Dissimilatory Iron-reducing Bacteria Research Articles

Enhancing anaerobic digestion of actual papermaking wastewater with addition of Fenton sludge

The effect of Fenton sludge on anaerobic digestion of actual papermaking wastewater was investigated in this study. The results showed the iron in the Fenton sludge primarily exists in the form of needle-like iron oxide (FeOOH) and showed high electron transfer capability. Fenton sludge promoted electron transport in anaerobic digestion and electron transport system activity increased by 59 %. Fenton sludge enhanced the metabolic activity of anaerobic microorganisms, especially that of the hydrogenotrophic methanogens, the content of coenzyme F420 increased by 48.9 %. Besides, the microbial community structure in anaerobic digestion was affected by Fenton sludge, the quantity of microorganisms increased significantly. The dissimilatory iron-reducing bacteria (Desulfobacterota) and hydrogenotrophic methanogens (Methanobacterium and Methanolinea) were enriched, which promoted the methane production. As a result, the anaerobic digestion performance of papermaking wastewater was promoted significantly by adding Fenton sludge, the organic matter removal efficiency and methane production increased by 11.17 % and 15.12 %. This study provided an effective solution for the optimisation of anaerobic treatment of actual refractory organic wastewater.

Morphological, Microstructural, and In Situ Chemical Characteristics of Siderite Produced by Iron-Reducing Bacteria.

Dissimilatory iron-reducing bacteria (DIRB) oxidize organic matter or hydrogen and reduce ferric iron to form Fe(II)-bearing minerals, such as magnetite and siderite. However, compared with magnetite, which was extensively studied, the mineralization process and mechanisms of siderite remain unclear. Here, with the combination of advanced electron microscopy and synchrotron-based scanning transmission X-ray microscopy (STXM) approaches, we studied in detail the morphological, structural, and chemical features of biogenic siderite via a growth experiment with Shewanella oneidensis MR-4. Results showed that along with the growth of cells, Fe(II) ions were increasingly released into solution and reacted with CO32- to form micrometer-sized siderite minerals with spindle, rod, peanut, dumbbell, and sphere shapes. They are composed of many single-crystal siderite plates that are fanned out from the center of the particles. Additionally, STXM revealed Fh and organic molecules inside siderite. This suggests that the siderite crystals might assemble around a Fh-organic molecule core and then continue to grow radially. This study illustrates the biomineralization and assembly of siderite by a successive multistep growth process induced by DIRB, also provides evidences that the distinctive shapes and the presence of organic molecules inside might be morphological and chemical features for biogenic siderite.

Incorporation of Shewanella oneidensis MR-1 and goethite stimulates anaerobic Sb(III) oxidation by the generation of labile Fe(III) intermediate

Dissimilatory iron-reducing bacteria (DIRB) affect the geochemical cycling of redox-sensitive pollutants in anaerobic environments by controlling the transformation of Fe morphology. The anaerobic oxidation of antimonite (Sb(III)) driven by DIRB and Fe(III) oxyhydroxides interactions has been previously reported. However, the oxidative species and mechanisms involved remain unclear. In this study, both biotic phenomenon and abiotic verification experiments were conducted to explore the formed oxidative intermediates and related processes that lead to anaerobic Sb(III) oxidation accompanied during dissimilatory iron reduction. Sb(V) up to 2.59 μmol L−1 combined with total Fe(II) increased to 188.79 μmol L−1 when both Shewanella oneidensis MR-1 and goethite were present. In contrast, no Sb(III) oxidation or Fe(III) reduction occurred in the presence of MR-1 or goethite alone. Negative open circuit potential (OCP) shifts further demonstrated the generation of interfacial electron transfer (ET) between biogenic Fe(II) and goethite. Based on spectrophotometry, electron spin resonance (ESR) test and quenching experiments, the active ET production labile Fe(III) was confirmed to oxidize 94.12% of the Sb(III), while the contribution of other radicals was elucidated. Accordingly, we proposed that labile Fe(III) was the main oxidative species during anaerobic Sb(III) oxidation in the presence of DIRB and that the toxicity of antimony (Sb) in the environment was reduced. Considering the prevalence of DIRB and Fe(III) oxyhydroxides in natural environments, our findings provide a new perspective on the transformation of redox sensitive substances and build an eco-friendly bioremediation strategy for treating toxic metalloid pollution.

