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

Molecular mechanisms of iron nanominerals formation in fungal extracellular polymeric substances (EPS) layers during fungus-mineral interactions

Extracellular polymeric substances (EPS), which envelop on fungal hyphae surface, interact strongly with minerals and play a crucial role in the formation of nanoscale minerals during biomineralization in nature environments. However, it remains poorly understood about the molecular mechanisms of nanominerals (i.e., iron nanominerals) formation in fungal EPS halos during fungus-mineral interactions. This process is vital because fungi typically grow attached to various mineral surfaces in nature. According to the changes of thickness of the fungal cell and EPS layers during the Trichoderma guizhouense NJAU 4742 and hematite cultivation experiments, we found that fungal biomineralization could trigger the formation of EPS layers. Fe-dominated nanominerals, aromatic C (283-286.1 eV), alkyl C (287.6-288.3 eV), and carboxylic C (288.4-289.1 eV) were the dominant chemical groups on the EPS layers, as determined by nanoscale secondary ion mass spectrometry (NanoSIMS), high-resolution transmission electron microscope (HRTEM), and carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Further, evidence from Fe K-edge X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) spectra indicated that oxygen vacancy (OV) was formed on the Fe-dominated nanomineral surface during fungus-mineral interactions, which played an important role in catalyzing H2O2 decomposition and HO∗ production. Taken together, the intrinsic peroxidase-like activity by reactive oxygen species (ROS) could modulate the Fe-dominated nanominerals formation in EPS layers to newly form a physical barrier between the cell and the external environments around hyphae, providing novel insights into the effects of ROS-mediated fungal-mineral interactions on fungal nutrient recycling, attenuation of contaminants, and biological control in nature environments.

Hematite enhances microbial autotrophic nitrate removal in carbonate and phosphate-rich environments by increasing Fe(II) activity

Groundwater contamination by nitrates presents significant risks to both human health and the environment. In groundwater characterized as oligotrophic-low in organic carbon, but abundant in carbonate and phosphate-chemolithoautotrophic bacteria, including nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB), play a vital role in denitrification. The chemoautotrophic nitrate reduction is sensitive to environmental factors, including widespread iron oxides like hematite in nature. However, the specific mechanisms of this influence remain unclear. We examined the mechanism of how hematite impacts autotrophic nitrate reduction in a model NRFeOB community known as culture KS. We found that hematite enhances the rate of autotrophic nitrate reduction by promoting Fe(II) oxidation. Mössbauer spectroscopy detected a significant amount of adsorbed Fe(II) when hematite was present, leading to a reduction in dissolved ferrous iron. In conjunction with XRD data, it can be inferred that the formation of vivianite decreased, thereby increasing the Fe(II) activity in the reaction system. Within the culture KS bacterial consortium, hematite fosters the proliferation of autotrophic microorganisms, specifically Gallionellaceae, and amplifies the presence of denitrifying microbes, notably Rhodanobacter. This dual enhancement improves Fe(II) utilization and nitrate reduction capabilities. Our findings highlight intricate interactions between hematite and a model NRFeOB community, offering insights into groundwater nitrate removal mechanisms and the ecological strategies of autotrophic bacteria in mineral-rich environments.

How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review

Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

Community assembly and microbial interactions in an alkaline vanadium tailing pond

Intensive development of vanadium-titanium mines leads to an increasing discharge of vanadium (V) into the environment, imposing potential risks to both environmental system and public health. Microorganisms play a key role in the biogeochemical cycling of V, influencing its transformation and distribution. In addition, the characterization of microbial community patterns serves to assess potential threats imposed by elevated V exposure. However, the impact of V on microbial community remains largely unknown in alkaline V tailing areas with a substantial amounts of V accumulation and nutrient-poor conditions. This study aims to explore the characteristics of microbial community in a wet tailing pond nearby a large-scale V mine. The results reveal V contamination in both water (0.60 mg/L) and sediment tailings (340 mg/kg) in the tailing pond. Microbial community diversity shows distinctive pattern between environmental metrices. Genera with the functional potential of metal reduction\resistance, nitrogen metabolism, and carbon fixation have been identified. In this alkaline V tailing pond, V and pH are major drivers to induce community variation, particularly for functional bacteria. Stochastic processes primarily govern the assemblies of microbial community in the water samples, while deterministic process regulate the community assemblies of sediment tailings. Moreover, the co-occurrence network pattern unveils strong selective pattern for sediment tailings communities, where genera form a complex network structure exhibiting strong competition for limited resource. These findings reveal the patterns of microbial adaptions in wet vanadium tailing ponds, providing insightful guidelines to mitigate the negative impact of V tailing and develop sustainable management for mine-waste reservoir.

Anaerobic ammonium oxidation coupled to iron(III) reduction catalyzed by a lithoautotrophic nitrate-reducing iron(II) oxidizing enrichment culture

The last two decades have seen nitrogen/iron-transforming bacteria at the forefront of new biogeochemical discoveries, such as anaerobic ammonium oxidation coupled to ferric iron reduction (feammox) and lithoautotrophic nitrate-reducing ferrous iron-oxidation (NRFeOx). These emerging findings continue to expand our knowledge of the nitrogen/iron cycle in nature and also highlight the need to re-understand the functional traits of the microorganisms involved. Here, as a proof-of-principle, we report compelling evidence for the capability of an NRFeOx enrichment culture to catalyze the feammox process. Our results demonstrate that the NRFeOx culture predominantly oxidizes NH4+ to nitrogen gas, by reducing both chelated nitrilotriacetic acid (NTA)-Fe(III) and poorly soluble Fe(III)-bearing minerals (γ-FeOOH) at pH 4.0 and 8.0, respectively. In the NRFeOx culture, Fe(II)-oxidizing bacteria of Rhodanobacter and Fe(III)-reducing bacteria of unclassified_Acidobacteriota coexisted. Their relative abundances were dynamically regulated by the supplemented iron sources. Metagenomic analysis revealed that the NRFeOx culture contained a complete set of denitrifying genes along with hao genes for ammonium oxidation. Additionally, numerous genes encoding extracellular electron transport-associated proteins or their homologs were identified, which facilitated the reduction of extracellular iron by this culture. More broadly, this work lightens the unexplored potential of specific microbial groups in driving nitrogen transformation through multiple pathways and highlights the essential role of microbial iron metabolism in the integral biogeochemical nitrogen cycle.

