The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of Fe^III reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory Fe^III-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

Disentangling Microbial Syntrophic Mechanisms for Hexavalent Chromium Reduction in Autotrophic Biosystems

Hexavalent chromium [Cr(VI)] is one of the common heavy-metal contaminants in groundwater, and the availability of electron donors is considered to be a key parameter for Cr(VI) biotransformation. During the autotrophic remediation process, however, much remains to be illuminated about how complex syntrophic microbial communities couple Cr(VI) reduction with other elemental cycles. Two series of Cr(VI)-reducing groundwater bioreactors were independently amended by elemental sulfur and iron and inoculated with the same inoculum. After 160 days of incubation, both bioreactors showed similar archaea-dominating microbiota compositions, whereas a higher Cr(VI)-reducing rate and more methane production were detected in the Fe⁰-driven one. Metabolic reconstruction of 23 retrieved genomes revealed complex symbiotic relationships driving distinct elemental cycles coupled with Cr(VI) reduction in bioreactors. In both bioreactors, these Cr(VI) reducers were assumed to live in syntrophy with oxidizers of sulfur, iron, hydrogen, and volatile fatty acids and methane produced by carbon fixers and multitrophic methanogens, respectively. The significant difference in methane production was mainly due to the fact that the yielded sulfate greatly retarded acetoclastic methanogenesis in the S-bioreactor. These findings provide insights into mutualistic symbioses of carbon, sulfur, iron, and chromium metabolisms in groundwater systems and have implications for bioremediation of Cr(VI)-contaminated groundwater.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Hematite facet-mediated microbial dissimilatory iron reduction and production of reactive oxygen species during aerobic oxidation

Microbial dissimilatory iron reduction and aerobic oxidation affect the biogeochemical cycles of many elements. Although the processes have been widely studied, the underlying mechanisms, and especially how the surface structures of iron oxides affect these redox processes, are poorly understood. Therefore, {001} facet-dominated hematite nanoplates (HNP) and {100} facet-dominated hematite nanorods (HNR) were used to explore the effects of surface structure on the microbial dissimilatory iron reduction and aerobic oxidation processes. During the reduction stage, the production of total Fe(II) normalized by specific surface area (SSA) was higher for HNP than HNR due to steric effects and the ligand-bound conformation of the connection between iron on different exposed facets and electron donors from microorganisms. However, during the aerobic oxidation stage, both the SSA- and Fe(II)-normalized reactive oxygen species (ROS), including hydrogen peroxide (H₂O₂) and hydroxyl radical (•OH), were higher for HNR than HNP. Theoretical calculation results showed that the {100} facets exhibited a lower activation energy barrier for oxygen reduction reaction than {001} facets, supporting the experimental observation that {100} facet-dominated HNR had a higher ROS production efficiency than {001} facet-dominated HNP. These results indicated that surface characteristics not only mediated the microbial reduction of Fe(III) but also affected the aerobic oxidation of microbially reduced Fe(II). Accessibility of electron donors to surface iron atom determined the reduction of Fe(III), and activation energy barrier for oxygen reduction by surface Fe(II) dominated the ROS production during the redox processes. This study advances our understanding of the mechanisms through which ROS are produced by iron (oxyhydr)oxides during microbial dissimilatory iron reduction and aerobic oxidation processes.

Nanosized non-proteinaceous complexes III and IV mimicking electron transfer of mitochondrial respiratory chain

Synthetic biology pursues the understanding of biological processes and their possible mimicry with artificial bioinspired materials. A number of materials have already been used to mimic the active site of simple redox proteins, including nanosized iron oxides due to their redox properties. However, the mimicry of membrane redox protein complexes is still a challenge. Herein, magnetic iron oxide nanoparticles (NPs), incorporated as non-proteinaceous complexes III and IV in a mitochondrial model membrane, catalyze electron transfer (ET) similarly to the natural complexes towards cytochrome c. The associated molecular mechanism is experimentally proven in solution and in a Langmuir-Blodgett film. A direct and entropy-driven ET, with rate constant of 2.63 ± 0.05Lmol^-1 at 25 °C, occurs between the iron sites of the NPs and the cytochrome c heme group, not affecting the protein secondary and tertiary structures. This process requires an activation energy of 40.2 ± 1.5 kJ mol^-1 resulting in an overall Gibbs free energy of -55.3 kJ mol^-1. Furthermore, the protein-NP system is governed by electrostatic and non-polar forces that contribute to an associative mechanism in the transition state. Finally, the incorporated NPs in a model membrane were able to catalyze ET, such as the natural complexes in respiratory chain. This work presents an experimental approach demonstrating that inorganic nanostructured systems may behave as embedded proteins in the eukaryotic cells membrane, opening the way for more sophisticated and robust mimicry of membrane protein complexes.

Effect of voltage intensity on the nutrient removal performance and microbial community in the iron electrolysis-integrated aerobic granular sludge system

The effects of voltage intensity on the nutrient removal performance and microbial community in the iron electrolysis-integrated aerobic granular sludge (AGS) system were investigated over a period of 15 weeks. Results revealed that the application outcomes of iron electrolysis for AGS systems relied on voltage intensity. When a constant voltage of 1.5 V was applied, the sludge granulation was most obviously accelerated with a specific growth rate of the sludge diameter of 0.078 day^-1, and the removal efficiencies of total nitrogen (TN) and total phosphorus (TP) increased by 14.1% and 20.2%, respectively, compared to the control reactor (without the iron electrolysis-integration). Moreover, the AGS developed at different voltages included different microbial communities, whose shifts were driven by the Fe content and the average diameter of AGS. Both heterotrophic nitrifiers and mixotrophic denitrifiers were significantly enriched in the AGS developed at 1.5 V, which effectively enhanced TN removal. Together with the response of the functional genes involved in Fe, N, and P metabolism, the electrolytic iron-driven nutrient degradation pathway was further elaborated. Overall, this study clarified the optimum voltage condition when iron electrolysis was integrated into the AGS system, and revealed the enhancement mechanism of this coupling technology on nutrient removal during the treatment of low-strength municipal wastewater.

Uranium and neptunium retention mechanisms in Gallionella ferruginea/ferrihydrite systems for remediation purposes

The ubiquitous β-Proteobacterium Gallionella ferruginea is known as stalk-forming, microaerophilic iron(II) oxidizer, which rapidly produces iron oxyhydroxide precipitates. Uranium and neptunium sorption on the resulting intermixes of G. ferruginea cells, stalks, extracellular exudates, and precipitated iron oxyhydroxides (BIOS) was compared to sorption to abiotically formed iron oxides and oxyhydroxides. The results show a high sorption capacity of BIOS towards radionuclides at circumneutral pH values with an apparent bulk distribution coefficient (Kd) of 1.23 × 104 L kg-1 for uranium and 3.07 × 105 L kg-1 for neptunium. The spectroscopic approach by X-ray absorption spectroscopy (XAS) and ATR FT-IR spectroscopy, which was applied on BIOS samples, showed the formation of inner-sphere complexes. The structural data obtained at the uranium LIII-edge and the neptunium LIII-edge indicate the formation of bidentate edge-sharing surface complexes, which are known as the main sorption species on abiotic ferrihydrite. Since the rate of iron precipitation in G. ferruginea-dominated systems is 60 times faster than in abiotic systems, more ferrihydrite will be available for immobilization processes of heavy metals and radionuclides in contaminated environments and even in the far-field of high-level nuclear waste repositories.

