Microaerophilic Oxidation of Fe(II) Coupled with Simultaneous Carbon Fixation and As(III) Oxidation and Sequestration in Karstic Paddy Soil

New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions

Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O₂ limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.

Iron at the helm: Steering arsenic speciation through redox processes in soils

The toxicity and bioavailability of arsenic (As) in soils are largely determined by its speciation. Iron (Fe) is widely present in soils with a strong affinity for As, and therefore the environmental behaviors of As and Fe oxides (including oxides, hydrates and hydrated oxides) are closely correlated with each other. The redox fluctuations of Fe driven by changes in the environment can significantly affect As speciation and its fate in soils. The interaction between Fe and As has garnered widespread attention, and the adsorption mechanisms of As by Fe oxides have also been well-documented. However, there is still a lack of systematic understanding of how Fe redox dynamics affects As speciation depending on the soil environmental conditions. In this review, we summarize the mechanisms for As speciation transformation and redistribution, as well as the role of environmental factors in the main Fe redox processes in soils. These processes include the biotic Fe oxidation mediated by Fe-oxidizing bacteria, abiotic Fe oxidation by oxygen or manganese oxides, dissimilatory Fe reduction mediated by Fe-reducing bacteria, and Fe(II)-catalyzed transformation of Fe oxides. This review contributes to a deeper understanding of the environmental behaviors of Fe and As in soils, and provides theoretical guidance for the development of remediation strategies for As-contaminated soils.

Custom-made medium approach for effective enrichment and isolation of chemolithotrophic iron-oxidizing bacteria

Chemolithotrophic neutrophilic iron (Fe)-oxidizing bacteria, which mainly belong to the family Gallionellaceae, universally prevail in terrestrial environments changing Fe cycling. However, they are typically recognized as difficult-to-culture microbes. Despite efforts, there are few Fe(II)-oxidizing lithotroph isolates; hence, their physiological and ecological knowledge remains limited. This limitation is largely owing to difficulties in their cultivation, and we hypothesize that the difficulty exists because substrate and mineral concentrations in the cultivation medium are not tuned to a specific environmental condition under which these organisms live. To address this hypothesis, this study proposes a novel custom-made medium approach for chemolithotrophic Fe(II)-oxidizing bacteria; a method that manipulates medium components through diligent analysis of field environment. A new custom-made medium simulating energy substrates and nutrients under the field condition was prepared by modifying both chemical composition and physical setup in the glass-tube medium. In particular, the modification of the physical setup in the tube had a significant effect on adjusting dissolved Fe(II) and O2 concentrations to the field environment. Using the medium, Gallionellaceae members were successfully enriched and a new Gallionellaceae species was isolated from a natural hot spring site. Compared with conventional medium, the custom-made medium has significantly higher ability in enriching Gallionellaceae members.

Intercropping improves the yield by increasing nutrient metabolism capacity and crucial microbial abundance in root of Camellia oleifera in purple soil

Intercropping system influences the endophytic microbial abundance, hormone balance, nutrient metabolism and yield, but the molecular mechanism of yield advantage in Camellia oleifera intercropping with peanut is not clear. In this study, the C. oleifera monoculture (CK) and C. oleifera-peanut intercropping (CP) treatments in purple soil were conducted, and the physicochemical properties, gene expressions, signal pathways and crucial microbial abundances were investigated to reveal the molecular mechanism of the yield advantage of intercropped C. oleifera. The results showed that the intercropping system increased in contents of pigment, carbohydrate, available nitrogen and phosphorus in leaf and root, as well as the abundances of Burkholderia, Ralstonia, Delftia, Pseudoalteromonas and Caulobacter, enhanced the relative expression levels of CoSPS, CoGBE, CoGlgP, CoGBSS/GlgA genes to promote sugar metabolism, decreased the relative expression levels of CoASA, CoTSB, CoPAI, CoTDC and CoCYP71A13 genes for inhibiting IAA biosynthesis and signal transduction, as well as microbial diversity, Fusarium, Albifimbria and Coniosporium abundances in root, ultimately improved the fruit yield of C. oleifera. These findings indicate that intercropping system improves the fruit yield by enhancing the nutrient metabolism capability and crucial microbial abundances in root of C. oleifera in purple soil.

