Bacteriogenic Iron Oxides Research Articles

First evidence of Pleistocene ochre production from bacteriogenic iron oxides. A case study of the Upper Palaeolithic site at the San Teodoro Cave (Sicily, Italy)

The use of iron pigments is well documented in the archaeological horizons of the different parts of the world since the Middle Pleistocene. The mineralogical and chemical composition of the pigments allowed defining, in most cases, their inorganic origin, which were then used after a limited transformation and manipulation. The use of a biogenic ochraceous pigment and its manipulation has recently been described in a late Holocene archaeological horizon of the American continent.Here we describe the earliest case of archaeological use of ferrous pigment produced by iron-oxidising bacteria (FeOB), the first identified in a European Epigravettian (late Upper Palaeolithic) layer, at the San Teodoro site in Sicily, Italy. Samples of the ochraceous archaeological deposit, overlying a large burial site, were analysed according to current methods of physical analysis and SEM highlighting a matrix of bacterial structures and a chemical composition coherent with biogenic productions. The physical-chemical analysis of the archaeological material from the Palaeolithic site, and of the modern bacteriogenic iron sediments from two close springs gave consistent results even after heat treatment. In absence of Terra Rossa or other easily available inorganic ferrous materials in the hinterland of their site, the hunter-gatherers identified several possible water sources rich of pigment used for covering a multiple burial.The implications of these results influence interpretations of the ecology of the late-glacial and Epigravettian sites in Europe, especially in relation to problems such as the increasing complexity of behaviours, the need to establish rituals and the search for materials.

Influence of Water Flow on In Situ Rates of Bacterial Fe(II) Oxidation

A survey of a low-flow wetland drainage channel rich in flocculent bacteriogenic iron oxide (BIOS) deposits was conducted to investigate the in situ kinetic behaviors of bacterial Fe(II) oxidation and its dependence on water flow. On the basis of analytical solutions to the advection-dispersion-reaction (ADR) equation and the channel’s Fe(II) concentration profile, the pseudo-first order rate constant for Fe(II) oxidation () was 0.78 ± 0.20 min−1. The difference in this estimate from that obtained in a previous study on a lotic groundwater discharge channel with an intact BIOS mat (1.70 ± 0.20 min−1) demonstrates the effects of water flow on Fe(II) oxidation kinetics in circumneutral pH, Fe(II)-rich settings. Importantly, these results also re-emphasize the discrepancies between rates obtained from in situ geochemical data and those of conventional ex situ batch studies in assessing the dependencies of in situ reaction rates on water flow and reactive transport across a range of hydraulic regimes characterizing natural systems.

Long Range Correlation in Redox Potential Fluctuations Signals Energetic Efficiency of Bacterial Fe(II)\xa0Oxidation

Differentiating biotic and abiotic processes in nature remains a persistent challenge, specifically in evaluating microbial contributions to geochemical processes through time. Building on previous work reporting that biologically-influenced systems exhibit stronger long-range correlation than abiotic systems, this study evaluated the relationship between long-range correlation of redox potential and oxidation rates of circumneutral microaerophilic bacterial Fe(II) oxidation using a series of batch microcosms with bacteriogenic iron oxides (BIOS). Initial detrended fluctuation analysis (DFA) scaling exponents of the abiotic microcosms were lower (ca. 1.20) than those of the biotic microcosms (ca. 1.80). As Fe(II) oxidation proceeded, correlation strength decayed as a logistic function of elapsed reaction time, exhibiting direct dependence on the free energy of reaction. Correlation strength for all microcosms decayed sharply from strong correlation to uncorrelated fluctuations. The decay rates are greater for abiotic microcosms than biotic microcosms. The ΔGm relaxation edges for biotic microcosms were lower, indicating less remaining free energy for Fe(II) oxidation than abiotic systems, with the implication that biologically-catalyzed reactions are likely more energetically efficient than abiotic reactions. These results strengthen the case for employing novel DFA techniques to distinguish in situ microbial metabolic activity from abiotic processes, as well as to potentially differentiate metabolisms among different chemoautotrophs.

