3-D analysis of bacterial cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using complementary microscopy tomography approaches

Novel Insight into Microbially Mediated Nitrate-Reducing Fe(II) Oxidation by Acidovorax sp. Strain BoFeN1 Using Dual N-O Isotope Fractionation

Microbially mediated nitrate reduction coupled with Fe(II) oxidation (NRFO) plays an important role in the Fe/N interactions in pH-neutral anoxic environments. However, the relative contributions of the chemical and microbial processes to NRFO are still unclear. In this study, N-O isotope fractionation during NRFO was investigated. The ratios of O and N isotope enrichment factors (18ε:15ε)-NO3- indicated that the main nitrate reductase functioning in Acidovorax sp. strain BoFeN1 was membrane-bound dissimilatory nitrate reductase (Nar). N-O isotope fractionation during chemodenitrification [Fe(II) + NO2-], microbial nitrite reduction (cells + NO2-), and the coupled process [cells + NO2- + Fe(II)] was explored. The ratios of (18ε:15ε)-NO2- were 0.58 ± 0.05 during chemodenitrification and -0.41 ± 0.11 during microbial nitrite reduction, indicating that N-O isotopes can be used to distinguish chemical from biological reactions. The (18ε:15ε)-NO2- of 0.70 ± 0.05 during the coupled process was close to that obtained for chemodenitrification, indicating that chemodenitrification played a more important role than biological reactions during the coupled process. The results of kinetic modeling showed that the relative contribution of chemodenitrification was 99.3% during the coupled process, which was consistent with that of isotope fractionation. This study provides a better understanding of chemical and biological mechanisms of NRFO using N-O isotopes and kinetic modeling.

Continuous cultivation of the lithoautotrophic nitrate-reducing Fe(II)-oxidizing culture KS in a chemostat bioreactor

Laboratory-based studies on microbial Fe(II) oxidation are commonly performed for 5-10 days in small volumes with high substrate concentrations, resulting in geochemical gradients and volumetric effects caused by sampling. We used a chemostat to enable uninterrupted supply of medium and investigated autotrophic nitrate-reducing Fe(II)-oxidizing culture KS for 24 days. We analysed Fe- and N-speciation, cell-mineral associations, and the identity of minerals. Results were compared to batch systems (50 and 700 mL-static/shaken). The Fe(II) oxidation rate was highest in the chemostat with 7.57 mM Fe(II) d^-1 , while the extent of oxidation was similar to the other experimental setups (average oxidation of 92% of all Fe(II)). Short-range ordered Fe(III) phases, presumably ferrihydrite, precipitated and later goethite was detected in the chemostat. The 1 mM solid phase Fe(II) remained in the chemostat, up to 15 μM of reactive nitrite was measured, and 42% of visualized cells were partially or completely mineral-encrusted, likely caused by abiotic oxidation of Fe(II) by nitrite. Despite (partial) encrustation, cells were still viable. Our results show that even with similar oxidation rates as in batch cultures, cultivating Fe(II)-oxidizing microorganisms under continuous conditions reveals the importance of reactive nitrogen intermediates on Fe(II) oxidation, mineral formation and cell-mineral interactions.

Effect of Environmental pH on Mineralization of Anaerobic Iron-Oxidizing Bacteria

Freshwater lakes are often polluted with various heavy metals in the Anthropocene. The iron-oxidizing microorganisms and their mineralized products can coprecipitate with many heavy metals, including Al, Zn, Cu, Cd, and Cr. As such, microbial iron oxidation can exert a profound impact on environmental remediation. The environmental pH is a key determinant regulating microbial growth and mineralization and then influences the structure of the final mineralized products of anaerobic iron-oxidizing bacteria. Freshwater lakes, in general, are neutral-pH environments. Understanding the effects of varying pH on the mineralization of iron-oxidizing bacteria under neutrophilic conditions could aid in finding out the optimal pH values that promote the coprecipitation of heavy metals. Here, two typical neutrophilic Fe(II)-oxidizing bacteria, the nitrate-reducing Acidovorax sp. strain BoFeN1 and the anoxygenic phototrophic Rhodobacter ferrooxidans strain SW2, were selected for studying how their growth and mineralization response to slight changes in circumneutral pH. By employing focused ion beam/scanning electron microscopy (FIB–SEM) and transmission electron microscopy (TEM), we examined the interplay between pH changes and anaerobic iron-oxidizing bacteria and observed that pH can significantly impact the microbial mineralization process and vice versa. Further, pH-dependent changes in the structure of mineralized products of bacterial iron oxidation were observed. Our study could provide mechanical insights into how to manipulate microbial iron oxidation for facilitating remediation of heavy metals in the environment.