Ferrihydrite Reduction by Photosynthetic Synechocystis sp. PCC 6803 and Its Correlation With Electricity Generation

Microbial extracellular electron transfer (EET) to solid-state electron acceptors such as anodes and metal oxides, which was originally identified in dissimilatory metal-reducing bacteria, is a key process in microbial electricity generation and the biogeochemical cycling of metals. Although it is now known that photosynthetic microorganisms can also generate (photo)currents via EET, which has attracted much interest in the field of biophotovoltaics, little is known about the reduction of metal (hydr)oxides via photosynthetic microbial EET. The present work quantitatively assessed the reduction of ferrihydrite in conjunction with the EET of the photosynthetic microbe Synechocystis sp. PCC 6803. Microbial reduction of ferrihydrite was found to be initiated in response to light but proceeded at higher rates when exogenous glucose was added, even under dark conditions. These results indicate that current generation from Synechocystis cells does not always need light irradiation. The qualitative trends exhibited by the ferrihydrite reduction rates under various conditions showed significant correlation with those of the microbial currents. Notably, the maximum concentration of Fe(II) generated by the cyanobacterial cells under dark conditions in the presence of glucose was comparable to the levels observed in the photic layers of Fe-rich microbial mats.

Phylogenetic diversity contributes more to sediment magnetism than abundance during incubation of iron-reducing sediment from a non-active volcanic lake in Northeast China

AIM

This study aimed to analyse bacterial community and biomineralization products from Wudalianchi non-active volcanic field and the relationship between magnetization and bacterial community.

METHODS AND RESULTS

Eighteen sediment samples obtained from Wenbo Lake, high-throughput sequencing and quantitative PCR (qPCR) were separately employed to investigate the bacterial community composition dynamics and abundance variation of the sediment sample with the highest iron-reducing capacity during incubation. The mineralization products were characterized by transmission electron microscopy, scanning electron microscopy, X-ray diffraction (XRD), Raman spectroscopy, vibrating sample magnetometer (VSM) and variable-temperature magnetism analyses. The results showed that the highest iron reduction rate was 98·06%. Seven phyla were identified as dominant bacterial phyla during the incubation process. Iron-reducing bacteria (FeRB) including Geobacter, Desulfosporosinus and Clostridium were involved in the iron mineralization process. The 16S rDNA copy numbers of sediment decreased quickly and then stayed steady during the incubation. Bacteria with rod-shaped and spheroid species were involved in extracellular iron reduction to produce magnetic particles with massive aggregation and columnar structures on the mineral surface morphologies. The materials produced by the microbial community over the incubation period were sequentially identified as siderite, magnetite and maghemite. The magnetism of the mineral samples gradually increased from 0·31748 to 33·58423 emu g^-1 with increased incubation time. The final products showed relatively stable magnetism under 0-400 K. Meanwhile, the saturation magnetization (M_S ) of the mineralized substance was tightly associated with bacterial diversity (P < 0·05).

CONCLUSIONS

Bacterial community varied during incubation of iron-reducing sediment of volcanic lake. Various iron mineral crystals were in turn formed extracellularly by FeRB. The magnetism of mineralized products was tightly associated with bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results not only help us to better understand the iron mineralization of FeRB in the volcanic lake sediments but also provide basic information for the future application of FeRB in environmental bioremediation.

Community Composition and Spatial Distribution of N-Removing Microorganisms Optimized by Fe-Modified Biochar in a Constructed Wetland

Microbial nitrogen (N) removal capability can be significantly enhanced in a horizontal subsurface flow constructed wetland (HSCW) amended by Fe-modified biochar (FeB). To further explore the microbiological mechanism of FeB enhancing N removal, nirS- and nirK-denitrifier community diversities, as well as spatial distributions of denitrifiers and anaerobic ammonium oxidation (anammox) bacteria, were investigated in HSCWs (C-HSCW: without biochar and FeB; B-HSCW: amended by biochar; FeB-HSCW: amended by FeB) treating tailwater from a wastewater treatment plant, with C-HSCW without biochar and FeB and B-HSCW amended by biochar as control. The community structures of nirS- and nirK-denitrifiers in FeB-HSCW were significantly optimized for improved N removal compared with the two other HSCWs, although no significant differences in their richness and diversity were detected among the HSCWs. The spatial distributions of the relative abundance of genes involved in denitrification and anammox were more heterogeneous and complex in FeB-HSCW than those in other HSCWs. More and larger high-value patches were observed in FeB-HSCW. These revealed that FeB provides more appropriate habitats for N-removing microorganisms, which can prompt the bacteria to use the habitats more differentially, without competitive exclusion. Overall, the Fe-modified biochar enhancement of the microbial N-removal capability of HSCWs was a result of optimized microbial community structures, higher functional gene abundance, and improved spatial distribution of N-removing microorganisms.

Stringent Starvation Protein Regulates Prodiginine Biosynthesis via Affecting Siderophore Production in Pseudoalteromonas sp. Strain R3

Prodiginines are a family of red-pigmented secondary metabolites with multiple biological activities. The biosynthesis of prodiginines is affected by various physiological and environmental factors. Thus, prodiginine biosynthesis regulation is highly complex and multifaceted. Although the regulatory mechanism for prodiginine biosynthesis has been extensively studied in Serratia and Streptomyces species, little is known about that in the marine betaproteobacterium Pseudoalteromonas In this study, we report that stringent starvation protein A (SspA), an RNA polymerase-associated regulatory protein, is required for the biosynthesis of prodiginine in Pseudoalteromonas sp. strain R3. The strain lacking sspA (ΔsspA) fails to produce prodiginine, which resulted from the downregulation of the prodiginine biosynthetic gene (pig) cluster. The effect of SspA on prodiginine biosynthesis is independent of histone-like nucleoid structuring protein (H-NS) and RpoS (σ^S). Further analysis demonstrates that the ΔsspA strain has a significant decrease in the transcription of the siderophore biosynthesis gene (pvd) cluster, leading to the inhibition of siderophore production and iron uptake. The ΔsspA strain regains the ability to synthesize prodiginine by cocultivation with siderophore producers or the addition of iron. Therefore, we conclude that SspA-regulated prodiginine biosynthesis is due to decreased siderophore levels and iron deficiency. We further show that the iron homeostasis master regulator Fur is also essential for pig transcription and prodiginine biosynthesis. Overall, our results suggest that SspA indirectly regulates the biosynthesis of prodiginine, which is mediated by the siderophore-dependent iron uptake pathway.IMPORTANCE The red-pigmented prodiginines are attracting increasing interest due to their broad biological activities. As with many secondary metabolites, the biosynthesis of prodiginines is regulated by both environmental and physiological factors. At present, studies on the regulation of prodiginine biosynthesis are mainly restricted to Serratia and Streptomyces species. This work focused on the regulatory mechanism of prodiginine biosynthesis in Pseudoalteromonas sp. R3. We found that stringent starvation protein A (SspA) positively regulates prodiginine biosynthesis via affecting the siderophore-dependent iron uptake pathway. The connections among SspA, iron homeostasis, and prodiginine biosynthesis were investigated. These findings uncover a novel regulatory mechanism for prodigiosin biosynthesis.

Strategies to Overcome Intermediate Accumulation During in situ Nitrate Remediation in Groundwater by Hydrogenotrophic Denitrification

Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L-1, largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches.