The dual roles of dissimilatory iron reduction in the carbon cycle: The "iron mesh" effect can increase inorganic carbon sequestration.

Dissimilatory iron reduction (DIR) can drive the release of organic carbon (OC) as carbon dioxide (CO2 ) by mediating electron transfer between organic compounds and microbes. However, DIR is also crucial for carbon sequestration, which can affect inorganic-carbon redistribution via iron abiotic-phase transformation. The formation conditions of modern carbonate-bearing iron minerals (ICFe ) and their potential as a CO2 sink are still unclear. A natural environment with modern ICFe , such as karst lake sediment, could be a good analog to explore the regulation of microbial iron reduction and sequential mineral formation. We find that high porosity is conducive to electron transport and dissimilatory iron-reducing bacteria activity, which can increase the iron reduction rate. The iron-rich environment with high calcium and OC can form a large sediment pore structure to support rapid DIR, which is conducive to the formation and growth of ICFe . Our results further demonstrate that the minimum DIR threshold suitable for ICFe formation is 6.65 μmol g-1 dw day-1 . DIR is the dominant pathway (average 66.93%) of organic anaerobic mineralization, and the abiotic-phase transformation of Fe2+ reduces CO2 emissions by ~41.79%. Our findings indicate that as part of the carbon cycle, DIR not only drives mineralization reactions but also traps carbon, increasing the stability of carbon sinks. Considering the wide geographic distribution of DIR and ICFe , our findings suggest that the "iron mesh" effect may become an increasingly important vector of carbon sequestration.

Effect of EDDS on the rhizosphere ecology and microbial regulation of the Cd-Cr contaminated soil remediation using king grass combined with Piriformospora indica

The negative impacts of soil heavy metals composite pollution on agricultural production and human health are becoming increasingly prevalent. The applications of green chelating agents and microorganisms have emerged as promising alternate methods for enhancing phytoremediation. The regulatory effects of root secretion composition, microbial carbon source utilization, key gene expression, and soil microbial community structure were comprehensively analyzed through a combination of HPLC, Biolog EcoPlates, qPCR, and high-throughput screening techniques. The application of EDDS resulted in a favorable rhizosphere ecological environment for the king grass Piriformospora indica, characterized by a decrease in soil pH by 0.41 units, stimulation of succinic acid and fumaric acid secretion, and an increase in carbon source metabolic activity of amino acids and carbohydrates. Consequently, this improvement enhanced the bioavailability of Cd/Cr and increased the biomass of king grass by 25.7%. The expression of dissimilatory iron-reducing bacteria was significantly upregulated by 99.2%, while there was no significant difference in Clostridium abundance. Furthermore, the richness of the soil rhizosphere fungal community (Ascomycota: 45.8%, Rozellomycota: 16.7%) significantly increased to regulate the proportion of tolerant microbial dominant groups, promoting the improvement of Cd/Cr removal efficiency (Cd: 23.4%, Cr: 18.7%). These findings provide a theoretical basis for the sustainable development of chelating agent-assisted plants-microorganisms combined remediation of heavy metals in soil.

Transcriptome Analysis Reveals the Inhibitory Effect of Cu2+ on Polyferric Sulfate Floc Reduction by Shewanella putrefaciens CN32.

