F. Grant Ferris

Could bacteria have formed the Precambrian banded iron formations

Banded iron formations (BIFs) are prominent sedimentary deposits of the Precambrian, but despite a century of endeavor, the mechanisms of their deposition are still unresolved. Interactions between microorganisms and dissolved ferrous iron in the ancient oceans offer one plausible means of mineral precipitation, in which bacteria directly generate ferric iron either by chemolithoautotrophic iron oxidation or by photoferrotrophy. On the basis of chemical analyses from BIF units of the 2.5 Ga Hamersley Group, Western Australia, we show here that even during periods of maximum iron precipitation, most, if not all, of the iron in BIFs could be precipitated by iron-oxidizing bacteria in cell densities considerably less than those found in modern Fe-rich aqueous environments. Those ancient microorganisms would also have been easily supported by the concentrations of nutrients (P) and trace metals (V, Mn, Co, Zn, and Mo) found within the same iron-rich bands. These calculations highlight the potential importance of early microbial activity on ancient metal cycling.

Microbially Mediated Calcium Carbonate Precipitation: Implications for Interpreting Calcite Precipitation and for Solid-Phase Capture of Inorganic Contaminants

Microbial degradation of urea was investigated as a potential geochemical catalyst for Ca carbonate precipitation and associated solid phase capture of common groundwater contaminants (Sr, UO2, Cu) in laboratory batch experiments. Bacterial degradation of urea increased pH and promoted Ca carbonate precipitation in both bacterial control and contaminant treatments. Associated solid phase capture of Sr was highly effective, capturing 95% of the 1 mM Sr added within 24 h. The results for Sr are consistent with solid solution formation rather than discrete Sr carbonate phase precipitation. In contrast, UO2 capture was not as effective, reaching only 30% of the initial 1 mM UO2 added, and also reversible, dropping to 7% by 24 h. These results likely reflect differing sites of incorporation of these two elements-Ca lattice sites for Sr versus crystal defect sites for UO2. Cu sequestration was poor, resulting from toxicity of the metal to the bacteria, which arrested urea degradation and concomitant Ca carbonate precipitation. Scanning electron microscopy (SEM) indicated a variety of morphologies reminiscent of those observed in the marine stromatolite literature. In bacterial control treatments, X-ray diffraction (XRD) analyses indicated only calcite; while in the presence of either Sr or UO2, both calcite and vaterite, a metastable polymorph of Ca carbonate, were identified. Tapping mode atomic force microscopy (AFM) indicated differences in surface microtopography among abiotic, bacterial control, and bacterial contaminant systems. These results indicate that Ca carbonate precipitation induced by passive biomineralization processes is highly effective and may provide a useful bioremediation strategy for Ca carbonate-rich aquifers where Sr contamination issues exist.Microbial degradation of urea was investigated as a potential geochemical catalyst for Ca carbonate precipitation and associated solid phase capture of common groundwater contaminants (Sr, UO2, Cu) in laboratory batch experiments. Bacterial degradation of urea increased pH and promoted Ca carbonate precipitation in both bacterial control and contaminant treatments. Associated solid phase capture of Sr was highly effective, capturing 95% of the 1 mM Sr added within 24 h. The results for Sr are consistent with solid solution formation rather than discrete Sr carbonate phase precipitation. In contrast, UO2 capture was not as effective, reaching only 30% of the initial 1 mM UO2 added, and also reversible, dropping to 7% by 24 h. These results likely reflect differing sites of incorporation of these two elements-Ca lattice sites for Sr versus crystal defect sites for UO2. Cu sequestration was poor, resulting from toxicity of the metal to the bacteria, which arrested urea degradation and concomitant Ca carbonat...

