Iron reduction in the DAMO/Shewanella oneidensis MR-1 coculture system and the fate of Fe(II)

Active anaerobic methane oxidation in the groundwater table fluctuation zone of rice paddies

Rice paddies are globally important sources of methane emissions and also active regions for methane consumption. However, the impact of fluctuating groundwater levels on methane cycling has received limited attention. In this study, we delved into the activity and microbial mechanisms underlying anaerobic oxidation of methane (AOM) in paddy fields. A comprehensive approach was employed, including 13C stable isotope assays, inhibition experiments, real-time quantitative reverse transcription PCR, metagenomic sequencing, and binning technology. Geochemical profiles revealed the abundant coexistence of both methane and electron acceptors in the groundwater table fluctuation (GTF) zone, at a depth of 40-60 cm. Notably, the GTF zone exhibited the highest rate of AOM, potentially linked to the reduction of iron oxides and nitrate. Within this zone, Candidatus Methanoperedens (belonging to the ANME-2d group) dominated the Archaea population, accounting for a remarkable 85.4 %. Furthermore, our results from inhibition experiments, RT-qPCR, and metagenome-assembled genome (MAG) analysis highlighted the active role of Ca. Methanoperedens GTF50 in the GTF zone. This microorganism could independently mediate AOM process through the intriguing "reverse methanogenesis" pathway. Considering the similarity in geochemical conditions across different paddy fields, it is likely that Ca. Methanoperedens-mediated AOM is prevalent in the GTF zones.

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications

Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.

Geogenic Phosphorus Enrichment in Groundwater due to Anaerobic Methane Oxidation-Coupled Fe(III) Oxide Reduction

Accumulation of geogenic phosphorus (P) in groundwater is an emerging environmental concern, which is closely linked to coupled processes involving FeOOH and organic matter under methanogenic conditions. However, it remains unclear how P enrichment is associated with methane cycling, particularly the anaerobic methane oxidation (AMO). This study conducted a comprehensive investigation of carbon isotopes in dissolved inorganic carbon (DIC), CO2, and CH4, alongside Fe isotopes, microbial communities, and functions in quaternary aquifers of the central Yangtze River plain. The study found that P concentrations tended to increase with Fe(II) concentrations, δ56Fe, and δ13C-DIC, suggesting P accumulation due to the reductive dissolution of FeOOH under methanogenic conditions. The positive correlations of pmoA gene abundance versus δ13C-CH4 and Fe concentrations versus δ13C-CH4, and the prevalent presence of Candidatus_Methanoperedens, jointly demonstrated the potential significance of Fe(III)-mediated AMO process (Fe-AMO) alongside traditional methanogenesis. The increase of P concentration with δ13C-CH4 value, pmoA gene abundance, and Fe concentration suggested that the Fe-AMO process facilitated P enrichment in groundwater. Redundancy analysis confirmed this assertion, identifying P concentration as the primary determinant and the cooperative influence of Fe-AMO microorganisms such as Candidatus_Methanoperedens and Geobacter on P enrichment. Our work provided new insights into P dynamics in subsurface environments.

Enhancement of electron transfer via magnetite in nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane oxidation (n-DAMO) is a novel denitrification process that simultaneously further removes and utilizes methane from anaerobic effluent from wastewater treatment plants. However, the metabolic activity of n-DAMO bacteria is relative low for practical application. In this study, conductive magnetite was added into lab-scale sequencing batch reactor inoculated with n-DAMO bacteria to study the influence on n-DAMO process. With magnetite amendment, the nitrogen removal rate could reach 34.9 mg N·L-1d-1, nearly 2.5 times more than that of control group. Magnetite significantly facilitated the interspecies electron transfer and built electrically connected community with high capacitance. Enzymatic activities of electron transport chain were significantly elevated. Functional gene expression and enzyme activities associated with nitrogen and methane metabolism had been highly up-regulated. These results not only propose a useful strategy in n-DAMO application but also provide insights into the stimulating mechanism of magnetite in n-DAMO process.

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

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

Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization

Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.

Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism

The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.

Mineral transformation of poorly crystalline ferrihydrite to hematite and goethite facilitated by an acclimated microbial consortium in electrodes of soil microbial fuel cells

In this study, we investigated the biogenic mineral transformation of poorly crystalline ferrihydrite in the presence of an acclimated microbial consortium after confirming successful soil microbial fuel cell optimization. The acclimated microbial consortia in the electrodes distinctly transformed amorphous ferrihydrite into crystallized hematite (cathode) and goethite (anode) under ambient culture conditions (30 °C). Serial analysis, including transmission/scanning electron microscopy and X-ray/selected area electron diffraction, confirmed that the biogenically synthesized nanostructures were iron nanospheres (~100 nm) for hematite and nanostars (~300 nm) for goethite. Fe(II) ion production with acetate oxidation via anaerobic respiration was much higher in the anode electrode sample (3.2- to 17.8-fold) than for the cathode electrode or soil samples. Regarding the culturable bacteria from the acclimated microbial consortium, the microbial isolates were more abundant and diverse at the anode. These results provide new insights into the biogeochemistry of iron minerals and microbial fuel cells in a soil environment, along with physiological characters of microbes (i.e., iron-reducing bacteria), for in situ applications in sustainable energy research.