Polyferric sulfate (PFS), an economical coagulant widely used for removing heavy metal contaminants from water, is susceptible to reduction and transformation by iron-reducing bacteria prevalent in sediments. However, the effect of heavy metal ions adsorbed in PFS flocs on this biological process remains unclear. According to our results, compared with other heavy metal cations (e.g., Cu2+, Cd2+, Zn2+, Ni2+, Pb2+, and Co2+), Cu2+ had a stronger inhibitory effect on PFS floc reduction by Shewanella putrefaciens CN32, a typical dissimilatory iron-reducing bacterium. The presence of Cu2+ remarkably influenced the global transcription of CN32, resulting in 782 upregulated genes and 713 downregulated genes that are mainly annotated in energy production, amino acid metabolism, protein biosynthesis, and oxidation‒reduction processes. The anaerobic TCA cycle for energy (electron) production was significantly activated in the presence of Cu2+, while the transcription of many genes related to the extracellular electron transfer pathway was downregulated, which is responsible for the decreased Fe3+ reduction. Moreover, the pathways of assimilatory sulfate reduction and subsequent cysteine biosynthesis were significantly enriched, which is hypothesized to result in the consumption of abundant energy produced from the enhanced anaerobic TCA cycle, revealing a strategy to address the oxidative stress caused by Cu2+. This work elucidates the unusual suppressive effects of Cu2+ on the microbial reduction of PFS flocs, which reveals the high resistance of PFS flocs to microbial destruction when used to treat Cu2+ pollution in water, thus demonstrating their tremendous practical prospects.

The Impact of Phosphorus Level on Vivianite Precipitation during Microbial Reduction of Ferrihydrite

Iron minerals play a pervasive role in the cycling of phosphorus (P) within both terrestrial and aquatic environments. The behavior of P, especially in oxygen-depleted environments, is frequently regulated by changing redox conditions and the associated phase transformations of Fe (III) (hydr)oxides (Borch and Fendorf 2007). Although the stability of Fe (III) hydroxides under changing redox conditions is well established, the relationship between specific minerals and their influence on the mechanisms of P retention and release remain unclear. In particular, the minerals vivianite (Fe3(PO4)2·8H2O) and ferrihydrite (Fe2O3·0.5H2O) are of interest. Vivianite crystallization in sediments has attracted increasing attention as a major contributor to P retention during early diagenesis (Slomp et al. 2013) and ferrihydrite reduction has been linked to fluctuating P concentrations which can impact vivianite crystallization. Additionally, there exists strong biological controls on these minerals as the reduction of Fe (III) oxides by dissimilatory iron-reducing bacteria may result in the formation of a suite of Fe (II)-bearing secondary minerals (O’Loughlin et al. 2021). To better understand the biogeochemical mechanisms behind these interactions, we examined the effects of fluctuating P concentrations on the reduction of ferrihydrite by Shewanella putrefaciens CN32 and resulting vivianite formation. In this study, bio-reduction experiments were conducted under sterile conditions in serum bottles containing 80 mL of mineral medium, with 80 mM Fe (III) in the form of Ferrihydrite, and various P concentrations (0, 1 mM, and 10 mM). The bottles were placed on a roller drum (180 rpm) and incubated at 30 oC in the dark for 15 days. Dissolved Fe (II), P concentrations, pH, and optical density (OD) values throughout the experiments were also measured. Our results showed that during incubation, Shewanella putrefaciens CN32 accelerated Ferrihydrite reduction as the dissolved iron (Fe2+) concentration increased significantly when compared to other bacterial and ferrihydrite treatments, as well as the control treatment. Additionally, P in both the 1mM and 10mM treatments was depleted after 5 and 7 days, respectively, and resulted in crystalline precipitates. Scanning electron microscopy (SEM) analyses of precipitates showed well-formed and highly crystalline vivianite particles of up to 30 µm in length in high P level. Some crystalline precipitates were confirmed as vivianite through SEM and Raman spectroscopy matching a known vivianite reference (Taylor et al. 2008), but only within the 10mM P incubations. After 15 days of incubation the morphology of the vivianite changed from aggregates of lath-shaped crystals to acicular crystals (Fig. 1). Based on our results, fluctuating P concentrations do indeed have a pronounced effect on ferrihydrite reduction and thus vivianite formation.