The effect of cyanobacteria on silica precipitation at neutral pH: implications for bacterial silicification in geothermal hot springs

In this study, we performed silica precipitation experiments with the cyanobacteria Calothrix sp. to investigate the mechanisms of silica biomineralization. Batch silica precipitation experiments were conducted at neutral pH as a function of time, Si saturation states, temperature and ferrihydrite concentrations. The experimental results show that in solutions undersaturated with respect to amorphous silica, the interaction between Si and cell surface functional groups is weak and minimal Si sorption onto cyanobacterial surfaces occurs. In solutions at high Si supersaturation states, abiotic Si polymerization is spontaneous, and at the time scales of our experiments (1–50 h) the presence of cyanobacteria had a negligible effect on silica precipitation kinetics. At lower supersaturation states, Si polymerization is slow and the presence of cyanobacteria do not promote Si–solid phase nucleation. In contrast, experiments conducted with ferrihydrite-coated cyanobacteria significantly increase the rate of Si removal, and the extent to which Si is removed increases as a function of ferrihydrite concentration. Experiments conducted with inorganic ferrihydrite colloids (without cyanobacteria) removes similar amounts of Si, suggesting that microbial surfaces play a limited role in the silica precipitation process. Therefore, in supersaturated hydrothermal waters, silica precipitation is largely nonbiogenic and cyanobacterial surfaces have a negligible effect on silica nucleation. D 2003 Elsevier Science B.V. All rights reserved.

The Influence of Bacillus pasteurii on the Nucleation and Growth of Calcium Carbonate

Microcosm experiments were performed to identify the influence of bacterial cell surfaces on the morphology, mineralogy, size and solubility of CaCO3 precipitated in response to the enzymatic hydrolysis of urea in an artificial groundwater (AGW) by the ureolytic bacteria, Bacillus pasteurii. In each microcosm, B. pasteurii were contained within a cellulose dialysis membrane (10 K Dalton MWCO), resulting in bacteria-inclusive and bacteria-free AGW solution. Urea hydrolysis by B. pasteurii resulted in the production of ammonium and an increase in pH in the whole AGW solution. This initiated predominantly rhombohedral calcite precipitation at the same critical saturation state ( S critical = 12) in the B. pasteurii-inclusive and bacteria-free zone of the AGW, indicating the mineralogy and morphology of CaCO3 precipitation is not controlled by B. pasteurii surfaces. However, the temporal evolution of distinctly different lognormal crystal-size-distributions in the B. pasteurii-inclusive and bacteria-free zone of the AGW resulted from identical changes in bulk solution chemistry. Specifically, B. pasteurii increased the size and size variance of crystals, and led to a greater crystal growth rate throughout the experiments, relative to bacteria-free AGW. Calculated crystal solubility (ln K S0 ) was lower for crystals > 4000 nm in diameter, reflecting smaller molar surface areas. This suggests that the larger crystals generated in the presence of B. pasteurii have a lower affinity for re-dissolution than those generated in the bacteria-free AGW, which may act as a positive feedback to maintain larger crystal sizes in the presence of B. pasteurii. During ureolysis, higher bacterial concentrations may therefore generate larger and less soluble carbonate crystals. This has important implications for the adaptation of bacterial ureolysis as a method for precipitating calcium carbonate and co-precipitating metals and radionuclides in contaminated aquifers.

Biomineralization by Gallionella

A new environmental scanning electron microscopic (ESEM) technique at low vacuum (5 torr) and 99% humidity, where the sample never has been exposed to high vacuum and coating of carbon or gold, has revealed a new insight into the nature of iron mineralization that develops in association with the stalked bacteria Gallionella. The stalk fibers contain minute flaky iron precipitates. The size of the crystallites is 0.1–0.5 micron and some of them exhibit a hexagonal feature. EDAX analyses on individual crystallites give an atomic ratio between Fe and O very close to 0.67. The stoichiometric formula would thus be Fe2O3. Stoichiometry and crystallinity are in accordance with the mineral hematite. The mineralization seems to take place inside the fibers of the stalk. With time the Gallionella stalk is covered with iron oxihydroxides of different kinds that probably are controlled by inorganic processes more than by the organic chemistry of the stalk. From a thermodynamic point of view, oxygen as well as carbon dioxide are required to explain the formation of hematite inside the fibers. The precipitation takes probably place at a pH close to 5.

Characterization of Iron-Oxides Formed by Oxidation of Ferrous Ions in the Presence of Various Bacterial Species and Inorganic Ligands

The oxidation of ferrous ions in the presence of an excess of dissolved oxygen at neutral pH generally leads to the formation of lepidocrocite. The effect of inorganic ligands (PO4, SO4, or Si(OH)4) in concentrations typical of those in sediment pore waters, and of microorganisms (Escherichia coli K12, Pseudomonas aeruginosa PA01, Bacillus subtilis or Bacillus licheniformis) on the mineralogy, chemical composition, morphology and spatial distribution of the iron-oxides were examined using various complementary techniques, including TEM, XRD, and EXAFS. The presence of inorganic ligands during the oxidation can affect the mineralogy as well as the size and structure of the Fe-oxide particles. While the presence of sulfate (SO4/Fe = 0.5) had little effect on the outcome of the Fe-oxide synthesis, low quantities of phosphate (PO4/Fe = 0.05) inhibited lepidocrocite and large quantities of aqueous silica (Si/Fe = 5) favored the formation of 2-line ferrihydrite. The presence of any of the four representative species of bacterial cells in the various systems did not modify the mineralogy of the Fe-oxides. However, the size of the Fe-oxide particles tended to be reduced, and the presence of the cells also affected the spatial organization and the morphology of the particles. In addition, in some systems, some of the iron remains adsorbed on the cells and does not contribute to the formation of mineral phases.

Immobilization of strontium during iron biomineralization coupled to dissimilatory hydrous ferric oxide reduction

The potential for incorporation of strontium (Sr) into biogenic Fe(II)-bearing minerals formed during microbial reduction of synthetic hydrous ferric oxide (HFO) was investigated in circumneutral bicarbonate-buffered medium containing SrCl2 at concentrations of 10 μM, 100 μM, or 1.0 mM. CaCl2 (10 mM) was added to some experiments to simulate a Ca-rich groundwater. In Ca-free systems, 89 to 100% of total Sr was captured in solid-phase compounds formed during reduction of 30 to 40 mmol Fe(III) L−1 over a 1-month period. A smaller fraction of total Sr (25 to 34%) was incorporated into the solid phase in cultures amended with 10 mM CaCl2. X-ray diffraction identified siderite and ferroan ankerite as major end products of HFO reduction in Ca-free and Ca-amended cultures, respectively. Scanning electron microscopy–energy dispersive x-ray spectroscopy revealed the presence of Sr associated with carbonate phases. Selective extraction of HFO reduction end products indicated that 46 to 100% of the solid-phase Sr was associated with carbonates. The sequestration of Sr into carbonate phases in the Ca-free systems occurred systematically according to a heterogeneous (Doerner-Hoskins) partition coefficient (DD-H) of 1.81 ± 0.15. This DD-H value was 2 to 10 times higher than values determined for incorporation of Sr (10 μM) into FeCO3(s) precipitated abiotically at rates comparable to or greater than rates observed during HFO reduction, and fivefold higher than theoretical partition coefficients for equilibrium Fe(Sr)CO3 solid solution formation. Surface complexation and entrapment of Sr by rapidly growing siderite crystals (and possibly other biogenic Fe(II) solids) provides an explanation for the intensive scavenging of Sr in the Ca-free systems. The results of abiotic siderite precipitation experiments in the presence and absence of excess Ca indicate that substitution of Ca for Sr at foreign element incorporation sites (mass action effect) on growing FeCO3(s) surfaces can account for the inhibition of Sr incorporation into the siderite component of ankerite formed in the Ca-amended HFO reduction experiments. Likewise, substitution of Fe(II) for Sr may explain the absence of major Sr partitioning into the calcite component of ankerite. The findings indicate that under appropriate conditions, sequestration of metals in siderite produced during bacterial Fe(III) oxide reduction may provide a mechanism for retarding the migration of Sr and other divalent metal contaminants in anaerobic, carbonate-rich sedimentary environments.

Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden

The objectives of this study were to determine if viruses exist in deep granitic groundwater and to analyse their abundance and morphological diversity. Fluorescent microscopy counts on 10 groundwater samples ranging from 69 to 450 m depth were in the range of 104–106 TNC ml−1 (TNC, total number of prokaryotic cells) and 105–107 VLP ml−1 (VLP, virus-like particles). A good positive correlation of VLP with TNC (r=0.91, P=0.0003) was found with an average VLP/TNC ratio of 12. Transmission electron microscopy revealed four distinct bacteriophage groups (polyhedral, tailed, filamentous and pleomorphic) with at least seven phage families of which some are known to be lytic. Our results suggest the presence of viruses in deep granitic groundwater up to 450 m depth. If they are active and lytic, they will constitute an important group of predators that might control the numbers of microorganisms in the analysed groundwater.

Modern freshwater microbialites from Kelly Lake, British Columbia, Canada

Small stromatolites and thrombolites occur in Kelly Lake, British Columbia, Canada. Thrombolites appear as welllithified, irregular calcite crusts on hard submerged surfaces, whereas poorly mineralized stromatolites exist on the thrombolite crusts as small laminated hemispherical domes 1.0 to 2.0 cm in diameter and height. Microscopic examination of the thrombolitic crusts reveal the presence of many coccoid and fewer small filamentous cyanobacteria. In contrast, large filamentous cyanobacteria are predominant in the stromatolitic domes. The inorganic carbon and elemental content of the two different microbialites are similar; however, the stromatolites contain more organic carbon (0.5% dry wt) than the thrombolites (0.2% dry wt). This implies that the production rate of organic matter in the stromatolites is higher, relative to the calcification rate, than in the thrombolites. Stable carbon isotope analyses show that the calcite precipitated within the microbialites is enriched in 13C compared to the dissolved inorganic carbon (DIC) source. The enrichments are the result of photosynthetic 12C fractionation by the respective microbial communities. Calcite precipitated within the stromatolites is even more enriched in 13C than that within the thrombolites, corresponding to an enhanced productivity level for the filamentous cyanobacteria in the stromatolites. These data indicate that the degree of mineralization, isotopic fractionation, and morphogenesis of modern microbialites are controlled to a large extent by relative rates of microbial growth and calcification.

Effect of the presence of bacterial surfaces during the synthesis of Fe oxides by oxidation of ferrous ions

Natural iron-oxides are often found in close association with bacterial cells in aquatic environments, but the effect of bacteria on their formation is still under investigation. The present study was undertaken to assess the effect of two common bacteria, Bacillus subtilis and Escherichia coli , on the morphology and mineralogy of Fe oxides. All Fe oxides were synthesised by oxidation of Fe(II) (2 × 10 −4 M) at pH = 7. Three systems were studied, i.e. , abiotic Fe oxides, Fe oxides formed in the presence of bacteria (which we call “biogenic” Fe oxides) and abiotic Fe oxides mixed with bacterial cells. Samples were analysed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). Fe oxide particles in all systems showed a needle-like morphology, with many needles seeming to be attached to a sheet, and were identified as lepidocrocite. However, the biogenic lepidocrocite crystals were generally shorter than the abiotic ones, and the crystals were found in association with the bacterial cell-wall, especially with B. subtilis , a Gram-positive bacterium. Biogenic lepidocrocite crystals also displayed an attenuation of the XRD 120 line, which is indicative of a low crystallinity. Growth limitation and poor crystalline order are then likely to affect the surface area of Fe oxides and indirectly, their sorptive capacity.