Enhanced anaerobic oxidation of methane with the coexistence of iron oxides and sulfate fertilizer in paddy soil

Iron oxides and sulfate are usually abundant in paddy soil, but their role in reducing methane emissions is little known. In this work, paddy soil was anaerobically cultivated with ferrihydrite and sulfate for 380 days. An activity assay, inhibition experiment, and microbial analysis were conducted to evaluate the microbial activity, possible pathways, and community structure, respectively. The results showed that anaerobic oxidation of methane (AOM) was active in the paddy soil. The AOM activity was much higher with ferrihydrite than sulfate, and an extra 10% of AOM activity was stimulated when ferrihydrite and sulfate coexisted. The microbial community was highly similar to the duplicates but totally different with different electron acceptors. The microbial abundance and diversity decreased due to the oligotrophic condition, but mcrA-carrying archaea increased 2-3 times after 380 days. Both the microbial community and the inhibition experiment implied that there was an intersection between iron and sulfur cycles. A "cryptic sulfur cycle" might link the two cycles, in which sulfate was quickly regenerated by iron oxides, and it might contribute 33% of AOM in the tested paddy soil. Complex links between methane, iron, and sulfur geochemical cycles occur in paddy soil, which may be significant in reducing methane emissions from rice fields.

Vivianite-induced peroxymonosulfate activation for containment removal under dark conditions: Performance, mechanism and regeneration

The performance and intrinsic mechanism of vivianite, a natural mineral containing structural Fe(II), for peroxymonosulfate (PMS) activation and pollutant degradation under dark conditions were comprehensively explored in this study. It was found that vivianite was able to efficiently activate PMS to degrade various pharmaceutical pollutants under dark conditions, in which the corresponding reaction rate constant of ciprofloxacin (CIP) degradation was 47- and 32-fold higher than that of magnetite and siderite, respectively. SO₄^·-, ^·OH, Fe(IV) and electron-transfer processes were found in the vivianite-PMS system, while SO₄^·- was the main contributor to CIP degradation. Moreover, mechanistic explorations revealed that the Fe site on the surface of vivianite could bind PMS in the form of a bridge position, and thus vivianite could rapidly activate absorbed PMS due to its strong electron-donating ability. Additionally, it was illustrated that the used vivianite could be efficiently regenerated by either chemical or biological reduction. This study may provide an alternative application of vivianite in addition to phosphorus recovery from wastewater.

Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria

The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood–Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.

Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems

Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH₄). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH₄ emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH₄ emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH₄ sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH₄ mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Heterotrophic denitrification: An overlooked factor that contributes to nitrogen removal in n-DAMO mixed culture

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) has been recognized as a sustainable process for simultaneous removal of nitrogen and methane. The metabolisms of denitrifying anaerobic methanotrophs, including Candidatus Methanoperedens and Candidatus Methylomirabilis, have been well studied. However, potential roles of heterotrophs co-existing with these anaerobic methanotrophs are generally overlooked. In this study, we pulse-fed methane and nitrate into an anaerobic laboratory sequencing batch bioreactor and enriched a mixed culture with stable nitrate removal rate (NRR) of ∼28 mg NO₃^--N L^-1 d^-1. Microbial community analysis indicates abundant heterotrophs, e.g., Arenimonas (5.3%-18.9%) and Fimbriimonadales ATM1 (6.4%), were enriched together with denitrifying anaerobic methanotrophs Ca. Methanoperedens (10.8%-13.2%) and Ca. Methylomirabilis (27.4%-34.3%). The results of metagenomics and batch tests suggested that the denitrifying anaerobic methanotrophs were capable of generating methane-derived intermediates (i.e., formate and acetate), which were employed by non-methanotrophic heterotrophs for denitrification and biomass growth. These findings offer new insights into the roles of heterotrophs in n-DAMO mixed culture, which may help to optimize n-DAMO process for nitrogen removal from wastewater.

Anaerobic methane oxidation coupled to ferrihydrite reduction by Methanosarcina barkeri

Fe(III) has been recognized as a potential electron sink for the anaerobic oxidation of methane (Fe-AOM) in diverse environments. However, most of previous Fe-AOM processes are limited to ANME archaea and the Fe-AOM mechanism remains unclear. Here we investigate, for the first time, the Fe-AOM performance and mechanisms by a single methanogen Methanosarcina barkeri. The results showed that M. barkeri was capable of oxidizing methane to CO₂ and reducing ferrihydrite to siderite simultaneously. The presence of methane enhanced both the abundances of redox-active species (such as cytochromes) and electrochemical activity of M. barkeri. The proteomic analyses revealed that M. barkeri up-regulated the expressions of a number of methanogenic enzymes during Fe-AOM, and significantly enriched metabolic pathways of amino acid synthesis and nitrogen fixation. Metabolic inhibition experiments indicated that membrane-bound redox-active components (cytochromes, methanophenazine and F₄₂₀H₂:quinone oxidoreductase) were probably involved in extracellular electron transfer (EET) from cells to ferrihydrite. Overall, these results provide a deep insight into the single‑carbon metabolism and survival strategy for methanogens and suggest that methanogens may play an important role in linking methane and iron cycling in the substrate-limited environments.

