Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments

Iron-dependent autotrophic denitrification as a novel microbial driven and iron-mediated denitrification process: A critical review

Based on previous research results, iron-dependent autotrophic denitrification (IDAD) was evaluated in an all-around way to provide a theoretical basis for further research. First, this review systematically and comprehensively summarizes the development of IDAD technology and describes the physiological properties of relevant functional microorganisms and their potential mechanisms from different perspectives. Second, the possible Fe-N pathways involved in the reaction of different iron-based materials are discussed in detail. Then, the theoretical advantages of the IDAD process and potential problems are described, and the corresponding control strategies are summarized. The influence of key factors on denitrification is discussed in terms of operational and water quality parameters. In addition, the application and research direction of this technology in engineering are summarized. Finally, the latest development trends and prospects for future applications are discussed to promote an in-depth understanding of IDAD and its practical application in sewage treatment.

Promotion of nitrogen removal in a denitrification process elevated by zero-valent iron under low carbon-to-nitrogen ratio

The nitrogen removal efficiency and distribution of microbial community in a denitrification process aided by zero-valent iron (ZVI) under low carbon-to-nitrogen ratio (C/N) were assessed in this study. Experimental results demonstrated that the nitrogen removal efficiency (TNRE) increased to 96.4 ± 2.72% and 63.3 ± 4.02% after continuous addition of ZVI with molar ratio of ZVI to nitrate (NO3--N) (ZVI/N) of 6 at C/N of 3 and 2, respectively, which was 4% and 7.7% higher than the blank one. Meanwhile, extracellular polymeric substance (EPS) could be used as electron transfer medium and endogenous carbon source for denitrification system and also the production of which increased by 28.43% and 53.10% under ZVI stimulation compared to the control group. Finally, a symbiotic system composed by autotrophic and heterotrophic denitrification bacteria was formed by aid of ZVI. This study proposed new insights into denitrification process improved by ZVI.

Microbially mediated Fe-N coupled cycling at different hydrological regimes in riparian wetland

Although the significance of the coupled Fe- and N- cycling processes on biogeochemical transformation in riparian wetlands is well-known, the regulation associated with the changes on the microbiotas during different hydrological regimes remains unclear. This study performed field investigations on the bacterial community compositions (BCC) and specific genera associated to Fe- and N- cycling in the rhizosphere soil and sediments in a riparian wetland in Poyang lake, China. The predominant phyla Proteobacteria, Acidobacteria, and Nitrospirae from all the samples remarkably decreased after long-term continuous flooding, while Actinobacteria, Firmicutes and Bacteroidetes were enriched. For the family level, the relative abundances of iron-oxidizing bacteria (FeOB) Gallionellaceae, and N fixing bacteria Nitrospiraceae and Bradyrhizobiaceae significantly declined upon the long-term flooding and then increased with dewatering, which were consistent with the functional genes sequencing analysis. In which, the Bradyrhizobiaceae (RA 2.0 %-34.6 %) was the dominant nirS denitrifier and potential iron-reducing bacteria (FeRB), Sideroxydans lithotrophicus was one of the dominant FeOB (RA 1.7 %-23 %), which was also identified to be the nirS dentrifier (RA 0.2 %-4.3 %). The absolute quantification of the functional genes levels including nirS, nirK, FeRB (Geobacter spp.) showed their significant increases by 3-7 times upon desiccation compared to that under post-CF. The PCA and RDA results indicated the linkage between redox changes of N and Fe during inundation mediated by FeRB, NOB, and FeOB, which were closely related to hydrochemical indices NO₃^-, Fe²⁺ and SO₄^2-. These evidences all implied the likely occurrence of nitrate reduction coupled to Fe(II) oxidation (NRFeOx) under oligotrophic conditions, which was potentially facilitated by metabolizers consisting of highly correlated Bradyrhizobiaceae and Sideroxydans (rho = 0.86, p < 0.01). These findings provide an interpretation of the biological reactions in the microbially mediated NRFeOx processes driven by hydrological change, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in riparian wetlands.

Evidence for the occurrence of Feammox coupled with nitrate-dependent Fe(II) oxidation in natural enrichment cultures