Elucidating heterogeneous iron biomineralization patterns in a denitrifying As(iii)-oxidizing bacterium: implications for arsenic immobilization

Anaerobic nitrate-dependent iron(ii) oxidation is a process common to many bacterial species, which promotes the formation of Fe(iii) minerals that can influence the fate of soil and groundwater pollutants, such as arsenic. Herein, we investigated simultaneous nitrate-dependent Fe(ii) and As(iii) oxidation by Acidovorax sp. strain ST3 with the aim of studying the Fe biominerals formed, their As immobilization capabilities and the metabolic effect on cells. X-ray powder diffraction (XRD) and scanning transmission electron microscopy (STEM) nanodiffraction were applied for biomineral characterization in bulk and at the nanoscale, respectively. NanoSIMS (nanoscale secondary ion mass spectrometry) was used to map the intra and extracellular As and Fe distribution at the single-cell level and to trace metabolically active cells, by incorporation of a ¹³C-labeled substrate (acetate). Metabolic heterogeneity among bacterial cells was detected, with periplasmic Fe mineral encrustation deleterious to cell metabolism. Interestingly, Fe and As were not co-localized in all cells, indicating delocalized sites of As(iii) and Fe(ii) oxidation. The Fe(iii) minerals lepidocrocite and goethite were identified in XRD, although only lepidocrocite was identified via STEM nanodiffraction. Extracellular amorphous nanoparticles were formed earlier and retained more As(iii/v) than crystalline "flakes" of lepidocrocite, indicating that longer incubation periods promote the formation of more crystalline minerals with lower As retention capabilities. Thus, the addition of nitrate promotes Fe(ii) oxidation and formation of Fe(iii) biominerals by ST3 cells which retain As(iii/v), and although this process was metabolically detrimental to some cells, it warrants further examination as a viable mechanism for As removal in anoxic environments by biostimulation with nitrate.

Recovery of Iron-Dependent Autotrophic Denitrification Activity from Cell-Iron Mineral Aggregation-Induced Reversible Inhibition by Low-Intensity Ultrasonication

Iron-dependent autotrophic denitrification (IDAD) has garnered increasing interests as an efficient method for removing nitrogen from wastewater with a low carbon to nitrogen ratio. However, an inevitable deterioration of IDAD performance casts a shadow over its further development. In this work, the hidden cause for such a deterioration is uncovered, and a viable solution to this problem is provided. Batch test results reveal that the aggregation of microbial cells and iron-bearing minerals induced a cumulative and reversible inhibition on the activity of IDAD sludge. Extracellular polymeric substances were found to play a glue-like role in the cell-iron mineral aggregates, where microbial cells were caged, and their metabolisms were suppressed. Adopting low-intensity ultrasound treatment efficiently restored the IDAD activity by disintegrating such aggregates rather than stimulating the microbial metabolism. Moreover, the ultrasonication-assisted IDAD bioreactor exhibited an advantageous nitrogen removal efficiency (with a maximum enhancement of 72.3%) and operational stability compared to the control one, demonstrating a feasible strategy to achieve long-term stability of the IDAD process. Overall, this work provides a better understanding about the mechanism for the performance deterioration and a simple approach to maintain the stability of IDAD.