DNA-stable isotope probing and metagenomics reveal Fe(II) oxidation by core microflora in microoxic rhizospheric habitats to mitigate the accumulation of cadmium and phenanthrene in rice

Rice rhizosphere soil-porewater microdomains exist within an iron (Fe)-rich microoxic habitat during paddy soil flooding. However, the response mechanisms of core microflora in this habitat to Fe(II)-oxidation-mediated cadmium (Cd) and phenanthrene (Phen) remain unclear. Using gel-stabilized gradient systems to replicate the microoxic conditions in the rice rhizosphere porewater, we found that microaerophilic rhizobacteria drove Fe(II) oxidation to yield iron oxides, thereby reducing the Cd and Phen contents in the rhizosphere porewater and rice (Cd and Phen decreased by 15.9%-78.0% and 10.1%-37.4%, respectively). However, co-exposure to Cd and Phen resulted in a greater reduction in the Cd uptake and a greater increase in the Phen uptake in rice as compared to those in the Cd or Phen treatments, possibly attributing to the cation-π interactions between Cd and Phen, as well as competition between the adsorption sites on the roots. The elevation of Cd-tolerant genes and Phen-degradation genes in biogenic cell-mineral aggregates unveiled the survival strategies of rhizobacteria with respect to Cd and Phen in the microoxic habitat. Potential Cd-tolerant rhizobacteria (e.g., Pandoraea and Comamonas) and Phen-degradation rhizobacteria (e.g., Pseudoxanthobacter) were identified through the DNA-SIP and 16S rRNA gene amplicon sequencing. Metagenomic analysis further confirmed that these core microbes harbor Cd-tolerant, Phen-degradation, and Fe(II) oxidation genes, supporting their metabolic potential for Cd and/or Phen in the microoxic habitat of the rice rhizosphere. These findings suggest the potential mechanism and ecological significance of core rhizospheric microbial-driven Fe(II) oxidation in mitigating the bioavailability of Cd and Phen in paddy soil during flooding.

Hydrogeochemical differences drive distinct microbial community assembly and arsenic biotransformation in unconfined and confined groundwater of the geothermal system

High‑arsenic (As) groundwater in geothermal aquifers poses a serious threat to public health. Assembly processes governing groundwater microbial community related to As biotransformation are still unexplored in geothermal groundwater across different aquifers. To fill this gap, groundwater microorganisms, community assembly processes, and microbially metabolic coupling of carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and arsenic (As) were investigated in unconfined and confined groundwater in the thermal reservoirs of the Guide Basin. The difference in groundwater hydrogeochemicals led to the heterogeneity of the microbial community and microbially mediated C, N, P, S, and As cycling between unconfined and confined groundwater. Higher temperature and As concentrations, low nutrient supply, and reduced conditions in confined groundwater supported stronger interspecific coexistence and environmental selection, thus promoting the proliferation of As-resistant microorganisms (ARMs) and simplifying the community assemblage. Abundant available nutrient supply and oxidizing conditions supported an increased species diversity and metabolic functionality in unconfined groundwater. S oxidizers, C fixation, and C degradation bacteria potentially contributed to the decreased As concentrations in unconfined groundwater. However, ARMs, ammonification, and anaerobic ammonia-oxidizing bacteria potentially caused As mobilization in confined groundwater. Overall, our results give a comprehensive insight into the interaction between As and microorganisms in geothermal groundwater.

Migration, transformation of arsenic, and pollution controlling strategies in paddy soil-rice system: A comprehensive review

Arsenic pollution in paddy fields has become a public concern by seriously threatening rice growth, food security and human health. In this review, we delve into the biogeochemical behaviors of arsenic in paddy soil-rice system, systemically revealing the complexity of its migration and transformation processes, including the release of arsenic from soil to porewater, uptake and translocation of arsenic by rice plants, as well as transformation of arsenic species mediated by microorganism. Especially, microbial processes like reduction, oxidation and methylation of arsenic, and the coupling of arsenic with carbon, iron, sulfur, nitrogen cycling through microbes and related mechanisms were highlighted. Environmental factors like pH, redox potential, organic matter, minerals, nutrient elements, microorganisms and periphyton significantly influence these processes through different pathways, which are discussed in this review. Furthermore, the current progress in remediation strategies, including agricultural interventions, passivation, phytoremediation and microbial remediation is explored, and their potential and limitations are analyzed to address the gaps. This review offers comprehensive perspectives on the complicated behaviors of arsenic and influence factors in paddy soil-rice system, and provides a scientific basis for developing effective arsenic pollution control strategies.