Cultivation and biogeochemical analyses reveal insights into biomineralization caused by piezotolerant iron-reducing bacteria from petroleum reservoirs and their application in MEOR

Interactions between minerals and iron-reducing bacteria under in-situ pressure and temperature conditions play important roles in oil extraction, residual oil methanation, and CO2 storage in petroleum reservoirs. However, the impacts of pressure on dissimilatory iron-reducing bacteria (DIRB) are poorly understood. Herein, the interactions between clay minerals and microbes under elevated hydrostatic pressure conditions were elucidated through enrichment experiments. Bioreduction experiments were performed under hydrostatic pressures of 0.1–40 MPa. Microbial diversity analysis revealed that high pressures significantly increased microbial diversity in petroleum reservoirs, which is helpful for restoring underground ecosystems in situ. The key piezotolerant iron-reducing bacteria in the samples were Shewanella and Flaviflexus. These two genera were isolated for the first time from petroleum reservoirs and identified as piezophiles. The SEM results clearly showed mineral surface dissolution. Moreover, nanoscale secondary minerals were produced during biomineralization. XRD analysis revealed that illite, albite, and clinoptilolite were present after bioreduction. The isolates showed the capacity to inhibit hydro-swelling and prevent plugging-related damage in reservoirs.

Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32.

Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.

Sub-MIC antibiotics affect microbial ferrihydrite reduction by extracellular membrane vesicles

Environmental concentrations of antibiotics, usually below MIC, have significant biological effects on bacterial cells. Sub-MIC antibiotics exposure induces bacteria to produce outer membrane vesicles (OMVs). Recently, OMVs is discovered as a novel pathway for dissimilatory iron reducing bacteria (DIRB) to mediate extracellular electron transfer (EET). Whether and how the antibiotic-induced OMVs modulate iron oxides reduction by DIRB have not been studied. This study showed the sub-MIC antibiotics (ampicillin or ciprofloxacin) increased OMVs secretion in Geobacter sulfurreducens, and the antibiotic-induced OMVs contained more redox active cytochromes facilitating iron oxides reduction, especially for the ciprofloxacin-induced OMVs. Deduced from a combination of electron microscopy and proteomic analysis, the influence of ciprofloxacin on SOS response triggered prophage induction and led to the formation of outer-inner membrane vesicles (OIMVs) in, which was a first report in Geobacter species. While ampicillin disrupting cell membrane integrity resulted in more formation of classic OMVs from outer membrane blebbing. The results indicated that the different structure and composition of vesicles were responsible for the antibiotic-dependent regulation on iron oxides reduction. This newly identified regulation on EET-mediated redox reactions by sub-MIC antibiotics expands our knowledge about the impact of antibiotics on microbial processes or “non-target” organisms.

Vertical distribution of dissimilatory iron reducing communities in the sediments of Taihu Lake

The reduction of Fe(III) coupled with the oxidation of organic matter, primarily stimulated by dissimilatory iron-reducing bacteria (DIRB) under anoxic conditions, is a critical biogeochemical process in lacustrine sediments. Many single strains have been recovered and investigated, however, the changes in the diversity of culturable DIRB communities with sedimentary depth have not been fully revealed. In this study, 41 DIRB strains affiliated to ten genera of phylum Firmicutes, Actinobacteria, and Proteobacteria were isolated from the sediments of Taihu Lake at three depths (0–2 cm, 9–12 cm, and 40–42 cm), referring to distinct nutrient conditions. Fermentative metabolisms were identified in nine genera (except genus Stenotrophomonas). The DIRB community diversity and the microbial iron reduction (MIR) patterns vary in vertical profiles. The community abundance varied with the TOC contents in vertical profiles. The DIRB communities, containing 17 strains of 8 genera, were most diverse in the surface sediments (0–2 cm), where organic matter was most abundant among the three depths. 11 DIRB strains of five genera were identified in the 9–12 cm sediments with the lowest content of organic matter, while 13 strains of seven genera were identified in deep sediments (40–42 cm). Among the isolated strains, phylum Firmicutes dominated the DIRB communities at three depths, while its relative abundance increased with depth. Fe2+ ion was recognized as the dominant microbial ferrihydrite-reducing product of DIRB from 0 to 12 cm sediments. Instead, lepidocrocite and magnetite were the main MIR products of DIRB retrieved from 40 to 42 cm. The results indicate that the MIR driven by fermentative DIRB is crucial in lacustrine sediments and that the distribution of nutrients and iron (minerals) likely influences the diversity of DIRB communities in the lacustrine sediments.

