Potential role of nitrite for abiotic Fe (II) oxidation and cell encrustation during nitrate reduction by denitrifying bacteria (original) (raw)
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Environmental Science & Technology, 2018
Fe(II)-organic-matter (Fe(II)-OM) complexes are abundant in the environment and may play a key role for the behavior of Fe and pollutants. Mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) reduce nitrate coupled to the oxidation of organic compounds and Fe(II). Fe(II) oxidation may occur enzymatically or abiotically by reaction with nitrite that forms during heterotrophic denitrification. However, it is unknown whether Fe(II)-OM complexes can be oxidized by NRFeOx. We used cellsuspension experiments with the mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium Acidovorax sp. strain BoFeN1 to reveal the role of non-organically-bound Fe(II) (aqueous Fe(II)) and nitrite for the rates and extent of oxidation of Fe(II)-OM-complexes (Fe(II)-citrate, Fe(II)-EDTA, Fe(II)-humic-acid, and Fe(II)fulvic-acid). We found that Fe(II)-OM complexation inhibited microbial nitrate-reducing Fe(II) oxidation; large colloidal and negatively charged complexes showed lower oxidation rates than aqueous Fe(II). Accumulation of nitrite and fast abiotic oxidation of Fe(II)-OM complexes only happened in the presence of aqueous Fe(II) that probably interacted with (nitrite-reducing) enzymes in the periplasm causing nitrite accumulation in the periplasm and outside of the cells, whereas Fe(II)-OM complexes probably could not enter the periplasm and cause nitrite accumulation. These results suggest that Fe(II) oxidation by mixotrophic nitrate-reducers in the environment depends on Fe(II) speciation, and that aqueous Fe(II) potentially plays a critical role in regulating microbial denitrification processes.
Geobiology, 2005
Understanding the mechanisms of anaerobic microbial iron cycling is necessary for a full appreciation of presentday biogeochemical cycling of iron and carbon and for drawing conclusions about these cycles on the ancient Earth. Towards that end, we isolated and characterized an anaerobic nitrate-dependent Fe(II)-oxidizing bacterium from a freshwater sediment. The 16SrRNA gene sequence of the isolated bacterium (strain BoFeN1) places it within the β -Proteobacteria, with Acidovorax sp. strain G8B1 as the closest known relative. During mixotrophic growth with acetate plus Fe(II) and nitrate as electron acceptor, strain BoFeN1 forms Fe(III) mineral crusts around the cells. The amount of the organic cosubstrate acetate present seems to control the rate and extent of Fe(II) oxidation and the viability of the cells. The crystallinity of the mineral products is influenced by nucleation by Fe minerals that are already present in the inoculum.
Environmental science & technology, 2018
Fe(II)-organic matter (Fe(II)-OM) complexes are abundant in the environment and may play a key role for the behavior of Fe and pollutants. Mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) reduce nitrate coupled to the oxidation of organic compounds and Fe(II). Fe(II) oxidation may occur enzymatically or abiotically by reaction with nitrite that forms during heterotrophic denitrification. However, it is unknown whether Fe(II)-OM complexes can be oxidized by NRFeOx. We used cell-suspension experiments with the mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium Acidovorax sp. strain BoFeN1 to reveal the role of nonorganically bound Fe(II) (aqueous Fe(II)) and nitrite for the rates and extent of oxidation of Fe(II)-OM complexes (Fe(II)-citrate, Fe(II)-EDTA, Fe(II)-humic acid, and Fe(II)-fulvic acid). We found that Fe(II)-OM complexation inhibited microbial nitrate-reducing Fe(II) oxidation; large colloidal and negatively charged complexes showed lower oxidation rates...