The degree of soil arsenic background enrichment by carbonate weathering is mainly controlled by climate in large spatial scale

Spatial distribution of soil arsenic (As) is heterogeneous. Making clear the dominant factor(s) controlling its spatial variation contributes to the differentiation of its natural background from anthropogenic pollution. Recent studies have found that the "high background" of soil heavy metals may be induced by the process of carbonate weathering. However, the extent, process, and factors that controls the degree of this enrichment, is still unclear, especially in large spatial scales. In this study, this problem is to be revealed by a compilation and spatial data mining of soil geochemical data for Australia, North America, Europe, and China with a collection and chemical analysis of bedrock and soil profiles in a typical region. The results indicated that the process of carbonate weathering strengthened the As enrichment in the soil; therefore, the carbonate rock underlaid regions could be distinguished from those of other bedrocks in the soil As maps. In the southwest region of China, an area larger than 12,000 km2 exceeding the intervention value of 100 mg/kg could be produced according to the national standard. Iron minerals play an important role for this enrichment as they serve as carriers for As during the stages of both carbonate leaching and the decomposition of silicate minerals. Geodetector results indicated a significant dependence on climate for the degree of enrichment, and both higher temperature and precipitation were necessary, which caused a decreasing trend of soil As on carbonate region from the warm and humid south to the cold and dry north in China. The dependence of soil As concentration on the mean average precipitation (MAP) and mean average temperature (MAT) was formulated using the data of the wider geographical regions across the world, and a theoretically predicted map has been produced to show the extent caused by this causation.

Hematite enhances microbial autotrophic nitrate removal in carbonate and phosphate-rich environments by increasing Fe(II) activity

Groundwater contamination by nitrates presents significant risks to both human health and the environment. In groundwater characterized as oligotrophic-low in organic carbon, but abundant in carbonate and phosphate-chemolithoautotrophic bacteria, including nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB), play a vital role in denitrification. The chemoautotrophic nitrate reduction is sensitive to environmental factors, including widespread iron oxides like hematite in nature. However, the specific mechanisms of this influence remain unclear. We examined the mechanism of how hematite impacts autotrophic nitrate reduction in a model NRFeOB community known as culture KS. We found that hematite enhances the rate of autotrophic nitrate reduction by promoting Fe(II) oxidation. Mössbauer spectroscopy detected a significant amount of adsorbed Fe(II) when hematite was present, leading to a reduction in dissolved ferrous iron. In conjunction with XRD data, it can be inferred that the formation of vivianite decreased, thereby increasing the Fe(II) activity in the reaction system. Within the culture KS bacterial consortium, hematite fosters the proliferation of autotrophic microorganisms, specifically Gallionellaceae, and amplifies the presence of denitrifying microbes, notably Rhodanobacter. This dual enhancement improves Fe(II) utilization and nitrate reduction capabilities. Our findings highlight intricate interactions between hematite and a model NRFeOB community, offering insights into groundwater nitrate removal mechanisms and the ecological strategies of autotrophic bacteria in mineral-rich environments.

Metagenomic and FT-ICR MS insights into the mechanism for the arsenic biogeochemical cycling in groundwater

Arsenic (As) is a groundwater contaminant of global concern. The degradation of dissolved organic matter (DOM) can provide a reducing environment for As release. However, the interaction of DOM with local microbial communities and how different sources and types of DOM influence the biotransformation of As in aquifers is uncertain. This study used optical spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomics, and structural equation modeling (SEM) to demonstrate the how the biotransformation of As in aquifers is promoted. The results indicated that the DOM in high-As groundwater is dominated by highly unsaturated low-oxygen(O) compounds that are quite humic and stable. Metagenomics analysis indicated Acinetobacter, Pseudoxanthomonas, and Pseudomonas predominate in high-As environments; these genera all contain As detoxification genes and are members of the same phylum (Proteobacteria). SEM analyses indicated the presence of Proteobacteria is positively related to highly unsaturated low-O compounds in the groundwater and conditions that promote arsenite release. The results illustrate how the biogeochemical transformation of As in groundwater systems is affected by DOM from different sources and with different characteristics.