Promoting vivianite recovery: Crucial role of tightly-bound extracellular polymeric substances

Vivianite is an important bio-induced product of dissimilated iron reduction (DIR), which exists widely in activated sludge and digested sludge of wastewater treatment plants (WWTPs). Extracellular polymeric substances (EPS) surrounding dissimilatory iron-reducing bacteria (DIRB) were reported to be transient media for microbial extracellular electron transfer (EET) and DIR. However, what happens when a layer of EPS envelops microbial cells during vivianite recovery? This study tried to assess the relationship between iron reduction and electron transfer by stripping EPS layer-by-layer, then clarified the delamination of different EPS layers on the performance of vivianite recovery. After stripping total EPS (PC-EPS batches) of DIRB, the Fe (III) reduction efficiencies (RFe), Fe (III) reduction rate (VFe), and vivianite formation efficiency (RV) decreased by 33%, 37%, and 30%, respectively. Tightly bound-EPS (TB-EPS) was confirmed to play a crucial role in vivianite formation, which contributed 28–51% to vivianite recovery and 34–55% to iron reduction. Electronic shuttle substances were contained in TB-EPS, which enhanced the EET rate and efficiency between cells and Fe (III). The polysaccharide content of TB-EPS was positively related to adhesiveness between cells and mineral, as well as the iron reduction efficiency. Furthermore, redox proteins (PpcA, OmcB) were embedded in EPS, which shortened the distance of electron hopping to across the EPS layer and further accelerated vivianite recovery from wastewater. Long-term operation of anaerobic reactors confirmed that TB-EPS played critical roles in bio-induced vivianite formation.

Coupled reduction of structural Fe(III) in nontronite and oxidation of petroleum hydrocarbons

Fe-bearing clay minerals are frequently present in oil reservoirs as potential electron acceptor. Compounds in crude oil may mediate microbial reduction of structural Fe(III) in clay minerals through their roles as electron donor and shuttle. However, there is limited knowledge about these roles and resulting transformation of oil compounds. In this study, bio-reduction of structural Fe(III) in nontronite (NAu-2, Fe-rich smectite) by the dissimilatory iron-reducing bacterium (DIRB) Shewanella putrefaciens CN32 was investigated in the presence of either crude oil or specific fractions of oil. Lactate was added in some experiments as extra electron donor. The fractions of saturates (nC14-nC20 alkanes and nC8-nC14-alkyl cyclohexanes), aromatics (with two/three benzene rings), and polar compounds (carboxylic acids) of crude oil were adsorbed to NAu-2 surface. Without CN32, crude oil was able to slightly reduce structural Fe(III) in NAu-2. In the presence of CN32, reduction of Fe(III) in NAu-2 was coupled with oxidation of bulk oil and saturated/aromatic fractions. The reduction extent (21.5 ± 0.3%) and rate (0.04 ± 0.00 mM/h) by the saturated oil fraction (nC17-nC30 alkanes and nC10-nC23-alkyl cyclohexanes as electron donors) were slightly lower than those by bulk oil (22.8 ± 0.4% and 0.05 ± 0.00 mM/h, respectively), but those by the aromatic fraction with two benzene rings were much higher (30.8 ± 0.2% and 0.15 ± 0.00 mM/h, respectively). Fe(III) bio-reduction was coupled with oxidative transformation of oil compounds. Specifically, n-alkanes and alkyl cyclohexanes with shorter carbon chains and aromatic isomers with fewer methyl groups were more easily degraded (i.e., dibenzothiophene series) and/or desorbed (i.e., phenanthrene series) than n-alkanes and alkyl cyclohexanes with longer carbon chains and aromatic isomers with more methyl groups. These hydrocarbons were degraded to oxygen-containing compounds, mainly saturated fatty acids, monocyclic naphthenic acids, and phenols. In the presence of lactate as extra electron donor, the aromatic fraction significantly promoted the Fe(III) bio-reduction extent and rate, suggesting its role as electron shuttle. The oxidative transformation of oil compounds driven by bio-reduction of clay minerals has broad implications for the coupled biogeochemical cycles of carbon and iron in oil reservoirs and organic-rich sedimentary rocks.