FEMS Microbiology Ecology, 2009
In order to assess the importance of nitrate-dependent Fe(II) oxidation and its impact on the growth physiology of dominant Fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. Most probable number counts of nitrate-reducing Fe(II)-oxidizing bacteria in the sediment of Lake Constance, a freshwater lake in Southern Germany, yielded about 10 5 cells mL À1 of the total heterotrophic nitrate-reducing bacteria, with about 1% (10 3 cells mL À1 ) of nitrate-reducing Fe(II) oxidizers. We investigated the growth physiology of Acidovorax sp. strain BoFeN1, a dominant nitrate-reducing mixotrophic Fe(II) oxidizer isolated from this sediment. Strain BoFeN1 uses several organic compounds (but no sugars) as substrates for nitrate reduction. It also reduces nitrite, dinitrogen monoxide, and O 2 , but cannot reduce Fe(III). Growth experiments with cultures amended either with acetate plus Fe(II) or with acetate alone demonstrated that the simultaneous oxidation of Fe(II) and acetate enhanced growth yields with acetate alone (12.5 g dry mass mol À1 acetate) by about 1.4 g dry mass mol À1 Fe(II). Also, pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans strains can oxidize Fe(II) with nitrate, whereas Pseudomonas fluorescens and Thiobacillus denitrificans strains did not. Our study demonstrates that nitrate-dependent Fe(II) oxidation contributes to the energy metabolism of these bacteria, and that nitrate-dependent Fe(II) oxidation can essentially contribute to anaerobic iron cycling.
Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite
Applied and Environmental Microbiology, 2012
Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 10 7 cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations simila...
Geochimica et Cosmochimica Acta, 2013
The importance of microbial nitrate-dependent Fe(II) oxidation to iron biogeochemistry is well recognized. Past research has focused on oxidation of aqueous Fe 2+ and structural Fe(II) in oxides, carbonates, and phosphate, but the importance of structural Fe(II) in phyllosilicates in this reaction is only recently studied. However, the effect of clay mineralogy on the rate and the mechanism of the reaction, and subsequent mineralogical end products are still poorly known. The objective of this research was to study the coupled process of microbial oxidation of Fe(II) in clay mineral nontronite (NAu-2), and nitrate reduction by Pseudogulbenkiania species strain 2002, and to determine mineralogical changes associated with this process. Bio-oxidation experiments were conducted using Fe(II) in microbially reduced nontronite as electron donor and nitrate as electron acceptor in bicarbonate-buffered medium under both growth and nongrowth conditions to investigate cell growth on this process. The extents of Fe(II) oxidation and nitrate reduction were measured by wet chemical methods. X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), and 57 Fe-Mö ssbauer spectroscopy were used to observe mineralogical changes associated with Fe(III) reduction and Fe(II) oxidation in NAu-2. The bio-oxidation extent under growth and nongrowth conditions reached 67% and 57%, respectively. Over the same time period, nitrate was completely reduced under both conditions to nitrogen gas (N 2 ), via an intermediate product nitrite. Abiotic oxidation by nitrite partly accelerated Fe(II) oxidation rate under the growth condition. The oxidized Fe(III) largely remained in the nontronite structure, but secondary minerals such as vivianite, ferrihydrite, and magnetite formed depending on specific experimental conditions. The results of this study highlight the importance of iron-bearing clay minerals in the global nitrogen cycle with potential applications in nitrate removal in natural environments.
Formation of Fe(III)-minerals by Fe(II)-oxidizing photoautotrophic bacteria
Geochimica et Cosmochimica Acta, 2004
It has been suggested that Fe(II)-oxidizing photoautotrophic bacteria may have catalyzed the precipitation of an ancient class of sedimentary deposits known as Banded Iron Formations. In order to evaluate this claim, it is necessary to define and understand this process at a molecular level so that putative Fe-isotope "biosignatures" in ancient rocks can be interpreted. In this report, we characterize the substrates and products of photoautotrophic Fe(II)-oxidation by three phylogenetically distinct Fe(II)-oxidizing bacteria. In every case, dissolved Fe(II) is used as the substrate for oxidation, and there is no evidence for active dissolution of poorly soluble Fe(II)-minerals by biogenic organic ligands. Poorly crystalline Fe(III) (hydr)oxide mineral phases are initially precipitated, and as they age, rapidly convert to the crystalline minerals goethite and lepidocrocite. Although the precipitates appear to associate with the cell wall, they do not cover it entirely, and precipitate-free cells represent a significant portion of the population in aged cultures. Citrate is occasionally detected at nanomolar concentrations in all culture fluids, whereas an unknown organic molecule is always present in two out of the three bacterial cultures. Whether these molecules are released by the cell to bind Fe(III) and prevent the cell from encrustation by Fe(III) (hydr)oxides is uncertain, but seems unlikely if we assume Fe(II)-oxidation occurs at the cell surface. In light of the energetic requirement the cell would face to produce ligands for this purpose, and given the local acidity metabolically generated in the microenvironment surrounding Fe(II)-oxidizing cells, our results suggest that Fe(III) is released in a dissolved form as an inorganic aqueous complex and/or as a colloidal aggregate prior to mineral precipitation. The implication of these results for the interpretation of Fe-isotope fractionation measured for this class of bacteria is that equilibrium processes involving free biological ligands do not account for the observed fractionation.
Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria
Geochimica Et Cosmochimica Acta, 2009
Minerals formed by bio-oxidation of ferrous iron (Fe(II)) at neutral pH, their association with bacterial ultrastructures as well as their impact on the metabolism of iron-oxidizing bacteria remain poorly understood. Here, we investigated iron biomineralization by the anaerobic nitrate-dependent iron-oxidizing bacterium Acidovorax sp. strain BoFeN1 in the presence of dissolved Fe(II) using electron microscopy and Scanning Transmission X-ray Microscopy (STXM). All detected minerals consisted mainly of amorphous iron phosphates, but based on their morphology and localization, three types of precipitates could be discriminated: (1) mineralized filaments at distance from the cells, (2) globules of 100 ± 25 nm in diameter, at the cell surface and (3) a 40-nm thick mineralized layer within the periplasm. All of those phases were shown to be intimately associated with organic molecules. Periplasmic encrustation was accompanied by an accumulation of protein moieties. In the same way, exopolysaccharides were associated with the extracellular mineralized filaments. The evolution of cell encrustation was followed by TEM over the time course of a culture: cell encrustation proceeded progressively, with rapid precipitation in the periplasm (in a few tens of minutes), followed by the formation of surface-bound globules. Moreover, we frequently observed an asymmetric mineral thickening at the cell poles. In parallel, the evolution of iron oxidation was quantified by STXM: iron both contained in the bacteria and in the extracellular precipitates reached complete oxidation within 6 days. While a progressive oxidation of Fe in the bacteria and in the medium could be observed, spatial redox (oxido-reduction state) heterogeneities were detected at the cell poles and in the extracellular precipitates after 1 day. All these findings provide new information to further the understanding of molecular processes involved in iron biomineralization by anaerobic iron-oxidizing bacteria and offer potential signatures of those metabolisms that can be looked for in the geological record.
bioRxiv (Cold Spring Harbor Laboratory), 2022
Anaerobic nitrate-dependent iron(II) oxidation is a process common to many bacterial species, which promotes the formation of Fe(III) minerals that can influence the fate of soil and groundwater pollutants, such as arsenic. Herein, we investigated simultaneous nitrate-dependent Fe(II) and As(III) oxidation by Acidovorax sp. strain ST3 with the aim of studying the Fe biominerals formed, their As immobilization capabilities and the metabolic effect on cells. X-ray powder diffraction (XRD) and scanning transmission electron microscopy (STEM) nanodiffraction were applied for biomineral characterization in bulk and at the nanoscale, respectively. NanoSIMS (nanoscale secondary ion mass spectrometry) was used to map the intra and extracellular As and Fe distribution at the singlecell level and to trace metabolically active cells, by incorporation of a 13 C-labeled substrate (acetate). Metabolic heterogeneity among bacterial cells was detected, with periplasmic Fe mineral encrustation deleterious to cell metabolism. Interestingly, Fe and As were not co-localized in all cells, indicating delocalized sites of As(III) and Fe(II) oxidation. The Fe(III) minerals lepidocrocite and goethite were identified in XRD, although only lepidocrocite was identified via STEM nanodiffraction. Extracellular amorphous nanoparticles were formed earlier and retained more As(III/V) than crystalline "flakes" of lepidocrocite, indicating that longer incubation periods promote the formation of more crystalline minerals with lower As retention capabilities. Thus, the addition of nitrate promotes Fe(II) oxidation and formation of Fe(III) biominerals by ST3 cells which retain As(III/V), and although this process was metabolically detrimental to some cells, it warrants further examination as a viable mechanism for As removal in anoxic environments by biostimulation with nitrate. .