Iron minerals enhance Fe(II)-mediated abiotic As(III) oxidation

The abiotic oxidation of As(III) is simultaneously mediated by the oxidation of Fe(II) in microaerobic environment, but the role of Fe minerals in the Fe(II)-mediated As(III) oxidation have been neglected. This work mimicked the microaerobic environment and examined the mechanisms of Fe(II) mediated the As(III) oxidation in the presence of Fe minerals using a variety of iron minerals (lepidocrocite, goethite, etc.). The results indicated the Fe(II) and As(III) oxidation rate were improved with Fe minerals, while As(III) oxidation efficiency increased by 1.3-1.8 times in comparison to that without minerals. Fe(II) mediated the As(III) oxidation happened on Fe minerals surface in the presence of Fe minerals. The As(III) oxidation efficiency increased with increasing Fe mineral concentrations (from 0.5 to 2 g L-1) but decreased with increasing pH values. Reactive oxygen species (ROS) that play a crucial role in As(III) oxidation were Fe(IV) and ·O2-, accounting for 42.7%-47.9% and 24.1%-29.8%, respectively. The Fe minerals facilitated the oxidation of As(III) by ROS and stimulated the release of ROS through the adsorbed-Fe(II) oxidation, both of which favored As(III) oxidation. This work highlighted the potential mechanisms of Fe minerals in promoting Fe(II) mediated the As(III) oxidation in microaerobic environment, especially in terms of As(III) oxidation efficiency, shedding a valuable insight on optimization of arsenic contaminated wastewater treatment processes.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

BACKGROUND

Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS

Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION

Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.

Biotransformation of HBCDs by the microbial communities enriched from mangrove sediments

1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are a sort of persistent organic pollutants (POPs). This research investigated 12 microbial communities enriched from sediments of four mangroves in China to transform HBCDs. Six microbial communities gained high transformation rates (27.5-97.7%) after 12 generations of serial transfer. Bacteria were the main contributors to transform HBCDs rather than fungi. Analyses on the bacterial compositions and binning genomes showed that Alcanivorax (55.246-84.942%) harboring haloalkane dehalogenase genes dadAH and dadBH dominated the microbial communities with high transformation rates. Moreover, expressions of dadAH and dadBH in the microbial communities and Alcanivorax isolate could be induced by HBCDs. Further, it was found that purified proteins DadAH and DadBH showed high conversion rates on HBCDs in 36 h (91.9 ± 7.4 and 101.0 ± 1.8%, respectively). The engineered Escherichia coli BL21 strains harbored two genes could convert 5.7 ± 0.4 and 35.1 ± 0.1% HBCDs, respectively, lower than their cell-free crude extracts (61.2 ± 5.2 and 56.5 ± 8.7%, respectively). The diastereoisomer-specific transforming trend by both microbial communities and enzymes were γ- > α- > β-HBCD, differed from α- > β- > γ-HBCD by the Alcanivorax isolate. The identified transformation products indicated that HBCDs were dehalogenated via HBr elimination (dehydrobromination), hydrolytic and reductive debromination pathways in the enriched cultures. Two enzymes converted HBCDs via hydrolytic debromination. The present research provided theoretical bases for the biotransformation of HBCDs by microbial community and the bioremediation of HBCDs contamination in the environment.