Volatile fatty acids changed the microbial community during feammox in coastal saline-alkaline paddy soil.

In order to indicate the effect of volatile fatty acids (VFAs) on the characteristics of feammox and dissimilatory iron reducing bacteria (DIRB) in paddy soils, different VFAs were selected with paddy soils for anaerobic cultivation. Five treatments were set up, respectively, only adding N and both adding N and C (formate + NH4+ (Fo-N), acetate + NH4+ (Ac-N), propionate + NH4+ (Pr-N), and butyrate + NH4+ (Bu-N)) treatments. The concentration of Fe(II), Fe(III), NH4+, and VFAs was assessed within 45 d, and the bacterial community was determined after cultivation. The oxidation rates of NH4+ were the highest in N treatment, while it was the lowest in Fo-N treatment. Under the four C treatments, the consumption of NH4+ and Fe(III) was the fastest in Pr-N treatment, which was consumed by 31.2% and 76.3%, respectively. Different VFAs selected for distinct DIRB. Compared with N treatment, Ac-N and Bu-N treatment increased the relative abundance of DIRB, such as Geobacter and Clostridia, which increased the consumption of VFAs during incubation. Overall, VFAs, especially formate, could promote Fe(III) reduction and compete with the feammox process for the electron acceptors to decrease the feammox reaction, and prohibited soil NH4+ loss. Therefore, VFAs, which was released from organic fertilizer, could reduce NH4+ loss in feammox process of saline-alkaline paddy soils.

Anaerobic syntrophic system composed of phosphate solubilizing bacteria and dissimilatory iron reducing bacteria induces cadmium immobilization via secondary mineralization

Secondary mineralization is a promising method for remediating cadmium (Cd) pollution in sediments, but the poor stability of Cd-containing secondary minerals is a bottleneck that limits the development of this approach. The existence of phosphate can enhance the formation of stable secondary minerals and points a new direction for Cd immobilization. In this research, a novel syntrophic system composed of phosphate solubilizing bacteria (PSB) and dissimilatory iron reducing bacteria (DIRB) was established and the effect and mechanism of Cd immobilization in the system were also explored. The results showed that under the conditions of DIRB:PSB (V:V)= 3:1, syntrophic bacteria dosage of 5% and glucose dosage of 5 g/L, Cd incorporated in the secondary minerals could account for about 60% of the total Cd. In the pH range of 5–9, alkaline environment was conducive to the immobilization of Cd and the percentage of combined Cd was up to 58%, while the combined Cd in secondary minerals decreased from 62% to 56% with the increase of initial Cd concentration from 0.1 to 0.3 mmol/L. In addition, XRD, XPS, Mössbauer and other characterization results showed that secondary minerals, such as Cd exchange hydroxyapatite (Cd-HAP) and kryzhanovskite (Fe3(PO4)2(OH)3) were formed in this new system. The established syntrophic system of PSB and DIRB is thus a prospective bioremediation technology for Cd immobilization in sediments and can avoid the potential risk might be caused by the addition of phosphorus-containing materials.