Feammox is a newly discovered process of anaerobic ammonium oxidation driven by Fe(III) reduction. Nitrate-dependent Fe(II) oxidation (NDFO) is the coupling of Fe(II) oxidation and nitrate reduction to produce N₂ under anaerobic conditions. It has not been reported whether the coupling of the two reactions exists in natural enrichment. In this study, enrichment culture experiments were carrired out to prove the occurrence of Feammox with NDFO. The results indicated that the nitrogen and iron cycle were formed during natural enrichment cultures, including Fe(III) reduction and NH₄⁺-N was oxidation to NO₃^--N, NO₂^--N and N₂, Fe(III) and Fe(II) were cyclically formed, and Fe(II) was oxidized with NO₃^--N reduced to N₂. The removal efficiencies of ammonium nitrogen and total nitrogen in the incubation were about 92.9% and 20% respectively. Organic carbon experiments indicate that sodium acetate can promote the initial NO₃^--N removal and a low concentration of organic carbon limited the NDFO process because iron-oxidizing bacteria are mixotrophic microorganisms. The added 9,10-anthraquinone-2,6-disulfonate (AQDS) in the later stage can promote NDFO to remove nitrate, thereby increasing the TN removal efficiency to 50%. ¹⁵N-isotope tracer incubations provided direct evidence for the occurrence of Feammox coupled to NDFO, with rates producing ³⁰N₂ of Feammox (0.024-0.0288 mg N·L^-1·d^-1) and NDFO (0.0465-0.0833 mg N·L^-1·d^-1) in three groups (Wetland/Wheat soil/Sediment). 16S rRNA sequencing further demonstrated that Pseudomonas, Rhodanobacter, Acinetobacter and Thermomonas were the dominant generas among the enrichment cultures, and these bacteria belonged to FeOB and FeRB, which may further promote Feammox coupled to NDFO in the cultivation system.

Fe(II) enhances simultaneous phosphorus removal and denitrification in heterotrophic denitrification by chemical precipitation and stimulating denitrifiers activity

Using Fe(II) salt as the precipitant in heterotrophic denitrification achieves improved TP removal, and enhancement in denitrification was often observed. This study aimed to obtain a better understanding of Fe(II)-enhanced denitrification with sufficient carbon source supply. Laboratory-scale experiments were conducted in SBRs with or without Fe(II) addition. Remarkably improved TP removal was experienced. TP removal efficiency in Fe(II) adding reactor was 85.8 ± 3.4%; whereas, that in the reactor without Fe(II) addition was 31.1 ± 2.8%. Besides improved TP removal, better TN removal efficiency (94.1 ± 1.1%) were recorded when Fe(II) was added, and that in the reactor without Fe(II) addition was 89 ± 0.8%. The specific denitrification rate were observed increase by 12.6% when Fe(II) was added. Further microbial analyses revealed increases in the abundances of typical denitrifiers (i.e. Niastella, Opitutus, Dechloromonas, Ignavibacterium, Anaeromyxobacter, Pedosphaera, and Myxococcus). Their associated denitrifying genes, narG, nirS, norB, and nosZ, were observed had 14.2%, 19.4%, 21.6%, and 9.9% elevation, respectively. Such enhancement in denitrification shall not be due to nitrate-dependent ferrous oxidation, which prevails in organic-deficient environments. In an environment with a continuous supply of Fe(II) and plenty of carbon sources, a cycle of denitrifying enzyme activity enhancement in the presence of Fe(II) facilitating nitrogen substrate utilization, stimulating denitrifier metabolism and growth, elevating denitrifying genes abundance, and increasing denitrifying enzymes expression were thought to be responsible for the Fe(II)-enhanced heterotrophic denitrification. Fe(II) salt is often a less expensive precipitant and has recently become attractive for TP removal in wastewater. The findings of this study solidify previous observation of enhancement of both TP and TN removal by adding Fe(II) in denitrification, and would be helpful for developing cost-effective pollutant removal processes.

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.

A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant Gallionellaceae sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a Gallionellaceae sp., Noviherbaspirillum sp., and Thiobacillus sp., were likely involved in metal oxidation (e.g., cyc2, mtoA), denitrification (e.g., nirK/S, norBC), carbon fixation (e.g., rbcL), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the Gallionellaceae sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms in situ. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct Gallionellaceae taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance in situ). Since several of these in situ-detected Gallionellaceae taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.

Coupling of Fe-C and aerobic granular sludge to treat refractory wastewater from a membrane manufacturer in a pilot-scale system

A novel pilot-scale system based on aerobic granular sludge (AGS) as a biological treatment step was proposed to treat refractory wastewater from a membrane manufacturer. The components of the system included a microelectrolysis Fe-C filter, a hydrolysis acidification bioreactor (HA), sequence batch reactor 1 (AGS SBR1), sequence batch reactor 2 (AGS SBR2), and a membrane bioreactor (MBR). The Fe-C filter effectively improved the biodegradability of the wastewater components and introduced some byproducts (such as Fe²⁺, Fe³⁺, and Fe minerals) that are beneficial for the cultivation and stability of the AGS. Ideal conditions for aerobic granulation were maintained in the SBR, such as alternating feast and famine conditions. A selection pressure, including a hydraulic shear force and settling time, was also created therein. The results showed that the AGS was formed successfully in both SBR1 and SBR2, the sludge volume index after 30 min (SVI₃₀) and mean particle size reached 34.2 mL/g and 720 µm, and 36.7 mL/g and 610 µm, respectively, and a satisfactory nutrient removal capacity was achieved in the system. During the entire experimental period, the microbial community changed significantly; enrichment of microbes with the secretion of extracellular polymeric substances (EPS), granule stabilization functions in the AGS, and the differentiation of microbes corresponding to the function of each unit were observed. The use of Fe-C, application of SBRs, and use of dewatered sludge as an inoculant played key roles in the cultivation and stability of the AGS.