Ligand Effects on Biotic and Abiotic Fe(II) Oxidation by the Microaerophile Sideroxydans lithotrophicus

Organic ligands are widely distributed and can affect microbially driven Fe biogeochemical cycles, but effects on microbial iron oxidation have not been well quantified. Our work used a model microaerophilic Fe(II)-oxidizing bacterium Sideroxydans lithotrophicus ES-1 to quantify biotic Fe(II) oxidation rates in the presence of organic ligands at 0.02 atm O₂ and pH 6.0. We used two common Fe chelators with different binding strengths: citrate (log K_{Fe(II)-citrate} = 3.20) and nitrilotriacetic acid (NTA) (log K_Fe(II)-NTA = 8.09) and two standard humic substances, Pahokee peat humic acid (PPHA) and Suwannee River fulvic acid (SRFA). Our results provide rate constants for biotic and abiotic Fe(II) oxidation over different ligand concentrations and furthermore demonstrate that various models and natural iron-binding ligands each have distinct effects on abiotic versus biotic Fe(II) oxidation rates. We show that NTA accelerates abiotic oxidation and citrate has negligible effects, making it a better laboratory chelator. The humic substances only affect biotic Fe(II) oxidation, via a combination of chelation and electron transfer. PPHA accelerates biotic Fe(II) oxidation, while SRFA decelerates or accelerates the rate depending on concentration. The specific nature of organic-Fe microbe interactions may play key roles in environmental Fe(II) oxidation, which have cascading influences on cycling of nutrients and contaminants that associate with Fe oxide minerals.

An efficient way to achieve stable and high-rate ferrous ion-dependent nitrate removal (FeNiR): Batch sludge replacement

Ferrous ion can be used as electron donor for denitrification in the ferrous ion-dependent nitrate removal (FeNiR). To prevent the FeNiR performance decrease caused by iron encrustation, a modified FeNiR process with batch sludge replacement was developed. Based on the decay kinetics of sludge mass and sludge activity, the sludge retention time (SRT) was determined as 40 days in the modified FeNiR process. To keep the FeNiR rate at 0.70 kg-N/(m³·d), the sludge replacement amount was 25% of total sludge every 10 days. The FeNiR efficiency stabilized around 70%. The batch sludge replacement could be an effective method to offset the active sludge decay caused by iron encrustation, and therefore led to the good FeNiR performance. The wasted FeNiR sludge was found to adsorb phosphate at a rate of 0.9 mg-P/(g VS min). The modified FeNiR process was proposed to be coupled with phosphate removal, achieving the co-removal of nitrate and phosphate. The coupled technology is promising due to the less consumption of resources and energy, as well as the less production of excessive sludge.

Improvement of ferrous ion-dependent nitrate removal (FeNiR) process with chelating ferrous ion as substrate

In order to improve the ferrous ion-dependent nitrate removal (FeNiR) process, hexametaphosphate chelated ferrous ion was used as substrate to replace the free ferrous ion. With hexametaphosphate chelated ferrous ion as substrate, the influent pH was adjusted to 6.8, and as a result a higher effluent pH (7.2) was detected. The volumetric removal rate (VRR) of nitrate kept at 0.42 ± 0.03 kg-N/(m³∙d) for 48 days and the corresponding nitrogen removal efficiency was 94.39 ± 4.57%. After 88 days of cultivation, FeNiR granules became small because of the oligotrophic substrate. The transmission electron microscope (TEM) analysis showed that less iron encrustation was formed on the surface or in the periplasm of FeNiR cells. The linear curve of the living cell percentage versus time showed that the death rate of FeNiR cells with chelated ferrous ion as substrate was much lower than that with free ferrous ion as substrate (0.4210 vs 0.9221). Without iron encrustation, both the FeNiR activity and alkaline phosphatase (ALP) activity of FeNiR cells kept at high level and thus the efficiency of the FeNiR reactor kept stable and high. With hexametaphosphate chelated ferrous ion as substrate, the pH in bulk liquid was high (pH = 7.2) resulting in the high FeNiR rate, and less iron encrustation was formed around cells ensuring the stability of high FeNiR rate. Therefore, using hexametaphosphate chelated ferrous ion as substrate was an efficient way to improve the FeNiR process.

