electrolyte (KCl) control decreased by 20–50%. In soils with high amounts of exchangeable calcium (Ca), the proton-induced Ca solubilization reduced soluble P_i, presumably due to ionic-strength-driven changes in the electric surface potential favoring a higher P_i retention. Across a wider soil pH range (pH 3–8), P_i solubility increased with increasing alkalinity, as a result of both, more negatively charged sorption sites, as well as DOC-driven changes in Fe and Al solubility, which were further enhanced by the presence of citrate. Overall, the relative efficiency of carboxylates in solubilizing P_i was greatest in soils with medium to high amounts of anionic binding sites (mainly Fe- and Al-oxy(hydr)oxides) and a medium P sorption site coverage, with citrate being most effective in solubilizing P_i.     

From Knock-Out Phenotype to Three-Dimensional Structure of a Promising Antibiotic Target from Streptococcus pneumoniae

Given the rise in drug-resistant Streptococcus pneumoniae, there is an urgent need to discover new antimicrobials targeting this pathogen and an equally urgent need to characterize new drug targets. A promising antibiotic target is dihydrodipicolinate synthase (DHDPS), which catalyzes the rate-limiting step in lysine biosynthesis. In this study, we firstly show by gene knock out studies that S. pneumoniae (sp) lacking the DHDPS gene is unable to grow unless supplemented with lysine-rich media. We subsequently set out to characterize the structure, function and stability of the enzyme drug target. Our studies show that sp-DHDPS is folded and active with a k _cat = 22 s^-1, K _M ^PYR = 2.55 ± 0.05 mM and K _M ^ASA = 0.044 ± 0.003 mM. Thermal denaturation experiments demonstrate sp-DHDPS exhibits an apparent melting temperature (T _M ^app) of 72 °C, which is significantly greater than Escherichia coli DHDPS (Ec-DHDPS) (T _M ^app = 59 °C). Sedimentation studies show that sp-DHDPS exists in a dimer-tetramer equilibrium with a K _D ^4→2 = 1.7 nM, which is considerably tighter than its E. coli ortholog (K _D ^4→2 = 76 nM). To further characterize the structure of the enzyme and probe its enhanced stability, we solved the high resolution (1.9 Å) crystal structure of sp-DHDPS (PDB ID 3VFL). The enzyme is tetrameric in the crystal state, consistent with biophysical measurements in solution. Although the sp-DHDPS and Ec-DHDPS active sites are almost identical, the tetramerization interface of the s. pneumoniae enzyme is significantly different in composition and has greater buried surface area (800 Ų) compared to its E. coli counterpart (500 Ų). This larger interface area is consistent with our solution studies demonstrating that sp-DHDPS is considerably more thermally and thermodynamically stable than Ec-DHDPS. Our study describe for the first time the knock-out phenotype, solution properties, stability and crystal structure of DHDPS from S. pneumoniae, a promising antimicrobial target.     

Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment,Juan de Fuca Ridge hydrothermal vent chimneys