Potentially bioavailable iron produced through benthic cycling in glaciated Arctic fjords of Svalbard

The Arctic has the highest warming rates on Earth. Glaciated fjord ecosystems, which are hotspots of carbon cycling and burial, are extremely sensitive to this warming. Glaciers are important for the transport of iron from land to sea and supply this essential nutrient to phytoplankton in high-latitude marine ecosystems. However, up to 95% of the glacially-sourced iron settles to sediments close to the glacial source. Our data show that while 0.6-12% of the total glacially-sourced iron is potentially bioavailable, biogeochemical cycling in Arctic fjord sediments converts the glacially-derived iron into more labile phases, generating up to a 9-fold increase in the amount of potentially bioavailable iron. Arctic fjord sediments are thus an important source of potentially bioavailable iron. However, our data suggests that as glaciers retreat onto land the flux of iron to the sediment-water interface may be reduced. Glacial retreat therefore likely impacts iron cycling in coastal marine ecosystems.

Abundant sediment organic matter potentially facilitates chemical iron reduction and surface water blackness in a Chinese deep lake

Black bloom has become an increasingly severe environmental and ecological problem in lots of lakes. Ferrous monosulfide (FeS), which is closely related to chemical iron reduction (CIR), is considered the major cause for black water in shallow lakes, but few studies focus on the effect of organic matters (OM) content on iron and sulfate reduction and its contribution to the black bloom in deep lakes. Here, in Lake Fuxian, a Chinese deep lake which has also suffered from black bloom, FeS was identified responsible for the surface water blackness by using multiple microscopy and element analyses. Dissolved oxygen (DO) penetrated 1.6-4.2 mm in all sediment sites, further indicating FeS formed in the sediments instead of the permanently oxic water column. Geochemical characteristics revealed by diffusive gradients in thin films (DGT) showed that DGT-Fe²⁺ concentration was 57.6-1919.4 times higher than the DGT-S^2- concentration and both were positively correlated with DGT-PO₄^3-. Combining DGT profiles and anaerobic OM remineralization rate according to bag incubation, iron reduction is more effective than sulfate reduction although the two processes coexisted. Moreover, correlation of DGT-Fe²⁺ and DGT-PO₄^3- was better than that of DGT-PO₄^3- and DGT-S^2- at OM-depleted sites but opposite at OM-rich sites. In addition, total organic carbon (TOC) was significantly positively related to acid volatile sulfide (AVS). We therefore conclude that abundant OM potentially exacerbate chemical iron reduction and further lead to surface water blackness. Our study revealed the mechanisms behind the black bloom and gives credence to the management strategy of reducing OM loading to protect water quality in deep lakes.

Changes in the microbial community during microbial microaerophilic Fe(II) oxidation at circumneutral pH enriched from paddy soil

Fe(II)-oxidizing bacteria (FeOB) are important catalysts for iron cycling in iron-rich marine, groundwater, and freshwater environments. However, few studies have reported the distribution and diversity of these bacteria in flooded paddy soils. This study investigates the microbial structure and diversity of microaerophilic Fe(II)-oxidizing bacteria (mFeOB) and their possible role in Fe(II) oxidation in iron-rich paddy soils. Using enrichment experiments that employed serial transfers, the changes in microaerophilic microbial community were examined via 16S rRNA gene high-throughput sequencing. During enrichments, the Fe(II) oxidation rate decreased as transfers increased, and the maximum rate of Fe(II) oxidation was observed in the first transfer (0.197 mM day^-1). Results from X-ray diffraction of minerals and scanning electron microscopy of the cell-mineral aggregates revealed that cell surfaces in all transfers were partly covered with amorphous iron oxide formed by FeOB. After four transfers, the phyla of Proteobacteria had a dominant presence that reached up to 95%. Compared with the original soil, the relative abundances of Cupriavidus, Massilia, Pseudomonas, Ralstonia, Sphingomonas, and Variovorax increased in FeS gradient tubes and became dominant genera after transfers. Cupriavidus, Pseudomonas, and Ralstonia have been identified as FeOB previously. Furthermore, the structure of the microbial community tended to be stable as transfers increased, indicating that other bacterial species might perform important roles in Fe(II) oxidation. These results suggest the potential involvement of mFeOB and these other microorganisms in the Fe(II)-oxidizing process of soils. It will be helpful for future studies to consider their role in related biogeochemical processes, such as transformation of organic matters and heavy metals.

Dissimilatory Iron-Reducing Microorganisms Are Present and Active in the Sediments of the Doce River and Tributaries Impacted by Iron Mine Tailings from the Collapsed Fundão Dam (Mariana, MG, Brazil)

On 5 November 2015, a large tailing deposit failed in Brazil, releasing an estimated 32.6 to 62 million m3 of iron mining tailings into the environment. Tailings from the Fundão Dam flowed down through the Gualaxo do Norte and Carmo riverbeds and floodplains and reached the Doce River. Since then, bottom sediments have become enriched in Fe(III) oxyhydroxides. Dissimilatory iron-reducing microorganisms (DIRMs) are anaerobes able to couple organic matter oxidation to Fe(III) reduction, producing CO2 and Fe(II), which can precipitate as magnetite (FeO·Fe2O3) and other Fe(II) minerals. In this work, we investigated the presence of DIRMs in affected and non-affected bottom sediments of the Gualaxo do Norte and Doce Rivers. The increase in Fe(II) concentrations in culture media over time indicated the presence of Fe(III)-reducing microorganisms in all sediments tested, which could reduce Fe(III) from both tailings and amorphous ferric oxyhydroxide. Half of our enrichment cultures converted amorphous Fe(III) oxyhydroxide into magnetite, which was characterized by X-ray diffraction, transmission electron microscopy, and magnetic measurements. The conversion of solid Fe(III) phases to soluble Fe(II) and/or magnetite is characteristic of DIRM cultures. The presence of DIRMs in the sediments of the Doce River and tributaries points to the possibility of reductive dissolution of goethite (α-FeOOH) and/or hematite (α-Fe2O3) from sediments, along with the consumption of organics, release of trace elements, and impairment of water quality.

Natural organic matter inhibits Ni stabilization during Fe(II)-catalyzed ferrihydrite transformation

Trace metals, such as nickel (Ni), are often found associated with ferrihydrite (Fh) in soil and sediment and have been shown to redistribute during Fe(II)-catalyzed transformation of Fh. Fe(II)-catalyzed transformation of Fh, however, is often inhibited when natural organic matter (NOM) is associated with Fh. To explore whether NOM affects the behavior of Ni during Fe(II)-catalyzed transformation of Fh, we tracked Ni distribution, Fe atom exchange, and mineral transformation of Fh and Fh coprecipitated with Suwannee River natural organic matter (SRNOM-Fh). As expected, in the absence of Fe(II), Fh and SRNOM-Fh did not transform to secondary Fe minerals after two weeks. We further observed little difference in Ni adsorption on SRNOM-Fh compared to Fh. In the presence of Fe(II), however, we found that Ni associated with SRNOM-Fh was more susceptible to acid extraction than Fh. Specifically, we found almost double the amount of Ni remaining in the Fh after mild extraction compared to SRNOM-Fh. XRD showed that Fh transformed to goethite and magnetite whereas SRNOM-Fh did not transform despite ⁵⁷Fe isotope tracer experiments confirmed that SRNOM-Fh underwent extensive atom exchange with aqueous Fe(II). Our findings suggest that Fe atom exchange may not be sufficient for obvious Ni stabilization and that transformation to secondary minerals may be necessary for Ni stabilization to occur.