Sulfate availability drives the reductive transformation of schwertmannite by co-cultured iron- and sulfate-reducing bacteria

Schwertmannite (Sch) is a highly bioavailable iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment rich in sulfate (SO42-). Microbial-mediated Sch transformation has been well-studied, however, the understanding of how SO42- availability affects the microbial-mediated Sch transformation and the secondary minerals influence microbes is relatively limited. This study examined the effect of SO42- availability on the iron-reducing bacteria (FeRB) and SO42--reducing bacteria (SRB) consortium-mediated Sch transformation and the resulting secondary minerals in turn on bacteria. Increased SO42- accelerated the onset of microbial SO42- reduction, which significantly accelerated Sch reduction transformation. The extent of intermediate products such as lepidocrocite (22.1 % ~ 76.3 %, all treatments) and goethite (15.3 %, 10 mM SO42-, 5 d) formed by Sch transformation depended on SO42- concentrations. Vivianite, siderite and iron‑sulfur minerals (e.g., FeS and FeS2) were the dominant secondary minerals, in which the relative content of vivianite and siderite decreased while iron‑sulfur minerals increased with increasing SO42- concentration. Correspondingly, the abundance of FeRB and SRB was negatively and positively correlated with SO42- concentration, respectively; 1 mM SO42- promoted the cymA and omcA expression of FeRB, but 10 mM SO42- lowerd the cymA and omcA expression compared to the 1 mM SO42-; the dsr expression of SRB related linearly to the SO42- concentration. These secondary minerals accumulated on the cell surface to form cell encrustations, which limited the growth and gene expression of FeRB and SRB, and even inhibited the activity of SRB in the 10 mM SO42- treatment group. The 10 mM SO42- treatment group with low-intensity ultrasound effectively restored the SRB activity for reducing SO42- by disintegrating the cell-mineral aggregation, further indicating that cell encrustations limited the microbial metabolism. The results highlight the critical role that SO42- availability can play in controlling microbial transformation of mineral, and the influence of secondary minerals on microbial metabolism.

Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils

Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2- accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4+ to the reduced NO3- were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2--to-NH4+ reduction in the cytoplasm. Dechloromonas dominated the NO2--to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2--to-NH4+ during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4+ production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.

Cu(II) and Cd(II) Removal Efficiency of Microbially Redox-Activated Magnetite Nanoparticles

Heavy metal pollutants in the environment are of global concern due to their risk of contaminating drinking water and food supplies. Removal of these metals can be achieved by adsorption to mixed-valent magnetite nanoparticles (MNPs) due to their high surface area, reactivity, and ability for magnetic recovery. The adsorption capacity and overall efficiency of MNPs are influenced by redox state as well as surface charge, the latter of which is directly related to solution pH. However, the influence of microbial redox cycling of iron (Fe) in magnetite alongside the change of pH on the metal adsorption process by MNPs remains an open question. Here we investigated adsorption of Cd2+ and Cu2+ by MNPs at different pH values that were modified by microbial Fe(II) oxidation or Fe(III) reduction. We found that the maximum adsorption capacity increased with pH for Cd2+ from 256 μmol/g Fe at pH 5.0 to 478 μmol/g Fe at pH 7.3 and for Cu2+ from 229 μmol/g Fe at pH 5.0 to 274 μmol/g Fe at pH 5.5. Microbially reduced MNPs exhibited the greatest adsorption for both Cu2+ and Cd2+ (632 μmol/g Fe at pH 7.3 for Cd2+ and 530 μmol/g Fe at pH 5.5 for Cu2+). Magnetite oxidation also enhanced adsorption of Cu2+ but inhibited Cd2+. Our results show that microbial modification of MNPs has an important impact on the (im-)mobilization of aqueous contaminations like Cu2+ and Cd2+ and that a change in stoichiometry of the MNPs can have a greater influence than a change of pH.

Novel insight into the inhibitory effects and mechanisms of Fe(II)-mediated multi-metabolism in anaerobic ammonium oxidation (anammox)

Fe(II) participates in complex Fe-N cycles and effects on the microbial metabolism in the anaerobic ammonium oxidation (anammox) dominated system. In this study, the inhibitory effects and mechanisms of Fe(II)-mediated multi-metabolism in anammox were revealed, and the potential role of Fe(II) in the nitrogen cycle was evaluated. The results showed that the long-term accumulation of high Fe(II) concentrations (70-80 mg/L) led to a hysteretic inhibition of anammox. High Fe(II) concentrations induced the generation of high levels of intracellular ·O2-, whereas the antioxidant capacity was insufficient to eliminate the excess ·O2-, thus causing ferroptosis to anammox cells. In addition, Fe(II) was oxidized via nitrate-dependent anaerobic ferrous-oxidation (NAFO) process, and mineralized to coquimbite and phosphosiderite. They formed crusts on the surface of the sludge, leading to mass transfer obstruction. The results of the microbial analysis showed that the addition of appropriate Fe(II) increased the abundance of Candidatus Kuenenia, and served as a potential electron donor to enrich Denitratisoma, promoting anammox and NAFO coupled with nitrogen removal, while high Fe(II) concentrations reduced the enrichment level. In this study, the understanding of Fe(II)-mediated multi-metabolism in the nitrogen cycle was deepened, providing the basis for the development of Fe(II)-based anammox technologies.

Goethite Formed in the Periplasmic Space of Pseudomonas sp. JM-7 during Fe Cycling Enhances Its Denitrification in Water

Denitrification-driven Fe(II) oxidation is an important microbial metabolism that connects iron and nitrogen cycling in the environment. The formation of Fe(III) minerals in the periplasmic space has a significant effect on microbial metabolism and electron transfer, but direct evidence of iron ions entering the periplasm and resulting in periplasmic mineral precipitation and electron conduction properties has yet to be conclusively determined. Here, we investigated the pathways and amounts of iron, with different valence states and morphologies, entering the periplasmic space of the denitrifier Pseudomonas sp. JM-7 (P. JM-7), and the possible effects on the electron transfer and the denitrifying ability. When consistently provided with Fe(II) ions (from siderite (FeCO3)), the dissolved Fe(II) ions entered the periplasmic space and were oxidized to Fe(III), leading to the formation of a 25 nm thick crystalline goethite crust, which functioned as a semiconductor, accelerating the transfer of electrons from the intracellular to the extracellular matrix. This consequently doubled the denitrification rate and increased the electron transport capacity by 4-30 times (0.015-0.04 μA). However, as the Fe(II) concentration further increased to above 4 mM, the Fe(II) ions tended to preferentially nucleate, oxidize, and crystallize on the outer surface of P. JM-7, leading to the formation of a densely crystallized goethite layer, which significantly slowed down the metabolism of P. JM-7. In contrast to the Fe(II) conditions, regardless of the initial concentration of Fe(III), it was challenging for Fe(III) ions to form goethite in the periplasmic space. This work has shed light on the likely effects of iron on environmental microorganisms, improved our understanding of globally significant iron and nitrogen geochemical cycles in water, and expanded our ability to study and control these important processes.