Aerobic microbial communities in the sediments of a marine oxygen minimum zone

The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15–30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 10⁷ (g sediment)^-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates’ genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.

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.

Role of organic carbon, nitrate and ferrous iron on the partitioning between denitrification and DNRA in constructed stormwater urban wetlands

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed wetlands. An important factor that controls DNRA in an aquatic ecosystem is the electron donor, commonly organic carbon (OC) or alternatively ferrous iron and sulfide. In this study, we investigated the role of natural organic carbon (NOC) and acetate at different OC/NO₃^- ratios and ferrous iron on the partitioning between DNF and DNRA using the ¹⁵N-tracer method in slurries from four constructed stormwater urban wetlands in Melbourne, Australia. The carbon and nitrate experiments revealed that DNF dominated at all OC/NO₃^- ratios. The higher DNF and DNRA rates observed after the addition of NOC indicates that nitrate reduction was enhanced more by NOC than acetate. Moreover, addition of NOC in slurries stimulated DNRA more than DNF. Interestingly, slurries amended with Fe²⁺ showed that Fe²⁺ had significant control on the balance between DNF and DNRA. From two out of four wetlands, a significant increase in DNRA rates (p < .05) at the cost of DNF in the presence of available Fe²⁺ suggests DNRA is coupled to Fe²⁺ oxidation. Rates of DNRA increased 1.5-3.5 times in the Fe²⁺ treatment compared to the control. Overall, our study provides direct evidence that DNRA is linked to Fe²⁺ oxidation in some wetland sediments and highlights the role of Fe²⁺ in controlling the partitioning between removal (DNF) and recycling (DNRA) of bioavailable N in stormwater urban constructed wetlands. In our study we also measured anammox and found that it was always <0.05% of total nitrate reduction in these sediments.

The enhancement of iron fuel cell on bio-cathode denitrification and its mechanism as well as the microbial community analysis of bio-cathode

To address the issue of insufficient electrons during denitrification, an iron fuel cell (IFC) bioreactor using iron as abiotic anode was designed. The nitrogen removal efficiency (NRE) of IFC (2.54 ± 0.016%) was significantly lower than microbial fuel cell (MFC) (32.58 ± 0.033%) with same bio-cathode under autotrophic conditions, which was due to the permeation of acetate on proton exchange membrane (PEM) affected the process of enriching autotrophic denitrifying bacteria by MFC. When used in heterotrophic conditions, the NRE of the closed-circuits of IFC was 29.04%, 10.53%, 8.33% higher than open-circuits, respectively, when the COD/nitrogen (C/N) ratios was 1, 2 and 3. The enhancement of IFC was the iron anode could convert a portion of nitrate to nitrite according to the abiotic cathode control experiments. The mainly functional bacteria of bio-cathode was Paracoccus (53.04%). In conclusion, the IFC could be a theoretical model for using inorganic electron donor during denitrification.

High diversity of potential nitrate-reducing Fe(II)-oxidizing bacteria enriched from activated sludge

Nitrate-dependent Fe(II) oxidation (NDFO) has been discovered in various environments including activated sludge and can potentially be used to remove nitrate from wastewater. In this study, NDFO sludge was successfully enriched from activated sludge under high Fe(II) concentrations over 100 days and the denitrification rate achieved 1.37 mmol N/(gVSS day). High-throughput sequencing of the bacterial 16S rRNA gene was used to investigate the microbial community structure dynamics during the enrichment process. The results showed that the microbial community changed significantly and high diversity of potential Fe(II)-oxidizing bacteria (FeOB) was observed in the enriched sludge. Thermomonas and Gallionella were the dominant bacterial genera in the enriched sludge and their relative abundances accounted for 9.49 and 4.08%, respectively. Furthermore, it was found that potential FeOB were also abundantly present in activated sludge samples of common municipal wastewater treatment plants. Collectively, this study demonstrated that NDFO could be successfully performed by enriched activated sludge and high diversity of bacteria is involved in this process, and the results also provide baseline information for future research and engineering application of NDFO process.

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.

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

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

A novel organotrophic nitrate-reducing Fe(ii)-oxidizing bacterium isolated from paddy soil and draft genome sequencing indicate its metabolic versatility

Physiological and genomic information of this strain provide preliminary evidence for nitrate-reduction coupled Fe(ii)-oxidation in microorganisms from paddy soil.

Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.

Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.

