Sequestration of Labile Organic Matter by Secondary Fe Minerals from Chemodenitrification: Insight into Mineral Protection Mechanisms

Labile organic matter (OM) immobilized by secondary iron (Fe) minerals from chemodenitrification may be an effective way to immobilize organic carbon (OC). However, the underlying mechanisms of coupled chemodenitrification and OC sequestration are poorly understood. Here, OM immobilization by secondary Fe minerals from chemodenitrification was investigated at different C/Fe ratios. Kinetics of Fe(II) oxidation and nitrite reduction rates decreased with increasing C/Fe ratios. Despite efficient sequestration, the immobilization efficiency of OM by secondary minerals varied with the C/Fe ratios. Higher C/Fe ratios were conducive to the formation of ferrihydrite and lepidocrocite, with defects and nanopores. Three contributions, including inner-core Fe-O and edge- and corner-shared Fe-Fe interactions, constituted the local coordination environment of mineral-organic composites. Microscopic analysis at the molecular scale uncovered that labile OM was more likely to combine with secondary minerals with poor crystallinity to enhance its stability, and OM distributed within nanopores and defects had a higher oxidation state. After chemodenitrification, high molecular weight substances and substances high in unsaturation or O/C ratios including phenols, polycyclic aromatics, and carboxylic compounds exhibited a stronger affinity to Fe minerals in the treatments with lower C/Fe ratios. Collectively, labile OM immobilization can occur during chemodenitrification. The findings on OM sequestration coupled with chemodenitrification have significant implications for understanding the long-term cycling of Fe, C, and N, providing a potential strategy for OM immobilization in anoxic soils and sediments.

Magnetite enhances As immobilization during nitrate reduction and Fe(II) oxidation by Acidovorax sp. strain BoFeN1

Arsenic (As) cycling in groundwater is commonly coupled to the biogeochemical cycling of iron (Fe) and the associated transformation of Fe minerals present. Numerous laboratory studies suggested that Fe minerals can act as nucleation sites for further crystal growth and as catalysts for abiotic Fe(II) oxidation. In view of the widespread existence of magnetite in anoxic environments where As is often dissolved, we firstly exploited magnetite to enhance As immobilization during nitrate-reducing Fe(II) oxidation (NRFO) induced by Acidovorax sp. strain BoFeN1, a mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium that can oxidize Fe(II) through both enzymatic and abiotic pathways. Subsequently, we investigated how magnetite affects NRFO and As immobilization. Results demonstrated a significant increase in As(III) removal efficiency from 75.4 % to 97.2 % with magnetite, attributed to the higher amount of NRFO and As(III) oxidation promoted by magnetite. It was found that magnetite stimulated the production of extracellular polymeric substances (EPS), which could decrease the diffusion of nitrate in the periplasm of bacteria and shield them against encrustation, resulting in a more rapid reduction of nitrate in the system with magnetite than that without magnetite. Meanwhile, Fe(II) was almost completely oxidized in the presence of magnetite during the whole 72 h experiment, while in the absence of magnetite, 47.7 % of Fe(II) remained, indicating that magnetite could obviously accelerate the chemical oxidation of Fe(II) with nitrite (the intermediates of nitrate bioreduction). Furthermore, the formation of labile Fe(III), an intermediate product of electron transfer between Fe(II) and magnetite, was reasonably deduced to be vital for anoxic As(III) oxidation. Additionally, the XPS analysis of the solid phase confirmed the oxidation of 43.8 % of As(III) to As(V). This study helps to understand the biogeochemical cycling of Fe and As in the environment, and provides a cost-effective and environmentally friendly option for in situ remediation of As-contaminated groundwater.