Filtration columns containing waste iron shavings, loofah, and plastic shavings for further removal of nitrate and phosphate from wastewater effluent

A novel pilot-scale advanced treatment system combining waste products as fillers is proposed and established to enhance the removal of nitrate (NO₃^--N) and phosphate (PO₄^3--P) from secondary treated effluent. The system consists of four modular filter columns, one containing iron shavings (R1), two containing loofahs (R2 and R3), and one containing plastic shavings (R4). The monthly average concentration of total nitrogen (TN) and total phosphorus (TP) decreased from 8.87 to 2.52 mg/L and 0.607 to 0.299 mg/L, respectively. Micro-electrolysis of iron shavings produces Fe²⁺ and Fe³⁺ to remove PO₄^3--P, while oxygen (O₂) consumption creates anoxic conditions for subsequent denitrification. Gallionellaceae, iron-autotrophic Microorganisms, enriched the surface of iron shavings. The loofah served as a carbon source to remove NO₃^--N, and its porous mesh structure facilitated the attachment of biofilm. The plastic shavings intercepted suspended solids and degraded excess carbon sources. This system can be scaled up and installed at wastewater plants to improve the water quality of effluent cost-effectively.

Selective pressure of PFOA on microbial community: Enrichment of denitrifiers harboring ARGs and the transfer of ferric-electrons

Perfluorooctanoic acid (PFOA), a class of permanent organic pollutants, is frequently detected in surface and ground water, with the latter made up primarily of porous media (such as soils, sediments, and aquifers) that harbor microbial communities. Therefore, we investigated the effects of PFOA on water ecosystems and found that, under stimulation by 2.4 μM PFOA, denitrifiers were significantly enriched due to their hosting antibiotic resistant genes (ARGs), which were 1.45 times more abundant than the control. Furthermore, denitrifying metabolism was enhanced by Fe(II) electron donation. Specifically, 2.4 μM PFOA significantly enhanced the removal of total inorganic nitrogen by 178.6%. The microbial community became predominated by denitrifying bacteria (67.8% abundance). Notably, the nitrate-reduction ferrous-oxidizing (NRFO) bacteria Dechloromonas, Acidovorax, Bradyrhizorium, etc. were significantly enriched. The selective pressures of PFOA driving the enrichment of denitrifiers were twofold. First, the toxic PFOA induced denitrifying bacteria to produce ARGs, mainly including the efflux (occupying 55.4%) and antibiotic inactivation (occupying 41.2%) types, which improved microbial tolerance to PFOA. The risk of horizontal ARGs transmission was elevated as the overall number of horizontally transmissible ARGs increased by 47.1%. Second, Fe(II) electrons were transported via the porin-cytochrome c extracellular electrons transfer system (EET), promoting the expression of nitrate reductases, which in turn further enhanced denitrification. In summary, PFOA regulated the microbial community structure and influenced microbial TN removal functions and increased the contribution of ARGs by the denitrifier hosts, but the PFOA-induced production of ARGs may pose a serious ecological threat that needs to be comprehensively investigated.

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.

Metabolic Performance and Fate of Electrons during Nitrate-Reducing Fe(II) Oxidation by the Autotrophic Enrichment Culture KS Grown at Different Initial Fe/N Ratios

Autotrophic nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms fix CO2 and oxidize Fe(II) coupled to denitrification, influencing carbon, iron, and nitrogen cycles in pH-neutral, anoxic environments. However, the distribution of electrons from Fe(II) oxidation to either biomass production (CO2 fixation) or energy generation (nitrate reduction) in autotrophic NRFeOx microorganisms has not been quantified. We therefore cultivated the autotrophic NRFeOx culture KS at different initial Fe/N ratios, followed geochemical parameters, identified minerals, analyzed N isotopes, and applied numerical modeling. We found that at all initial Fe/N ratios, the ratios of Fe(II)oxidized to nitratereduced were slightly higher (5.11 to 5.94 at Fe/N ratios of 10:1 and 10:0.5) or lower (4.27 to 4.59 at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1) than the theoretical ratio for 100% Fe(II) oxidation being coupled to nitrate reduction (5:1). The main N denitrification product was N2O (71.88 to 96.29% at Fe/15N ratios of 10:4 and 5:1; 43.13 to 66.26% at an Fe/15N ratio of 10:1), implying that denitrification during NRFeOx was incomplete in culture KS. Based on the reaction model, on average 12% of electrons from Fe(II) oxidation were used for CO2 fixation while 88% of electrons were used for reduction of NO3- to N2O at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1. With 10 mM Fe(II) (and 4, 2, 1, or 0.5 mM nitrate), most cells were closely associated with and partially encrusted by the Fe(III) (oxyhydr)oxide minerals, whereas at 5 mM Fe(II), most cells were free of cell surface mineral precipitates. The genus Gallionella (>80%) dominated culture KS regardless of the initial Fe/N ratios. Our results showed that Fe/N ratios play a key role in regulating N2O emissions, for distributing electrons between nitrate reduction and CO2 fixation, and for the degree of cell-mineral interactions in the autotrophic NRFeOx culture KS. IMPORTANCE Autotrophic NRFeOx microorganisms that oxidize Fe(II), reduce nitrate, and produce biomass play a key role in carbon, iron, and nitrogen cycles in pH-neutral, anoxic environments. Electrons from Fe(II) oxidation are used for the reduction of both carbon dioxide and nitrate. However, the question is how many electrons go into biomass production versus energy generation during autotrophic growth. Here, we demonstrated that in the autotrophic NRFeOx culture KS cultivated at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1, ca. 12% of electrons went into biomass formation, while 88% of electrons were used for reduction of NO3- to N2O. Isotope analysis also showed that denitrification during NRFeOx was incomplete in culture KS and the main N denitrification product was N2O. Therefore, most electrons stemming from Fe(II) oxidation seemed to be used for N2O formation in culture KS. This is environmentally important for the greenhouse gas budget.