Effect of metal cations on antimicrobial activity and compartmentalization of silver in Shewanella oneidensis MR-1 upon exposure to silver ions

Silver is an antimicrobial agent that is used extensively in consumer products, such as fabrics and humidifiers. Silver ion (Ag⁺) uptake in bacteria represents a crucial phase of antimicrobial activity. However, the uptake mechanism of Ag⁺ in bacteria remains largely unknown. The genus Shewanella drives many geochemical processes of nutrients and pollutants in soils. In the present study, Ag⁺ uptake by Shewanella oneidensis MR-1 was first investigated in a laboratory in defined anaerobic, oligotrophic, and inorganic media with or without cations (potassium ions [K⁺], magnesium ions [Mg²⁺], and zinc ions [Zn²⁺]). Our results revealed variations in antimicrobial activity of Ag⁺ in the presence of Mg²⁺ and Zn²⁺. First, Mg²⁺ significantly decreased antimicrobial activity of Ag⁺ in S. oneidensis MR-1 by inhibiting cellular Ag⁺ uptake when compared with K⁺. The results were consistent with that of Co²⁺ (Mg²⁺ channel blocker) decreased Ag⁺ uptake by S. oneidensis MR-1. Moreover, Mg²⁺ promoted riboflavin secretion and facilitated the formation of metallic Ag nanoparticles on bacterial surfaces, which was beneficial for extracellular electron transfer and consequently reduced antibacterial activity of Ag⁺. Second, Zn²⁺ increased the antimicrobial activity of Ag⁺ in S. oneidensis MR-1, although the effect on Ag⁺ uptake was minimal. A synergistic interaction between Zn²⁺ and Ag⁺ led to an increase in dead cells and decreased ferrihydrite reduction capacity. The findings suggest that Mg²⁺ could reduce the environmental risk of Ag⁺ to soil bacteria, while Zn²⁺ should be of particular concern due to its synergistic antimicrobial effect on bacteria.

Shewanella shenzhenensis sp. nov., a novel Fe(III)-reducing bacterium with abundant possible cytochrome genes, isolated from mangrove sediment

A facultative anaerobic bacterium, designated as A25^T, was isolated from a mangrove sediment sample collected in Shenzhen, China. Cells of strain A25^T were found to be Gram-staining negative, rod-shaped, flagella-harboring, and oxidase- and catalase-positive. The isolate was able to grow at 4-40 °C (optimum 28 °C) and pH 5.0-9.0 (optimum pH 6.0), and in 0-10% NaCl concentration (w/v) (optimum 1%). Strain A25^T was capable of reducing Fe(III) citrate under anaerobic conditions. The major fatty acids of this strain was C_16:1ω7c/C_16:1ω6c (summed feature 3), C_17:1ω8c and iso-C_15:0. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain A25^T is affiliated with the genus Shewanella, showing the highest similarity to Shewanella seohaensis S7-3^T (98.4% similarity). The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain A25^T and its closely related strains were ≤ 79.0% and ≤ 22.8%, respectively. Based on its phenotypic, phylogenetic properties and physiological and biochemical characteristics, strain A25^T (= JCM 34900^T = GDMCC 1.2731^T) was designated as the type strain of a novel species of the genus Shewanella, for which the name Shewanella shenzhenensis sp. nov. was proposed.

Control the greenhouse gas emission via mediating the dissimilatory iron reduction: Fulvic acid inhibit secondary mineralization of ferrihydrite

Reducing methane emission is of great importance to control the global greenhouse effect. Dissimilatory iron reduction (DIR) coupling of organic matter decomposition may suppress methane production via reducing primary electron donors available for methanogenesis. However, during DIR, the amorphous iron oxides (e.g., ferrihydrite) are easy to transform into more stable crystalline iron minerals, which slowdowns the rate of DIR. Humic substance (HS) with redox activity has been extensively reported to facilitate DIR via "electron shuttles" mechanism, yet little known about the effect of HS on mediating the mineralization of iron oxides and the subsequent influences on DIR and methanogenesis. To clarify this, ferrihydrite and fulvic acid (FA) (as the model substance of HS) were supplied to anaerobic methanogenesis systems. Results showed that FA could significantly decrease the formation of crystalline iron oxides, enhance DIR rate by 13.72% and suppress methanogenesis by 25.13% compared to ferrihydrite supplemented only. By X-ray absorption spectra analysis, it was found that FA could complex with ferrihydrite via forming a Fe-C/O structure on the second shell of Fe atom. Quantum chemical calculation further confirmed that FA reduced the adsorption energy between Fe(II) and ferrihydrite. Our study suggested that rational use of HS to mediate mineralization pathway of iron oxides could efficiently improve the availability of iron oxides to drive DIR and control the conversion of organics into CH₄ in natural or engineered systems.

Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria

Soil protists are essential but often overlooked in soil and could impact microbially driven element cycling in natural ecosystems. However, how protists influence heavy metal cycling in soil remains poorly understood. In this study, we used a model protist, Dictyostelium discoideum, to explore the effect of interactions between soil amoeba and metal-reducing bacteria on the reduction of soil Fe(III) and Cr(VI). We found that D. discoideum could preferentially prey on the Fe(III)-reducing bacterium Shewanella decolorationis S12 and significantly decrease its biomass. Surprisingly, this predation pressure also stimulated the activity of a single S. decolorationis S12 bacterium to reduce Fe(III) by enhancing the content of electron-transfer protein cyt c, intracellular ATP synthesis, and reactive oxygen species (e.g., H₂O₂). We also found that D. discoideum could not prey on the Cr(VI)-reducing bacterium Brevibacillus laterosporus. In contrast, B. laterosporus became edible to amoebae in the presence of S. decolorationis S12, and their Cr(VI) reduction ability decreased under amoeba predation pressure. This study provides direct evidence that protists can affect the Cr and Fe cycling via the elective predation pressure on the metal-reducing bacteria, broadening our horizons of predation of protists on soil metal cycling.

Conductive property of secondary minerals triggered Cr(VI) bioreduction by dissimilatory iron reducing bacteria

Although secondary minerals have great potential for heavy metal removal, their impact on chromium biogeochemistry in subsurface environments associated with dissimilatory iron reducing bacteria (DIRB) remains poorly characterized. Here, we have investigated the mechanisms of biogenic secondary minerals on the rate of Cr(VI) bioreduction with shewanella oneidensis MR-1. Batch results showed that the biogenic secondary minerals, schwertmannite and jarosite, appreciably increased the Cr(VI) bioreduction rate. UV-vis diffuse reflection spectra showed that schwertmannite and jarosite are semiconductive minerals, which can be activated by MR-1, followed by transferred conduction electrons toward Cr(VI). Cyclic voltammetry and Tafel analysis suggested that the resistance of secondary minerals is a dominant factor controlling Cr(VI) bioreduction. In addition, Cr(VI) adsorption on secondary minerals through ligand exchange promoted Cr(VI) bioreduction by decreasing the electron transfer distance between MR-1 and chromate. Fe(III)/Fe(II) cycling in schwertmannite and jarosite also contributed to Cr(VI) bioreduction as reflected by X-ray photoelectron spectroscopy and Fourier transform infrared spectrometer. Complementary characterizations further verified the contributions of Fe(III)/Fe(II) cycling, Cr(VI) adsorption, and conduction band electron transfer to enhanced Cr(VI) bioreduction. This study provides new insights on the understanding of Cr(VI) bioreduction by semiconductor minerals containing sulfate in subsurface environments.

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Heavy metal reduction coupled to methane oxidation：Mechanisms, recent advances and future perspectives

Methane emission has contributed greatly to the global warming and climate change, and the pollution of heavy metals is an important concern due to their toxicity and environmental persistence. Recently, multiple heavy metals have been demonstrated to be electron acceptors for methane oxidation, which offers a potential for simultaneous methane emission mitigation and heavy metal detoxification. This review provides a comprehensive discussion of heavy metals reduction coupled to methane oxidation, and identifies knowledge gaps and opportunities for future research. The functional microorganisms and possible mechanisms are detailed in groups under aerobic, hypoxic and anaerobic conditions. The potential application and major environmental significances for global methane mitigation, the elements cycle and heavy metals detoxification are also discussed. The future research opportunities are also discussed to provide insights for further research and efficient practical application.

Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea

Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.

Chemotrophic profiling of prokaryotic communities thriving on organic and mineral nutrients in a submerged coastal cave

The geothermal system of the Salento peninsula (Italy) is characterized by the presence of many hydrogen sulfide-rich underground waters and thermal springs. We focused our attention on the submerged section of Zinzulùsa (Castro, Italy), a cave of both naturalistic and archaeological interest. In pioneer studies, some hypotheses about the origin of the sulfurous waters of this area were proposed. The most accredited one is that sulfate-enriched waters of marine origin infiltrate deep along bands with greater permeability, and warm-up going upwards, due to the geothermal gradient. During their route, marine waters interact with organic deposits and generate hydrogen sulfide as a result of sulfate reduction. To date, no studies have been conducted to elucidate the hydrogen sulfide origin in this site. The nature of reducing power and energy sources supporting microbial life in this submerged habitat is currently unknown. Here we present a multidisciplinary experimental approach aimed at defining geochemical features and microbiological diversity of the submerged habitat of Zinzulùsa cave. Our integrated data provide strong evidence that the sulfate content of the marine water and the activity of sulfate-reducing bacteria may account for the hydrogen sulfide content of the thermal springs. Anaerobic, sulfate-reducing, thermophilic Thermodesulfovibrio and hyperthermophilic Fervidobacterium genera show a high percentage contribution in 16S rRNA gene metabarcoding analyses, despite the mesophilic conditions of the sampling site. Besides, supported by PICRUSt functional analysis, we propose a chemotrophic model in which hydrocarbon deposits, entrapped in the stratifications of the seafloor, may be exploited by anaerobic oil-degrading bacteria as carbon and energy sources to sustain efficient hydrogen, sulfur, and nitrogen biogeochemical cycles. The Zinzulùsa hydrothermal site represents an ecosystem useful to obtain new insights into prokaryotic mutual interactions in oligotrophic and aphotic conditions, which constitute the largest environment of the biosphere.

Enhancement of nitrite reduction and enrichment of Methylomonas via conductive materials in a nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane-oxidizing (n-damo) process has a promising prospect in anaerobic wastewater treatment, utilizing methane as the sole electron source to remove nitrite. However, the metabolic activity of n-damo bacteria is too low for practical application. This study aimed to stimulate n-damo process by introducing conductive nano-magnetite and/or electron shuttle anthraquinone-2,6-disulfonate (AQDS), and also set a comparative treatment of adding insulated ferrihydrite. The results showed that the nitrite reduction rate was enhanced the most significantly in treatment with nano-magnetite, approximately 1.6 times higher than that of the control without any supplement. While ferrihydrite application showed an adverse effect on n-damo process. The well-known aerobic methane oxidizer Methylomonas spp. was found to be enriched under n-damo condition with the supplementation of nano-magnetite and/or AQDS, but abundance of n-damo bacteria did not exhibit significant increase. It was hypothesized that Methylomonas spp. could be survived under anaerobic n-damo condition using oxygen produced by n-damo bacteria for the self-growth, and the nitrite reduction could be promoted through the enhancement of microbial interspecies electron transfer triggered by the introduction of conductive materials. It opens a new direction for the stimulation of n-damo activity, which needs more evidences to verify the hypothetic mechanism.

A new insight on the effects of iron oxides and dissimilated metal-reducing bacteria on CH4 emissions in constructed wetland matrix systems

Iron oxides and dissimilated metal-reducing bacteria (DMRB) have been reported to result in a reduction in methane (CH₄) emissions in constructed wetlands (CWs), but their mechanisms on CH₄ production and oxidation remains unclear. Here, a set of CW matrix systems (Control, Fe-CWs, and FeB-CWs) was established to analyze the CH₄ emission reduction from various angles, including the valencies of iron, microbial community structure and enzyme activity. The results revealed that the addition of iron oxides promoted the electron transfer between methanogens and Geobacter to promote CH₄ production, but it was interesting that iron oxides also reduced the enzymes involved in the carbon dioxide (CO₂) reduction pathway and promoted the enzymes that participated in anaerobic oxidation of methane (AOM) thereby leading to the overall reduction in CH₄ emissions. Moreover, DMRB could promote iron reduction thereby further reducing CH₄ emissions by promoting AOM and competing with methanogens for organic substrates.

Mechanistic insights into iodine enrichment in groundwater during the transformation of iron minerals in aquifer sediments

Long-term intake of groundwater with elevated iodine concentration can cause thyroid dysfunction in humans; however, little is known on the mechanisms controlling the fate of iodine in groundwater systems. In this study, the groundwater and aquifer sediment samples from the Datong basin, a geologic iodine-affected area, were collected to perform the batch incubation experiments to understand the release and enrichment of iodine in groundwater systems. The results showed that the groundwater from the deep confined aquifer had a total iodine concentration of 473 μg/L, higher than that of shallow groundwater, and iodide is the dominant species of iodine. The deep confined aquifer was characterized by the reducing conditions. Meanwhile, a higher ratio of Fe(II) to total Fe was observed in bulk deep aquifer sediments (59%) in comparison with that of shallow sediments (33%). The results of batch incubation experiments showed that during the reductive transformation of Fe minerals in shallow aquifer sediments, iodide concentration in solution was gradually increasing from 24.7 to 101.5 μg/L after 10 days. It suggests that the transformation of Fe minerals in aquifer sediments acts as a diver causing the release of iodine from sediment into groundwater, which was further supported by the features Fe K-edge EXAFS before and after the batch experiments. Moreover, the changes in iodine species from iodate or organic iodine into iodide during the release further promotes the release of sediment iodine, which was supported by the developed geochemical models. The prevalence of reducing condition in deep aquifer favors the enrichment of released iodide. This study provides new insights into the mechanisms of iodide enrichment observed in deep confined aquifer.

Iron Transformation and Its Role in Phosphorus Immobilization in a UCT-MBR with Vivianite Formation Enhancement

The formation of vivianite (Fe₃(PO₄)₂·8H₂O) in iron (Fe)-dosed wastewater treatment facilities has the potential to develop into an economically feasible method of phosphorus (P) recovery. In this work, a long-term steady Fe^III-dosed University of Cape Town process-membrane bioreactor (UCT-MBR) system was investigated to evaluate the role of Fe transformations in immobilizing P via vivianite crystallization. The highest fraction of Fe^II, to total Fe (Fe_tot), was observed in the anaerobic chamber, revealing that a redox condition suitable for Fe^III reduction was established by improving operational and configurational conditions. The supersaturation index for vivianite in the anaerobic chamber varied but averaged ∼4, which is within the metastable zone and appropriate for its crystallization. Vivianite accounted for over 50% of the Fe_tot in the anaerobic chamber, and its oxidation as it passed through the aerobic chambers was slow, even in the presence of high dissolved oxygen concentrations at circumneutral pH. This study has shown that the high stability and growth of vivianite crystals in oxygenated activated sludge can allow for the subsequent separation of vivianite as a P recovery product.

Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps

Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.

Operation strategies of n-DAMO and Anammox process based on microbial interactions for high rate nitrogen removal from landfill leachate

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) coupling to Anaerobic ammonium oxidation (Anammox) provides an opportunity for simultaneous nitrogen removal and methane emissions mitigation from wastewater. However, to achieve high nitrogen removal rate in such a process remains a critical challenge in practical application. This work investigated the interactions between n-DAMO and Anammox in membrane biofilm reactor (MBfR) and then developed operational strategies of MBfR for high rate nitrogen removal from landfill leachate. Initially, influent containing nitrate and ammonium facilitated the development of n-DAMO and Anammox microorganisms in MBfR, but nitrogen removal performance is hard to be further improved even deteriorated. Detailed investigations of interactions among n-DAMO and Anammox microorganisms confirmed that extra addition of nitrite into MBfR fed with nitrate and ammonium not only stimulated the activities of Anammox bacteria, but also enhanced the activities of n-DAMO archaea from 172.3 to 356.9 mg NO₃^--N L^-1 d^-1. Functional gene analysis also indicated that mcrA and hzsA genes increased after nitrite addition. Based on this finding, influent containing NO₃^-, NO₂^- and NH₄⁺ enabled nitrogen removal rates of MBfR increase from 224.9 to 888.2 mg N L^-1 d^-1. Finally, nitrate in the influent was gradually replaced with nitrite to mimic the effluent from partial nitriation of landfill leachate, but maintain the nitrate availability for n-DAMO archaea through increasing nitrate production from Anammox. These operation strategies enabled MBfR achieve the steady state with a nitrogen removal rate of 6.1 kg N m^-3 d^-1. Microbial community analysis revealed n-DAMO archaea, n-DAMO bacteria and Anammox bacteria jointly dominated the biofilm, and their relative abundance dynamically shifted with feeding regime. This work provides promising operational strategies for high rate of nitrogen removal from landfill leachate through integrating n-DAMO and Anammox process.

Behaviors of heavy metal(loid)s in a cocontaminated alkaline paddy soil throughout the growth period of rice

A pot experiment was conducted to investigate uptake of cadmium (Cd), arsenic (As) and antimony (Sb) by rice from a lime-treated paddy soil contaminated with the three pollutants. The results showed that the content of Cd in the total rice plants decreased as the plant grew, whereas the As and Sb contents increased steadily. The concentration of As in the pore water showed steady increase throughout the growth period, likely due to the reductive dissolution of iron (Fe)-bearing minerals and the reduction of As(V). In contrast, the concentrations of Cd and Sb in the pore water increased initially, likely attributable to the reductive dissolution of Fe-bearing minerals, and then decreased likely due to their adsorptions onto carbonate and Fe sulfides, the reduction of Sb(V), and the formation of CdS. A random forest model was used to quantitatively evaluate the relative contributions of environmental factors to the accumulation of Cd, As, and Sb in the rice plants. The results suggest that sulfides produced through sulfate reduction and the formation of Cd forms associated with sulfur (S) might significantly affected the Cd content in the rice plants. In addition, the dissolved Fe species, the oxidation-reduction potential, and the abundance of the As(V)-respiring gene were major contributors to the As content in the rice plants, suggesting the important role of the reduction of Fe-bearing minerals and As(V). The results also showed that the Sb content in the rice plants was correlated with Fe species, Sb(V) reduction, and acid volatile S. The environmental behaviors of Cd, As, and Sb in the cocontaminated paddy soil exhibited significant differences. Such differences should be considered in remedy of soils contaminated with multiple heavy metals and metalloids.

Microbial vanadate and nitrate reductions coupled with anaerobic methane oxidation in groundwater

Vanadate contaminant in groundwater receives increasing attentions, but little is known on its biogeochemical transformation with gaseous electron donors. This study investigated bio-reduction of vanadate coupled with anaerobic methane oxidation and its relationship with nitrate reduction. Results showed 95.8 ± 3.1% of 1 mM vanadate was removed within 7 days using methane as the sole electron donor. Tetravalent vanadium compounds were the main reduction products, which precipitated naturally in groundwater environment. The introduction of nitrate inhibited vanadate reduction, though both were reduced in parallel. Accumulations of volatile fatty acids (VFAs) were observed from methane oxidation. Preliminary microbial community structure and metabolite analyses indicated that vanadate was likely reduced via Methylomonas coupled with methane oxidation or through synergistic relationships between methane oxidizing bacteria and heterotrophic vanadate reducers with VFAs served as the intermediates.

Electron shuttles enhance anaerobic oxidation of methane coupled to iron(III) reduction

Anaerobic oxidation of methane (AOM) has recently been coupled with the reduction of insoluble electron acceptors such as iron minerals. However, effects of electron shuttles (ESs) on this process and the underlying coupling mechanisms remain not well understood. Here, we evaluated AOM-coupled ferrihydrite reduction by a mixed culture in the absence and presence of ESs. The results showed that ESs (AQS, flavin, HA and AQDS) significantly enhanced the rate (up to 7.4 times) of AOM-dependent ferrihydrite reduction compared with the control. The enhancements were linearly related with the electron transfer capacity of ESs. Illumina high-throughput sequencing and DNA-based stable isotope probing revealed that the AOM-coupled iron reduction depended on the syntrophic interaction of Methanobacterium and the partner bacteria. Methanobacterium as the dominant microorganism, did not assimilate methane into its biomasses. However, it played a crucial role in the partial oxidation of methane into an intermediate (i.e. propionate), which was then assimilated by the partner bacteria (e.g. Cellulomonas, Desulfovibrio, Actinotalea, etc.) for ferrihydrite reduction. This work suggests that ESs in natural environments can mitigate the methane emissions by facilitating the AOM process and biogeochemical cycles of iron.

Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction

In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia

This study evaluates rates and pathways of methane (CH₄ ) oxidation and uptake using ¹⁴ C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^-1  day^-1 to 117 μmol L^-1  day^-1 ) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂ ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂ ) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Integration of nanoscale zero-valent iron and functional anaerobic bacteria for groundwater remediation: A review

The technology of integrating nanoscale zero-valent iron (nZVI) and functional anaerobic bacteria has broad prospects for groundwater remediation. This review focuses on the interactions between nZVI and three kinds of functional anaerobic bacteria: organohalide-respiring bacteria (OHRB), sulfate reducing bacteria (SRB) and iron reducing bacteria (IRB), which are commonly used in the anaerobic bioremediation. The coupling effects of nZVI and the functional bacteria on the contaminant removal in the integrated system are summarized. Generally, nZVI could create a suitable living condition for the growth and activity of anaerobic bacteria. OHRB and SRB could synergistically degrade organic halides and remove heavy metals with nZVI, and IRB could reactive the passivated nZVI by reducing the iron (hydr)oxides on the surface of nZVI. Moreover, the roles of these anaerobic bacteria in contaminant removal coupling with nZVI and the degradation mechanisms are illustrated. In addition, this review also discusses the main factors influencing the removal efficiency of contaminants in the integrated treatment system, including nZVI species and dosage, inorganic ions, organic matters, pH, type of pollutants, temperature, and carbon/energy sources, etc. Among these factors, the nZVI species and dosage play a fundamental role due to the potential cytotoxicity of nZVI, which might exert a negative impact on the performance of this integrated system. Lastly, the future research needs are proposed to better understand this integrated technology and effectively apply it in groundwater remediation.

Degradation of organic pollutants by anaerobic methane-oxidizing microorganisms using methyl orange as example

Anaerobic oxidation of methane (AOM) microorganisms widespread in nature and they are able to utilize methane as electron donor to reduce sulfate, nitrate, nitrite, and high valence metals. However, whether persistent organic contaminants can also be degraded remains unknown. In this study, the organic pollutant methyl orange (MO) was used to address this open question. The initial concentration of MO affected its degradation efficiency and higher concentration (>100 mg/L) caused considerable inhibition. A ¹³CH₄ isotope experiment indicated that methane oxidation was involved in MO degradation, which produced N, N-dimethyl-p-phenylenediamine, and 4-aminobenzenesulfonic acid corresponded stoichiometrically. During the long-term experiment, the maximum degradation rate was 47.91 mg/(L·d). The percentage of Candidatus Methanoperedens and Pseudoxanthomonas significantly increased after 30-d of MO degradation under CH₄ conditions; moreover, Candidatus Methanoperedens dominated (46.83%) the microbial community. Candidatus Methanoperedens, either alone or in combination with Pseudoxanthomonas, utilized methane as the sole carbon source to degrade MO via direct interspecies electron transfer or the syntrophy pathway. This study will add to our understanding of the functions and applications of AOM microorganisms.

Electron shuttling mediated by humic substances fuels anaerobic methane oxidation and carbon burial in wetland sediments

Key pathways for the anaerobic oxidation of methane (AOM) have remained elusive, particularly in organic rich ecosystems. In this work, the occurrence of AOM driven by humus-catalyzed dissimilatory iron reduction was investigated in sediments from a coastal mangrove swamp. Anoxic sediment incubations supplied with both goethite (α-FeOOH) and leonardite (humic substances (HS)) displayed an average AOM rate of 10.7 ± 0.8 μmol CH₄ cm^-3 day^-1, which was 7 and 3 times faster than that measured in incubations containing only goethite or HS, respectively. Additional incubations performed with ¹³C-methane displayed Pahokee Peat HS-mediated carbonate precipitation linked to ¹³CH₄ oxidation and ferrihydrite reduction (~1.3 μmol carbonate cm^-3 day^-1). These results highlight the role of HS on mitigating greenhouse gases released from wetlands, not only by mediating the AOM process, but also by enhancing carbon sequestration as inert minerals (calcite, aragonite and siderite).