Genetic mechanism of Carboniferous-Permian coal measures siderite nodules in an epicontinental sea basin—An example from the Zibo area in North China

Siderite is a mineral resource and a climate sensitive mineral. Siderite nodule layers are widely developed in coal measures within the marine-ontinental transitional facies of North China epicontinental sea basin, yet their formation environment and genetic mechanism are poorly understood. In this paper, taking the siderite nodule layers in the coal measures of the Late Paleozoic Taiyuan Formation in Zibo area of North China as an example, the formation environment and genetic mechanism of siderite nodules in the transitional facies of the epicontinental sea basin are studied through detailed petrological, sedimentological and geochemical analysis. It is found that the siderite nodules in the research area were formed in a tidal flat-lagoon environment. The siderite nodules are formed in the synsedimentary stage, the original information of chemical composition and characteristics of the nodules being largely retained. Most of the carbon in the siderite nodules originates from inorganic carbon from marine carbonate rocks, with the remainder originating from inorganic carbon formed by dissimilatory iron reducing bacteria (DIR) degrading organic matter. Meanwhile, most of the iron in the siderite nodules originates from hydrothermal fluids, and the remainder from terrigenous sediments. The content of iron input from hydrothermal fluids and terrestrial sediment represents a trade-off relationship. The two genetic mechanisms of the siderite nodules are as follows: 1) Chemical genetic mechanism: The siderite nodules are mainly formed by the combination of low-valence iron (Fe2+) and inorganic carbon in seawater through reduction with iron input from hydrothermal fluids as the main source. 2) Biochemical genetic mechanism: Some is formed by the combination of low-valence iron (Fe2+) and inorganic carbon with high-valence iron (Fe3+) as an oxidant to degrade the organic matter and convert organic carbon into inorganic carbon through DIR. On this basis, a genetic model of the Late Paleozoic coal measures siderite nodules in the epicontinental sea basin is established.

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor.

A hydrogen-based membrane biofilm reactor (H2-MBfR) was operated to investigate the bioreduction of antimonate [Sb(V)] in terms of Sb(V) removal, the fate of Sb, and the pathways of reduction metabolism. The MBfR achieved up to 80% Sb(V) removal and an Sb(V) removal flux of 0.55 g/m2·day. Sb(V) was reduced to Sb(III), which mainly formed Sb2O3 precipitates in the biofilm matrix, although some Sb(III) was retained intracellularly. High Sb(V) loading caused stress that deteriorated performance that was not recovered when the high Sb(V) loading was removed. The biofilm community consisted of DSbRB (dissimilatory Sb-reduction bacteria), SbRB (Sb-resistant bacteria), and DIRB (dissimilatory iron-reducing bacteria). Dissimilatory antimonate reduction, mediated by the respiratory arsenate reductase ArrAB, was the main reduction route, but respiratory reduction coexisted with cytoplasmic Sb(V)-reduction mediated by arsenate reductase ArsC. Increasing Sb(V) loading caused stress that led to increases in the expression of arsC gene and intracellular accumulation of Sb(III). By illuminating the roles of the dissimilatory and cytoplasmic Sb(V) reduction mechanism in the biofilms of the H2-MBfR, this study reveals that the Sb(V) loading should be controlled to avoid stress that deteriorates Sb(V) reduction.

Exploring the secondary mineral products generated by microbial iron respiration in Archean ocean simulations.