New insights on simultaneous nitrate and phosphorus removal in pyrite-involved mixotrophic denitrification biofilter for a long-term operation: Performance change and its underlying mechanism

Simultaneous nitrate and phosphorus removal can be completed by pyrite- and influent organics-involved mixotrophic denitrification and chemical phosphorus removal via iron precipitation. However, so far, how their removal performances change with iron precipitation accumulation remains unclear. In this study, the differences in nitrate and phosphorus removal from municipal tailwater between volcanic and pyrite supported biofilters (V-BF, P-BF) for a long-term operation were investigated, as well as the underlying mechanism for these differences. The nitrate removal efficiencies (NREs) in P-BF were greater than those in V-BF due to the synergistic effect of influent organic and pyrite, as evidenced by comparable TOC consumption and Fe²⁺/SO₄^2- production. The NREs in P-BF were gradually lower than in V-BF as a result of bacterial cell-iron encrustation observed in TEM images, which would deteriorate microbial activity. However, the phosphorus removal efficiencies (PREs) in P-BF remained consistently higher than in V-BF, resulting from chemical phosphorus removal which was confirmed that P, Fe and O elements dominated on the pyrite surface after use by SEM-EDS. The dominant denitrifying bacteria differed significantly, autotrophic and heterotrophic denitrifying microorganisms coexisted in P-BF. The relative abundances of the narG coding gene in P-BF were higher than that in V-BF, which was consistent with the total relative abundances of identified denitrifying bacteria. Besides, the mechanism of simultaneous nitrogen and phosphorus removal in the pyrite-involved mixotrophic denitrification process has been deduced. This work has significant implications for the practical application of a pyrite-involved mixotrophic denitrification process for low C/N wastewater treatment.

Promotion of nitrogen removal in a zero-valent iron-mediated nitrogen removal system operated in co-substrate mode

In this study, the performance and mechanism of nitrogen removal were investigated in a zero-valent iron-mediated nitrogen removal system operated in co-substrate mode with sodium acetate as the organic carbon source. The results showed that the additional organic matter had the capacity to promote NH4+-N and total inorganic nitrogen (TIN) removal with efficiencies of 91.09% and 84.10%, and increases of 60.06% and 75.32% compared with the control group, respectively. The organic matter also stimulated the production of extracellular polymer substances that reduced the passivation and toxicity of iron to microorganisms. The ammonia oxidation activity was 2.5 times higher than that in the control group, and the anammonia oxidation activity and denitrification activity were substantially higher than in the control group with TIN removal efficiencies of 1.02 and 1.19 mgN/(gVSS·d), respectively. In addition, the organic matter increased the enrichment of the heterotrophic denitrification bacterium Diaphorobacter and facultative iron salt-based bacterium Dechloromonas.

Bacterial community structure and metabolic activity of drinking water pipelines in buildings: A new perspective on dual effects of hydrodynamic stagnation and algal organic matter invasion

Eutrophication and algal blooms have become global issues. The drinking water treatment process suffers from pollution by algal organic matter (AOM) through cell lysis during the algal blooms. Nevertheless, it remains unclear how AOM invasion affects water quality and microbial communities in drinking water, particularly in the stagnant settings. In this study, the addition of AOM caused the residual chlorine to rapidly degrade and below the limit of 0.05 mg/L, while the NO₂^--N concentration ranged from 0.11 to 3.71 mg/L. Additionally, total bacterial counts increased and subsequently decreased. The results of Biolog demonstrated that the AOM significantly improved the utilization capacity of carbon sources and changed the preference for carbon sources. Full-length 16S rRNA gene sequencing and network modeling revealed a considerable reduction in the abundance of Proteobacteria, whereas that of Bacteroidetes increased significantly under the influence of AOM. Furthermore, the species abundance distributions of the Microcystis group and Scenedesmus group was most consistent with the Mandelbrot model. According to redundancy analysis and structural equation modeling, the bacterial community structure of the control group was most positively regulated by the free residual chlorine concentrations, whereas the Microcystis group and Scenedesmus group were positively correlated with the total organic carbon (TOC) concentration. Overall, these findings provide a scientific foundation for the evolution of drinking water quality under algae bloom pollution.

Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation

Natural-abundance measurements of nitrate and nitrite (NO_x) isotope ratios (δ¹⁵N and δ¹⁸O) can be a valuable tool to study the biogeochemical fate of NO_x species in the environment. A prerequisite for using NO_x isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (¹⁵ε, ¹⁸ε) associated with the biotic and abiotic NO_x transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NO_x reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO₃^–) and nitrite (NO₂^–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that ¹⁵ε and ¹⁸ε values obtained for heterotrophic (¹⁵ε-NO₃^–: 17.6 ± 2.8‰, ¹⁸ε-NO₃^–:18.1 ± 2.5‰; ¹⁵ε-NO₂^–: 14.4 ± 3.2‰) vs. mixotrophic (¹⁵ε-NO₃^–: 20.2 ± 1.4‰, ¹⁸ε-NO₃^–: 19.5 ± 1.5‰; ¹⁵ε-NO₂^–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NO_x reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (¹⁵ε-NO₂^–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NO_x reduction. The similar isotope effects detected during mixotrophic and heterotrophic NO_x reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NO_x reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.

Underestimation about the Contribution of Nitrate Reducers to Iron Cycling Indicated by Enterobacter Strain

Nitrate-reducing iron(II) oxidation (NRFO) has been intensively reported in various bacteria. Iron(II) oxidation is found to be involved in both enzymatic and chemical reactions in nitrate-reducing Fe(II)-oxidizing microorganisms (NRFOMs). However, little is known about the relative contribution of biotic and abiotic reactions to iron(II) oxidation for the common nitrate reducers during the NRFO process. In this study, the typical nitrate reducers, four Enterobacter strains E. hormaechei, E. tabaci, E. mori and E. asburiae, were utilized as the model microorganisms. The comparison of the kinetics of nitrate, iron(II) and nitrite and N₂O production in setups with and without iron(II) indicates a mixture of enzymatic and abiotic oxidation of iron(II) in all four Enterobacter strains. It was estimated that 22−29% of total oxidized iron(II) was coupled to microbial nitrate reduction by E. hormaechei, E. tabaci, E. mori, and E. asburiae. Enterobacter strains displayed an metabolic inactivity with heavy iron(III) encrustation on the cell surface in the NRFOmedium during days of incubation. Moreover, both respiratory and periplasmic nitrate-reducing genes are encoded by genomes of Enterobacter strains, suggesting that cell encrustation may occur with periplasmic iron(III) oxide precipitation as well as the surface iron(II) mineral coating for nitrate reducers. Overall, this study clarified the potential role of nitrate reducers in the biochemical cycling of iron under anoxic conditions, in turn, re-shaping their activity during denitrification because of cell encrustation with iron(III) minerals.