The reduction of nitrobenzene by extracellular electron transfer facilitated by Fe-bearing biochar derived from sewage sludge

In this work, the incorporation of Fe-bearing sludge-derived biochar greatly enhanced both biotic and abiotic reduction of nitrobenzene (NB) to aniline, which was attributed to the concomitant microbial dissimilatory iron reduction. Biogenic Fe(II) produced by Geobacter sulfurreducens dominated the anaerobic reduction of NB following the pseudo-first-order kinetic. Besides, the increase of pyrolysis temperature from 600 to 900 ℃ to generate biochar resulted in an accelerated removal rate of NB in Geobacter-biochar combined system. The morphology and structural characterization of biochar with G. sulfurreducens confirmed the formation of conductive bacteria-biochar aggregates. Electrochemical measurements suggested the presence of graphitized domains and quinone-like moieties in biochar as redox-active centers, which might play an important role in accelerating electron transfer for microbial dissimilatory iron reduction and NB degradation. This study provides a feasible way of using Fe-bearing sludge as a valuable feedstock for biochar generation and its application with electrochemically active bacteria for the bioremediation of nitroaromatic compounds-polluted wastewater.

How do phytogenic iron oxide nanoparticles drive redox reactions to reduce cadmium availability in a flooded paddy soil?

While soil redox reactions are known to determine heavy metal soil availability, specific information on how iron (Fe) nanomaterials reduce heavy metal availability in bulk soil and in the rice rhizosphere is limited. Here a pot experiment was performed to examine the effect of phytogenic iron oxide nanoparticles (PION) on the availability of cadmium (Cd) in flooded soil. PION significantly reduced soil Cd availability, with Cd in rice shoot being 2.72, 1.21 and 0.40 mg kg^-1 for the control, 1 and 5% PION treatments, respectively. In addition, following PION application, Illumina MiSeq sequencing indicated that the abundance of Lentimicrobium and Anaeromyxobacter increased, while the abundance of Geobacter and Thiobacillus decreased. Structural equation model analysis revealed that redox reactions, driven by carbon, nitrogen, iron and sulfur cycling related functional groups, played an important role in the immobilization of Cd in flooded soil. Co-occurrence network analysis showed that the rhizosphere soil was far more complex than the bulk soil. Overall, PION addition enhanced the inherent soil microbe's activity and the involved in reducing Cd availability to rice by converting mobile Cd into stabler forms. This initial result paves the way for establishing a practical low-cost remediation strategy for Cd contaminated paddy soils.

Transformation of redox-sensitive to redox-stable iron-bound phosphorus in anoxic lake sediments under laboratory conditions

Phosphorus (P) can be retained in mineral association with ferrous iron (Fe) as vivianite, Fe(II)₃(PO₄)₂ ∙ 8 H₂O, in lake sediments. The mineral is formed and remains stable under anoxic non-sulphidogenic conditions and, therefore, acts as a long-term P sink. In laboratory experiments under anoxic conditions, we investigated whether P adsorbed to amorphous Fe(III)-hydroxide functioned as a precursor phase of vivianite when added to different sediments as a treatment. The untreated sediments served as controls and were naturally Fe-rich (559 µmol/g DW) and Fe-poor (219 µmol/g DW), respectively. The solid P binding forms analysed by sequential extraction and X-ray diffraction were related to coinciding pore water analyses and the bacterial community compositions of the sediments by bacterial 16S rRNA gene amplicon sequencing. In the treatments, within a period of 40 d, 70 % of the redox-sensitive Fe(III)-P was transformed into redox-stable P, which contained vivianite. The mineral was supersaturated in the pore water, but the presence of Fe(III)-P functioning as a precursor was sufficient for measurable vivianite formation. The composition of the microbial community did not differ significantly (PERMANOVA, p = 0.09) between treatment and control of the naturally Fe-rich sediment. In the naturally Fe-poor sediment, the microbial community changed significantly (PERMANOVA, p = 0.001) in response to the addition of Fe(III)-P to the sediment. The freshly formed redox-stable P was not retransferred to a redox-sensitive compound by aeration for 24 h until 90 % O₂ saturation was reached in the sediment slurry. We conclude that 1) Fe(III)-hydroxide bound P, resulting from oxic conditions at the sediment-water interface, is immobilised during anoxic conditions and stable even after re-oxygenation; 2) the process is feasible within the time scales of anoxic lake stratification periods; and 3) in relatively Fe-poor lakes, Fe dosing can provide excess Fe to form the precursor.

Using Fe(II)/Fe(III) as catalyst to drive a novel anammox process with no need of anammox bacteria

A novel 'anammox' in the absence of anammox bacteria was confirmed to occur in an anaerobic sludge slurry system, in which Fe(II)/Fe(III) cycle driven by NO₂^--induced Fe(II) oxidation and subsequent NH₄⁺-induced Fe(III) reduction (Feammox) pushed the nitrogen removal. Results showed that Fe(II) contents significantly (p<0.05) decreased and Fe(III) accordingly increased with NO₂^- addition, indicating that Fe(II) was anaerobically oxidized to Fe(III). With depletion of NO₂^-, the Fe(II) content began to increase which was a result of Feammox. Consequently, 96.0% NH₄⁺-N of the NO₂^--added reactor was removed during 18 days operation, while NH₄⁺-N content remained essentially unchanged in the control in which NO₂^- was not added. X-ray diffraction (XRD) and X-ray Photoelectron Spectroscopy (XPS) analysis indicated that FeOOH was produced from chemical Fe(II) oxidation with NO₂^-. During the treatment, anammox bacteria was not detected, but the relative abundance of Geobacter of the NO₂^--added group increased by 13 folds. Isotope experiment in ¹⁵NH₄⁺-containing reactors found that much more ³⁰N₂ and ²⁹N₂ in the ¹⁴NO₂^--added group were produced than those in the control (without ¹⁴NO₂^-), confirming that ¹⁴NO₂^- induced Fe(II) oxidation to participate in Feammox for ¹⁵NH₄⁺ removal. Also, NO₂^- could be produced from partial denitrification of NO₃^-, meaning that NO₃^- as a more common species might substitute NO₂^- to trigger this new anammox process.

An evolving view on biogeochemical cycling of iron

Biogeochemical cycling of iron is crucial to many environmental processes, such as ocean productivity, carbon storage, greenhouse gas emissions and the fate of nutrients, toxic metals and metalloids. Knowledge of the underlying processes involved in iron cycling has accelerated in recent years along with appreciation of the complex network of biotic and abiotic reactions dictating the speciation, mobility and reactivity of iron in the environment. Recent studies have provided insights into novel processes in the biogeochemical iron cycle such as microbial ammonium oxidation and methane oxidation coupled to Fe(III) reduction. They have also revealed that processes in the biogeochemical iron cycle spatially overlap and may compete with each other, and that oxidation and reduction of iron occur cyclically or simultaneously in many environments. This Review discusses these advances with particular focus on their environmental consequences, including the formation of greenhouse gases and the fate of nutrients and contaminants.

More than redox, biological organic ligands control iron isotope fractionation in the riparian wetland

Although redox reactions are recognized to fractionate iron (Fe) isotopes, the dominant mechanisms controlling the Fe isotope fractionation and notably the role of organic matter (OM) are still debated. Here, we demonstrate how binding to organic ligands governs Fe isotope fractionation beyond that arising from redox reactions. The reductive biodissolution of soil Fe(III) enriched the solution in light Fe isotopes, whereas, with the extended reduction, the preferential binding of heavy Fe isotopes to large biological organic ligands enriched the solution in heavy Fe isotopes. Under oxic conditions, the aggregation/sedimentation of Fe(III) nano-oxides with OM resulted in an initial enrichment of the solution in light Fe isotopes. However, heavy Fe isotopes progressively dominate the solution composition in response to their binding with large biologically-derived organic ligands. Confronted with field data, these results demonstrate that Fe isotope systematics in wetlands are controlled by the OM flux, masking Fe isotope fractionation arising from redox reactions. This work sheds light on an overseen aspect of Fe isotopic fractionation and calls for a reevaluation of the parameters controlling the Fe isotopes fractionation to clarify the interpretation of the Fe isotopic signature.