The dynamic role of pH in microbial reduction of uranium(VI) in the presence of bicarbonate

The negative effect of carbonate on the rate and extent of bioreduction of aqueous U(VI) has been commonly reported. The solution pH is a key chemical factor controlling U(VI)_aq species and the Gibbs free energy of reaction. Therefore, it is interesting to study whether the negative effect can be diminished under specific pH conditions. Experiments were conducted using Shewanella putrefaciens under anaerobic conditions with varying pH values (4-9) and bicarbonate concentrations ( [Formula: see text] , 0-50 mmol/L). The results showed a clear correlation between the pH-bioreduction edges of U(VI)_aq and the [Formula: see text] . The specific pH at which the maximum bioreduction occurred (pH_mbr) shifted from slightly basic to acidic pH (∼7.5-∼6.0) as the [Formula: see text] increased (2-50 mmol/L). At [Formula: see text]  = 0, however, no pH_mbr was observed in terms of increasing bioreduction with pH (∼100%, pH > 7). In the presence of [Formula: see text] , significant bioreduction was observed at pH_mbr (∼100% at 2-30 mmol/L [Formula: see text] , 93.7% at 50 mmol/L [Formula: see text] ), which is in contrast to the previously reported infeasibility of bioreduction at high [Formula: see text] . The pH-bioreduction edges were almost comparable to the pH-biosorption edges of U(VI)_aq on heat-killed cells, revealing that biosorption is favorable for bioreduction. The end product of U(VI)_aq bioreduction was characterized as insoluble nanobiogenic uraninite by HRTEM. The redox potentials of the master complex species of U(VI)_aq, such as [Formula: see text] , [Formula: see text] , and [Formula: see text] , were calculated to obtain insights into the thermodynamic reduction mechanism. The observed dynamic role of pH in bioreduction suggests the potential for bioremediation of uranium-contaminated groundwater containing high carbonate concentrations.

Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium

The aim of this work was to study the effects of key trace elements (i.e., iron, copper and molybdenum) on the development of co-cultured n-damo and methanogenic bacteria consortium, which could realize in situ CH₄ production and utilization. The results showed that rational dosage, which was 50 mg/L of Fe, 1 mg/L of Cu and 5 mg/L of Mo, significantly stimulated the removal of NO₂^-. However, the activity of microbes was noticeably inhibited at 5 mg/L of Cu and 1 mg/L of Mo. Microbial community analysis indicated that the abundances of n-damo bacteria and methanogens showed a positive response to the rational dosage. Furthermore, the expression of key functional genes was enhanced under the rational dosage condition.

Autotrophic Vanadium(V) Bioreduction in Groundwater by Elemental Sulfur and Zerovalent Iron

Vanadium (V) is an emerging contaminant in groundwater that can adversely affect human health. Although bioremediation has been shown effective, little is known on autotrophic V(V) bioreduction in the context of oligotrophic characteristics of groundwater. In this study, we demonstrate that efficient V(V) bioreductions can be coupled with bio-oxidation of elemental sulfur (S(0)) or zerovalent iron (Fe(0)), and the V(V) removal efficiencies reached 97.5 ± 1.2% and 86.6 ± 2.5% within 120 h using S(0) and Fe(0), respectively. V(IV) is the main reduction product and precipitates naturally in near-neutral conditions. Microbial community, functional gene, and metabolites analyses reveal that synthetic metabolisms among autotrophs and heterotrophs played major roles in V(V) reduction using S(0) and Fe(0). These results demonstrate a new approach for V(V) contaminated groundwater remediation.

A simple method for assaying anaerobic biodegradation of dyes

Anaerobic dye degradation is usually assayed using serum vials, which is time-consuming and costly. In this work, a simple method was established for real-time nondestructive assay of dye biodegradation using 96-well microtiter plates with petrolatum oil to avoid the volatilization and high transmittance transparent tape to prevent the permeation of oxygen. With the anaerobic degradation of methyl red and amaranth by Shewanella oneidensis MR-1, this assay method was verified. Further experiments revealed that blocking Mtr pathway had no substantial effect on the degradation of methyl red and dose of riboflavin also failed to promote the degradation of methyl red. On the contrary, the anaerobic degradation of amaranth depended mainly on the electron transmembrane transfer through Mtr pathway. Our work clearly indicates that Mtr pathway had different effects on intra- and extra-cellular degradation of azo dyes by S. oneidensis MR-1. Such a developed method is helpful for investigating anaerobic dye decolorization.

Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane

Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies. In this article, we discuss the discovery of this process, the microorganisms and mechanisms involved, environmental significance and factors influencing metal-AOM. Since metal-AOM is poorly studied to date, some discussion is included on the present understanding of sulfate- and nitrate-AOM and traditional metal reduction processes using organic substrates or hydrogen as electron donors. Metal-AOM is a relatively new research field, and therefore more studies are needed to fully characterize the process. This review summarizes current studies and discusses the many unanswered questions, which should be useful for future research in this field.

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Reactive Fe(III) minerals can influence methane (CH4 ) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4 oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4 -stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.