Oxidation of Fe(II)-EDTA by nitrite and by two nitrate-reducing Fe(II)-oxidizing Acidovorax strains

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.

Hematite-promoted nitrate-reducing Fe(II) oxidation by Acidovorax sp. strain BoFeN1: Roles of mineral catalysis and cell encrustation

Although nitrate-reducing Fe(II) oxidizing (NRFO) bacteria can grow sustainably in natural environments, numerous laboratory studies suggested that cell encrustation-induced metabolism limitations and cell death occurred more seriously in the absence of natural minerals. Hence, a study on how natural minerals could affect NRFO is warranted. This study examined the impact of hematite on NRFO by Acidovorax sp. BoFeN1 with different electron donors (acetate and Fe(II), acetate alone, and Fe(II) alone) and with nitrate as an electron acceptor. When acetate and Fe(II) were used as the electron donors, the amount of Fe(II) oxidation and nitrate reduction was enhanced in the presence of hematite, whereas no promotion was observed when only acetate was added as an electron donor. Under the conditions with only Fe(II) added as an electron donor, the level of Fe(II) oxidation was increased from 3.07 ± 0.06 to 3.92 ± 0.02 mM in the presence of hematite and nitrate reduction was enhanced. This suggests that hematite promotes microbial nitrate reduction by accelerating the biological oxidation of Fe(II). The main secondary minerals were goethite and lepidocrocite. After adding hematite, the assemblage of iron minerals on the cell surface decreased, and the cell crusts became thinner, indicating that hematite effectively mitigated cell encrustation. Furthermore, hematite accelerated the chemical oxidation of Fe(II) by nitrite. Hence, hematite can promote the NRFO of Acidovorax sp. BoFeN1 via two possible pathways: (i) hematite acts as nucleation sites to mitigate cell encrustation; (ii) hematite catalyzes the biological and chemical oxidation of Fe(II) through the mineral catalysis effects. This study highlights the importance of existing iron minerals on NRFO and sheds light on the survival strategy of NRFO bacteria in anoxic subsurface environments.

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.

Co-response of Fe-reducing/oxidizing bacteria and Fe species to the dynamic redox cycles of natural sediment

Fe(III)-reducing bacteria (FRB) and Fe(II)-oxidizing bacteria (FOB) play essential roles in the biogeochemical cycling of iron (Fe). Although the redox transformation of Fe species mediated by FRB/FOB has been extensively studied, the co-responses of FRB and FOB and Fe species transformation in natural sediment under dynamic redox conditions are poorly known. This study explored the variations of potential FRB and FOB abundances and Fe species transformation in natural sediment during successive anoxic-oxic-anoxic-oxic-anoxic cycles. Compared with the pristine sediment sample, the FRB abundance increased 121-793% (initial: (2.6 ± 0.6) × 10⁷ copies/g) in the anoxic stages, while it decreased by 38-64% in the oxic stages. The increase in FRB abundance was ascribed to energy gain of FRB from the reduction of the amorphous Fe(III) (Fe(III)_am) and the crystalline Fe(III) (Fe(III)_cry) to the aqueous Fe(II) (Fe(II)_aq), the adsorbed Fe(II) (Fe(II)_ad) and the amorphous Fe(II) (Fe(II)_am), while the decrease was attributed to the oxidative stress caused by the reactive oxidant produced from the abiotic oxidation of Fe(II)_aq, Fe(II)_ad and Fe(II)_am to Fe(III)_am and Fe(III)_cry. The FOB abundance decreased 38-44% (initial: (5 ± 1.8) × 10⁷ copies/g) in the second and third anoxic stages, while slightly fluctuated in the oxic periods. This observation was contrary to the variation of FRB, which might be attributed to the strong resistance to oxidative stress of FOB and its ability to obtain energy under oxic conditions. Although the functions of FRB and FOB were impaired during anoxic-oxic cycles, the transformation of Fe(II)/Fe(III) was not immediately affected, which may be related to the residual reactivity of dead bacteria and the bio-availability of Fe(II)/Fe(III) species. In the anoxic-oxic alternation process, the iron cycle is mainly the mutual transformation between Fe(II)_aq, Fe(II)_ad, Fe(II)_am and Fe(III)_am, Fe(III)_cry. This finding deepens our understanding of the biogeochemical cycling of Fe in the redox-dynamic environments.