Electrostimulation enhanced ammonium removal during Fe(III) reduction coupled with anaerobic ammonium oxidation (Feammox) process

Ammonium removal in wastewater treatment plants requires a large number of energy input, such as aeration and the addition of organics. Alternative, more economical technologies for nitrogen removal from wastewater are required. This study comprehensively investigated the feasible of microbial electricity coupled with Fe(III) reduction promoting the anaerobic ammonium removal. It was found that electrostimulation coupled with Fe(III) reduction (bioelectrochemical systems-Fe(III) (BES-Fe(III)) reactor) enhanced the anaerobic ammonium removal by 50.38% and 38.8% compared with the BES reactor and Fe(III) reactor, respectively. The ammonium removal rate reached the highest value of 80.62 ± 0.26 g N m^-3·d^-1 in the Fe(III)-BES reactor comparable to conventional wastewater treatment plants (WWWTPs). The improvement of ammonium removal might be the synergistic effect of BES and Feammox process on reaction process and microorganisms. Firstly, the addition of Fe₂O₃ could improve the electrochemical characteristics by enriching iron-reducing bacterial (FeRB). Secondly, the improved ammonium removal could be due to nitrite generated from Feammox process driving the anodic ammonium oxidation. Additionally, the ammonium removal improvement might be the effect of BES on the Fe²⁺ leaching so as to accelerate the Fe (II)/Fe(III) cycle. In agreement, higher abundance of FeRB and iron-oxidizing bacteria was detected in the Fe(III)-BES reactor. This study provides a lower energy consumption and operational cost technology compared with the conventional partial nitrification/denitrification, which was more than 800 times less than for the conventional wastewater treatment.

Conditions that promote the formation of black bloom in aquatic microcosms and its effects on sediment bacteria related to iron and sulfur cycling

Black bloom occurs frequently in eutrophic waters. We investigated the conditions promoted the formation of black bloom via in-situ measurement in two aquatic microcosms and the effects of black bloom on the bacterial community composition. Although larger changes in dissolved oxygen (DO) were detected in the Hydrilla verticillata-dominated microcosm over the 90-day simulation, black bloom occurred more readily in the phytoplankton-dominated than macrophyte-dominated microcosm under conditions of O₂ depletion and temperature above 30 °C. The sediment bacterial community composition shifted after black bloom; the relative abundance of Thiobacillus and Sideroxydans, which oxidize iron (Fe) and sulfur (S), decreased by 47% and 48%, respectively, in the phytoplankton-dominated microcosm and by 18% and 20% in the macrophyte-dominated microcosm. By contrast, Desulfatiglans increased by 13% and 19%, respectively, after black bloom. Furthermore, inter-taxa correlations remarkably changed according to co-occurrence network analysis. Thirty-six different taxa from the phylum to the genus level were identified as biomarkers of sediments collected before and after the black bloom event. Most of these biomarkers are related to Fe/S cycling in aquatic ecosystems.

Arsenic removal from natural groundwater using 'green rust': Solid phase stability and contaminant fate

Arsenic (As) contamination in groundwater remains a pressing global challenge. In this study, we evaluated the potential of green rust (GR), a redox-active iron phase frequently occurring in anoxic environments, to treat As contamination at a former wood preservation site. We performed long-term batch experiments by exposing synthetic GR sulfate (GR_SO4) to As-free and As-spiked (6 mg L^-1) natural groundwater at both 25 and 4 °C. At 25 °C, GR_SO4 was metastable in As-free groundwater and transformed to GR_CO3, and then fully to magnetite within 120 days; however, GR_SO4 stability increased 7-fold by lowering the temperature to 4 °C, and 8-fold by adding As to the groundwater at 25 °C. Highest GR_SO4 stability was observed when As was added to the groundwater at 4 °C. This stabilizing effect is explained by GR solubility being lowered by adsorbed As and/or lower temperatures, inhibiting partial GR dissolution required for transformation to GR_CO3, and ultimately to magnetite. Despite these mineral transformations, all added As was removed from As-spiked samples within 120 days at 25 °C, while uptake was 2 times slower at 4 °C. Overall, we have successfully documented that GR is an important mineral substrate for As immobilization in anoxic subsurface environments.

Bio-imaging with the helium-ion microscope: A review

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

Impact of Fe(III) (Oxyhydr)oxides Mineralogy on Iron Solubilization and Associated Microbial Communities

Iron-reducing bacteria (IRB) are strongly involved in Fe cycling in surface environments. Transformation of Fe and associated trace elements is strongly linked to the reactivity of various iron minerals. Mechanisms of Fe (oxyhydr)oxides bio-reduction have been mostly elucidated with pure bacterial strains belonging to Geobacter or Shewanella genera, whereas studies involving mixed IRB populations remain scarce. The present study aimed to evaluate the iron reducing rates of IRB enriched consortia originating from complex environmental samples, when grown in presence of Fe (oxyhydr)oxides of different mineralogy. The abundances of Geobacter and Shewanella were assessed in order to acquire knowledge about the abundance of these two genera in relation to the effects of mixed IRB populations on kinetic control of mineralogical Fe (oxyhydr)oxides reductive dissolution. Laboratory experiments were carried out with two freshly synthetized Fe (oxyhydr)oxides presenting contrasting specific surfaces, and two defined Fe-oxides, i.e., goethite and hematite. Three IRB consortia were enriched from environmental samples from a riverbank subjected to cyclic redox oscillations related to flooding periods (Decize, France): an unsaturated surface soil, a flooded surface soil and an aquatic sediment, with a mixture of organic compounds provided as electron donors. The consortia could all reduce iron-nitrilotriacetate acid (Fe(III)-NTA) in 1–2 days. When grown on Fe (oxyhydr)oxides, Fe solubilization rates decreased as follows: fresh Fe (oxyhydr)oxides > goethite > hematite. Based on a bacterial rrs gene fingerprinting approach (CE-SSCP), bacterial community structure in presence of Fe(III)-minerals was similar to those of the site sample communities from which they originated but differed from that of the Fe(III)-NTA enrichments. Shewanella was more abundant than Geobacter in all cultures. Its abundance was higher in presence of the most efficiently reduced Fe (oxyhydr)oxide than with other Fe(III)-minerals. Geobacter as a proportion of the total community was highest in the presence of the least easily solubilized Fe (oxyhydr)oxides. This study highlights the influence of Fe mineralogy on the abundance of Geobacter and Shewanella in relation to Fe bio-reduction kinetics in presence of a complex mixture of electron donors.