Hyperthermophilic iron reducers are common in hydrothermal chimneys found along the Endeavour Segment in the northeastern Pacific Ocean based on culture‐dependent estimates. However, information on the availability of Fe(III) (oxyhydr) oxides within these chimneys, the types of Fe(III) (oxyhydr) oxides utilized by the organisms, rates and environmental constraints of hyperthermophilic iron reduction, and mineral end products is needed to determine their biogeochemical significance and are addressed in this study. Thin‐section petrography on the interior of a hydrothermal chimney from the Dante edifice at Endeavour showed a thin coat of Fe(III) (oxyhydr) oxide associated with amorphous silica on the exposed outer surfaces of pyrrhotite, sphalerite, and chalcopyrite in pore spaces, along with anhydrite precipitation in the pores that is indicative of seawater ingress. The iron sulfide minerals were likely oxidized to Fe(III) (oxyhydr) oxide with increasing pH and E_h due to cooling and seawater exposure, providing reactants for bioreduction. Culture‐dependent estimates of hyperthermophilic iron reducer abundances in this sample were 1740 and 10 cells per gram (dry weight) of material from the outer surface and the marcasite‐sphalerite‐rich interior, respectively. Two hyperthermophilic iron reducers, Hyperthermus sp. Ro04 and Pyrodictium sp. Su06, were isolated from other active hydrothermal chimneys on the Endeavour Segment. Strain Ro04 is a neutrophilic (pH_opt 7–8) heterotroph, while strain Su06 is a mildly acidophilic (pH_opt 5), hydrogenotrophic autotroph, both with optimal growth temperatures of 90–92 °C. Mössbauer spectroscopy of the iron oxides before and after growth demonstrated that both organisms form nanophase (<12 nm) magnetite [Fe₃O₄] from laboratory‐synthesized ferrihydrite [Fe₁₀O₁₄(OH)₂] with no detectable mineral intermediates. They produced up to 40 mm Fe²⁺ in a growth‐dependent manner, while all abiotic and biotic controls produced <3 mm Fe²⁺. Hyperthermophilic iron reducers may have a growth advantage over other hyperthermophiles in hydrothermal systems that are mildly acidic where mineral weathering at increased temperatures occurs.     

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.     

Zinc phytotoxicity to oilseed rape grown on zinc-loaded substrates consisting of Fe oxide-coated and calcite sand

The risk of zinc (Zn) phytotoxicity in soils has increased in various regions following application of different anthropogenic materials. In order to assess the relative efficiency of Fe oxide and calcite in sorbing Zn and hence alleviating Zn phytotoxicity, we grew oilseed rape for 28 days in pots containing Zn-loaded model substrates consisting of Fe oxide (ferrihydrite)-coated sand (FOCS, 0.2–0.5 mm, 0.3 m² ferrihydrite g^–1 sand) and calcium carbonate (calcite) sand (CCS, 0.2–0.5 mm, 0.3 m² calcite g^–1 sand). Five substrates containing 5, 10, 20, 40, and 80% FOCS and supplied with ZnSO₄ at a rate of 30, 100, 300, and 1000 mg Zn kg^–1 were used in the cropping experiment and in an in vitro study of Zn desorption for 62 days. Plants exhibited good growth and a similar dry matter yield (DMY) at the 30 and 100 mg Zn kg^–1 rates. On the other hand, DMY was markedly reduced at the 300 and, especially, at the 1000 mg Zn kg^–1 rate, particularly for the substrates with the higher FOCS proportions. Symptoms of phytotoxicity (viz. chlorosis, purple colouration due to P deficiency) were apparent at such rates and were accompanied by high Zn concentrations in both shoot (average values >1000 and >1500 mg Zn kg^–1 dry matter for the 300 and 1000 mg Zn kg^–1 rate, respectively) and root (average values >2500 and >6000 mg Zn kg^–1 dry matter for the 300 and 1000 mg Zn kg^–1 rate, respectively). Total Zn uptake was maximal at 300 mg Zn kg^–1. The results of water extractable Zn in the substrate after cropping and the dissolved Zn concentrations measured in substrate–water systems (desorption experiment) suggest that, on a surface area basis, calcite is more effective than Fe oxide to retain Zn and thus alleviate phytotoxicity at high Zn loadings. However, the Zn-sorption capacity of the Fe oxide cannot be neglected, particularly at low Zn loadings, where Fe oxide seems to exhibit a higher affinity for Zn – but not a higher Zn-sorption capacity – than does calcite.     