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.

Demethylation of the Antibiotic Methylarsenite is Coupled to Denitrification in Anoxic Paddy Soil

Arsenic (As) biomethylation is an important component of the As biogeochemical cycle, which produces methylarsenite [MAs(III)] as an intermediate product. Its high toxicity is used by some microbes as an antibiotic to kill off other microbes and gain a competitive advantage. Some aerobic microbes have evolved a detoxification mechanism to demethylate MAs(III) via the dioxygenase C-As lyase ArsI. How MAs(III) is demethylated under anoxic conditions is unclear. We found that nitrate addition to a flooded paddy soil enhanced MAs(III) demethylation. A facultative anaerobe Bacillus sp. CZDM1 isolated from the soil was able to demethylate MAs(III) under anoxic nitrate-reducing conditions. A putative C-As lyase gene (BcarsI) was identified in the genome of strain CZDM1. The expression of BcarsI in the As-sensitive Escherichia coli AW3110 conferred the bacterium the ability to demethylate MAs(III) under anoxic nitrate-reducing condition and enhanced its resistance to MAs(III). Both Bacillus sp. CZDM1 and E. coli AW3110 harboring BcarsI could not demethylate MAs(III) under fermentative conditions. Five conserved amino acid resides of cysteine, histidine, and glutamic acid are essential for MAs(III) demethylation under anoxic nitrate-reducing conditions. Putative arsI genes are widely present in denitrifying bacteria, with 75% of the sequenced genomes containing arsI, also possessing dissimilatory nitrate reductase genes narG or napA. These results reveal a novel mechanism in which MAs(III) is demethylated via ArsI by coupling to denitrification, and such a mechanism is likely to be common in an anoxic environment such as paddy soils and wetlands.

Anammox Bacteria Are Potentially Involved in Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction in the Wastewater Treatment System

Anaerobic ammonium oxidation coupled to nitrite reduction (termed as Anammox) was demonstrated as an efficient pathway to remove nitrogen from a wastewater treatment system. Recently, anaerobic ammonium oxidation was also identified to be linked to iron(III) reduction (termed Feammox) with dinitrogen, nitrite, or nitrate as end-product, reporting to enhance nitrogen removal from the wastewater treatment system. However, little is known about the role of Anammox bacteria in the Feammox process. Here, slurry from wastewater reactor amended with ferrihydrite was employed to investigate activity of Anammox bacteria in the Feammox process using the ¹⁵N isotopic tracing technique combined with 16S rRNA gene amplicon sequencing. A significantly positive relationship between rates of ¹⁵N₂ production and iron(III) reduction indicated the occurrence of Feammox during incubation. Relative abundances of Anammox bacteria including Brocadia, Kuenenia, Jettenia, and unclassified Brocadiaceae were detected with low relative abundances, whereas Geobacteraceae dominated in the treatment throughout the incubation. ¹⁵N₂ production rates significantly positively correlated with relative abundances of Geobacter, unclassified Geobacteraceae, and Anammox bacteria, revealing their contribution to nitrogen generation via Feammox. Overall, these findings suggested Anammox bacteria or cooperation between Anammox bacteria and iron(III) reducers serves a potential role in Feammox process.