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

Microbial extracellular electron transfer and strategies for engineering electroactive microorganisms

Electroactive microorganisms (EAMs) are ubiquitous in nature and have attracted considerable attention as they can be used for energy recovery and environmental remediation via their extracellular electron transfer (EET) capabilities. Although the EET mechanisms of Shewanella and Geobacter have been rigorously investigated and are well characterized, much less is known about the EET mechanisms of other microorganisms. For EAMs, efficient EET is crucial for the sustainable economic development of bioelectrochemical systems (BESs). Currently, the low efficiency of EET remains a key factor in limiting the development of BESs. In this review, we focus on the EET mechanisms of different microorganisms, (i.e., bacteria, fungi, and archaea). In addition, we describe in detail three engineering strategies for improving the EET ability of EAMs: (1) enhancing transmembrane electron transport via cytochrome protein channels; (2) accelerating electron transport via electron shuttle synthesis and transmission; and (3) promoting the microbe-electrode interface reaction via regulating biofilm formation. At the end of this review, we look to the future, with an emphasis on the cross-disciplinary integration of systems biology and synthetic biology to build high-performance EAM systems.

Geochemical and isotopic study of abiotic nitrite reduction coupled to biologically produced Fe(II) oxidation in marine environments

Estuarine sediments are often characterized by abundant iron oxides, organic matter, and anthropogenic nitrogen compounds (e.g., nitrate and nitrite). Anoxic dissimilatory iron reducing bacteria (e.g., Shewanella loihica) are ubiquitous in these environments where they can catalyze the reduction of Fe(III) (oxyhydr)oxides, thereby releasing aqueous Fe(II). The biologically produced Fe(II) can later reduce nitrite to form nitrous oxide. The effect on nitrite reduction by both biologically produced and artificially amended Fe(II) was examined experimentally. Ferrihydrite was reduced by Shewanella loihica in a batch reaction with an anoxic synthetic sea water medium. Some of the Fe(II) released by S. loihica adsorbed onto ferrihydrite, which was involved in the transformation of ferrihydrite to magnetite. In a second set of experiments with identical medium, no microorganism was present, instead, Fe(II) was amended. The amount of solid-bound Fe(II) in the experiments with bioproduced Fe(II) increased the rate of abiotic NO₂^- reduction with respect to that with synthetic Fe(II), yielding half-lives of 0.07 and 0.47 d, respectively. The δ¹⁸O and δ¹⁵N of NO₂^- was measured through time for both the abiotic and innoculated experiments. The ratio of ε¹⁸O/ε¹⁵N was 0.6 for the abiotic experiments and 3.1 when NO₂^- was reduced by S. loihica, thus indicating two different mechanisms for the NO₂^- reduction. Notably, there is a wide range of the ε¹⁸O/ε¹⁵N values in the literature for abiotic and biotic NO₂^- reduction, as such, the use of this ratio to distinguish between reduction mechanisms in natural systems should be taken with caution. Therefore, we suggest an additional constraint to identify the mechanisms (i.e. abiotic/biotic) controlling NO₂^- reduction in natural settings through the correlation of δ¹⁵N-NO₂^- and the aqueous Fe(II) concentration.

How Thermodynamics Illuminates Population Interactions in Microbial Communities

In traditional population models of microbial ecology, there are two central players: producers and consumers (including decomposers that depend on organic carbon). Producers support surface ecosystems by generating adenosine triphosphate (ATP) from sunlight, part of which is used to build new biomass from carbon dioxide. In contrast, the productivity of subsurface ecosystems with a limited supply of sunlight must rely on bacteria and archaea that are able generate ATP solely from chemical or electric energy to fix inorganic carbon. These “light-independent producers” are frequently not included in traditional food webs, even though they are ubiquitous in nature and interact with one another through the utilization of the by-products of others. In this review, we introduce theoretical approaches based on population dynamics that incorporate thermodynamics to highlight characteristic interactions in the microbial community of subsurface ecosystems, which may link community structures and ecosystem expansion under conditions of a limited supply of sunlight. In comparison with light-dependent producers, which compete with one another for light, the use of Gibbs free energy (chemical energy) can lead cooperative interactions among light-independent producers through the effects of the relative quantities of products and reactants on the available chemical energy, which is termed abundant resource premium. The development of a population theory that incorporates thermodynamics offers fundamental ecological insights into subsurface microbial ecosystems, which may be applied to fields of study such as environmental science/engineering, astrobiology, or the microbial ecosystems of the early earth.

Mechanistic insights into iodine enrichment in groundwater during the transformation of iron minerals in aquifer sediments

Long-term intake of groundwater with elevated iodine concentration can cause thyroid dysfunction in humans; however, little is known on the mechanisms controlling the fate of iodine in groundwater systems. In this study, the groundwater and aquifer sediment samples from the Datong basin, a geologic iodine-affected area, were collected to perform the batch incubation experiments to understand the release and enrichment of iodine in groundwater systems. The results showed that the groundwater from the deep confined aquifer had a total iodine concentration of 473 μg/L, higher than that of shallow groundwater, and iodide is the dominant species of iodine. The deep confined aquifer was characterized by the reducing conditions. Meanwhile, a higher ratio of Fe(II) to total Fe was observed in bulk deep aquifer sediments (59%) in comparison with that of shallow sediments (33%). The results of batch incubation experiments showed that during the reductive transformation of Fe minerals in shallow aquifer sediments, iodide concentration in solution was gradually increasing from 24.7 to 101.5 μg/L after 10 days. It suggests that the transformation of Fe minerals in aquifer sediments acts as a diver causing the release of iodine from sediment into groundwater, which was further supported by the features Fe K-edge EXAFS before and after the batch experiments. Moreover, the changes in iodine species from iodate or organic iodine into iodide during the release further promotes the release of sediment iodine, which was supported by the developed geochemical models. The prevalence of reducing condition in deep aquifer favors the enrichment of released iodide. This study provides new insights into the mechanisms of iodide enrichment observed in deep confined aquifer.

Genome reconstruction reveals distinct assemblages of Gallionellaceae in surface and subsurface redox transition zones

Fe-oxidizing bacteria of the family Gallionellaceae are major players in the Fe biogeochemical cycle in freshwater. These bacteria thrive in redox transition zones where they benefit from both high Fe concentrations and microaerobic conditions. We analysed the Gallionellaceae genomic diversity in an artesian hard-rock aquifer where redox transition zones develop (i) in the subsurface, where ancient, reduced groundwater mixes with recent oxygenated groundwater, and (ii) at the surface, where groundwater reaches the open air. A total of 15 new draft genomes of Gallionellaceae representing to 11 candidate genera were recovered from the two redox transition zones. Sulfur oxidation genes were encoded in most genomes while denitrification genes were much less represented. One genus dominated microbial communities belowground and we propose to name it 'Candidatus Houarnoksidobacter'. The two transition zones were populated by completely different assemblages of Gallionellaceae despite the almost constant upward circulation of groundwater between the two zones. The processes leading to redox transition zones, oxygen diffusion at the surface or groundwater mixing in subsurface, appear to be a major driver of the Gallionellaceae diversity.

Ferrihydrite Reduction Increases Arsenic and Uranium Bioavailability in Unsaturated Soil

Redox driven mobilization and plant uptake of contaminants under transiently saturated soil conditions need to be clarified to ensure food and water quality across different irrigation systems. We postulate that solid-phase iron reduction in anoxic microsites present in the rhizosphere of unsaturated soil is a key driver for mobilization and bioavailability of contaminants under nonflooded irrigation. To clarify this, two major crops, corn and soybean differing in iron uptake strategies, were grown in irrigated synthetic soil under semiarid conditions with gravimetric moisture content ∼12.5 ± 2.4%. 2-line ferrihydrite, which was coprecipitated with uranium and arsenic, served as the only iron source in soil. Irrespective of crop type, reduced iron was detected in pore water and postexperiment rhizosphere soil confirming ferrihydrite reduction. These results support the presence of localized anoxic microsites in the otherwise aerobic porous bulk soil causing reduction of ferrihydrite and concomitant increase in plant uptake of comobilized contaminants. Our findings indicate that reactive iron minerals undergo reductive dissolution inside anoxic microsites of primarily unsaturated soil, which may have implications on the mobility of trace element contaminants such as arsenic and uranium in irrigated unsaturated soils, accounting for 55% of the irrigated area in the US.