Dissolved Organic Matter Sorption and Molecular Fractionation by Naturally Occurring Bacteriogenic Iron (Oxyhydr)oxides.

Iron (oxyhydr)oxides are highly reactive, environmentally ubiquitous organic matter (OM) sorbents that act as mediators of terrestrial and aqueous OM cycling. However, current understanding of environmental iron (oxyhydr)oxide affinity for OM is limited primarily to abiogenic oxides. Bacteriogenic iron (oxyhydr)oxides (BIOs), common to quiescent waterways and soil redox transitions, possess a high affinity for oxyanions (i.e., arsenate and chromate) and suggests that BIOs may be similarly reactive for OM. Using adsorption and desorption batch reactions, paired with Fourier transform infrared spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry, this work demonstrates that BIOs are capable of sorbing leaf litter-extracted DOM and Suwannee River Humic/Fulvic Acid (SRHA/SRFA) and have sorptive preference for distinct organic carbon compound classes at the biomineral interface. BIOs were found to sorb DOM and SRFA to half the extent of 2-line ferrihydrite per mass of sorbent and was resilient to desorption at high ionic strength and in the presence of a competitive ligand. We observed the preferential sorption of aromatic and carboxylic-containing species and concurrent solution enrichment of aliphatic groups unassociated with carboxylic acids. These findings suggest that DOM cycling may be significantly affected by BIOs, which may impact nutrient and contaminant transport in circumneutral environments.

Hydrodynamic Shear-Induced Densification of Bacteriogenic Iron Oxides: Mechanisms and Implications

Bacterial–mineral aggregates are the products of a tight biogeochemical coupling between microbes and geological media and play an outsized role in governing the composition of natural waters through biogeochemical cycling and mineral formation and dissolution processes. The results of combined batch column settling experiments, volumetric analyses, and microscopic investigations demonstrate that composite bacteriogenic iron oxide aggregates are sensitive to densification in response to hydrodynamic shear, a physical fluid phenomenon that introduces significant alterations to aggregate size and structure, permeability, and settling and transport behaviour. After exposing aggregate suspensions to varying degrees of shear stress, final solids volume fractions decreased by as much as 75% from initial data, while aggregate bulk density saw increases from 999 kg∙m–3 to as much as 1010 kg∙m–3. Inverse modelling of time course data yielded estimates for settling rate constants and initial settling velocities that increased with shear stress application. As well as having implications for aqueous contaminant transport and potential bacterial bioenergetic strategies, these results suggest the preservation potential of microfossils formed from bacterial–mineral aggregates may be significantly reduced with shear-induced alterations, leading to a possible underrepresentation of these microfossils in the sedimentary record and a gap in our understanding of early life on Earth.

Dependence of In Situ Bacterial Fe(II)-Oxidation and Fe(III)-Precipitation on Sequential Reactive Transport

ABSTRACTA study was conducted to determine in situ rates of Fe(II) oxidation and Fe(III) precipitation along a 5.0 m reach of a ferruginous groundwater discharge zone under two distinct conditions; (i) the natural state featuring abundant flocculent mats of bacteriogenic iron oxides (BIOS) produced by Fe(II)-oxidizing bacteria, and (ii) after a manual washout of the streambed to remove the microbial mat. Examination of mat samples by differential interference contrast light microscopy revealed tangled meshworks of filamentous Leptothrix sheaths and helical Gallionella stalks intermixed with fine-grained hydrous ferric oxide (HFO) precipitates. The greatest accumulation of BIOS mat was 1.0 m downstream of the groundwater spring. Redox potential (Eh) increased sharply from 200 mV to over 300 mV over the last 2.0 m of the reach. Similarly, dissolved oxygen increased from < 10% saturation to almost 100% saturation over the last 2.0 m of the reach, whereas pH increased from 6.4 to 7.3. Pseudo-first-order rate constants determined on the basis of analytical solutions to sequential partial differential advection-dispersion-reaction equations for the linear Fe(II)→Fe(III)→HFO reaction network yielded in situ Fe(II) oxidation rate constants (kox) of 1.70 ± 0.20 min−1 in natural conditions and 0.48 ± 0.14 min−1 after washout. Corresponding Fe(III)-precipitation rates (kp) before and after washout were 3.45 ± 0.10 min−1 and 0.90 ± 0.01 min−1, respectively. These values for kox and kp are higher than estimates obtained from closed batch microcosm and laboratory experiments, underscoring the crucial dependence of in situ Fe(II) oxidation and Fe(III) precipitation rates on advective and dispersive mass transport. The results also highlight the influence that BIOS microbial mats exert on the reaction kinetics of the multiple heterogeneous reactions contributing not only to Fe(II)/Fe(III) redox transformations in groundwater discharge zones, but also the precipitation of HFO.