Preliminary characterization and biological reduction of putative biogenic iron oxides (BIOS) from the Tonga-Kermadec Arc, southwest Pacific Ocean

Sediment samples were obtained from areas of diffuse hydrothermal venting along the seabed in the Tonga sector of the Tonga‐Kermadec Arc, southwest Pacific Ocean. Sediments from Volcano 1 and Volcano 19 were analyzed by X‐ray diffraction (XRD) and found to be composed primarily of the iron oxyhydroxide mineral, two‐line ferrihydrite. XRD also suggested the possible presence of minor amounts of more ordered iron (hydr)oxides (including six‐line ferrihydrite, goethite/lepidocrocite and magnetite) in the biogenic iron oxides (BIOS) from Volcano 1; however, Mössbauer spectroscopy failed to detect any mineral phases more crystalline than two‐line ferrihydrite. The minerals were precipitated on the surfaces of abundant filamentous microbial structures. Morphologically, some of these structures were similar in appearance to the known iron‐oxidizing genus Mariprofundus spp., suggesting that the sediments are composed of biogenic iron oxides. At Volcano 19, an areally extensive, active vent field, the microbial cells appeared to be responsible for the formation of cohesive chimney‐like structures of iron oxyhydroxide, 2–3 m in height, whereas at Volcano 1, an older vent field, no chimney‐like structures were apparent. Iron reduction of the sediment material (i.e. BIOS) by Shewanella putrefaciens CN32 was measured, in vitro, as the ratio of [total Fe(II)]:[total Fe]. From this parameter, reduction rates were calculated for Volcano 1 BIOS (0.0521 day^?1), Volcano 19 BIOS (0.0473 day^?1), and hydrous ferric oxide, a synthetic two‐line ferrihydrite (0.0224 day^?1). Sediments from both BIOS sites were more easily reduced than synthetic ferrihydrite, which suggests that the decrease in effective surface area of the minerals within the sediments (due to the presence of the organic component) does not inhibit subsequent microbial reduction. These results indicate that natural, marine BIOS are easily reduced in the presence of dissimilatory iron‐reducing bacteria, and that the use of common synthetic iron minerals to model their reduction may lead to a significant underestimation of their biological reactivity.     

A Comparison of the Rates of Fe(III) Reduction in Synthetic and Bacteriogenic Iron Oxides by Shewanella putrefaciens CN32

The susceptibility of various bacteriogenic iron oxides (BIOS) to bacterial Fe(III) reduction was examined. Reduction resulted in complete dissolution of the iron mineral from the surfaces of the Fe-oxidizing consortium. Reduction rates were compared to that of synthetic ferrihydrite (HFO). The reduction rate of HFO (0.162 day^{? 1}) was significantly lower than that of Äspö (Gallionella dominated) BIOS (0.269 day^{? 1}). Two Canadian (Leptothrix dominated) BIOS samples showed statistically equivalent rates of reduction (0.541 day^?1 and 0.467 day^{? 1}), which were higher than both Äspö BIOS and HFO. BIOS produced by different iron-oxidizing genera have different susceptibilities to microbial reduction.     

Syntrophic Effects in a Subsurface Clostridial Consortium on Fe(III)-(Oxyhydr)oxide Reduction and Secondary Mineralization

In this study, we cultivated from subsurface sediments an anaerobic clostridial consortium that was composed of a fermentative Fe-reducer Clostridium species (designated as strain FGH) and a novel sulfate-reducing bacterium belonging to the clostridia family Vellionellaceae (designated as strain RU4). In pure culture, Clostridium sp. strain FGH mediated the reductive dissolution/transformation of iron oxides during growth on peptone. When Clostridium sp. FGH was grown with strain RU4 on peptone, the rates of iron oxide reduction were significantly higher. Iron reduction by the consortium was mediated by multiple mechanisms, including biotic reduction by Clostridium sp. FGH and biotic/abiotic reactions involving biogenic sulfide formed by strain RU4. The Clostridium sp. FGH produced hydrogen during fermentation, and the presence of hydrogen inhibited growth and iron reduction activity. The sulfate-reducing partner strain RU4 was stimulated by the presence of H₂and generated reactive sulfide which promoted the chemical reduction of the iron oxides. Characterization of Fe(II) mineral products showed the formation of nanoparticulate magnetite during ferrihydrite reduction, and the precipitation of iron sulfides during goethite and hematite reduction. The results suggest an important pathway for iron reduction and secondary mineralization by fermentative sulfate-reducing microbial consortia through syntrophy-driven biotic/abiotic reactions with biogenic sulfide.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.