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L^-1, iron ~ 35-61 mg L^-1 (waters), and ~ 8-293 g kg^-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L^-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

Role of clay-associated humic substances in catalyzing bioreduction of structural Fe(III) in nontronite by Shewanella putrefaciens CN32

Previous studies have shown that humic substances can serve as electron shuttle to catalyze bioreduction of structural Fe(III) in clay minerals, but it is unclear if clay-sorbed humic substances can serve the same function. It is unknown if the electron shuttling function is dependent on electron donor type and if humic substances undergo change as a result. In this study, humic acid (HA) and fulvic acid (FA) were sorbed onto nontronite (NAu-2) surface. Structural Fe(III) in HA- and FA-coated NAu-2 samples was bioreduced by Shewanella putrefaciens CN32 using H₂ and lactate as electron donors. The results showed a contrasting effect of humic substances on bioreduction of structural Fe(III), depending on the electron donor type. With H₂ as electron donor, humic substances had little effect on bioreduction of Fe(III) (the reduction extent: 26.2%, 27.4%, 29.3% for HA-coated, FA-coated, and uncoated NAu-2, respectively). In contrast, these substances significantly enhanced bioreduction of Fe(III) with lactate as electron donor (the reduction extent: 20.2%, 20.7%, 11.5% for HA-coated, FA-coated, and uncoated NAu-2, respectively). This contrasting behavior is likely caused by the difference in reaction free energy and electron transport process between H₂ and lactate. When H₂ served as electron donor, more energy was released than when lactate served as electron donor. In addition, because of different cellular locations of lactate dehydrogenase (inner membrane) and H₂ hydrogenase (the periplasm), electrons generated by H₂ hydrogenase may pass through the electron transport chain more rapidly than those generated from lactate dehydrogenase. Through their functions as electron shuttle and/or carbon source, clay-sorbed HA/FA underwent partial transformation to amino acids and other compounds. The availability of external carbon source played an important role in the amount and type of secondary product generation. These results have important implications for coupled iron and carbon biogeochemical cycles in clay- and humic substance-rich environments.

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms

Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or -oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.

Mineralogical associations with soil carbon in managed wetland soils

Carbon (C)-rich wetland soils are often drained for agriculture due to their capacity to support high net primary productivity. Increased drainage is expected this century to meet the agricultural demands of a growing population. Wetland drainage can result in large soil C losses and the concentration of residual soil minerals such as iron (Fe) and aluminum (Al). In upland soils, reactive Fe and Al minerals can contribute to soil C accumulation through sorption to poorly crystalline minerals and coprecipitation of organo-metal complexes, as well as C loss via anaerobic respiration by Fe-reducing bacteria. The role of these minerals in soil C dynamics is often overlooked in managed wetland soils and may be particularly important in both drained and reflooded systems with elevated mineral concentrations. Reflooding drained soils have been proposed as a means to sequester C for climate change mitigation, yet little is known about how reactive Fe and Al minerals affect C cycling in restored wetlands. We explored the interactions among soil C and reactive Fe and Al minerals in drained and reflooded wetland soils. In reflooded soils, soil C was negatively associated with reactive Fe and reduced Fe(II), a proxy for anaerobic conditions (reactive Fe: R²  = .54-.79; Fe(II): R²  = .59-.89). In drained soils, organo-Al complexes were positively associated with soil C and Fe(II) (Al R²  = .91; Fe(II): R²  = .54-.60). Soil moisture, organo-Al, and reactive Fe explained most of the variation observed in soil C concentrations across all sites (p < .01). Reactive Fe was negatively correlated to soil C concentrations across sites, suggesting these Fe pools may drive additional C losses in drained soils and limit C sequestration with reflooding. In contrast, reactive organo-Al in drained soils facilitates C storage via aggregation and/or formation of anaerobic (micro)sites that protect residual soil C from oxidation and may at least partially offset C losses.

Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes

Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.

Promotion of Microbial Oxidation of Structural Fe(II) in Nontronite by Oxalate and NTA

Iron redox cycling occurs extensively in soils and sediments. Previous research has focused on microbially mediated redox cycling of aqueous Fe. At circumneutral pH, most Fe occurs in solid phase, where Fe and organic ligands interact closely. However, the role of organic ligands in microbial oxidation of solid-phase Fe(II) is not well understood. Here, we incubated reduced nontronite NAu-2 (rNAu-2) with an iron-oxidizing bacterium and in the presence of oxalate and nitrilotriacetic acid. These ligands significantly enhanced the rate and extent of microbial oxidation of structural Fe(II) in rNAu-2. Aqueous and solid-phase analyses, coupled with biogeochemical modeling, revealed a pathway for ligand-enhanced bio-oxidation of solid-phase Fe(II): (1) dissolution of rNAu-2 to form aqueous Fe(II)-ligand complex; (2) bio-oxidation to Fe(III)-ligand complex; (3) rapid reduction of Fe(III)-ligand complex to Fe(II)-ligand complex by structural Fe(II) in rNAu-2. In this process, the Fe(II)-ligand and Fe(III)-ligand complexes effectively serve as electron shuttle to expand the bioavailable pool of solid-phase Fe(II). These results have important implications for a better understanding of the bioavailability and reactivity of solid-phase Fe pool in the environment.

Fe-modified biochar enhances microbial nitrogen removal capability of constructed wetland

To improve the nitrogen removal capability of constructed wetlands, the biochar, produced from bamboo, activated with HCl and coated with Fe (FeCl₃·6H₂O), and then was added as a substrate into the systems. Three horizontal subsurface flow constructed wetlands (HSCWs) was established to treat the low C/N tailwater from the wastewater treatment plant: C-HSCW (quartz sand + soil), B-HSCW (quartz sand + soil + unmodified biochar), and FeB-HSCW (quartz sand + soil + Fe-modified biochar). Under different combinations of hydraulic retention time and nitrogen loading, the FeB-HSCW revealed extremely effective nitrogen removal, compared to the C-HSCW and B-HSCW. The highest removal efficiencies of NO₃^--N (95.30%), TN (86.68%), NH₄⁺-N (86.33%), NO₂^--N (79.35%) and COD (63.36%) were obtained in FeB-HSCW with the hydraulic retention time of 96 h. and low influent nitrogen loading (C/N of 2.5). Nitrogen mass balance analysis showed that microbial processes played the most important role of nitrogen removal in HSCWs and the Fe-modified biochar significantly enhanced the microbial nitrogen removal. A total of 128.40 g nitrogen was removed by microorganisms in FeB-HSCW (average removal rate of 2.52 g N/(m³·d¹)), much higher than that in other two HSCWs. The contributions of microorganisms, substrate storage and plant uptake on the total amount of nitrogen removal in the FeB-HSCW was 92.69%, 2.97% and 4.34%, respectively. Moreover, FeB significantly increased the abundances of genes involved in nitrogen removal. The copy numbers of bacterial 16S rRNA and amx, as well as of genes nirS, nirK, nosZ-I, nosZ-II, and hzsA were 1.3- to 27.8-fold higher in the FeB-HSCW than that in the other two HSCWs. Thus, Fe-modified biochar provides a feasible and effective amendment for constructed wetlands to improve the nitrogen removal, particularly nitrate-N, for low C/N wastewaters by enhancing the microbial nitrogen removal capacity (mainly of the denitrification).