Marine chemical sedimentary deposits known as Banded Iron Formations (BIFs) archive Archean ocean chemistry and, potentially, signs of ancient microbial life. BIFs contain a diversity of iron- and silica-rich minerals in disequilibrium, and thus many interpretations of these phases suggest they formed secondarily during early diagenetic processes. One such hypothesis posits that the early diagenetic microbial respiration of primary iron(III) oxides in BIFs resulted in the formation of other iron phases, including the iron-rich silicates, carbonates, and magnetite common in BIF assemblages. Here, we simulated this proposed pathway in laboratory incubations combining a model dissimilatory iron-reducing (DIR) bacterium, Shewanella putrefaciens CN32, and the ferric oxyhydroxide mineral ferrihydrite under conditions mimicking the predicted Archean seawater geochemistry. We assessed the impact of dissolved silica, calcium, and magnesium on the bioreduced precipitates. After harvesting the solid products from these experiments, we analyzed the reduced mineral phases using Raman spectroscopy, electron microscopy, powder x-ray diffraction, and spectrophotometric techniques to identify mineral precipitates and track the bulk distributions of Fe(II) and Fe(III). These techniques detected a diverse range of calcium carbonate morphologies and polymorphism in incubations with calcium, as well as secondary ferric oxide phases like goethite in silica-free experiments. We also identified aggregates of curling, iron- and silica-rich amorphous precipitates in all incubations amended with silica. Although ferric oxides persist even in our electron acceptor-limited incubations, our observations indicate that microbial iron reduction of ferrihydrite is a viable pathway for the formation of early iron silicate phases. This finding allows us to draw parallels between our experimental proto-silicates and the recently characterized iron silicate nanoinclusions in BIF chert deposits, suggesting that early iron silicates could possibly be signatures of iron-reducing metabolisms on early Earth.

Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield

Fe(III) may be reasonably considered as one of the most important electron acceptors in petroleum reservoir ecosystems. The microbial mineralization of clay minerals, especially montmorillonite, is also of great significance to the exploration of petroleum and gas reservoirs. The bioreduction mechanisms of iron-poor minerals in petroleum reservoirs have been poorly investigated. This study investigated the bioreduction of montmorillonite by dissimilatory iron-reducing bacteria (DIRB) in petroleum reservoirs based on culture-independent and culture-dependent methods. Microbial diversity analysis revealed that Halolactibacillus, Bacillus, Alkaliphilus, Shewanella, Clostridium, and Pseudomonas were the key genera involved in the bioreduction of Fe(III). Through the traditional culture-dependent method, most of the key genera were isolated from the samples collected from petroleum reservoirs. Traditional culture-dependent methods can be used to reveal the metabolic characteristics of microorganisms (such as iron-reduction efficiency) to further elucidate the roles of different species (B. subtilis and B. alkalitelluris) in the environment. Moreover, many species with high iron-reduction efficiencies and relatively low abundances in the samples, such as Tessaracoccus and Flaviflexus, were isolated from petroleum reservoirs for the first time. The combination of culture-dependent and culture-independent methods can be used to further the understanding of the microbial communities and the metabolic characteristics of DIRB in petroleum reservoirs. Structural alterations that occurred during the interactions of microorganisms and montmorillonite were revealed through scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The physical and chemical analysis results demonstrated that microorganisms from petroleum reservoirs can dissolve iron-poor montmorillonite and promote the release of interlayer water. The secondary minerals illite and clinoptilolite were observed in bioreduced smectite. The formation of secondary minerals was closely related to the dissolution degrees of minerals based on iron reduction.

Dithionite extractable iron responsible for the production of hydroxyl radicals in soils under fluctuating redox conditions

Iron is a redox-active metal that is abundantly present in soils. Many recent studies have reported the production of reactive oxygen species (ROS) during the oxygenation of structural ferrous iron (Fe(II)). In soils, structural Fe(II) is mainly formed through microbial reduction of iron(III) under anoxic conditions, however, little is known about which iron species are preferred to be reduced by dissimilatory iron-reducing bacteria and further induce the production of ROS during oxygenation. The present study employed a variety of soils to investigate the microbial reduction of iron and the following production of ROS. Sustained production of hydroxyl radical (•OH) was observed during redox cycles, positively correlated to the contents of bio-reduced Fe(II). Furthermore, the yields of •OH, hydrogen peroxide, and Fe(II) were positively correlated to the content of crystalline Fe extracted using sodium dithionite rather than the total Fe in the soils. In addition, clay size fractions with higher dithionite extractable Fe contents were found to have greater contributions to the production of •OH compared to the coarse fractions. This study demonstrates the presence of •OH production in soils under fluctuating redox conditions and suggests that dithionite extractable Fe could serve as a feasible indicator to evaluate the potential of •OH production.