Two-step partial nitritation/Anammox process in granulation reactors: Start-up operation and microbial characterization

A two-stage Partial Nitritation (PN)/Anammox process was carried out at lab-scale conditions to treat reject water from a municipal WWTP. PN was achieved in a granular SBR obtaining an effluent with a NH4(+)-N/NO2(-)-N molar ratio around 1.0. The microbial characterization of this reactor revealed a predominance of Betaproteobacteria, with a member of Nitrosomonas as the main autotrophic ammonium oxidizing bacterium (AOB). Nitrite oxidizing bacteria (NOB) were under the detection limit of 16S rRNA gene pyrosequencing, indicating their effective inhibition. The effluent of the PN reactor was fed to an Anammox SBR where stable operation was achieved with a NH4(+)-N:NO2(-)-N:NO3(-)-N stoichiometry of 1:1.25:0.14. The deviation to the theoretical stoichiometry could be attributed to the presence of heterotrophic biomass in the Anammox reactor (mainly members of Chlorobi and Chloroflexi). Planctomycetes accounted for 7% of the global community, being members of Brocadia (1.4% of the total abundance) the main anaerobic ammonium oxidizer detected.

The origin and implications of clay minerals from Yellowknife Bay, Gale crater, Mars

The Mars Science Laboratory (MSL) rover Curiosity has documented a section of fluvio-lacustrine strata at Yellowknife Bay (YKB), an embayment on the floor of Gale crater, approximately 500 m east of the Bradbury landing site. X-ray diffraction (XRD) data and evolved gas analysis (EGA) data from the CheMin and SAM instruments show that two powdered mudstone samples (named John Klein and Cumberland) drilled from the Sheepbed member of this succession contain up to ~20 wt% clay minerals. A trioctahedral smectite, likely a ferrian saponite, is the only clay mineral phase detected in these samples. Smectites of the two samples exhibit different 001 spacing under the low partial pressures of H₂O inside the CheMin instrument (relative humidity <1%). Smectite interlayers in John Klein collapsed sometime between clay mineral formation and the time of analysis to a basal spacing of 10 Å, but largely remain open in the Cumberland sample with a basal spacing of ~13.2 Å. Partial intercalation of Cumberland smectites by metal-hydroxyl groups, a common process in certain pedogenic and lacustrine settings on Earth, is our favored explanation for these differences. The relatively low abundances of olivine and enriched levels of magnetite in the Sheepbed mudstone, when compared with regional basalt compositions derived from orbital data, suggest that clay minerals formed with magnetite in situ via aqueous alteration of olivine. Mass-balance calculations are permissive of such a reaction. Moreover, the Sheepbed mudstone mineral assemblage is consistent with minimal inputs of detrital clay minerals from the crater walls and rim. Early diagenetic fabrics suggest clay mineral formation prior to lithification. Thermodynamic modeling indicates that the production of authigenic magnetite and saponite at surficial temperatures requires a moderate supply of oxidants, allowing circum-neutral pH. The kinetics of olivine alteration suggest the presence of fluids for thousands to hundreds of thousands of years. Mineralogical evidence of the persistence of benign aqueous conditions at YKB for extended periods indicates a potentially habitable environment where life could establish itself. Mediated oxidation of Fe²⁺ in olivine to Fe³⁺ in magnetite, and perhaps in smectites provided a potential energy source for organisms.

The origin and implications of clay minerals from Yellowknife Bay, Gale crater, Mars

The Mars Science Laboratory (MSL) rover Curiosity has documented a section of fluvio-lacustrine strata at Yellowknife Bay (YKB), an embayment on the floor of Gale crater, approximately 500 m east of the Bradbury landing site. X-ray diffraction (XRD) data and evolved gas analysis (EGA) data from the CheMin and SAM instruments show that two powdered mudstone samples (named John Klein and Cumberland) drilled from the Sheepbed member of this succession contain up to ~20 wt% clay minerals. A trioctahedral smectite, likely a ferrian saponite, is the only clay mineral phase detected in these samples. Smectites of the two samples exhibit different 001 spacing under the low partial pressures of H₂O inside the CheMin instrument (relative humidity <1%). Smectite interlayers in John Klein collapsed sometime between clay mineral formation and the time of analysis to a basal spacing of 10 Å, but largely remain open in the Cumberland sample with a basal spacing of ~13.2 Å. Partial intercalation of Cumberland smectites by metal-hydroxyl groups, a common process in certain pedogenic and lacustrine settings on Earth, is our favored explanation for these differences. The relatively low abundances of olivine and enriched levels of magnetite in the Sheepbed mudstone, when compared with regional basalt compositions derived from orbital data, suggest that clay minerals formed with magnetite in situ via aqueous alteration of olivine. Mass-balance calculations are permissive of such a reaction. Moreover, the Sheepbed mudstone mineral assemblage is consistent with minimal inputs of detrital clay minerals from the crater walls and rim. Early diagenetic fabrics suggest clay mineral formation prior to lithification. Thermodynamic modeling indicates that the production of authigenic magnetite and saponite at surficial temperatures requires a moderate supply of oxidants, allowing circum-neutral pH. The kinetics of olivine alteration suggest the presence of fluids for thousands to hundreds of thousands of years. Mineralogical evidence of the persistence of benign aqueous conditions at YKB for extended periods indicates a potentially habitable environment where life could establish itself. Mediated oxidation of Fe²⁺ in olivine to Fe³⁺ in magnetite, and perhaps in smectites provided a potential energy source for organisms.