Driving mechanism of different nutrient conditions on microbial mediated nitrate reduction in magnetite-present river infiltration zone

Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings. Additionally, we aimed to use this information as a foundation for examining the effect of nutritional conditions on the nitrate reduction process in magnetite-present environments. These results emphasise the significance of organic matter in enabling dissimilatory nitrate reduction to ammonium (DNRA) and enhancing the connection between nitrate reduction and iron in sedimentary environments. In the later phases of nitrate reduction, nitrogen fixation was the prevailing process in low-carbon environments, whereas high-carbon environments tended to facilitate the breakdown of organic nitrogen. High-throughput sequencing analysis revealed a robust association between C/N ratios and alterations in microbial community composition, providing insights into notable modifications in essential functioning microorganisms. The nitrogen-fixing bacterium Ralstonia is more abundant in ecosystems with scarce organic matter. In contrast, in settings rich in organic matter, microorganisms, such as Acinetobacter and Clostridia, which may produce ammonia, play crucial roles. Moreover, the population of iron bacteria grows in such an environment. Hence, this study proposes that C/N ratios can influence Fe(II)/Fe(III) conversions and simultaneously affect the process of nitrate reduction by shaping the composition of specific microbial communities.

Soil carbon and nitrogen cycles driven by iron redox: A review

Soil carbon and nitrogen cycles affect agricultural production, environmental quality, and global climate. Iron (Fe), regarded as the most abundant redox-active metal element in the Earth's crust, is involved in a biogeochemical cycle that includes Fe(III) reduction and Fe(II) oxidation. The redox reactions of Fe can be linked to the carbon and nitrogen cycles in soil in various ways. Investigating the transformation processes and mechanisms of soil carbon and nitrogen species driven by Fe redox can provide theoretical guidance for improving soil fertility, and addressing global environmental pollution as well as climate change. Although the widespread occurrence of these coupling processes in soils has been revealed, explorations of the effects of Fe redox on soil carbon and nitrogen cycles remain in the early stages, particularly when considering the broader context of global climate and environmental changes. The key functional microorganisms, mechanisms, and contributions of these coupling processes to soil carbon and nitrogen cycles have not been fully elucidated. Here, we present a systematic review of the research progress on soil carbon and nitrogen cycles mediated by Fe redox, including the underlying reaction processes, the key microorganisms involved, the influencing factors, and their environmental significance. Finally, some unresolved issues and future perspectives are addressed. This knowledge expands our understanding of the interconnected cycles of Fe, carbon and nitrogen in soils.

Insights into nitrate-reducing Fe(II) oxidation by Diaphorobacter caeni LI3T through kinetic, nitrogen isotope fractionation, and genome analyses

Nitrate (NO3-)-reducing Fe(II) oxidation (NRFO) is prevalent in anoxic environments. However, it is uncertain in which step(s) the biological Fe(II) oxidation is coupled with denitrification during NRFO. In this study, a heterotrophic NRFO bacterium, Diaphorobacter caeni LI3T, was isolated from paddy soil and used to investigate the transformation of Fe(II) and nitrogen as well as nitrogen isotopic fractionation (δ15N-N2O) during NRFO. Fe(II) oxidation was observed in the Cell+NO3- +Fe(II), Cell+NO2- + Fe(II), and NO2- + Fe(II) treatments, resulting in precipitation of amorphous Fe(III) minerals and lepidocrocite on the surface and in the periplasm of cells. The presence of Fe(II) slightly accelerated microbial NO3- reduction in the Cell+NO3- + Fe(II) treatment relative to the Cell+NO3- treatment, but slowed down the NO2- reduction in the Cell+NO2- + Fe(II) treatment relative to the Cell+NO2- treatment likely due to cell encrustation that blocking microbial NO2- reduction in the periplasm. The δ15N-N2O results in the Cell+NO3- + Fe(II) treatment were close to those in the Cell+NO3- and Cell+NO2- treatments, indicating that the accumulative N2O is primarily of biological origin during NRFO. The genome analysis found a complete set of denitrification and oxidative phosphorylation genes in strain LI3T, the metabolic pathways of which were closely related with cyc2 and cytc as indicated by protein-protein interactions network analysis. It is proposed that Fe(II) oxidation is catalyzed by the outer membrane protein Cyc2, with the resulting electrons being transferred to the nitrite reductase NirS via CytC in the periplasm, and the CytC can also accept electrons from the oxidative phosphorylation in the cytoplasmic membrane. Overall, our findings provide new insights into the potential pathways of biological Fe(II) oxidation coupled with nitrate reduction in heterotrophic NRFO bacteria.