Soil indigenous microorganisms alleviate soluble vanadium release from industrial dusts

Vanadium-bearing dusts from industrial processes release abundant toxic vanadium, posing imminent ecological and human health concerns. Although the precipitation of these dusts has been recognized as the main source of soil vanadium pollution, little is known regarding the interrelationships between industrial dusts and soil inherent compositions. In this study, the interactions between dusts from vanadium smelting and soil indigenous microorganisms were investigated. Soluble vanadium (V) [V(V)] released from industrial dusts was reduced by 41.5 ± 0.39% with soil addition, compared to water leaching. Reducible fraction accounted for the highest proportion (55.1 ± 1.73%) of vanadium speciation in the resultant soils, while residual vanadium fraction increased to 83.7 ± 3.22% in the leached dusts. Functional genera (e.g., Aliihoeflea, Actinotalea) that transformed V(V) to insoluble vanadium (IV) alleviated dissolved vanadium release. Nitrate/nitrite reduction and glutathione metabolisms contributed to V(V) immobilization primarily. Structural equation model analysis indicated that V(V) reducers had significant negative impacts on soluble V(V) in the leachate. This first-attempt study highlights the importance of soil microorganisms in immobilizing vanadium from industrial dusts, which is helpful to develop novel strategies to reduce their environmental risks associated to vanadium smelting process.

Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes

Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0.67 g/L to 346 g/L). MPN results showed that the abundance of NRFeOx microorganisms significantly (P < 0.05) decreased with increasing lake salinity, from 7.55 × 10³ to 8.09 cells/g dry sediment. The community composition of the NRFeOx enrichment cultures obtained from the MPNs differed distinctly among the five lakes and clustered with lake salinity. Two stable enrichment cultures, named FeN-EHL and FeN-CKL, were obtained from microcosm incubations of sediment from freshwater Lake Erhai and hypersaline Lake Chaka. The culture FeN-EHL was dominated by genus Gallionella (68.4%), while the culture FeN-CKL was dominated by genus Marinobacter (71.2%), with the former growing autotrophically and the latter requiring an additional organic substrate (acetate) and Fe(II) oxidation, caused to a large extent by chemodenitrification [reaction of nitrite with Fe(II)]. Short-range ordered Fe(III) (oxyhydr)oxides were the product of Fe(II) oxidation, and the cells were partially attached to or encrusted by the formed iron minerals in both cultures. In summary, different types of interactions between Fe(II) and nitrate-reducing bacteria may exist in freshwater and hypersaline lakes, i.e., autotrophic NRFeOx and chemodenitrification in freshwater and hypersaline environments, respectively. IMPORTANCE NRFeOx microorganisms are globally distributed in various types of environments and play a vital role in iron transformation and nitrate and heavy metal removal. However, most known NRFeOx microorganisms were isolated from freshwater and marine environments, while their identity and activity under hypersaline conditions remain unknown. Here, we demonstrated that salinity may affect the abundance, identity, and nutrition modes of NRFeOx microorganisms. Autotrophy was only detectable in a freshwater lake but not in the saline lake investigated. We enriched a mixotrophic culture capable of nitrate-reducing Fe(II) oxidation from hypersaline lake sediments. However, Fe(II) oxidation was probably caused by abiotic nitrite reduction (chemodenitrification) rather than by a biologically mediated process. Consequently, our study suggests that in hypersaline environments, Fe(II) oxidation is largely caused by chemodentrification initiated by nitrite formation by chemoheterotrophic bacteria, and additional experiments are needed to demonstrate whether or to what extent Fe(II) is enzymatically oxidized.

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.

Reduction of Chlorinated Ethenes by Ag- and Cu-Amended Green Rust

Chlorinated ethenes have been used extensively as solvents, degreasers, and dry-cleaning agents in a range of commercial and industrial applications. This has created a legacy of contaminated soils and groundwater, particularly with respect to perchloroethylene (PCE; a.k.a. tetrachloroethene—C2Cl4), and trichloroethylene (TCE; a.k.a. trichloroethene—C2HCl3), prompting the development of a wide array of treatment technologies for remediation of chlorinated ethene-contaminated environments. Green rusts are highly redox-active layered Fe(II)-Fe(III) hydroxides that have been shown to be facile reductants for a wide range of organic and inorganic pollutants. The reduction of chlorinated ethenes [vinyl chloride (VC); 1,1-dichloroethene(11DCE), cis-1,2-dichloroethene (c12DCE), trans-1,2-dichloroethene (t12DCE), TCE, and PCE] was examined in aqueous suspensions of green rust, alone as well as with the addition of Ag(I) (AgGR) or Cu(II) (CuGR). Green rust alone was ineffective as a reductant for the reductive dechlorination for all of the chlorinated ethenes. Near-complete removal of PCE was observed in the presence of AgGR, but all other chlorinated ethenes were essentially non-reactive. Partial removal of chlorinated ethenes was observed in the presence of CuGR, particularly 11DCE (34%), t12DCE (51%), and VC (66%). Significant differences were observed in the product distributions of chlorinated ethene reduction by AgGR and CuGR. The effectiveness of Ag(I)- and Cu(II)-amended green rusts for removal of chlorinated ethenes may be improved under different conditions (e.g., pH and interlayer anion) and warrants further investigation.

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.

Impact of Periodic Polarization on Groundwater Denitrification in Bioelectrochemical Systems

Nitrate contamination is a common problem in groundwater around the world. Nitrate can be cathodically reduced in bioelectrochemical systems using autotrophic denitrifiers with low energy investment and without chemical addition. Successful denitrification was demonstrated in previous studies in both microbial fuel cells and microbial electrolysis cells (MECs) with continuous current flow, whereas the impact of intermittent current supply (e.g., in a fluidized-bed system) on denitrification and particularly the electron-storing capacity of the denitrifying electroactive biofilms (EABs) on the cathodes have not been studied in depth. In this study, two continuously fed MECs were operated in parallel under continuous and periodic polarization modes over 280 days, respectively. Under continuous polarization, the maximum denitrification rate reached 233 g NO₃^--N/m³/d with 98% nitrate removal (0.6 mg NO₃^--N/L in the effluent) with negligible intermediate production, while under a 30 s open-circuit/30 s polarization mode, 86% of nitrate was removed at a maximum rate of 205 g NO₃^--N/m³/d (4.5 mg NO₃^--N/L in the effluent) with higher N₂O production (6.6-9.3 mg N/L in the effluent). Conversely, periodic polarization could be an interesting approach in other bioelectrochemical processes if the generation of chemical intermediates (partially reduced or oxidized) should be favored. Similar microbial communities dominated byGallionellaceaewere found in both MECs; however, swapping the polarization modes and the electrochemical analyses suggested that the periodically polarized EABs probably developed a higher ability for electron storage and transfer, which supported the direct electron transfer pathway in discontinuous operation or fluidized biocathodes.