Removal of chlorpyrifos and its hydrolytic metabolite in microcosm-scale constructed wetlands under soda saline-alkaline condition: Mass balance and intensification strategies

Chlorpyrifos (CP) is a typical organophosphorus insecticide, which poses serious threats to the natural environment and human health. Strategies for the fast elimination of CP and its toxic hydrolytic metabolite 3,5,6-trichloro-2(1H)-pyridianol (TCP) in drainage water are urgently needed. The fate of CP and TCP in microcosm-scale subsurface batch constructed wetlands (SSBCWs) was quantified with different macrophyte species under soda saline-alkaline (SSA) condition and effective intensification strategies were developed. The macrophyte species Canna indica outperformed Phragmites australis and Typha orientalis for CP and TCP removal in SSBCWs. Mass balance calculation indicates the fate of CP in SSBCWs was residue in water (≤8%), alkaline hydrolysis (18.93-57.42%), microbial degradation (37.75-61.91%), substrate adsorption (~4-14%), and macrophyte uptake (≤3%). The addition of ferric-carbon (Fe-C) as a substrate amendment in SSBCWs increased the CP removal percentage by 35% and reduced the effluent TCP concentration by ~70% during Day 1-4 on average compared with the unintensified control. Fe-C addition simplified the microbial community diversity, while increasing the relative abundance of Proteobacteria which tolerates the microelectrolytic environment. A single application of liquid microbial agent improved CP removal percentage by 84% and decreased the effluent TCP concentration by two orders of magnitude during Day 1-4. The hydraulic retention time for thorough removal of TCP reduced from over 8 d to 4 d. Although only two dominant microbial genera (i.e., Sphingomonas and Pseudomonas) adapted to the environment with CP and SSA, they accelerated CP and TCP degradation via their own metabolism and co-metabolism with other indigenous microorganisms.

Visualizing Microorganism-Mineral Interaction in the Iberian Pyrite Belt Subsurface: The Acidovorax Case

Despite being considered an extreme environment, several studies have shown that life in the deep subsurface is abundant and diverse. Microorganisms inhabiting these systems live within the rock pores and, therefore, the geochemical and geohydrological characteristics of this matrix may influence the distribution of underground biodiversity. In this study, correlative fluorescence and Raman microscopy (Raman-FISH) was used to analyze the mineralogy associated with the presence of members of the genus Acidovorax, an iron oxidizing microorganisms, in native rock samples of the Iberian Pyrite Belt subsurface. Our results suggest a strong correlation between the presence of Acidovorax genus and pyrite, suggesting that the mineral might greatly influence its subsurface distribution.

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.

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

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

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.

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.

Methane and nitrous oxide temporal and spatial variability in two midwestern USA streams containing high nitrate concentrations

Concentrations and emissions of greenhouse gases CO₂, CH₄, and N₂O commonly are examined individually in aquatic environments in which each is expected to be relatively important; however, their co-occurrence and dynamic interactions in fluvial settings could provide important information about their controlling biogeochemical processes and potential contributions to global climate change. Spatial and temporal variability of CH₄, N₂O, and CO₂ concentrations were measured from June 1999 to September 2003 in two nitrate-rich (40-1200 μM) streams draining agricultural land in the midwestern USA that differed ~13-fold in flow. Seasonal (biweekly), diel (hourly), and transport-oriented (reach-scale) sampling approaches were compared. Dissolved gas concentrations exceeded atmospheric equilibrium values up to 700- and 16-fold, for CH₄ and N₂O, respectively. Mean concentrations were higher in the larger stream than in the smaller stream. In both streams, CH₄ emissions were generally higher in summer-fall and negatively correlated with flow and NO₃^- concentration while N₂O emissions were generally higher in winter/spring and positively correlated with flow and NO₃^-. In the small stream, diel variations in the concentrations, emissions, and isotopic compositions of CH₄, N₂O, and NO₂^- resulted from diel variations in sources, sinks, and air-water gas exchange velocities. Seasonal mean total (CH₄ + N₂O) area-normalized emission rates, expressed as CO₂ warming potential equivalents, were similar for the two streams, but the total reach-scale emission rate for the larger stream, including CO₂, was about 2.9 times that of the smaller stream (131.6 vs 46.0 kg CO₂ equivalents km^-1 day^-1, respectively). The CH₄ contribution to this flux was 9-28%, despite the relatively high NO₃^- and O₂ concentrations in the streams, indicating contributions from upwelling groundwater or reactions in streambed sediment.