The origin and implications of clay minerals from Yellowknife Bay, Gale crater, Mars

The Mars Science Laboratory (MSL) rover Curiosity has documented a section of fluvio-lacustrine strata at Yellowknife Bay (YKB), an embayment on the floor of Gale crater, approximately 500 m east of the Bradbury landing site. X-ray diffraction (XRD) data and evolved gas analysis (EGA) data from the CheMin and SAM instruments show that two powdered mudstone samples (named John Klein and Cumberland) drilled from the Sheepbed member of this succession contain up to ~20 wt% clay minerals. A trioctahedral smectite, likely a ferrian saponite, is the only clay mineral phase detected in these samples. Smectites of the two samples exhibit different 001 spacing under the low partial pressures of H₂O inside the CheMin instrument (relative humidity <1%). Smectite interlayers in John Klein collapsed sometime between clay mineral formation and the time of analysis to a basal spacing of 10 Å, but largely remain open in the Cumberland sample with a basal spacing of ~13.2 Å. Partial intercalation of Cumberland smectites by metal-hydroxyl groups, a common process in certain pedogenic and lacustrine settings on Earth, is our favored explanation for these differences. The relatively low abundances of olivine and enriched levels of magnetite in the Sheepbed mudstone, when compared with regional basalt compositions derived from orbital data, suggest that clay minerals formed with magnetite in situ via aqueous alteration of olivine. Mass-balance calculations are permissive of such a reaction. Moreover, the Sheepbed mudstone mineral assemblage is consistent with minimal inputs of detrital clay minerals from the crater walls and rim. Early diagenetic fabrics suggest clay mineral formation prior to lithification. Thermodynamic modeling indicates that the production of authigenic magnetite and saponite at surficial temperatures requires a moderate supply of oxidants, allowing circum-neutral pH. The kinetics of olivine alteration suggest the presence of fluids for thousands to hundreds of thousands of years. Mineralogical evidence of the persistence of benign aqueous conditions at YKB for extended periods indicates a potentially habitable environment where life could establish itself. Mediated oxidation of Fe²⁺ in olivine to Fe³⁺ in magnetite, and perhaps in smectites provided a potential energy source for organisms.

Autotrophic denitrification with anaerobic Fe(2+) oxidation by a novel Pseudomonas sp. W1

In the present study, a novel Pseudomonas sp. W1 was characterized in terms of its ability to perform nitrate removal coupled with anaerobic Fe⁻¹ oxidation under autotrophic growth condition. The effects of operating parameters with respect to the initial solution pH, temperature and initial Fe⁻¹ concentration on nitrate removal were investigated by central composite design. Based on the results of response surface methodology, the maximal nitrate removal efficiency was achieved under the following conditions: pH 7.0, temperature 30 °C and initial Fe⁻¹ concentration 1,100 mg L⁻¹. Under this optimal condition and with an initial NO(3)(-)-N concentration of 55 mg L⁻¹, this strain could remove NO(3)(-)-N with 90% reduction of NO(3)(-)-N, corresponding to oxidizing Fe⁻¹ with 71% oxidation of Fe⁻¹ after 7 days of incubation. The result of kinetic evaluation indicated that this bacterium showed significant substrate affinity to both NO(3)(-)-N and Fe⁻¹.

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575^T under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575^T grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575^T are dominant under anoxic conditions. Furthermore, strain DSM 6575^T forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575^T, and could contribute to biogeochemical cycles of Fe and N in the environment.

Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate

This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O.

Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitrate-dependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitrate-dependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 × 10(4) autotrophic and 1 × 10(7) heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to ~0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using (13)CO2 was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.

Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions

Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO(3)(-)) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO(2)(-)/NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO(2)(-), NO, and N(2)O in the environment.