The role of available phosphorous in vanadate decontamination by soil indigenous microbial consortia

Indigenous microbial consortia are closely associated with soil inherent components including nutrients and minerals. Although indigenous microbial consortia present great prospects for bioremediation of vanadate [V(V)] contaminated soil, influences of some key components, such as available phosphorus (AP), on V(V) biodetoxification are poorly understood. In this study, surface soils sampled from five representative vanadium smelter sites were employed as inocula without pretreatment. V(V) removal efficiency ranged from 81.7 ± 1.4% to 99.5 ± 0.2% in batch experiment, and the maximum V(V) removal rates were positively correlated with AP contents. Long-term V(V) removal was achieved under fluctuant hydrodynamic and hydrochemical conditions in column experiment. Geobacter and Bacillus, which were found in both original soils and bioreactors, catalytically reduced V(V) to insoluble tetravalent vanadium. Phosphate-solubilizing bacterium affiliated to Gemmatimonadaceae were also identified abundantly. Microbial functional characterization indicated the enrichment of phosphate ABC transporter, which could accelerate V(V) transfer into intercellular space for efficient reduction due to the structural similarity of V(V) and phosphate. This study reveals the critical role of AP in microbial V(V) decontamination and provides promising strategy for in situ bioremediation of V(V) polluted soil.

Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum

Photoferrotrophy allows anoxygenic phototrophs to use reduced iron as an electron donor for primary productivity. Recent work shows that freshwater photoferrotrophs can use electrons from solid-phase conductive substances via phototrophic extracellular electron uptake (pEEU), and the two processes share the underlying electron uptake mechanism. However, the ability of marine phototrophs to perform photoferrotrophy and pEEU, and the contribution of these processes to primary productivity is largely unknown. To fill this knowledge gap, we isolated 15 new strains of the marine anoxygenic phototroph Rhodovulum sulfidophilum on electron donors such as acetate and thiosulfate. We observed that all of the R. sulfidophilum strains isolated can perform photoferrotrophy. We chose strain AB26 as a representative strain to study further, and find that it can also perform pEEU from poised electrodes. We show that during pEEU, AB26 transfers electrons to the photosynthetic electron transport chain. Furthermore, systems biology-guided mutant analysis shows that R. sulfidophilum AB26 uses a previously unknown diheme cytochrome c protein, which we call EeuP, for pEEU but not photoferrotrophy. Homologs of EeuP occur in a range of widely distributed marine microbes. Overall, these results suggest that photoferrotrophy and pEEU contribute to the biogeochemical cycling of iron and carbon in marine ecosystems.

Inhibition effects of long-term calcium-magnesia phosphate fertilizer application on Cd uptake in rice: Regulation of the iron-nitrogen coupling cycle driven by the soil microbial community

Cadmium (Cd) pollution in paddy soil seriously endangers food safety production. To investigate the effects and microbiological mechanisms of calcium-magnesium-phosphate (CMP) fertilizer application on Cd reduction in rice, field experiments were conducted in Cd-contaminated paddy soil. Compared with conventional compound fertilizer, CMP fertilizer treatments inhibited Cd uptake through plant roots, significantly decreasing Cd content in rice grains from 0.340 to 0.062 mg/kg. Soil pH and total Ca, Mg and P contents increased after CMP fertilizer application, resulting in a further decrease in soil available Cd content from 0.246 to 0.181 mg/kg. Specific extraction analysis recorded a decrease in both available Fe content and the ratio of nitrate to ammonium nitrogen, indicating that the soil Fe-N cycle was affected by the addition of CMP fertilizer. This finding was also recorded using soil bacterial community sequencing, with CMP fertilizer promoting the progress of nitrate-dependent Fe-oxidation driven by Thiobacillus (1.60-2.83%) and subsequent dissimilatory nitrate reduction to ammonium (DNRA) driven by Ignavibacteriae (1.01-1.92%); Fe-reduction driven by Anaeromyxobacter (3.09-2.23%) was also inhibited. Our results indicate that CMP fertilizer application regulates the Fe-N coupling cycle driven by the soil microbial community to benefit remediation of Cd contaminated paddy soil.

Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer, and as such, there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic cosubstrates for growth, within 7 to 11 days, 0.3 to 0.5 mM nitrate was reduced and 1.3 to 2 mM iron(II) was oxidized, leading to a stoichiometric NO₃^-/Fe(II) ratio of 0.2, with N₂ and N₂O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals, but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, and microaerophilic iron(II) oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically affected aquifers. IMPORTANCE Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment, and as such, there are no model cultures available to study the rate-limiting factors of this potentially important process. Here, we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II) oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N₂O and N₂ formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.

Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS

Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.

Fe(II) Redox Chemistry in the Environment

Iron (Fe) is the fourth most abundant element in the earth's crust and plays important roles in both biological and chemical processes. The redox reactivity of various Fe(II) forms has gained increasing attention over recent decades in the areas of (bio) geochemistry, environmental chemistry and engineering, and material sciences. The goal of this paper is to review these recent advances and the current state of knowledge of Fe(II) redox chemistry in the environment. Specifically, this comprehensive review focuses on the redox reactivity of four types of Fe(II) species including aqueous Fe(II), Fe(II) complexed with ligands, minerals bearing structural Fe(II), and sorbed Fe(II) on mineral oxide surfaces. The formation pathways, factors governing the reactivity, insights into potential mechanisms, reactivity comparison, and characterization techniques are discussed with reference to the most recent breakthroughs in this field where possible. We also cover the roles of these Fe(II) species in environmental applications of zerovalent iron, microbial processes, biogeochemical cycling of carbon and nutrients, and their abiotic oxidation related processes in natural and engineered systems.

Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept

Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm³ densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.

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.

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.