Magnetic Attachment of Lipase Immobilized on Bacteriogenic Iron Oxide Inside a Microtube Reactor for the Kinetic Resolution of Secondary Alcohols

A PTFE microtube reactor was constructed with lipase immobilized on magnetized bacteriogenic iron oxide, which was retained inside of the tube by attraction to an external magnet. The reactor was used for the lipase-promoted kinetic resolution of secondary alcohols and gave sufficient catalytic activity, which was maintained during long-term flow over 14 days.

Spatially Resolved Distribution of Fe Species around Microbes at the Submicron Scale in Natural Bacteriogenic Iron Oxides.

Natural bacteriogenic iron oxides (BIOS) were investigated using local-analyzable synchrotron-based scanning transmission X-ray microscopy (STXM) with a submicron-scale resolution. Cell, cell sheath interface (EPS), and sheath in the BIOS were clearly depicted using C-, N-, and O- near edge X-ray absorption fine structure (NEXAFS) obtained through STXM measurements. Fe-NEXAFS obtained from different regions of BIOS indicated that the most dominant iron mineral species was ferrihydrite. Fe(II)- and/or Fe(III)-acidic polysaccharides accompanied ferrihydrite near the cell and EPS regions. Our STXM/NEXAFS analysis showed that Fe species change continuously between the cell, EPS, and sheath under several 10-nm scales.

Divalent metal cation adsorption onto Leptothrix cholodnii SP-6SL bacterial cells

Bacteriogenic iron oxide (BIOS) particles have a high affinity to adsorb inorganic nutrients such as Ca, Mg, Zn, and Ni, raising the question of how Fe(II) oxidizing bacteria (FeOB) compete for these same cations while the BIOS are in such close proximity to the cells. Answering this question requires a detailed understanding of metal binding properties of FeOB.In this study, the adsorption behaviors of aqueous Ni, Cu, Zn, Sr, Cd, and Pb onto the sheathless FeOB Leptothrix cholodnii SP-6SL were measured separately, and the adsorption behaviors were compared to that of Bacillus subtilis in order to determine if the iron oxidizing bacterial species exhibits similar binding properties to those of most previously studied bacterial species. The experiments for both species were performed aerobically; ionic strength was held constant with 0.1M NaClO4; the experiments were conducted as a function of pH over the range of 2 to 9; and biomass and metal concentrations were 10g (wet weight)/L and 2ppm, respectively.Our results show that the two studied bacterial species exhibit similar adsorption of the tested metals, and that although some iron oxides formed during L. cholodnii SP-6SL liquid culture growth, they are present in low enough concentrations not to significantly affect the extent of metal adsorption. We apply a linear free-energy approach to define relationships between the stability constants for site-specific metal-bacterial surface complexes and corresponding metal-acetate binding constants. We use these relationships to estimate binding constants for L. cholodnii for some metals that have not been studied, and we apply these results to calculate the ability of L. cholodnii to compete for nutrients with BIOS particles that form during Fe(II) oxidation by the bacteria.