Metabolic Inactivity and Re-awakening of a Nitrate Reduction Dependent Iron(II)-Oxidizing Bacterium Bacillus ferrooxidans

Microorganisms capable of anaerobic nitrate-dependent Fe(II) (ferrous iron) oxidation (ANDFO) contribute significantly to iron and nitrogen cycling in various environments. However, lab efforts in continuous cultivation of ANDFO strains suffer from loss of activity when ferrous iron is used as sole electron donor. Here, we used a novel strain of nitrate-dependent Fe(II)-oxidizing bacterium Bacillus ferroxidians as a model and focused on the physiological activity of cells during ANDFO. It was shown that B. ferrooxidans entered a metabolically inactive state during ANDFO. B. ferrooxidans exhibited nitrate reduction coupled with Fe(II) oxidation, and the activity gradually declined and was hardly detected after 48-h incubation. Propidium monoazide (PMA) assisted 16S rRNA gene real-time PCR suggested that a large number of B. ferrooxidans cells were alive during incubation. However, ²H(D)-isotope based Raman analysis indicated that the cells were metabolically inactive after 120-h of ANDFO. These inactive cells re-awakened in R2A medium and were capable of growth and reproduction, which was consistent with results in Raman analysis. Scanning electron microscopy (SEM) observation and x-ray diffraction (XRD) revealed the formation of Fe minerals in close proximity of cells in the Fe(II)-oxidizing medium after Fe(II) oxidation. Overall, our results demonstrated that continued ANDFO can induce a metabolically inactive state in B. ferrooxidans, which was responsible for the loss of activity during ANDFO. This study provides an insight into the ANDFO process and its contribution to iron and nitrogen cycling in the environments.

Effect of Fe(II) on reactivity of heterotrophic denitrifiers in the remediation of nitrate- and Fe(II)-contaminated groundwater

Heterotrophic denitrifiers, capable of simultaneous nitrate reduction and Fe(II) oxidation, can be applied for the remediation of nitrate and Fe(II) combined contamination in groundwater. Under strictly anaerobic condition, denitrifying microbial communities were enriched with the coexistence of soluble nitrate, Fe(II) and associated nutrient elements to monitor the denitrification process. Low abundance of Fe(II) (e.g., 10 mg L^-1 in this study) tended to stimulate the activity of denitrifying microbial communities. However, elevated Fe(II) concentration (50 and 100 mg L^-1 in this study), acted as a stress, strongly inhibited the activity and reproduction of denitrifiers. Besides, through thermodynamics calculations, methanol rather than Fe(II) was proved to be the preferable electron donors for both energy metabolism and anabolism. Betaproteobacteria was found to be the most predominant (sub)phylum in all enriched microbial assemblages. Methylovesartilis was the most predominant group mainly catalyzed for methanol based denitrification, and others denitrifiers included Methylophilaceae, Dechloromonas and Denitratisoma. Excessive Fe(II) in the solution greatly reduced the proportions of these denitrifying groups, while the influence seemed to be less apparent on functional genes composition. As such, a conceptional metabolism pathway of the most dominant genus (i.e., Methylovesartilis) for nitrate reducing as well as methanol and Fe(II) oxidation confirmed that biotic nitrate reducing and Fe(II) oxidizing were potentially proceeded in cytoplasm by enzymes such as NarGHI. The Fe(II) oxidation rate depended on the rate of Fe(II) entering into the cell. These findings provide a clear mechanistic understanding of heterotrophic denitrification coupling with Fe(II) oxidation, and environmental implication for the bioremediation of nitrate and Fe(II) contaminated groundwater.

Bacillus ferrooxidans sp. nov., an iron(II)-oxidizing bacterium isolated from paddy soil

An endospore-forming bacterium, designated YT-3^T, was isolated from a paddy soil in Yingtan, Jiangxi, China. Cells of strain YT-3^T were Gram-positive, rod-shaped, facultative anaerobic, catalase, and oxidase positive. The optimum growth temperature and pH were 30°C (ranged from 15 to 50°C) and 6.5-7.0 (ranged from 3 to 11), respectively. Analysis of the 16S rRNA gene sequence showed that strain YT-3^T was affiliated to the genus Bacillus and displayed the highest similarity to that of Bacillus drentensis JCM 21707^T (98.3%), followed by B. ginsengisoli JCM 17335^T (97.8%) and B. fumarioli JCM 21708^T (97.0%). The similarity of rpoB gene sequence between strain YT-3^T and B. drentensis JCM 21707^T, B. ginsengisoli JCM 17335^T and B. fumarioli JCM 21708T was 80.4%, 81.5%, and 82.1%, respectively. The genomic DNA G + C content was 44.9 mol%. The predominant respiratory quinone was Menaquinone-7, and meso-diaminopimelic acid was present in the peptidoglycan layer of cell wall. The major fatty acids were C_15:0 anteiso (36.2%), C_14:0 iso (19.6%), C_15:0 iso (17.4%), and C_16:0 iso (9.8%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and ammoniac phospholipids. The DNA-DNA hybridization values between isolate YT-3^T and B. drentensis (JCM 21707^T), B. ginsengisoli (JCM 17335^T), and B. fumarioli (JCM 21708^T) were 36.3%, 30.3%, and 25.3%, respectively. On the basis of physiological, genetic and biochemical data, strain YT-3^T represented a novel species of the genus Bacillus, for which the name Bacillus ferrooxidans sp. nov was proposed. The type strain is YT-3^T (= KCTC 33875T = CCTCC AB 2017049T).

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

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

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).

Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism

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

Abiotic nitrate loss and nitrogenous trace gas emission from Chinese acidic forest soils

There are an increasing number of studies, which have shown the potential importance of abiotic denitrification in nitrogen biogeochemistry through pure chemical coupling between nitrate/nitrite reduction and Fe(II) oxidation. However, there is little direct evidence showing the environmental significance of abiotic nitrate (NO₃^-) reduction in acidic soils. We assessed the magnitude and gaseous product stoichiometry of abiotic nitrate reduction in acidic forest soils based on sterilized anoxic soil incubations at different soil pHs and nitrate loadings. The results showed that 24.9, 53.4, and 88.7% of added nitrate (70 mg N kg^-1) were lost during 15 days incubation at pHs 3.9, 4.8, and 5.6, respectively. Nitrous oxide (N₂O) was found as the dominant gaseous product of abiotic nitrate reduction, accounting for 5.0, 28.9, and 47.9% of nitrate losses at three pH levels, respectively. Minor but clear NO accumulations were observed for all nitrate-amended treatments, with the maxima at intermediate pH 4.8. The percentage of NO increased significantly with soil pH decline, leading to a negative correlation between NO/N₂O ratio and soil pH. Though saturations were found under excessive nitrogen loading (i.e., 140 mg N kg^-1), we still pose that abiotic nitrate reduction may represent a potentially important pathway for nitrate loss from acidic forest soils receiving nitrogen deposition. Our results here highlight the importance of abiotic nitrate reduction in the soil nitrogen cycle, with special relevance to nitrate removal and nitrogenous trace gas (NO and N₂O) emissions from acidic soils.