Phosphorus Recovery from Wastewater Prominently through a Fe(II)-P Oxidizing Pathway in the Autotrophic Iron-Dependent Denitrification Process

Phosphorus (P) recovery from wastewater can be completed by iron-involved autotrophic denitrification via forming Fe(III)-P precipitates and/or adsorbing P onto Fe(III) oxyhydroxides. However, so far, most studies focused on the final P-containing products, while the P-capturing pathways in such a process remain unclear. In this work, autotrophic iron-dependent denitrification (AIDD) was used as a typical anoxic iron-involved P-capturing biosystem to investigate the main P recovery pathways. The AIDD biosystem showed a relatively stable capability of capturing P coupled with nitrate reduction. Direct formation of amorphous Fe(II)-P precipitates after the phosphate was fed, followed by microbially driven oxidation into Fe(III)-P minerals, was found to be the primary pathway for the P capture. In addition, adsorption of phosphate onto the formed iron oxyhydroxides also contributed to the P recovery. This work provides better understanding about recovering P in AIDD and iron-involved denitrification and highlights the important roles of iron oxidizers in the iron-related biological wastewater treatment processes.

Controls of H2S, Fe2 +, and Mn2 + on Microbial NO3 --Reducing Processes in Sediments of an Eutrophic Lake

Understanding the biogeochemical controls on the partitioning between nitrogen (N) removal through denitrification and anaerobic ammonium oxidation (anammox), and N recycling via dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) is crucial for constraining lacustrine N budgets. Besides organic carbon, inorganic compounds may serve as electron donors for NO3 - reduction, yet the significance of lithotrophic NO3 - reduction in the environment is still poorly understood. Conducting incubation experiments with additions of 15N-labeled compounds and reduced inorganic substrates (H2S, Fe2+, Mn2+), we assessed the role of alternative electron donors in regulating the partitioning between the different NO3 --reducing processes in ferruginous surface sediments of Lake Lugano, Switzerland. In sediment slurry incubations without added inorganic substrates, denitrification and DNRA were the dominant NO3 --reducing pathways, with DNRA contributing between 31 and 46% to the total NO3 - reduction. The contribution of anammox was less than 1%. Denitrification rates were stimulated by low to moderate additions of ferrous iron (Fe2+ ≤ 258 μM) but almost completely suppressed at higher levels (≥1300 μM). Conversely, DNRA was stimulated only at higher Fe2+ concentrations. Dissolved sulfide (H2S, i.e., sum of H2S, HS- and S2-) concentrations up to ∼80 μM, strongly stimulated denitrification, but did not affect DNRA significantly. At higher H2S levels (≥125 μM), both processes were inhibited. We were unable to find clear evidence for Mn2+-supported lithotrophic NO3 - reduction. However, at high concentrations (∼500 μM), Mn2+ additions inhibited NO3 - reduction, while it did not affect the balance between the two NO3 - reduction pathways. Our results provide experimental evidence for chemolithotrophic denitrification or DNRA with Fe2+ and H2S in the Lake Lugano sediments, and demonstrate that all tested potential electron donors, despite the beneficial effect at low concentrations of some of them, can inhibit NO3 - reduction at high concentration levels. Our findings thus imply that the concentration of inorganic electron donors in lake sediments can act as an important regulator of both benthic denitrification and DNRA rates, and suggest that they can exert an important control on the relative partitioning between microbial N removal and N retention in lakes.

Natural sphalerite nanoparticles can accelerate horizontal transfer of plasmid-mediated antibiotic-resistance genes

Minerals and microorganisms are integral parts of natural environments, and they inevitably interact. Antibiotic-resistance genes (ARGs) significantly threaten modern healthcare. However, the effects of natural minerals on ARG propagation in aquatic systems are not fully understood. The present work studied the effects of natural sphalerite (NS) nanoparticles on the horizontal transfer of ARGs from Escherichia coli DH5α (CTX) (donor) to E. coli C600 (Sm) (recipient), and from E. coli DH5α (MCR) (donor) to E. coli C600 (Sm), and their underlying mechanisms. NS particles (0.5-50 mg L^-1) induced an NS-concentration-dependent increase in conjugative transfer frequency. The underlying mechanisms associated with the facilitated ARG transfer included the production of intracellular reactive oxygen species, the SOS response, changes in bacterial cell morphology, and alteration of mRNA levels of bacterial cell membrane protein-related genes and genes associated with conjugative ARG transfer. The information herein offers new mechanistic understanding of risks of bacterial resistance resulting from NS.

Exclusive microbially driven autotrophic iron-dependent denitrification in a reactor inoculated with activated sludge

Autotrophic iron-dependent denitrification (AIDD) is arising as a promising process for nitrogen removal from wastewater with a low carbon to nitrogen ratio. However, there is still a debate about the existence of such a process in activated sludge systems. This work provides evidence and elucidated the feasibility of autotrophic Fe(II)-oxidizing nitrate-reducing culture for nitrogen removal by long-term reactor operation, batch experimental verification, unstructured kinetic modeling and microbial community analyses. A relatively stable nitrate removal rate was achieved coupled with the oxidation of ferrous ions in 3-month operation of reactor. The kinetic modeling suggests that the iron oxidation was a growth-associated process in AIDD. Utilization of extracellular polymeric substances (and/or soluble microbial products) as electron donor for denitrification by heterotrophic denitrifiers was not mainly responsible for nitrogen removal in the reactor. After long-term operation of the reactor with activated sludge as inoculum, the enrichment culture KS-like consortium, dominated by Fe(II) oxidizer, Gallionellaceae, was successfully acclimated for autotrophic Fe(II)-oxidizing nitrate reduction. This work extents our understanding about the existence of such an autotrophic Fe(II)-oxidizing nitrate-reducing culture in both natural and engineered systems, and opens a door for its potential application in wastewater treatment.

Anaerobic Bacterial Immobilization and Removal of Toxic Sb(III) Coupled With Fe(II)/Sb(III) Oxidation and Denitrification

Antimony (Sb) pollution is a worldwide problem. In some anoxic sites, such as Sb mine drainage and groundwater sediment, the Sb concentration is extremely elevated. Therefore, effective Sb remediation strategies are urgently needed. In contrast to microbial aerobic antimonite [Sb(III)] oxidation, the mechanism of microbial anaerobic Sb(III) oxidation and the effects of nitrate and Fe(II) on the fate of Sb remain unknown. In this study, we discovered the mechanism of anaerobic Sb(III) oxidation coupled with Fe(II) oxidation and denitrification in the facultative anaerobic Sb(III) oxidizer Sinorhizobium sp. GW3. We observed the following: (1) under anoxic conditions with nitrate as the electron acceptor, strain GW3 was able to oxidize both Fe(II) and Sb(III) during cultivation; (2) in the presence of Fe(II), nitrate and Sb(III), the anaerobic Sb(III) oxidation rate was remarkably enhanced, and Fe(III)-containing minerals were produced during Fe(II) and Sb(III) oxidation; (3) qRT-PCR, gene knock-out and complementation analyses indicated that the arsenite oxidase gene product AioA plays an important role in anaerobic Sb(III) oxidation, in contrast to aerobic Sb(III) oxidation; and (4) energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and powder X-ray diffraction (XRD) analyses revealed that the microbially produced Fe(III) minerals were an effective chemical oxidant responsible for abiotic anaerobic Sb(III) oxidation, and the generated Sb(V) was adsorbed or coprecipitated on the Fe(III) minerals. This process included biotic and abiotic factors, which efficiently immobilize and remove soluble Sb(III) under anoxic conditions. The findings revealed a significantly novel development for understanding the biogeochemical Sb cycle. Microbial Sb(III) and Fe(II) oxidation coupled with denitrification has great potential for bioremediation in anoxic Sb-contaminated environments.