Microbe interactions drive the formation of floating iron films in circumneutral wetlands

Floating iron (Fe) films are widely found in wetlands that can form oxic-anoxic boundaries under circumneutral conditions. These films play a crucial role in the redox transformations and bioavailability of nutrients and trace metals. Current studies mainly focus on chemical oxidation during Fe film formation under circumneutral conditions. The functional microorganisms and associated microbial processes involved in Fe film formation have yet to be investigated in detail. Here, we investigated the microbial communities and involved microbial processes for the formation of floating Fe films in wetlands. Ferrihydrite was the dominant Fe(III) phase in films, accompanied by moderate levels of carbon and silicon. The Fe species and microbial analysis indicated that Fe films contain mixed-valent Fe and can form biotically. Microbial community analysis showed that the dominant genera in these Fe films were Fe-oxidizing and reducing bacteria and methanotrophs, including Leptothrix, Ferriphasclus, Gallionella, Geobacter and Methylococcales. Leptothrix, Ferriphasclus and Gallionella, as classical Fe(II)-oxidizing bacteria (FeOB), can oxidize Fe(II) with limited oxygen and form special structures that are consistent with Fe film morphology. Geobacter can provide a source of Fe(II) for FeOB growth, and Methylococcales can perform methane oxidation to provide energy for Fe cycling. The high ratios of Gallionella- and Geobacter-related microorganisms and carbon fixation genes proved the contribution of potential of Fe cycling and autotrophic microbial communities to the formation of Fe films. The diversity of microbial community suggested that Fe(II) oxidation could trigger carbon fixation, while Fe(III) reduction accelerated Fe and carbon cycling through anaerobic respiration and autotrophic chemosynthesis. These results highlight the contribution of these multiple microbial processes to Fe and carbon cycling during the formation of floating Fe films in wetlands. However, further studies are required to fully elucidate the interaction of functional microorganisms involved in floating film formation and their biogeochemical role in wetlands.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

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.

Polystyrene microplastics biodegradation by gut bacterial Enterobacter hormaechei from mealworms under anaerobic conditions: Anaerobic oxidation and depolymerization

Synthetic plastic is used throughout daily life and industry, threatening organisms with microplastic pollution. Polystyrene is a major plastic polymer and also widely found sources of plastic wastes and microplastics. Here, we report that Enterobacter hormaechei LG3 (CP118279.1), a facultative anaerobic bacterial strain isolated from the gut of Tenebrio molitor larvae (mealworms) can oxidize and depolymerize polystyrene under anaerobic conditions. LG3 performed biodegradation while forming a biofilm on the plastic surface. PS biodegradation was characterized by analyses of surface oxidation, change in morphology and molecular weights, and production of biodegraded derivative. The biodegradation performance by LG3 was compared with PS biodegradation by Bacillus amyloliquefaciens SCGB1 under both anaerobic and aerobic conditions. In addition, through nanopore sequencing technology, we identified degradative enzymes, including thiol peroxidase (tpx), alkyl hydroperoxide reductase C (ahpC) and bacterioferritin comigratory protein (bcp). Along with the upregulation of degradative enzymes for biodegradation, changes in lipid A and biofilm-associated proteins were also observed after the cells were incubated with polystyrene microplastics. Our results provide evidence for anaerobic biodegradation by polystyrene-degrading bacteria and show alterations in gene expression patterns after polystyrene microplastics treatment in the opportunistic pathogen Enterobacter hormaechei.

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

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

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.

Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils

Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.