Bacterial Fe(II) oxidation distinguished by long‐range correlation in redox potential

AbstractThe kinetics of bacterial Fe(II) oxidation was investigated 297 m underground at the Äspö Hard Rock Laboratory (near Oskarshamn, Sweden) under steady state groundwater flow conditions in a flow‐through cell containing well‐developed flocculent mats of bacteriogenic iron oxides (BIOS). Pseudo first‐order rate constants of 0.004 min−1 and 0.009 min−1 were obtained for chemical and bacterial Fe(II) oxidation, respectively, based on the 104 min retention time of groundwater in the flow cell, inlet Fe(II) concentration of 21.0 ± 0.5 µm, outlet Fe(II) concentration of 8.5 ± 0.7 µm, as well as constant pH = − log H+ of 7.42 ± 0.01, dissolved O2 concentration of 0.11 ± 0.01 mg/L, and groundwater temperature of 12.4 ± 0.1°C. Redox potential was lower at the BIOS‐free inlet (−135.4 ± 1.16 mV) compared to inside BIOS within the flow cell (−112.6 ± 1.91 mV), consistent with the Nernst relationship and oxidation of Fe(II) to Fe(III). Further evaluation of the redox potential time series data using detrended fluctuation analysis (DFA) revealed power law scaling in the amplitude of fluctuations over increasing intervals of time with significantly different (p &lt; 0.01) DFA α scaling exponents of 1.89 ± 0.03 for BIOS and 1.67 ± 0.06 at the inlet. These α values not only signal the presence of long‐range correlation in the redox potential time series measurements but also distinguish between the slower rate of chemical Fe(II) oxidation at the inlet and faster rate accelerated by FeOB in BIOS.

ChemInform Abstract: Bacteriogenic Iron Oxide as an Effective Catalyst for Baeyer—Villiger Oxidation with Molecular Oxygen and Benzaldehyde.

AbstractIron oxide produced by Leptothrix ochracea catalyzes the Baeyer—Villiger oxidation with molecular oxygen in the presence of benzaldehyde at 25°C.

Rates of Fe(II)-Oxidation and Solubility of Bacteriogenic Iron Oxides

ABSTRACTThe oxidation of Fe(II) at circumneutral pH by natural bacterial consortia capable of oxidizing Fe(II) in flocculent mats of bacteriogenic iron oxides (BIOS) was investigated in a series of microcosm experiments under constant pH and pO2 conditions. The oxidation of Fe(II) was faster in the presence BIOS compared to chemical oxidation in solution with pseudo–first-order rate constants ranging from 0.036 to 0.248 min−1 for BIOS compared to 0.004 min−1 for the chemical control. The Fe(II)-oxidation rates exhibited a kinetic dependency on BIOS concentrations, measured in terms of a pseudo–second-order rate constant at 0.066 Lg−1min−1. From the asymptotic decline in Fe(total) in the microcosms, apparent rate constants for HFO dissolution (zero-order values 0.001 to 0.046 mgL−1min−1) and precipitation (second-order values 0.007 to .297 min−1) were obtained from the BIOS and control microcosms, which yield an apparent equilibrium BIOS solubility of 0.157 mgL−1 (i.e., 2.8 μM). These results reflect the complex interplay of Fe(II) oxidation reactions associated with BIOS including homogenous chemical oxidation in solution, chemical oxidation on HFO surfaces, and bacterially mediated oxidation. Furthermore, BIOS precipitated in response to Fe(II) oxidation exhibit a greater apparent solubility than more stable varieties of HFO. The implication is that the competitive advantage of Fe(II)-oxidizing bacteria over autocatalytic surface chemical Fe(II) oxidation on HFO might be enhanced by a reduction in the total amount of BIOS that is precipitated.

Design and performance of a compact scanning transmission X-ray microscope at the Photon Factory.

We present a new compact instrument designed for scanning transmission X-ray microscopy. It has piezo-driven linear stages, making it small and light. Optical components from the virtual source point to the detector are located on a single optical table, resulting in a portable instrument that can be operated at a general-purpose spectroscopy beamline without requiring any major reconstruction. Careful consideration has been given to solving the vibration problem common to high-resolution microscopy, so as not to affect the spatial resolution determined by the Fresnel zone plate. Results on bacteriogenic iron oxides, single particle aerosols, and rare-earth permanent magnets are presented as examples of its performance under diverse applications.