Arsenic bioremediation by biogenic iron oxides and sulfides

Microcosms containing sediment from an aquifer in Cambodia with naturally elevated levels of arsenic in the associated groundwater were used to evaluate the effectiveness of microbially mediated production of iron minerals for in situ As remediation. The microcosms were first incubated without amendments for 28 days, and the release of As and other geogenic chemicals from the sediments into the aqueous phase was monitored. Nitrate or a mixture of sulfate and lactate was then added to stimulate biological Fe(II) oxidation or sulfate reduction, respectively. Without treatment, soluble As concentrations reached 3.9 ± 0.9 μM at the end of the 143-day experiment. However, in the nitrate- and sulfate-plus-lactate-amended microcosms, soluble As levels decreased to 0.01 and 0.41 ± 0.13 μM, respectively, by the end of the experiment. Analyses using a range of biogeochemical and mineralogical tools indicated that sorption onto freshly formed hydrous ferric oxide (HFO) and iron sulfide mineral phases are the likely mechanisms for As removal in the respective treatments. Incorporation of the experimental results into a one-dimensional transport-reaction model suggests that, under conditions representative of the Cambodian aquifer, the in situ precipitation of HFO would be effective in bringing groundwater into compliance with the World Health Organization (WHO) provisional guideline value for As (10 ppb or 0.13 μM), although soluble Mn release accompanying microbial Fe(II) oxidation presents a potential health concern. In contrast, production of biogenic iron sulfide minerals would not remediate the groundwater As concentration below the recommended WHO limit.

Natural organic matter as global antennae for primary production

Humic substances (HS) are high-molecular-weight complex refractory organics that are ubiquitous in terrestrial and aquatic environments. While resistant to microbial degradation, these compounds nevertheless support microbial metabolism via oxidation or reduction of their (hydro)quinone moieties. As such, they are known to be important electron sinks for respiratory and fermentative bacteria and electron sources for denitrifying and perchlorate-reducing bacteria. HS also strongly promote abiotic reduction of Fe(III) when irradiated with light. Here, we show that HS-enhanced Fe(III) photoreduction can also drive chemolithotrophic microbial respiration by producing Fe(II), which functions as a respiratory electron donor. Due to their molecular complexity, HS absorb most of the electromagnetic spectrum and can act as broad-spectrum antennae converting radiant energy into bioavailable chemical energy. The finding that chemolithotrophic organisms can utilize this energy has important implications for terrestrial, and possibly extraterrestrial, microbial processes and offers an alternative mechanism of radiation-driven primary productivity to that of phototrophy.

Nitrate-dependent ferrous iron oxidation by anaerobic ammonium oxidation (anammox) bacteria

We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.

A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria

Abstract Using the MicroDrop((R)) microdispenser system, a novel approach for high throughput cultivation assays for the determination of numbers of culturable bacteria, and for the isolation of bacteria in liquid media was established. The MicroDrop device works similar to an ink jet printer. Droplets of 150-200 pl are created at the nozzle of a glass micropipette by means of a computer-driven piezo transducer, and are dispensed automatically at predetermined positions with the aid of a XYZ-positioning system. The actual drop volume is highly reproducible and is determined by the pulse duration, the pulse frequency and the micropipette geometry. Culture media in 96-well microtiter plates were inoculated with constant numbers of bacteria from three different natural freshwater lakes. The number of culturable bacteria in the sample can be calculated from the frequency of wells showing bacterial growth, based on a binomial distribution of culturable cells. Our method was compared to the conventional most probable number (MPN) approach, the technique presently most often used for the determination of bacterial culturability and for the isolation of numerically dominant culturable bacteria. As opposed to the MPN technique, our approach yields data with much higher statistical significance (i.e. a 10 times lower standard deviation) due to the higher number of parallels which can be performed in each microtiter plate. The values of culturable bacteria as determined by the MPN and MicroDrop techniques were only weakly correlated (r(2)=0.570, n=42, P<0.001). Cultivation efficiencies obtained with the MicroDrop technique were systematically lower than MPN values by a factor of 2.7, indicating a significant overestimation of culturability by the latter method. The composition of the cultured bacterial fraction was determined by denaturing gradient gel electrophoresis fingerprinting of 16S rDNA fragments and sequencing. This demonstrated that phylogenetically similar bacteria were recovered by both cultivation techniques. Both methods resulted in the recovery of many previously unknown aquatic bacteria affiliated to the same taxonomic groups and, in one case, in the isolation of a numerically dominant, but not-yet-cultured beta-Proteobacterium which was ubiquitous in all three lakes.

Microbial Iron(II) Oxidation in Littoral Freshwater Lake Sediment: The Potential for Competition between Phototrophic vs. Nitrate-Reducing Iron(II)-Oxidizers

The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediment, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e⁻ donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic most probable number counted 3.4·10⁵ cells·g⁻¹ and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totaled 1.8·10⁴ and 4.5·10⁴ cells·g⁻¹ dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e⁻ donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle.