Autotrophic denitrification using Fe(II) as an electron donor: A novel prospective denitrification process

As a newly identified nitrogen loss pathway, the nitrate-dependent ferrous oxidation (NDFO) process is emerging as a research hotspot in the field of low carbon to nitrogen ratio (C/N) wastewater treatment. This review article provides an overview of the NDFO process and summarizes the functional microorganisms associated with NDFO from different perspectives. The potential mechanisms by which external factors such as influent pH, influent Fe(II)/N (mol), organic carbon, and chelating agents affect NDFO performance are also thoroughly discussed. As the electron-transfer mechanism of the NDFO process is still largely unknown, the extensive chemical Fe(II)-oxidizing nitrite-reducing pathway (NDFO_chem) of the NDFO process is described here, and the potential enzymatic electron transfer mechanisms involved are summarized. On this basis, a three-stage electron transfer pathway applicable to low C/N wastewater is proposed. Furthermore, the impact of Fe(III) mineral products on the NDFO process is revisited, and existing crusting prevention strategies are summarized. Finally, future challenges facing the NDFO process and new research directions are discussed, with the aim of further promoting the development and application of the NDFO process in the field of nitrogen removal.

Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil

Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO₃, and Fe₃(PO₄)₂ as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d^-1) was obtained in the FeCO₃ tubes, and cells grown in the Fe₃(PO₄)₂ tubes yielded maximum assimilation amounts of ¹³C-NaHCO₃ of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.

The Nitrogen Dynamics of Newly Developed Lignite-Based Controlled-Release Fertilisers in the Soil-Plant Cycle

The effect of newly developed controlled-release fertilisers (CRFs); Epox5 and Ver-1 and two levels of Fe2+ applications (478 and 239 kg-FeSO4 ha−1) on controlling nitrogen (N) losses, were tested on ryegrass, in a climate-controlled lysimeter system. The Epox5 and Ver-1 effectively decreased the total N losses by 37 and 47%, respectively, compared to urea. Nitrous oxide (N2O) emissions by Ver-1 were comparable to urea. However, Epox5 showed significantly higher (p < 0.05) N2O emissions (0.5 kg-N ha−1), compared to other treatments, possibly due to the lock-off nitrogen in Epox5. The application of Fe2+ did not show a significant effect in controlling the N leaching loss and N2O emission. Therefore, a dissimilatory nitrate reduction and chemodenitrification pathways were not pronounced in this study. The total dry matter yield, N accumulation, N use efficiency and soil residual N were not significantly different among any N treatments. Nevertheless, the N accumulation of CRFs was lower in the first month, possibly due to the slow release of urea. The total root biomass was significantly (p < 0.05) lower for Epox5 (35%), compared to urea. The hierarchical clustering of all treatments revealed that Ver-1 outperformed other treatments, followed by Epox5. Further studies are merited to identify the potential of Fe2+ as a controlling agent for N losses.

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.

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.

How different nitrogen fertilizers affect arsenic mobility in paddy soil after straw incorporation?

In straw return fields, nitrogen-fertilizers are added to mitigate microbial competition for nitrogen with plants. However, in arsenic (As)-contaminated paddy fields, the specific effects of different nitrogen fertilizers on As mobility after straw incorporation and the interactions among iron(Fe)/carbon(C)/nitrogen(N)/As are not well understood. In the reported microcosm experiment we monitored As-mobility as a function of different dosages of KNO₃, NH₄Cl and rice straw incorporation. Addition of both KNO₃ and NH₄Cl significantly inhibited the As mobilization induced by straw incorporation. Following the KNO₃ addition, the As concentration in porewater dropped by 51-66% after 2 days of the incubation by restraining Fe reduction and enhancing Fe oxidation. High-dose NH₄Cl addition reduced As in porewater by 22-43% throughout the incubation by decreasing porewater pH. High-throughput sequencing results demonstrated that KNO₃ addition enriches both the denitrifying and Fe-oxidizing bacteria, while diminishing Fe-reducing bacteria; NH₄Cl addition has the opposite effect on Fe-reducing bacteria. Network analysis revealed that As and Fe concentrations in porewater were positively correlated with the abundance of denitrifying and Fe-reducing bacteria. This study broadens our insight into the As biogeochemistry associated with the N/C/Fe balance in soil, which are of great significance for agronomic management and mitigation the risk of As-contaminated paddy fields.

Anaerobic microbial manganese oxidation and reduction: A critical review

Manganese is a vital heavy metal abundant in terrestrial and aquatic environments. Anaerobic manganese redox reactions mediated by microorganisms have been recognized for a long time, which promote elements mobility and bioavailability in the environment. Biological anaerobic redox of manganese serves two reactions, including Mn(II) oxidation and Mn(IV) reduction. This review provides a comprehensive analysis of manganese redox cycles in the environment, closely related to greenhouse gas mitigation, the fate of nutrients, microbial bioremediation, and global biogeochemical cycle, including nitrogen, sulfur, and carbon. The oxidation and reduction of manganese occur cyclically and simultaneously in the environment. Anaerobic reduction of Mn(IV) receives electrons from methane, ammonium and sulfide, while Mn(II) can function as an electron source for manganese-oxidizing microorganisms for autotrophic denitrification and photosynthesis. The anaerobic redox transition between Mn(II) and Mn(IV) promotes a dynamic biogeochemical cycle coupled to microorganisms in water, soil and sediment environments. The discussion of reaction mechanisms, microorganism diversity, environmental influence bioremediation and application identify the research gaps for future investigation, which provides promising opportunities for further development of biotechnological applications to remediate contaminated environments.

Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment

The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg^-1 to 130 g·kg^-1 and content of antimony ranging from 0.25 g·kg^-1 up to 12 g·kg^-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.

Autotrophic Fe-Driven Biological Nitrogen Removal Technologies for Sustainable Wastewater Treatment

Fe-driven biological nitrogen removal (FeBNR) has become one of the main technologies in water pollution remediation due to its economy, safety and mild reaction conditions. This paper systematically summarizes abiotic and biotic reactions in the Fe and N cycles, including nitrate/nitrite-dependent anaerobic Fe(II) oxidation (NDAFO) and anaerobic ammonium oxidation coupled with Fe(III) reduction (Feammox). The biodiversity of iron-oxidizing microorganisms for nitrate/nitrite reduction and iron-reducing microorganisms for ammonium oxidation are reviewed. The effects of environmental factors, e.g., pH, redox potential, Fe species, extracellular electron shuttles and natural organic matter, on the FeBNR reaction rate are analyzed. Current application advances in natural and artificial wastewater treatment are introduced with some typical experimental and application cases. Autotrophic FeBNR can treat low-C/N wastewater and greatly benefit the sustainable development of environmentally friendly biotechnologies for advanced nitrogen control.

Interactions of Vallisneria natans and Iron-Oxidizing Bacteria Enhance Iron-Bound Phosphorus Formation in Eutrophic Lake Sediments

Submerged macrophyte restoration and in situ phosphorus (P) passivation are effective methods for the control of internal P loading from sediments. This study explored the synergistic effects of Vallisneria natans and iron (Fe)-oxidizing bacteria (IOB) on internal P loading from eutrophic freshwater lake sediments by taking into account Fe-bound P (FeP) formation and associated bacterial community structures. Sediment samples were prepared in glass tanks under four treatments, namely no V. natans planting or IOB inoculation (control), planting V. natans without IOB inoculation (Va), planting V. natans with IOB inoculation (Va-IOB), and planting V. natans with autoclaved IOB inoculation (Va-IOB[A]). Compared with the control, all three treatments with V. natans (Va, Va-IOB, and Va-IOB[A]) had significantly decreased organic matter contents and increased redox potential in sediments (p < 0.05), at the rapid growth and mature stages of V. natans. Planting V. natans with and without IOB inoculation also decreased the total P (TP) and Fe–P concentrations in sediments. Conversely, Fe³⁺ concentrations, Fe³⁺/Fe²⁺ ratios, and the proportions of Fe–P in TP all increased in sediments planted with V. natans, especially under the Va-IOB treatment (p < 0.05). Furthermore, bacterial community diversity increased in sediments due to the presence of V. natans. The relative abundances of IOB (including Acidovorax and Chlorobium) increased from the transplanting to the rapid growth stage of V. natans and then decreased afterwards. In the later stages, the relative abundances of IOB and their ratios to Fe-reducing bacteria were the highest under the Va-IOB treatment. Accordingly, synergistic interactions between V. natans and IOB could enhance Fe–P formation and reduce TP concentrations in eutrophic lake sediments by altering sediment physicochemical properties and Fe oxidation-related bacterial community structures.

Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis

Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.

Exobiology of the Venusian Clouds: New Insights into Habitability through Terrestrial Models and Methods of Detection

The search for life beyond Earth has focused on Mars and the icy moons Europa and Enceladus, all of which are considered a safe haven for life due to evidence of current or past water. The surface of Venus, on the other hand, has extreme conditions that make it a nonhabitable environment to life as we know it. This is in contrast, however, to its cloud layer, which, while still an extreme environment, may prove to be a safe haven for some extreme forms of life similar to extremophiles on Earth. We consider the venusian clouds a habitable environment based on the presence of (1) a solvent for biochemical reactions, (2) appropriate physicochemical conditions, (3) available energy, and (4) biologically relevant elements. The diversity of extreme microbial ecosystems on Earth has allowed us to identify terrestrial chemolithoautotrophic microorganisms that may be analogs to putative venusian organisms. Here, we hypothesize and describe biological processes that may be performed by such organisms in the venusian clouds. To detect putative venusian organisms, we describe potential biosignature detection methods, which include metal-microbial interactions and optical methods. Finally, we describe currently available technology that can potentially be used for modeling and simulation experiments.

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water

Woodchip bioreactors are increasingly used to remove nitrate (NO₃^–) from agricultural drainage water in order to protect aquatic ecosystems from excess nitrogen. Nitrate removal in woodchip bioreactors is based on microbial processes, but the microbiomes and their role in bioreactor efficiency are generally poorly characterized. Using metagenomic analyses, we characterized the microbiomes from 3 full-scale bioreactors in Denmark, which had been operating for 4–7 years. The microbiomes were dominated by Proteobacteria and especially the genus Pseudomonas, which is consistent with heterotrophic denitrification as the main pathway of NO₃^– reduction. This was supported by functional gene analyses, showing the presence of the full suite of denitrification genes from NO₃^– reductases to nitrous oxide reductases. Genes encoding for dissimilatory NO₃^– reduction to ammonium were found only in minor proportions. In addition to NO₃^– reducers, the bioreactors harbored distinct functional groups, such as lignocellulose degrading fungi and bacteria, dissimilatory sulfate reducers and methanogens. Further, all bioreactors harbored genera of heterotrophic iron reducers and anaerobic iron oxidizers (Acidovorax) indicating a potential for iron-mediated denitrification. Ecological indices of species diversity showed high similarity between the bioreactors and between the different positions along the flow path, indicating that the woodchip resource niche was important in shaping the microbiome. This trait may be favorable for the development of common microbiological strategies to increase the NO₃^– removal from agricultural drainage water.

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.

Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer

Neutrophilic microbial pyrite (FeS₂) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes (^NAFe-pyrite) and ⁵⁷Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO₃) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S⁰), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the ^NAFe-pyrite/⁵⁷Fe-siderite setups by maps of ⁵⁶FeO and ³²S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of ⁵⁶Fe(III) (oxyhydr)oxides that could solely originate from ⁵⁶FeS₂. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe³⁺ appeared to be negligible in our experimental setup.

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.

Electrochemical enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode of bioelectrochemical systems

Electrotrophic microorganisms have not been well studied in extreme environments. Here, we report on the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment. The biofilm enriched via electrochemical approach under 9.5 pH and 20 g NaCl/L salinity conditions achieved −43.5±7.2μA/cm2 current density and 49.5±13.2%nitrate reduction efficiency via partial and complete denitrification. Voltammetric characterization of the biocathodes revealed a redox center with −0.294±0.003V (vs. Ag/AgCl) formal potential putatively involved in the electron uptake process. The lack of soluble redox mediators and hydrogen-driven nitrate reduction suggests direct-contact cathodic electron uptake by the nitrate-reducing microorganisms in the enriched biofilm. 16S-rRNA amplicon sequencing of the cathodic biofilm revealed the presence of unreported Pseudomonas, Natronococcus, and Pseudoalteromonas spp. at 31.45%,11.82%, and 9.69% relative sequence abundances, respectively. The enriched nitrate-reducing microorganisms also reduced nitrate efficiently using soluble electron donors found in the lake sediments, thereby suggesting their role in N-cycling in such environments.

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Enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode

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Cathodic reduction current corresponded to the nitrate reduction process

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Pseudomonas, Natronococcus, and Pseudoalteromonas spp. enriched in the cathodic biofilm

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Enriched culture reduced nitrate efficiently with soluble electron donor sources

Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea

Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.

Simultaneous removal of nitrate and heavy metals in a continuous flow nitrate-dependent ferrous iron oxidation (NDFO) bioreactor

Nitrogen and heavy metals can co-occur in various industrial wastewaters such as coke-oven wastewater. Removal of these contaminants is important, but cost-efficient removal technology is limited. In this study, we examined the usefulness of nitrate-dependent ferrous iron oxidation (NDFO) for the simultaneous removal of nitrate and heavy metals (iron and zinc), by using an NDFO strain Pseudogulbenkiania sp. NH8B. Based on the batch culture assays, nitrate, Fe, and Zn were successfully removed from a basal medium as well as coke-oven wastewater containing 5 mM nitrate, 10 mM Fe(II), and 10 mg/L Zn. Zinc in the water was most likely co-precipitated with Fe(III) oxides produced during the NDFO reaction. Simultaneous removal of nitrate, Fe, and Zn was also achieved in a continuous-flow reactor fed with a basal medium containing 10 mM nitrate, 5 mM Fe(II), 4 mM acetate, and 10 mg/L Zn. However, when the reactor is fed with coke-oven wastewater supplemented with 10 mM nitrate, 5 mM Fe(II), 4 mM acetate, and 10 mg/L ZnCl₂, the reactor performance significantly decreased, most likely due to the inhibition of bacterial growth by thiocyanate or organic contaminants present in the coke-oven wastewater. Use of mixed culture of NDFO bacteria and thiocyanate/organic-degrading denitrifiers should help improve the reactor performance.

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

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

Substratum-associated microbiota

Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.

Nitrite Accumulation Is Required for Microbial Anaerobic Iron Oxidation, but Not for Arsenite Oxidation, in Two Heterotrophic Denitrifiers

Phylogenetically diverse species of bacteria can mediate anaerobic oxidation of ferrous iron [Fe(II)] and/or arsenite [As(III)] coupled to nitrate reduction, impacting the biogeochemical cycles of Fe and As. However, the mechanisms for nitrate-dependent anaerobic oxidation of Fe(II) and As(III) remain unclear. In this study, we isolated two bacterial strains from arsenic-contaminated paddy soils, Ensifer sp. ST2 and Paracoccus sp. QY30. Both strains were capable of anaerobic As(III) oxidation, but only QY30 could oxidize Fe(II) under nitrate-reducing conditions. Both strains contain the As(III) oxidase gene aioA, whose expression was induced greatly by As(III) exposure. Both strains contain the whole suite of genes for complete denitrification, but the nitrite reductase gene nirK was not expressed in QY30 and nitrite accumulated under nitrate-reducing conditions. When the functional nirK gene was knocked out in strain ST2, its nitrite reduction ability was completely abolished and nitrite accumulated in the medium. Moreover, the ST2^ΔnirK mutant gained the ability to oxidize Fe(II). When nirK gene from ST2 was introduced to QY30, the recombinant strain QY30::nirK gained the ability to reduce nitrite but lost the ability to oxidize Fe(II). These genetic manipulations did not affect the ability of both strains to oxidize As(III). Our results indicate that nitrite accumulation is required for anaerobic oxidation of Fe(II) but not for As(III) oxidation in these strains. The results suggest that anaerobic Fe(II) oxidation in the two bacterial strains is primarily driven by abiotic reaction of Fe(II) with nitrite, while reduction of nitrate to nitrite is sufficient for redox coupling with anaerobic As(III) oxidation catalyzed by Aio. Deletion of nirK gene in denitrifiers can enhance anaerobic Fe(II) oxidation.