Arsenic and cadmium simultaneous immobilization in arid calcareous soil amended with iron-oxidizing bacteria and organic fertilizer

Immobilization stands as the most widely adopted remediation technology for addressing heavy metal(loid) contamination in soil. However, it is crucial to acknowledge that this process does not eliminate pollutants; instead, it confines them, potentially leaving room for future mobilization. Presently, our comprehension of the temporal variations in the efficacy of immobilization, particularly in the context of its applicability to arid farmland, remains severely limited. To address this knowledge gap, our research delves deep into the roles of iron-oxidizing bacteria (FeOB) and organic fertilizer (OF) in the simultaneous immobilization of arsenic (As) and cadmium (Cd) in soils. We conducted laboratory incubation and field experiments to investigate these phenomena. When OF was combined with FeOB, a noteworthy transformation of available As and Cd into stable species, such as the residual state and combinations with Fe-Mn/Al oxides, was observed. This transformation coincided with changes in soil properties, including pH, Eh, soluble Fe, and dissolved organic carbon (DOC). Furthermore, we observed synergistic effects between available As and Cd when treated with bacteria and OF individually. The stabilization efficiency of As and Cd, as determined by the Toxicity Characteristic Leaching Procedure, reached its highest values at 33.39 % and 24.67 %, respectively, after 120 days. Nevertheless, the formation of iron‑calcium complexes was disrupted due to pH fluctuations. Hence, long-term monitoring and model development are essential to enhance our understanding of the remediation process. The application of organic fertilizer and the use of FeOB in calcareous soil hold promise for the restoration of polluted soil and the maintenance of soil health by mitigating the instability of heavy metals(loid).

Distribution and correlation of iron oxidizers and carbon-fixing microbial communities in natural wetlands

Most microaerophilic Fe(II)-oxidizing bacteria (mFeOB) belonging to the family Gallionellaceae are autotrophic microorganisms that can use inorganic carbon to drive carbon sequestration in wetlands. However, the relationship between microorganisms involved in Fe and C cycling is not well understood. Here, soil samples were collected from different wetlands to explore the distribution and correlation of Gallionella-related mFeOB and carbon-fixing microorganisms containing cbbL and cbbM genes. A significant positive correlation was found between the abundances of mFeOB and the cbbL gene, as well as a highly significant positive correlation between the abundances of mFeOB and the cbbM gene, indicating the distribution of mFeOB in co-occurrence with carbon-fixing microorganisms in wetlands. The mFeOB were mainly dominated by Sideroxydans lithotrophicus ES-1 and Gallionella capsiferriformans ES-2 in all wetland soils. The structures of the carbon-fixing microbial communities were similar in these wetlands, mainly consisting of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The extractable Fe(II) concentrations affected the community composition of mFeOB, resulting in a significant difference in the relative abundances of the dominant FeOB. The main factors affecting cbbL-related microbial communities were dissolved inorganic carbon and oxygen, soil redox potential, and sodium acetate-extracted Fe(II). The composition of cbbM-related microbial communities was mainly affected by acetate-extracted Fe(II) and soil redox potential. In addition, the positive correlation between these functional microorganisms suggests that they play a synergistic role in Fe(II) oxidation and carbon fixation in wetland soil ecosystems. Our results suggest a cryptic relationship between mFeOB and carbon-fixing microorganisms in wetlands and that the microbial community structure can be effectively altered by regulating their physicochemical properties, thus affecting the capacity of carbon sequestration.

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

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

Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia

Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 μmol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.

Insights on biotic and abiotic 2,4-dichlorophenoxyacetic acid degradation by anaerobic iron-cycling bacteria

The use of the phenoxy herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been steadily increasing in recent years due to its selectivity against broad-leafed weeds and use on genetically modified crops resistant to 2,4-D. This increases the likelihood of 2,4-D persisting in agriculturally impacted soils, sediments, and aquatic systems. Aerobic microorganisms are capable of degrading 2,4-D enzymatically. Anaerobic degradation also occurs, though the enzymatic pathway is unclear. Iron-reducing bacteria (FeRB) have been hypothesized to augment anaerobic degradation through the production of a chemically reactive Fe(II) adsorbed to Fe(III) oxyhydroxides. To test whether this iron species can catalyze abiotic degradation of 2,4-D, an enrichment culture (BLA1) containing a photosynthetic Fe(II)-oxidizing bacterium (FeOB) "Candidatus Chlorobium masyuteum" and the FeRB "Candidatus Pseudopelobacter ferreus", both of which lacked known 2,4-D degradation genes was investigated. BLA1 produces Fe(II)-adsorbed to Fe(III) oxyhydroxides during alternating photoautotrophic iron oxidation and dark iron reduction (amended with acetate) cycles. No 2,4-D degradation occurred during iron oxidation by FeOB Ca. C. masyuteum or during iron reduction by FeRB Ca. P. ferreus under any incubation conditions tested (i.e., +/-Fe(II), +/-cells, and +/-light), or due to the presence of Fe(II) adsorbed to Fe(III) oxyhydroxides. Our results cast doubt on the hypothesis that the mineral-bound Fe(II) species augments the anaerobic degradation of 2,4-D in anoxic soils and waters by iron-cycling bacteria, and further justify the need to identify the genetic underpinnings of anaerobic 2,4-D degradation.