Microbial biomodification of clay minerals

Clay minerals are important reactive centers in the soil system. Their interactions with microorganisms are ubiquitous and wide-ranging, affecting growth and function, interactions with other organisms, including plants, biogeochemical processes and the fate of organic and inorganic pollutants. Clay minerals have a large specific surface area and cation exchange capacity (CEC) per unit mass, and are abundant in many soil systems, especially those of agricultural significance. They can adsorb microbial cells, exudates, and enzymes, organic and inorganic chemical species, nutrients, and contaminants, and stabilize soil organic matter. Bacterial modification of clays appears to be primarily due to biochemical mechanisms, while fungi can exhibit both biochemical and biomechanical mechanisms, the latter aided by their exploratory filamentous growth habit. Such interactions between microorganisms and clays regulate many critical environmental processes, such as soil development and transformation, the formation of soil aggregates, and the global cycling of multiple elements. Applications of biomodified clay minerals are of relevance to the fields of both agricultural management and environmental remediation. This review provides an overview of the interactions between bacteria, fungi and clay minerals, considers some important gaps in current knowledge, and indicates perspectives for future research.

Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes

Arctic lakes emit methane (CH₄) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH₄ oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH₄ mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH₄ concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH₄ was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH₄ cycling in these Siberian Arctic lakes by mitigating the majority of produced CH₄ before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH₄ cycle in lakes, a crucial component of the global CH₄ cycle.

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of de-lignification, with a growing interest in the use of microbes. Here we investigate the physiology and molecular response of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, to lignin under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 accumulates higher biomass and has a shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in late logarithmic phase. Ferrozine assays of the supernatant confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

Oxidation of Fe(II) by Flavins under Anoxic Conditions

Flavin-mediated electron transfer is an important pathway for Fe(III) reduction by dissimilatory iron-reducing bacteria. Although the mechanisms and kinetics of Fe(III) reduction by reduced flavins have been widely studied, the reaction between Fe(II) and oxidized flavins is rarely investigated. Results of this study show that under anoxic conditions, Fe(II) can be oxidized by the oxidized forms of riboflavin (RBF) and flavin mononucleotide (FMN) at pH 7-9. For instance, at pH 9, 73% of 17.8 μM Fe(II) was oxidized by 10 μM RBF within 20 min. Both the rate and extent of oxidation increased with increasing concentrations of oxidized flavins and increasing solution pH. Thermodynamic calculations and kinetic analyses implied that the oxidation of Fe(II) proceeded predominantly via the autodecomposition of Fe²⁺-RBF^- and Fe²⁺-FMN^- complexes, along with minor contributions from direct oxidation of Fe(II) by flavins and flavin radicals. Our findings suggest that the reoxidation of Fe(II) by oxidized flavins may be a rate-controlling factor in microbial Fe(III) reduction via flavin-mediated electron transfer.

Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities

Long-chain fatty acids (LCFA) are common contaminants in municipal and industrial wastewater that can be converted anaerobically to methane. A low hydrogen partial pressure is required for LCFA degradation by anaerobic bacteria, requiring the establishment of syntrophic relationships with hydrogenotrophic methanogens. However, high LCFA loads can inhibit methanogens, hindering biodegradation. Because it has been suggested that anaerobic degradation of these compounds may be enhanced by the presence of alternative electron acceptors, such as iron, we investigated the effect of sub-stoichiometric amounts of Fe(III) on oleate (C18:1 LCFA) degradation by suspended and granular methanogenic sludge. Fe(III) accelerated oleate biodegradation and hydrogenotrophic methanogenesis in the assays with suspended sludge, with H₂-consuming methanogens coexisting with iron-reducing bacteria. On the other hand, acetoclastic methanogenesis was delayed by Fe(III). These effects were less evident with granular sludge, possibly due to its higher initial methanogenic activity relative to suspended sludge. Enrichments with close-to-stoichiometric amounts of Fe(III) resulted in a microbial community mainly composed of Geobacter, Syntrophomonas, and Methanobacterium genera, with relative abundances of 83-89%, 3-6%, and 0.2-10%, respectively. In these enrichments, oleate was biodegraded to acetate and coupled to iron-reduction and methane production, revealing novel microbial interactions between syntrophic LCFA-degrading bacteria, iron-reducing bacteria, and methanogens.

Intrinsic enzyme-like activity of magnetite particles is enhanced by cultivation with Trichoderma guizhouense

Fungal-mineral interactions can produce large amounts of biogenic nano-size (~ 1-100 nm) minerals, yet their influence on fungal physiology and growth remains largely unexplored. Using Trichoderma guizhouense NJAU4742 and magnetite (Mt) as a model fungus and mineral system, we have shown for the first time that biogenic Mt nanoparticles formed during fungal-mineral cultivation exhibit intrinsic peroxidase-like activity. Specifically, the average peroxidase-like activity of Mt nanoparticles after 72 h cultivation was ~ 2.4 times higher than that of the original Mt. Evidence from high resolution X-ray photoelectron spectroscopy analyses indicated that the unique properties of magnetite nanoparticles largely stemmed from their high proportion of surface non-lattice oxygen, through occupying surface oxygen-vacant sites, rather than Fe redox chemistry, which challenges conventional Fenton reaction theories that assume iron to be the sole redox-active centre. Nanoscale secondary ion mass spectrometry with a resolution down to 50 nm demonstrated that a thin (< 1 μm) oxygen-film was present on the surface of fungal hyphae. Furthermore, synchrotron radiation-based micro-FTIR spectra revealed that surface oxygen groups corresponded mainly to organic OH, mineral OH and carbonyl groups. Together, these findings highlight an important, but unrecognized, catalytic activity of mineral nanoparticles produced by fungal-mineral interactions and contribute substantially to our understanding of mineral nanoparticles in natural ecosystems.

His/Met heme ligation in the PioA outer membrane cytochrome enabling light-driven extracellular electron transfer by Rhodopseudomonas palustris TIE-1

A growing number of bacterial species are known to move electrons across their cell envelopes. Naturally this occurs in support of energy conservation and carbon-fixation. For biotechnology it allows electron exchange between bacteria and electrodes in microbial fuel cells and during microbial electrosynthesis. In this context Rhodopseudomonas palustris TIE-1 is of much interest. These bacteria respond to light by taking electrons from their external environment, including electrodes, to drive CO₂-fixation. The PioA cytochrome, that spans the bacterial outer membrane, is essential for this electron transfer and yet little is known about its structure and electron transfer properties. Here we reveal the ten c-type hemes of PioA are redox active across the window +250 to -400 mV versus Standard Hydrogen Electrode and that the hemes with most positive reduction potentials have His/Met and His/H₂O ligation. These chemical and redox properties distinguish PioA from the more widely studied family of MtrA outer membrane decaheme cytochromes with ten His/His ligated hemes. We predict a structure for PioA in which the hemes form a chain spanning the longest dimension of the protein, from Heme 1 to Heme 10. Hemes 2, 3 and 7 are identified as those most likely to have His/Met and/or His/H₂O ligation. Sequence analysis suggests His/Met ligation of Heme 2 and/or 7 is a defining feature of decaheme PioA homologs from over 30 different bacterial genera. His/Met ligation of Heme 3 appears to be less common and primarily associated with PioA homologs from purple non-sulphur bacteria belonging to the alphaproteobacteria class.