Influence of pH, EDTA/Fe(II) ratio, and microbial culture on Fe(II)-mediated autotrophic denitrification

Fe(II)-mediated autotrophic denitrification with four different microbial cultures under different pH and EDTA/Fe(II) conditions was investigated in batch bioassays. Initially, the highest nitrate removal (72%) was achieved with an activated sludge inoculum. The use of pure cultures of Pseudogulbenkiania strain 2002 and Thiobacillus denitrificans resulted in a 55 and 52% nitrate removal, respectively. No denitrification was observed for a mixed culture dominated by Thiobacillus thioparus and T. denitrificans. A longer enrichment on Fe(II) and the supplementation of thiosulfate as additional electron donor were needed to stimulate the denitrifying activity of the Thiobacillus-mixed culture. A second subculture on Fe(II) as sole electron donor resulted in higher denitrification efficiencies for all microbial cultures. In particular, nitrate removal reached up to 84% with a specific nitrate removal rate of 1.160 mM·(g VSS·day)^-1 in the bioassays seeded with the Thiobacillus-mixed culture. All cultures were favored by decreasing the EDTA/Fe(II) molar ratio from 2.0 to 0.5. The most significant denitrification enhancement was observed for the Pseudogulbenkiania species, indicating a lower tolerance to EDTA. The two pure cultures effectively maintained denitrification at pH 7.0 and were more sensitive to a pH decrease. Conversely, the optimal pH was 6.0 for the Thiobacillus-mixed and activated sludge cultures.

Nitrate Stimulates Anaerobic Microbial Arsenite Oxidation in Paddy Soils

Arsenic (As) bioavailability to rice plants is elevated in flooded paddy soils due to reductive mobilization of arsenite [As(III)]. However, some microorganisms are able to mediate anaerobic As(III) oxidation by coupling to nitrate reduction, thus attenuating As mobility. In this study, we investigated the impact of nitrate additions on As species dynamics in the porewater of four As-contaminated paddy soils. The effects of nitrate on microbial community structure and the abundance and diversity of the As(III) oxidase (aioA) genes were quantified using 16S rRNA sequencing, quantitative PCR, and aioA gene clone libraries. Nitrate additions greatly stimulated anaerobic oxidation of As(III) to As(V) and decreased total soluble As in the porewater in flooded paddy soils. Nitrate additions significantly enhanced the abundance of aioA genes and changed the microbial community structure by increasing the relative abundance of the operational taxonomic units (OTUs) from the genera Acidovorax and Azoarcus. The aioA gene sequences from the Acidovorax related OTU were also stimulated by nitrate. A bacterial strain (ST3) belonging to Acidovorax was isolated from nitrate-amended paddy soil. The strain was able to oxidize As(III) and Fe(II) under anoxic conditions using nitrate as the electron acceptor. Abiotic experiments showed that Fe(II), but not As(III), could be oxidized by nitrite. These results show that nitrate additions can stimulate As(III) oxidation in flooded paddy soils by enhancing the population of anaerobic As(III) oxidizers, offering a potential strategy to decrease As mobility in As-contaminated paddy soils.

Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment

Aquabacterium parvum strain B6 exhibited efficient nitrate-dependent Fe(II) oxidation ability using nitrate as an electron acceptor. A continuous up-flow bioreactor that included an aerobic and an anoxic section was constructed, and strain B6 was added to the bioreactor as inocula to explore the application of microbial nitrate-dependent Fe(II) oxidizing (NDFO) efficiency in wastewater treatment. The maximum NRE (anoxic section) and TNRE of 46.9% and 79.7%, respectively, could be obtained at a C/N ratio of 5.3:1 in the influent with HRT of 17. Meanwhile, the taxonomy composition of the reactor was assessed, as well. The NDFO metabolism of strain B6 could be expected because of its relatively dominant position in the anoxic section, whereas potential heterotrophic nitrification and aerobic denitrification developed into the prevailing status in the aerobic section after 50days of continuous operation.

Effects of Fe(ii) on microbial communities, nitrogen transformation pathways and iron cycling in the anammox process: kinetics, quantitative molecular mechanism and metagenomic analysis

Appropriate Fe(ii) concentration has been regarded as a significant factor for fast start-up of the anammox (anaerobic ammonium oxidizing) process.