Insight into the plant-associated bacterial interactions: Role for plant arsenic extraction and carbon fixation

This study investigated the interactions between rhizosphere and endosphere bacteria during phytoextraction and how the interactions affect arsenic (As) extraction and carbon (C) fixation of plants. Pot experiments, high-throughput sequencing, metabonomics, and network analysis were integrated. Results showed that positive correlations dominated the interconnections within modules (>95 %), among modules (100 %), and among keystone taxa (>72 %) in the bacterial networks of plant rhizosphere, root endosphere, and shoot endosphere. This confirmed that cooperative interactions occurred between bacteria in the rhizosphere and endosphere during phytoextraction. Modules and keystone taxa positively correlating with plant As extraction and C fixation were identified, indicating that modules and keystone taxa promoted plant As extraction and C fixation simultaneously. This is mainly because modules and keystone taxa in plant rhizosphere, root endosphere, and shoot endosphere carried arsenate reduction and C fixation genes. Meanwhile, they up-regulated the significant metabolites related to plant As tolerance. Additionally, shoot C fixation increased peroxidase activity and biomass thereby facilitating plant As extraction was confirmed. This study revealed the mechanisms of plant-associated bacterial interactions contributing to plant As extraction and C fixation. More importantly, this study provided a new angle of view that phytoextraction can be applied to achieve multiple environmental goals, such as simultaneous soil remediation and C neutrality.

Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater

Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N₁/N₂)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.

Arsenic release from microbial reduction of scorodite in the presence of electron shuttle in flooded soil

Scorodite (FeAsO₄·H₂O) is a common arsenic-bearing (As-bearing) iron mineral in near-surface environments that could immobilize or store As in a bound state. In flooded soils, microbe induced Fe(III) or As(V) reduction can increase the mobility and bioavailability of As. Additionally, humic substances can act as electron shuttles to promote this process. The dynamics of As release and diversity of putative As(V)-reducing bacteria during scorodite reduction have yet to be investigated in detail in flooded soils. Here, the microbial reductive dissolution of scorodite was conducted in an flooded soil in the presence of anthraquinone-2,6-disulfonate (AQDS). Anaeromyxobacter, Dechloromonas, Geothrix, Geobacter, Ideonella, and Zoogloea were found to be the dominant indigenous bacteria during Fe(III) and As(V) reduction. AQDS increased the relative abundance of dominant species, but did not change the diversity and microbial community of the systems with scorodite. Among these bacteria, Geobacter exhibited the greatest increase and was the dominant Fe(III)- and As(V)-reducing bacteria during the incubation with AQDS and scorodite. AQDS promoted both Fe(III) and As(V) reduction, and over 80% of released As(V) was microbially transformed to As(III). The increases in the abundance of arrA gene and putative arrA sequences of Geobacter were higher with AQDS than without AQDS. As a result, the addition of AQDS promoted microbial Fe(III) and As(V) release and reduction from As-bearing iron minerals into the environment. These results contribute to exploration of the transformation of As from As-bearing iron minerals under anaerobic conditions, thus providing insights into the bioremediation of As-contaminated soil.