Fabricating biogenic Fe(III) flocs from municipal sewage sludge using NAFO processes: Characterization and arsenic removal ability

This study involved fabricating biogenic Fe(III) flocs enriched from municipal sludge using microbial nitrate-dependent anaerobic Fe(II)-oxidizing (NAFO) processes. The research focused on bacterial community compositions and physicochemical properties of the biogenic Fe(III) flocs and their ability to adsorb arsenic (As). High-throughput sequencing analysis showed that significant microbial succession occurs in the raw sludge after the NAFO processes. The predominant bacterial communities in the biogenic Fe(III) flocs included Rhodanobacter, Parvibaculum, Gemmatimonas and Segetibacter genera. Microscopic and spectroscopic analyses included scanning electron microscopy - energy disperse spectroscopy (SEM-EDS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. These tests indicated that biogenic Fe(III) flocs were a mixture of NAFO bacteria and nanosized, poorly crystalline Fe(III) oxide particles. Batch experiments showed that after 120 min of reaction time, more than 95% of As(III) and As(V) (at an initial concentrations of 0.25 mg/L) were effectively removed with 120 ppm biogenic Fe(III) flocs. In addition, biogenic Fe(III) flocs removed As more effectively than abiotic Fe(III) flocs. These findings indicated that biogenic Fe(III) flocs produced from municipal sludge using NAFO processes performed well in removing As.

Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

Most isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer, Gallionellaceae sp., and less abundant heterotrophic strains (e.g., Bradyrhizobium sp., Nocardioides sp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the family Gallionellaceae dominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated with Bradyrhizobium sp. Gallionellaceae sp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II). Bradyrhizobium spp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O₂IMPORTANCE Nitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizer Gallionellaceae sp. and several heterotrophic strains (e.g., Bradyrhizobium sp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed and Bradyrhizobium became the dominant community member, Fe(II) was still oxidized by Gallionellaceae sp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.

Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture

The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing, Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of catalyzed amplification reporter deposition fluorescence in situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities, and interactions among the two most abundant microbial community members (i.e., Gallionellaceae sp. and Bradyrhizobium spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II) oxidizer Gallionellaceae sp. under autotrophic conditions as well as of Bradyrhizobium spp. under heterotrophic conditions. We used NanoSIMS to monitor the fate of ¹³C-labeled bicarbonate and acetate as well as ¹⁵N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions, only the Gallionellaceae sp. was actively incorporating ¹³C-labeled bicarbonate and ¹⁵N-labeled ammonium. Interestingly, both Bradyrhizobium spp. and Gallionellaceae sp. became enriched in [¹³C]acetate and [¹⁵N]ammonium under heterotrophic conditions. Our experiments demonstrated that Gallionellaceae sp. was capable of assimilating [¹³C]acetate while Bradyrhizobium spp. were not able to fix CO₂, although a metagenomics survey of culture KS recently revealed that Gallionellaceae sp. lacks genes for acetate uptake and that the Bradyrhizobium sp. carries the genetic potential to fix CO₂ The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment.IMPORTANCE Microbial mechanisms by which Fe(II) is oxidized with nitrate as the terminal electron acceptor are generally referred to as "nitrate-dependent Fe(II) oxidation" (NDFO). NDFO has been demonstrated in laboratory cultures (such as the one studied in this work) and in a variety of marine and freshwater sediments. Recently, the importance of NDFO for the transport of sediment-derived Fe in aquatic ecosystems has been emphasized in a series of studies discussing the impact of NDFO for sedimentary nutrient cycling and redox dynamics in marine and freshwater environments. In this article, we report results from an isotope labeling study performed with the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS, which was first described by Straub et al. (1) about 20 years ago. Our current study builds on the recently published metagenome of culture KS (2).

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.

Microbially Mediated Coupling of Fe and N Cycles by Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Littoral Freshwater Sediments

Nitrate-reducing iron(II)-oxidizing bacteria have been known for approximately 20 years. There has been much debate as to what extent the reduction of nitrate and the oxidation of ferrous iron are coupled via enzymatic pathways or via abiotic processes induced by nitrite formed by heterotrophic denitrification. The aim of the present study was to assess the coupling of nitrate reduction and iron(II) oxidation by monitoring changes in substrate concentrations, as well as in the activity of nitrate-reducing bacteria in natural littoral freshwater sediment, in response to stimulation with nitrate and iron(II). In substrate-amended microcosms, we found that the biotic oxidation of ferrous iron depended on the simultaneous microbial reduction of nitrate. Additionally, the abiotic oxidation of ferrous iron by nitrite in sterilized sediment was not fast enough to explain the iron oxidation rates observed in microbially active sediment. Furthermore, the expression levels of genes coding for enzymes crucial for nitrate reduction were in some setups stimulated by the presence of ferrous iron. These results indicate that there is a direct influence of ferrous iron on bacterial denitrification and support the hypothesis that microbial nitrate reduction is stimulated by biotic iron(II) oxidation.IMPORTANCE The coupling of nitrate reduction and Fe(II) oxidation affects the environment at a local scale, e.g., by changing nutrient or heavy metal mobility in soils due to the formation of Fe(III) minerals, as well as at a global scale, e.g., by the formation of the primary greenhouse gas nitrous oxide. Although the coupling of nitrate reduction and Fe(II) oxidation was reported 20 years ago and has been studied intensively since then, the underlying mechanisms still remain unknown. One of the main knowledge gaps is the extent of enzymatic Fe(II) oxidation coupled to nitrate reduction, which has frequently been questioned in the literature. In the present study, we provide evidence for microbially mediated nitrate-reducing Fe(II) oxidation in freshwater sediments. This evidence is based on the rates of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and on the effect of iron on the expression of genes required for denitrification.