Iron as electron donor for denitrification: The efficiency, toxicity and mechanism

For the treatment of low C/N wastewaters, methanol or acetate is usually dosed as electron donor for denitrification but such organics makes the process costly. To decrease the cost, iron which is the fourth most abundant element in lithosphere is suggested as the substitution of methanol and acetate. The peak volumetric removal rate (VRR) of nitrate nitrogen in the ferrous iron-dependent nitrate removal (FeNiR) reactor was 0.70 ± 0.04 kg-N/(m³·d), and the corresponding removal efficiency was 98%. Iron showed toxicity to cells by decreasing the live cell amount (dropped 56%) and the live cell activity (dropped 70%). The toxicity of iron was mainly expressed by the formation of iron encrustation. From microbial community data analysis, heterotrophs (Paracocccus, Thauera and Azoarcus) faded away while the facultative chemolithotrophs (Hyphomicrobium and Anaerolineaceae_uncultured) dominated in the reactor after replacing acetate with ferrous iron in the influent. Through scanning electron microscope (SEM) and transmission electron microscope (TEM), two iron oxidation sites in FeNiR cells were observed and accordingly two FeNiR mechanisms were proposed: 1) extracellular FeNiR in which ferrous iron was bio-oxidized extracellularly; and 2) intracellular FeNiR in which ferrous iron was chemically oxidized in periplasm. Bio-oxidation (extracellular FeNiR) and chemical oxidation (intracellular FeNiR) of ferrous iron coexisted in FeNiR reactor, but the former one predominated. Comparing with the control group without electron donor in the influent, FeNiR reactor showed 2 times higher and stable nitrate removal rate, suggesting iron could be used as electron donor for denitrification. However, further research works are still needed for the practical application of FeNiR in wastewater treatment.

A biophysiological perspective on enhanced nitrate removal from decentralized domestic sewage using gravitational-flow multi-soil-layering systems

Multi-soil-layering (MSL) system with brick-wall pattern structure and gravitational flow can be used for decentralized rural domestic sewage treatment. The capability of soil for contaminant removal is maximized within soil mixture blocks (SMBs). However, the performance of removing nitrate was still not ideal during operation. To improve its performance in MSL system, the relationship between biophysiological characteristics of denitrifying species and operating conditions was studied. Microbial species diversity of activated sludge and soil samples were analyzed. The significant effects of independent factors and their interactions on microbial species diversity and denitrifying species abundance were revealed on the basis of factorial analysis. The results indicated activated sludge in SMBs played a key role in increasing the richness of denitrifying species in MSL system. Slow-release poly (butylene succinate) (PBS) had the most dominant positive effect on increasing denitrifying species abundance. Submersion had significantly positive effect on species richness in SMBs. These three factors, including activated sludge, PBS in SMBs, and submersion condition had different significant effects on microbial responses. They were favorable for denitrification and ensuring a better removal efficiency of nitrate and total nitrogen. The porous zeolites were served as the habitats for most of aerobic bacteria to form biofilms, which could promote the oxygen consumption in both sewage and system to improve denitrification in SMBs. The results could help on the enhancement of denitrification in MSL system from biophysiological insights. It can provide a sound strategy for using MSL system with great performance on contaminant removal.

Facilitated arsenic immobilization by biogenic ferrihydrite-goethite biphasic Fe(III) minerals (Fh-Gt Bio-bi-minerals)

Biogenic iron(III) minerals (BIM) widely occur in aquatic systems. However, characteristics and mechanisms of As sequestration by biogenic biphasic Fe(III) minerals (Bio-bi-minerals) are not clearly understood. We investigated characteristics of Bio-bi-minerals induced by Pseudogulbenkiania sp. strain 2002 and explored their As sequestration mechanisms by monitoring particle morphology, mineralogical composition, and As binding properties. Results showed that Fe(II) oxidation (about 3 mM) by Pseudogulbenkiania sp. strain 2002 under growth condition produced biogenic ferrihydrite-goethite biphasic Fe(III) minerals (Fh-Gt Bio-bi-minerals), which showed better performance in As immobilization compared to corresponding biogenic monophasic Fe(III) minerals (Bio-mono-minerals). Decreased particle size, increased abundance of ferrihydrite and occurrence of bidentate mononuclear edge-sharing (²E) and monodentate mononuclear edge-sharing As complexes (¹V) contributed to enhanced As immobilization by Fh-Gt Bio-bi-minerals. We suggest that the Bio-bi-minerals have the potential to illuminate As biogeochemical cycles in aquatic systems and to remediate As and nitrate co-contaminated groundwater.

Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation

Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.

Oxidation of Fe(II)-Organic Matter Complexes in the Presence of the Mixotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacterium Acidovorax sp. BoFeN1

Fe(II)-organic matter (Fe(II)-OM) complexes are abundant in the environment and may play a key role for the behavior of Fe and pollutants. Mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) reduce nitrate coupled to the oxidation of organic compounds and Fe(II). Fe(II) oxidation may occur enzymatically or abiotically by reaction with nitrite that forms during heterotrophic denitrification. However, it is unknown whether Fe(II)-OM complexes can be oxidized by NRFeOx. We used cell-suspension experiments with the mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium Acidovorax sp. strain BoFeN1 to reveal the role of nonorganically bound Fe(II) (aqueous Fe(II)) and nitrite for the rates and extent of oxidation of Fe(II)-OM complexes (Fe(II)-citrate, Fe(II)-EDTA, Fe(II)-humic acid, and Fe(II)-fulvic acid). We found that Fe(II)-OM complexation inhibited microbial nitrate-reducing Fe(II) oxidation; large colloidal and negatively charged complexes showed lower oxidation rates than aqueous Fe(II). Accumulation of nitrite and fast abiotic oxidation of Fe(II)-OM complexes only happened in the presence of aqueous Fe(II) that probably interacted with (nitrite-reducing) enzymes in the periplasm causing nitrite accumulation in the periplasm and outside of the cells, whereas Fe(II)-OM complexes probably could not enter the periplasm and cause nitrite accumulation. These results suggest that Fe(II) oxidation by mixotrophic nitrate reducers in the environment depends on Fe(II) speciation, and that aqueous Fe(II) potentially plays a critical role in regulating microbial denitrification processes.

Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism

This work considers the hypothetical viability of microbial nitrate-dependent Fe2+ oxidation (NDFO) for supporting simple life in the context of the early Mars environment. This draws on knowledge built up over several decades of remote and in situ observation, as well as recent discoveries that have shaped current understanding of early Mars. Our current understanding is that certain early martian environments fulfill several of the key requirements for microbes with NDFO metabolism. First, abundant Fe2+ has been identified on Mars and provides evidence of an accessible electron donor; evidence of anoxia suggests that abiotic Fe2+ oxidation by molecular oxygen would not have interfered and competed with microbial iron metabolism in these environments. Second, nitrate, which can be used by some iron oxidizing microorganisms as an electron acceptor, has also been confirmed in modern aeolian and ancient sediment deposits on Mars. In addition to redox substrates, reservoirs of both organic and inorganic carbon are available for biosynthesis, and geochemical evidence suggests that lacustrine systems during the hydrologically active Noachian period (4.1-3.7 Ga) match the circumneutral pH requirements of nitrate-dependent iron-oxidizing microorganisms. As well as potentially acting as a primary producer in early martian lakes and fluvial systems, the light-independent nature of NDFO suggests that such microbes could have persisted in sub-surface aquifers long after the desiccation of the surface, provided that adequate carbon and nitrates sources were prevalent. Traces of NDFO microorganisms may be preserved in the rock record by biomineralization and cellular encrustation in zones of high Fe2+ concentrations. These processes could produce morphological biosignatures, preserve distinctive Fe-isotope variation patterns, and enhance preservation of biological organic compounds. Such biosignatures could be detectable by future missions to Mars with appropriate instrumentation.

Magnetite and Green Rust: Synthesis, Properties, and Environmental Applications of Mixed-Valent Iron Minerals

Mixed-valent iron [Fe(II)-Fe(III)] minerals such as magnetite and green rust have received a significant amount of attention over recent decades, especially in the environmental sciences. These mineral phases are intrinsic and essential parts of biogeochemical cycling of metals and organic carbon and play an important role regarding the mobility, toxicity, and redox transformation of organic and inorganic pollutants. The formation pathways, mineral properties, and applications of magnetite and green rust are currently active areas of research in geochemistry, environmental mineralogy, geomicrobiology, material sciences, environmental engineering, and environmental remediation. These aspects ultimately dictate the reactivity of magnetite and green rust in the environment, which has important consequences for the application of these mineral phases, for example in remediation strategies. In this review we discuss the properties, occurrence, formation by biotic as well as abiotic pathways, characterization techniques, and environmental applications of magnetite and green rust in the environment. The aim is to present a detailed overview of the key aspects related to these mineral phases which can be used as an important resource for researchers working in a diverse range of fields dealing with mixed-valent iron minerals.

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats.IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.

Iron Isotope Fractionation during Fe(II) Oxidation Mediated by the Oxygen-Producing Marine Cyanobacterium Synechococcus PCC 7002

In this study, we couple iron isotope analysis to microscopic and mineralogical investigation of iron speciation during circumneutral Fe(II) oxidation and Fe(III) precipitation with photosynthetically produced oxygen. In the presence of the cyanobacterium Synechococcus PCC 7002, aqueous Fe(II) (Fe(II)_aq) is oxidized and precipitated as amorphous Fe(III) oxyhydroxide minerals (iron precipitates, Fe_ppt), with distinct isotopic fractionation (ε⁵⁶Fe) values determined from fitting the δ⁵⁶Fe(II)_aq (1.79‰ and 2.15‰) and the δ⁵⁶Fe_ppt (2.44‰ and 2.98‰) data trends from two replicate experiments. Additional Fe(II) and Fe(III) phases were detected using microscopy and chemical extractions and likely represent Fe(II) and Fe(III) sorbed to minerals and cells. The iron desorbed with sodium acetate (Fe_NaAc) yielded heavier δ⁵⁶Fe compositions than Fe(II)_aq. Modeling of the fractionation during Fe(III) sorption to cells and Fe(II) sorption to Fe_ppt, combined with equilibration of sorbed iron and with Fe(II)_aq using published fractionation factors, is consistent with our resulting δ⁵⁶Fe_NaAc. The δ⁵⁶Fe_ppt data trend is inconsistent with complete equilibrium exchange with Fe(II)_aq. Because of this and our detection of microbially excreted organics (e.g., exopolysaccharides) coating Fe_ppt in our microscopic analysis, we suggest that electron and atom exchange is partially suppressed in this system by biologically produced organics. These results indicate that cyanobacteria influence the fate and composition of iron in sunlit environments via their role in Fe(II) oxidation through O₂ production, the capacity of their cell surfaces to sorb iron, and the interaction of secreted organics with Fe(III) minerals.

X-ray spectromicroscopy of nanoparticulate iron oxide phases

Soft x-ray spectromicroscopy techniques have seen great amount of development in the recent years, and with the development of new diffraction limited synchrotron source, many new nanoscale and mesoscale characterization opportunities of applied materials are foreseen. In this perspective, the authors present some examples that illustrate the capabilities of spectromicroscopy techniques, namely, 2D and 3D spatially resolved chemical quantification, surface and bulk sensitive measurements, and polarization dependent measurements as applied to iron oxide nanoparticulate materials of biological, geological, and other origins.

Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis

The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.

Protection of Nitrate-Reducing Fe(II)-Oxidizing Bacteria from UV Radiation by Biogenic Fe(III) Minerals

Due to the lack of an ozone layer in the Archean, ultraviolet radiation (UVR) reached early Earth's surface almost unattenuated; as a consequence, a terrestrial biosphere in the form of biological soil crusts would have been highly susceptible to lethal doses of irradiation. However, a self-produced external screen in the form of nanoparticular Fe(III) minerals could have effectively protected those early microorganisms. In this study, we use viability studies by quantifying colony-forming units (CFUs), as well as Fe(II) oxidation and nitrate reduction rates, to show that encrustation in biogenic and abiogenic Fe(III) minerals can protect a common soil bacteria such as the nitrate-reducing Fe(II)-oxidizing microorganisms Acidovorax sp. strain BoFeN1 and strain 2AN from harmful UVC radiation. Analysis of DNA damage by quantifying cyclobutane pyrimidine dimers (CPD) confirmed the protecting effect by Fe(III) minerals. This study suggests that Fe(II)-oxidizing microorganisms, as would have grown in association with mafic and ultramafic soils/outcrops, would have been able to produce their own UV screen, enabling them to live in terrestrial habitats on early Earth.

Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria

Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.

Bioaugmentation of nitrate-dependent anaerobic ferrous oxidation by heterotrophic denitrifying sludge addition: A promising way for promotion of chemoautotrophic denitrification

Nitrate-dependent anaerobic ferrous oxidation (NAFO) is a new and valuable bio-process for the treatment of wastewaters with low C/N ratio, and the NAFO process is in state of the art. The heterotrophic denitrifying sludge (HDS), possessing NAFO activity, was used as bioaugmentation to enhance NAFO efficiency. At a dosage of 6% (V/V), the removal of nitrate and ferrous was 2.4 times and 2.3 times of as primary, and the volumetric removal rate (VRR) of nitrate and ferrous was 2.4 times and 2.2 times of as primary. Tracing experiments of HDS indicated that the bioaugmentation on NAFO reactor was resulted from the NAFO activity by HDS itself. The predominant bacteria in HDS were identified as Thauera (52.5%) and Hyphomicrobium (20.0%) which were typical denitrifying bacteria and had potential ability to oxidize ferrous. In conclusion, HDS could serve as bioaugmentation or a new seeding sludge for operating high-efficiency NAFO reactors.

ScatterJ: An ImageJ plugin for the evaluation of analytical microscopy datasets

We present ScatterJ, an ImageJ plugin that allows for extracting qualitative as well as quantitative information from analytical microscopy datasets. A large variety of analytical microscopy methods are used to obtain spatially resolved chemical information. The resulting datasets are often large and complex, and can contain information that is not obvious or directly accessible. ScatterJ extends and complements existing methods to extract information on correlation and colocalization from pairs of species-specific or element-specific maps. We demonstrate the possibilities to extract information using example datasets from biogeochemical studies, although the plugin is not restricted to this type of research. The information that we could extract from our existing data helped to further our understanding of biogeochemical processes such as mineral formation or heavy metal sorption. ScatterJ can be used for a variety of different two-dimensional (2D) and three-dimensional (3D) datasets such as energy-dispersive X-ray spectroscopy maps, 3D confocal laser scanning microscopy maps, and 2D scanning transmission X-ray microscopy maps.

Three-dimensional mid-infrared tomographic imaging of endogenous and exogenous molecules in a single intact cell with subcellular resolution

Microscopy in the mid-infrared spectral range provides detailed chemical information on a sample at moderate spatial resolution and is being used increasingly in the characterization of biological entities as challenging as single cells. However, a conventional cellular 2D imaging measurement is limited in its ability to associate specific compositional information to subcellular structures because of the interference from the complex topography of the sample. Herein we provide a method and protocols that overcome this challenge in which tilt-series infrared tomography is used with a standard benchtop infrared microscope. This approach gives access to the quantitative 3D distribution of molecular components based on the intrinsic contrast provided by the sample. We demonstrate the method by quantifying the distribution of an exogenous metal carbonyl complex throughout the cell and by reporting changes in its coordination sphere in different locations in the cell.