The changes in the physicochemical properties of calcareous soils and the factors of arsenic (As) uptake by wheat were investigated after the cessation of effluent irrigation for nearly 20 years

It is not known what the buffering capacity of soils and arsenic (As) enrichment by crops is for calcareous agricultural soils after the end of long-term effluent irrigation. In this study, changes in soil physicochemical properties and factors of influencing As uptake by wheat were investigated in agricultural soils where sewage irrigation had been ceased for nearly 20 years. The results showed that the content of CaCO₃ and pH in soil increased compared to the period before the cessation of sewage irrigation, but remained below the soil background value. Furthermore, CaCO₃ is by far the main buffering substance in agricultural soils and indirectly contributes to the increase in pH. The As concentration in the soil was 36.4 ± 34.8 mg/kg, which was 0.56-10.28 times and 0.28-5.18 times higher than the soil background and risk screening values, respectively, but showed a decreasing trend. pH and Fe dissolution were the main reasons for the lower As concentration in the soil. Total As in soil was a better predictor of As in wheat, and soil electrical conductivity (EC) and soil organic matter (SOM) promoted As uptake by wheat. The competitive uptake of As by dissolved Si was an important reason for the mismatch between As concentrations in soil and wheat. This study highlighted the key issues of As transport transformation in soil-wheat systems after cessation of effluent irrigation, using agricultural soils, and provided a reference for soil risk management in agricultural soils in mining areas.

Microbial autotrophy explains large-scale soil CO2 fixation

Microbial communities play critical roles in fixing carbon from the atmosphere and fixing it in the soils. However, the large-scale variations and drivers of these microbial communities remain poorly understood. Here, we conducted a large-scale survey across China and found that soil autotrophic organisms are critical for explaining CO₂ fluxes from the atmosphere to soils. In particular, we showed that large-scale variations in CO₂ fixation rates are highly correlated to those in autotrophic bacteria and phototrophic protists. Paddy soils, supporting a larger proportion of obligate bacterial and protist autotrophs, display four-fold of CO₂ fixation rates over upland and forest soils. Precipitation and pH, together with key ecological clusters of autotrophic microbes, also played important roles in controlling CO₂ fixation. Our work provides a novel quantification on the contribution of terrestrial autotrophic microbes to soil CO₂ fixation processes at a large scale, with implications for global carbon regulation under climate change.

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

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

Co-incorporation of Chinese milk vetch (Astragalus sinicus L.), rice straw, and biochar strengthens the mitigation of Cd uptake by rice (Oryza sativa L.)

Soil cadmium (Cd) contamination is becoming a widespread concern because of its threat to global ecosystem health and food security. Co-incorporation of Chinese milk vetch (MV) and rice straw (RS) is a common agricultural practice in Southern China; however, the effects of combining these two materials with biochar on Cd bioavailability remain unclear. This study investigated the effects of MV, RS, rape straw biochar (RB), iron-modified biochar (FB), and their combinations on Cd uptake by rice through incubation and field experiments. The results showed that compared with the control without material input (CK), MV + RS (MR), MV + RS + RB (MRRB), and MV + RS + FB (MRFB) considerably reduced the Cd concentration in brown rice by 61.20 %, 65.38 %, and 62.65 %, respectively. Furthermore, the treatments increased the formation of iron‑manganese plaque (IMP) at different growth stages; MRRB and MRFB exhibited the highest increase rates among the treatments. Quantitatively, the Fe plaque and Mn plaque were increased by 20.61 %-47.23 % and 80.18 %-172.74 %, respectively. Compared with CK, the MRRB and MRFB treatments reduced the soil available Cd by 35.09 %-54.45 % and 38.20 %-50.20 %, respectively, at all stages. This decrease was substantially lower than that observed in the MV, RS, and MR treatments. Similar trends were observed in the incubation experiment. Additionally, the Community Bureau of Reference Sequential Extraction Analysis indicated that the MRRB and MRFB treatments converted the bioavailable Cd fractions into a stable form. Partial least squares path model and redundancy analysis revealed that pH was the major factor influencing Cd bioavailability. This study emphasized that the dual impact factors from the enhancement of Cd passivation capability and IMP formation jointly result in the reduction of Cd uptake by rice. Consequently, the co-incorporation of MV, RS, and biochar is promising for remediating Cd-contaminated paddy soils in Southern China.