Bacteriogenic iron oxide as an effective catalyst for Baeyer-Villiger oxidation with molecular oxygen and benzaldehyde

Iron oxide produced by iron-oxidizing bacteria, Leptothrix ochracea, (L-BIOX) obtained from a freshwater purification plant, Joyo City in Kyoto, Japan catalyzed Baeyer-Villiger oxidation with molecular oxygen in the presence of benzaldehyde at 25 °C more efficiently than usual iron compounds. L-BIOX can promote the reactions of various substrates to give the desired products in sufficient yields and was found to be reusable. Scanning transmission electron microscopy and 57Fe Mössbauer spectroscopy revealed that no change of the surface structure of L-BIOX was observed even after four times of the recycling test and the oxidation state of iron in L-BIOX is trivalent before and after the oxidation of cyclohexanone. An investigation with analogous amorphous iron oxides which contain silicon revealed that the catalytic activity of L-BIOX might stem from a synergetic effect of iron and silicon in the structure.

Fragmentation of Bacteriogenic Iron Oxides in Response to Hydrodynamic Shear Stress

A viscous shear stress of 1.97 Nm2 was applied to suspensions of freshwater, brackish and marine bacteriogenic iron oxides (BIOS) in shake flasks. Samples were taken at intervals over 480 minutes for scanning electron microscopy. The remains of three Fe2+-oxidizing bacteria (FeOB) genera were conspicuous biomass constituents in the BIOS samples; these included the filamentous extracellular sheaths of Leptothrix, as well as helical fibrous stalks of Gallionella and Mariprofundus. The applied hydrodynamic shear stress resulted in an exponential decrease in Leptothrix sheath and Gallionella-Mariprofundus stalk lengths; first-order breakage rate constants derived from the experimental measurements ranged from 0.009 to 0.023 min−1 and 0.014 to 0.021 min−1, respectively. Breakage half-times extended from 30 to 70 min. Shear strength values calculated from the time course data ranged from 27.8 to 29.6 Nm−2 for Leptothrix sheaths, and from 28.0 to 28.8 Nm−2 for Gallionella-Mariprofundus stalks. Computational analyses showed that breakage half-times decreased rapidly with increasing shear stress, implying that the accumulation of BIOS is constrained hydrodynamically to quiescent aqueous environments. These results imply that there is considerable potential for natural hydrodynamic fluctuations in basal shear stress levels to bring about resuspension and advective dispersal of BIOS. Immediate consequences anticipated from such events include enhanced particulate transport of BIOS-associated chemical species through aquatic systems, as well as reduced preservation potential and underrepresentation of BIOS bacteria structures as microfossils in the geological record.

Sphaerotilus natans, a Neutrophilic Iron-Related Sheath-Forming Bacterium: Perspectives for Metal Remediation Strategies

Sphaerotilus natans is a neutrophilic sheath-forming microorganism from the Sphaerotilus-Leptothrix group of iron-related bacteria, known to form bacteriogenic iron oxides (BIOS) frequently deposited on cell surfaces as well as on sheaths and extracellular polymeric substances. S. natans has been reported to be an excellent sorbent for inorganic pollutants, either due to direct sorption onto biological surfaces or due to sorption onto BIOS. However, its filaments can cause bulking problems in wastewater treatment plants. This article promotes the potential applications of Sphaerotilus natans in bioremediation by reviewing its physiology and the fundamental understanding of sheath-forming mechanisms as well as iron biomineralization processes.

FISH法とマイクロXAFS法を組み合わせた新しいバイオミネラル分析法(XAFS-FISH法)の開発

FISH法とマイクロXAFS法を組み合わせた新しいバイオミネラル分析法(XAFS-FISH法)の開発

Regulation of Fe3+-oxide Formation Among Fe2+-oxidizing Bacteria

Helical stalks (resembling Gallionella ferruginea, Mariprofundus ferrooxydans) and filamentous sheaths (resembling Leptothrix ochracea) of Fe2+-oxidizing bacteria (FeOB) are mineralized by hydrous ferric oxides (HFO). To perform both inter-species and inter-site size comparisons of HFO particles on stalks and sheaths we measured HFO particles in samples of natural bacteriogenic iron oxides (BIOS) from 3 contrasting field sites: the Loihi Seamount (southern Hawaii); Äspö Hard Rock Laboratory (eastern Sweden); and Chalk River Laboratories (northern Canada) representing seafloor saline, underground brackish, and surface freshwater aqueous conditions. Ambient temperatures were in the psychrophilic range and pHs measured for Loihi, CRL, and Äspö were 5.6, 6.9 and 7.4, respectively. Dissolved Fe was lowest for CRL (0.2 mg · L−1) followed by Äspö (1.5 mg · L−1), then Loihi (4.5–14.9 mg · L−1). L. ochraceasheaths appear to have surface properties that restrict HFO particle growth in comparison to G.ferruginea-M.ferrooxydans stalks in the same environment, which we attribute to interfacial surface energy (γ). An inverse relationship between particle size and stalk/sheath length due to restrictions in reactive surface area was also observed, which may provide insight into FeOB survival strategies to alleviate oxidative stress arising from Fe3+ production.

Seasonal Changes In Mineralogy, Geochemistry and Microbial Community of Bacteriogenic Iron Oxides (BIOS) Deposited in a Circumneutral Wetland

Changes in the mineralogy, microbial community structure and aquatic geochemistry of bacteriogenic iron oxides (BIOS) deposited at a circumneutral groundwater seep were recorded seasonally. X-ray diffraction and X-ray absorption spectroscopy demonstrated that 2-line ferrihydrite dominated the iron-bearing mineralogy of the BIOS (>60%). Minor proportions of the more crystalline lepidocrocite were also detected in BIOS collected throughout the year (<30%), but goethite (<15%) was only identified in sediments collected during the spring, summer and fall months. Subsurface porewater profiles generally showed an increase in dissolved equilibrium concentrations of Fe(II), indicative of microbial Fe(III) reduction, and the depth at which appreciable levels of dissolved Fe(II) (and to a lesser extent manganese) arose, and sulfate concentrations declined, become shallower as the seasons progressed from spring to fall. Clone libraries constructed from 16S rRNA gene sequence analysis of surficial BIOS showed the presence of sequences closely affiliated to known Fe(II)-oxidizing and Fe(III)-reducing prokaryotes, pointing towards a tightly coupled microbial iron cycle. Clones that showed closest identity to Fe(II)-oxidizing bacteria in culture, including Gallionella spp. and Sideroxydans spp., made up a significant portion of the clone library, but their relative proportion declined through the winter (73%), spring (26%) and summer (9%). The dominance of the putative microaerophilic Fe(II)-oxidizing chemolithoautotrophs in the winter clone library may be partly due to the lower temperature and dissolved organic carbon concentrations observed during this season, conditions that could have limited mixotrophic or organotrophic growth by mesophilic bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.

Retention of Iodide by Bacteriogenic Iron Oxides

This study was performed to determine the ability of wetland bacteriogenic iron oxides (BIOS) to immobilize iodide in contaminated groundwater systems near Chalk River, Canada. The sorption of iodide onto synthetic hydrous ferric oxide (HFO) and BIOS was investigated using an autotitrator and an I− ion-selective electrode to generate high-resolution anion sorption data over a pH range of 2.5 to 9. The effect of strontium sorption in the presence of I− was also investigated to determine its effect on iodide retention as it is also a common contaminant near Chalk River. Both HFO and BIOS correspond to 2-line ferrihydrite with surface areas of 227.7 m2 g−1 and 92.52 m2 g−1, respectively. Sorption of I− was found to be pH dependent for both HFO and BIOS and was most strongly immobilized at pH 2.5. The pH at which 50% of the I− was bound to HFO occurred at pH 4.0, whereas BIOS maintained 50% sorption to pH 9. Field data also indicated a 54% decrease for iodine and 75% for 129I in waters passing over in-situ BIOS at circumneutral pH. Iodide sorption to HFO is best explained by homogeneous functional groups, whereas sorption of I− to BIOS is best explained by heterogeneous functional groups, due to the presence of bacterial functional groups with pKa values that extend to 9.0. The presence of Sr2+ decreased iodide sorption on HFO by 10–20%, but had no effect on BIOS due to its surface functional groups being reactive over the pH range investigated in this study. These results imply that BIOS is a useful sorbent for natural retention of I− from groundwater and that the amount of organic material present in iron oxides is an important factor when considering remediation strategies for radionuclides in groundwater.