Abiotic and Microbial Interactions during Anaerobic Transformations of Fe(II) and [Formula: see text]

Microbial Fe(II) oxidation using [Formula: see text] as the terminal electron acceptor [nitrate-dependent Fe(II) oxidation, NDFO] has been studied for over 15 years. Although there are reports of autotrophic isolates and stable enrichments, many of the bacteria capable of NDFO are known organotrophic [Formula: see text]-reducers that require the presence of an organic, primary substrate, e.g., acetate, for significant amounts of Fe(II) oxidation. Although the thermodynamics of Fe(II) oxidation are favorable when coupled to either [Formula: see text] or [Formula: see text] reduction, the kinetics of abiotic Fe(II) oxidation by [Formula: see text] are relatively slow except under special conditions. NDFO is typically studied in batch cultures containing millimolar concentrations of Fe(II), [Formula: see text], and the primary substrate. In such systems, [Formula: see text] is often observed to accumulate in culture media during Fe(II) oxidation. Compared to [Formula: see text] abiotic reactions of biogenic [Formula: see text] and Fe(II) are relatively rapid. The kinetics and reaction pathways of Fe(II) oxidation by [Formula: see text] are strongly affected by medium composition and pH, reactant concentration, and the presence of Fe(II)-sorptive surfaces, e.g., Fe(III) oxyhydroxides and cellular surfaces. In batch cultures, the combination of abiotic and microbial Fe(II) oxidation can alter product distribution and, more importantly, results in the formation of intracellular precipitates and extracellular Fe(III) oxyhydroxide encrustations that apparently limit further cell growth and Fe(II) oxidation. Unless steps are taken to minimize or account for potential abiotic reactions, results of microbial NDFO studies can be obfuscated by artifacts of the chosen experimental conditions, the use of inappropriate analytical methods, and the resulting uncertainties about the relative importance of abiotic and microbial reactions. In this manuscript, abiotic reactions of [Formula: see text] and [Formula: see text] with aqueous Fe(2+), chelated Fe(II), and solid-phase Fe(II) are reviewed along with factors that can influence overall NDFO reaction rates in microbial systems. In addition, the use of low substrate concentrations, continuous-flow systems, and experimental protocols that minimize experimental artifacts and reduce the potential for under- or overestimation of microbial NDFO rates are discussed.

Toward a mechanistic understanding of anaerobic nitrate-dependent iron oxidation: balancing electron uptake and detoxification

The anaerobic oxidation of Fe(II) by subsurface microorganisms is an important part of biogeochemical cycling in the environment, but the biochemical mechanisms used to couple iron oxidation to nitrate respiration are not well understood. Based on our own work and the evidence available in the literature, we propose a mechanistic model for anaerobic nitrate-dependent iron oxidation. We suggest that anaerobic iron-oxidizing microorganisms likely exist along a continuum including: (1) bacteria that inadvertently oxidize Fe(II) by abiotic or biotic reactions with enzymes or chemical intermediates in their metabolic pathways (e.g., denitrification) and suffer from toxicity or energetic penalty, (2) Fe(II) tolerant bacteria that gain little or no growth benefit from iron oxidation but can manage the toxic reactions, and (3) bacteria that efficiently accept electrons from Fe(II) to gain a growth advantage while preventing or mitigating the toxic reactions. Predictions of the proposed model are highlighted and experimental approaches are discussed.

Anoxic iron cycling bacteria from an iron sulfide- and nitrate-rich freshwater environment

In this study, both culture-dependent and culture-independent methods were used to determine whether the iron sulfide mineral- and nitrate-rich freshwater nature reserve Het Zwart Water accommodates anoxic microbial iron cycling. Molecular analyses (16S rRNA gene clone library and fluorescence in situ hybridization, FISH) showed that sulfur-oxidizing denitrifiers dominated the microbial population. In addition, bacteria resembling the iron-oxidizing, nitrate-reducing Acidovorax strain BrG1 accounted for a major part of the microbial community in the groundwater of this ecosystem. Despite the apparent abundance of strain BrG1-like bacteria, iron-oxidizing nitrate reducers could not be isolated, likely due to the strictly autotrophic cultivation conditions adopted in our study. In contrast an iron-reducing Geobacter sp. was isolated from this environment while FISH and 16S rRNA gene clone library analyses did not reveal any Geobacter sp.-related sequences in the groundwater. Our findings indicate that iron-oxidizing nitrate reducers may be of importance to the redox cycling of iron in the groundwater of our study site and illustrate the necessity of employing both culture-dependent and independent methods in studies on microbial processes.

Enhanced growth of Acidovorax sp. strain 2AN during nitrate-dependent Fe(II) oxidation in batch and continuous-flow systems