The nature of metal atoms incorporated in hematite determines oxygen activation by surface-bound Fe(II) for As(III) oxidation

The incorporation of secondary metal atoms into iron oxyhydroxides may regulate the surface chemistry of mediating electron transfer (ET) and, therefore, the biogeochemical pollutant processes such as arsenic (As) in the subsurface and soils. The influence of incorporating two typical metals (Cu and Zn) into a specific {001} hematite facet on O₂ activation by surface-bound Fe(II) was addressed. The results showed that Cu-incorporated hematite enhances As(III) oxidation in the presence of Fe(II) under oxic conditions and increases with increasing Cu content. Conversely, Zn incorporation leads to the opposite trend. The As(III) oxidation induced by surface-bound Fe(II) is positively related to the Fe(II) content and is favorable under acidic conditions. Reactive oxygen species (ROS), such as superoxide (·O^2-) and H₂O₂, predominantly contribute to As(III) oxidation as a result of 1-electron transfer from bound Fe(II) to surface O₂ on hematite and radical propagation. Electrochemical analysis demonstrates that Cu incorporation significantly lower the oxidation potential of Fe(II) on hematite, whereas Zn led to a higher reaction potential for Fe(II) oxidation. Subsequently, distinct surface reactivities of hematite for the activation of O₂ to form ROS by surface-bound Fe(II) are evidenced by metal incorporation. Our study provides a new understanding of the changes in the surface chemistry of iron oxyhydroxides because of incorporating metals (Zn and Cu), and therefore impact the biogeochemical processes of pollutants in soils and subsurface environments.

Carbon fixation pathways across the bacterial and archaeal tree of life

Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes and discover carbon fixation pathways in 1,007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognized archaeal and bacterial phyla (i.e. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expand the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin-Benson-Bassham cycle. Finally, the genomic potential for carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation thus appears to be much more widespread than previously known, and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.

Arsenic and nitrate remediation by isolated FeOB strains coupled with additional ferrous iron in the iron-deficient arid soils

Remediation of As(III) by use of Fe(II) oxidation bacteria (FeOB) in iron-rich soils has been reported, but seldom used in the iron-deficient soil of arid areas. This study was aimed at selecting native bacterial strains to remediate As pollution in arid soils, coupled with the addition of Fe(II). The used methods included: The selection of two FeOB strains; XRD for solid phase identification based on peaks; SEM with EDS for morphology identification of newly formed minerals with chemical compositions; XPS for surface chemistry of the minerals; FTIR for functional groups of precipitates and 3DEEM for EPS determination, etc. The results were as follows: Sharp decrement curves of As(III) and NO₃^- with Fe(II) and total Fe contents and increment of NO₂^-; NH₄⁺ fluctuating during the experimental period of 11 days; and precipitation of Fe(III) hydroxides together with As(III) with broken FeOBs due to encrustation in the SEM scan. It was concluded that two selected Pseudomonas strains have NAFO functionality by addition of iron as iron reduction-oxidation pair in the arid soil, further potentially fixing NH₄⁺ while As(III) can be effectively remediated through the FeOB participation in forms of adsorption and co-precipitation of Fe(OH)₃ through an oxidation of Fe(II) process.

Active iron species driven hydroxyl radicals formation in oxygenation of different paddy soils: Implications to polycyclic aromatic hydrocarbons degradation

The frequently occurring redox fluctuations in paddy soil are critical to the cycling of redox-sensitive elements (e.g., iron (Fe) and carbon) due to the driving of microbial processes. However, the associated abiotic process, such as hydroxyl radical (^•OH) formation, was rarely investigated. Hence, we examined the under-appreciated role of ^•OH formation in driving polycyclic aromatic hydrocarbons (PAHs) degradation upon oxygenation of anoxic paddy slurries. Results showed that ^•OH production largely differed in different paddy slurries, in the range of 271.5-581.2 μmol kg^-1 soil after 12 h reaction. The ^•OH production was highly hinged on the contents of active Fe species, i.e., exchangeable, surface-bound Fe and Fe in low-crystalline phases rather than Fe in high-crystalline minerals or silicates. Besides, ^•OH production significantly decreased with increasing soil depth due to the declined active Fe species and abundance of functional microbes. Oxygenation also induced the transformation of these active Fe species into the low- and high-crystalline phases, which might affect the following redox process. The produced ^•OH can efficiently degrade PAHs with degradation extents depending on their physiochemical properties. Our findings highlight the key roles of active Fe species in driving ^•OH formation and organic contaminants degradation during redox fluctuations of paddy soils.