Microbial nitrate-dependent, Fe(II) oxidation (NDFO) is a ubiquitous biogeochemical process in anoxic sediments. Since most microorganisms that can oxidize Fe(II) with nitrate require an additional organic substrate for growth or sustained Fe(II) oxidation, the energetic benefits of NDFO are unclear. The process may also be self-limiting in batch cultures due to formation of Fe-oxide cell encrustations. We hypothesized that NDFO provides energetic benefits via a mixotrophic physiology in environments where cells encounter very low substrate concentrations, thereby minimizing cell encrustations. Acidovorax sp. strain 2AN was incubated in anoxic batch reactors in a defined medium containing 5 to 6 mM NO₃⁻, 8 to 9 mM Fe²⁺, and 1.5 mM acetate. Almost 90% of the Fe(II) was oxidized within 7 days with concomitant reduction of nitrate and complete consumption of acetate. Batch-grown cells became heavily encrusted with Fe(III) oxyhydroxides, lost motility, and formed aggregates. Encrusted cells could neither oxidize more Fe(II) nor utilize further acetate additions. In similar experiments with chelated iron (Fe(II)-EDTA), encrusted cells were not produced, and further additions of acetate and Fe(II)-EDTA could be oxidized. Experiments using a novel, continuous-flow culture system with low concentrations of substrate, e.g., 100 μM NO₃⁻, 20 μM acetate, and 50 to 250 μM Fe²⁺, showed that the growth yield of Acidovorax sp. strain 2AN was always greater in the presence of Fe(II) than in its absence, and electron microscopy showed that encrustation was minimized. Our results provide evidence that, under environmentally relevant concentrations of substrates, NDFO can enhance growth without the formation of growth-limiting cell encrustations.

Leaching behavior of iron from simulated landfills with different operational modes

The aim of the present study was to investigate the leaching behavior of iron from simulated landfills with different operation modes, with an emphasis on the variation of iron in different oxidation state, ferrous Fe(II) and ferric Fe(III) percentage and the distribution of iron content in different landfill leachate fractions. The leaching behavior and accumulated amounts of iron leached out by leachate from conventional landfill (CL) and leachate recirculated landfill (RL) exhibited decidedly different trends except for the initial 28 days. In addition, the percentage of iron leached from CL and RL accounted 1.00% and 0.14% for the total amount in landfills, respectively. No correlations between iron and selected characteristics in leachate were found were observed in the two simulated landfills. Significant positive correlations between particulate bound iron and Fe(III) were found in the leachates from RL (R(2)=0.748) and CL (R(2)=0.833).

Repeated anaerobic microbial redox cycling of iron

Some nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifying Betaproteobacteria (e.g., Dechloromonas) and Fe(III)-reducing Deltaproteobacteria (Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that both Geobacter and various Betaproteobacteria participated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments.

The iron-oxidizing proteobacteria

The ‘iron bacteria’ are a collection of morphologically and phylogenetically heterogeneous prokaryotes. They include some of the first micro-organisms to be observed and described, and continue to be the subject of a considerable body of fundamental and applied microbiological research. While species of iron-oxidizing bacteria can be found in many different phyla, most are affiliated with the Proteobacteria. The latter can be subdivided into four main physiological groups: (i) acidophilic, aerobic iron oxidizers; (ii) neutrophilic, aerobic iron oxidizers; (iii) neutrophilic, anaerobic (nitrate-dependent) iron oxidizers; and (iv) anaerobic photosynthetic iron oxidizers. Some species (mostly acidophiles) can reduce ferric iron as well as oxidize ferrous iron, depending on prevailing environmental conditions. This review describes what is currently known about the phylogenetic and physiological diversity of the iron-oxidizing proteobacteria, their significance in the environment (on the global and micro scales), and their increasing importance in biotechnology.

A comparative study on two extraction procedures in speciation of iron in municipal solid waste

Two extraction reagents, hydrochloric acid (HCl) and acid ammonium oxalate solution (Tamm's reagent), were used to evaluate the redox state of iron in municipal solid waste (MSW) with different deposit ages. Orthogonal experiments were conducted to optimize the extraction conditions for extractable iron speciation (ferric and ferrous) in MSW. The optimal extraction conditions for HCl were determined as follows: the liquid-to-solid ratio was set at 100, and then the samples were extracted at the shaking speed of 200 rpm at 35 degrees C for 60 min by 1.00 M HCl. For Tamm's reagent, the optimal extraction conditions were extracted at the shaking speed of 175 rpm at 30 degrees C for 12 h with the same liquid-to-solid ratio. However, Tamm's reagent extraction is much more laborious and time-consuming. Thus the HC1 extraction might be a better choice for the evaluation of the redox state of iron in MSW. The results also showed that the yield of extractable iron increased with deposited age. About 60-83% of extractable iron was presented as ferrous in the MSW deposited for 1-8 years. This study supplied a tool for investigating the role of iron on the fate of pollutants in the landfill.

Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen

The ecological importance of Fe(II)-oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O(2) where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ∼ 5) located in northern Bavaria, Germany. Mean O(2) penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid-tolerant FeOB cultivated in gradient tubes were most abundant (10(6) cells g(-1) peat) at the 10-20 cm depth interval. A stable enrichment culture was active at up to 29% O(2) saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid-tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD-1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale-goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid-tolerant population of FeOB is thriving at redox interfaces formed by diffusion-limited O(2) transport in acidic peatlands. Furthermore, this well-adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle.