Fate of Labile Organic Carbon in Paddy Soil Is Regulated by Microbial Ferric Iron Reduction

Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.

Enhancement of hydrogenotrophic methanogenesis for methane production by nano zero-valent iron in soils

Nanoscale zero-valent iron (nZVI) is attracting increasing attention as the most commonly used environmental remediation material. However, given the high surface area and strong reducing capabilities of nZVI, there is a lack of understanding regarding its effects on the complex anaerobic methane production process in flooded soils. To elucidate the mechanism of CH4 production in soil exposed to nZVI, paddy soil was collected and subjected to anaerobic culture under continuous flooding conditions, with various dosages of nZVI applied. The results showed that the introduction of nZVI into anaerobic flooded rice paddy systems promoted microbial utilization of acetate and carbon dioxide as carbon sources for methane production, ultimately leading to increased methane production. Following the introduction of nZVI into the soil, there was a rapid increase in hydrogen levels in the headspace, surpassing that of the control group. The hydrogen levels in both the experimental and control groups were depleted by the 29th day of culture. These findings suggest that nZVI exposure facilitates the enrichment of hydrogenotrophic methanogens, providing them with a favorable environment for growth. Additionally, it affected soil physicochemical properties by increasing pH and electrical conductivity. The metagenomic analysis further indicates that under exposure to nZVI, hydrogenotrophic methanogens, particularly Methanobacteriaceae and Methanocellaceae, were enriched. The relative abundance of genes such as mcrA and mcrB associated with methane production was increased. This study provides important theoretical insights into the response of key microbes, functional genes, and methane production pathways to nZVI during anaerobic methane production in rice paddy soils, offering fundamental insights into the long-term fate and risks associated with the introduction of nZVI into soils.

Composition of DOM along the depth gradients in the paddy field treated with crop straw for 10 years

Crop straw return is a widely used agricultural management practice. The addition of crop straw significantly alters the pool of dissolved organic matter (DOM) in agricultural soils and plays a pivotal role in the global carbon (C) cycle, which is sensitive to climate change. The DOM concentration and composition at different soil depths could regulate the turnover and further storage of organic C in terrestrial systems. However, it is still unclear how crop straw return influences the change in DOM composition in rice paddy soils. Therefore, a field experiment was conducted in which paddy soil was amended with crop straw for 10 years. Two crop straw-addition treatments [NPK with 50% crop straw (NPK+1/2S) and NPK with 100% crop straw (NPK + S)], a conventional mineral fertilization control (NPK) and a non-fertilized control were included. Topsoil (0-20 cm) and subsoil (20-40 cm) samples were collected to investigate the soil DOM concentration and compositional structure of the profile. Soil nutrients, iron (Fe) fraction, microbial biomass carbon (MBC), and concentration and optical properties (UV-Vis and fluorescence spectra) of soil DOM were determined. Here, we found that the DOM in the topsoil was more humified than that in the subsoil. The addition of crop straw further decreased the humidification degree of DOM in the subsoil. In crop straw-amended topsoil, microbial decomposition controlled the composition of DOM and induced the formation of aromatic DOM. In the straw-treated subsoil, selective adsorption by poorly crystalline Fe(oxyhydr)oxides and microbial decomposition controlled the composition of DOM. In particular, the formation of protein-like compounds could have played a significant role in the microbial degradation of DOM in the subsoil. Overall, this work conducted a case study within long-term agricultural management to understand the changes in DOM composition along the soil profile, which would be further helpful for evaluating C cycling in agricultural ecosystems.

Labile Carbon from Artificial Roots Alters the Patterns of N2O and N2 Production in Agricultural Soils

Labile carbon (C) continuously delivered from the rhizosphere profoundly affects terrestrial nitrogen (N) cycling. However, nitrous oxide (N2O) and dinitrogen (N2) production in agricultural soils in the presence of continuous root C exudation with applied N remains poorly understood. We conducted an incubation experiment using artificial roots to continuously deliver small-dose labile C combined with 15N tracers to investigate N2O and N2 emissions in agricultural soils with pH and organic C (SOC) gradients. A significantly negative exponential relationship existed between N2O and N2 emissions under continuous C exudation. Increasing soil pH significantly promoted N2 emissions while reducing N2O emissions. Higher SOC further promoted N2 emissions in alkaline soils. Native soil-N (versus fertilizer-N) was the main source of N2O (average 67%) and N2 (average 80%) emissions across all tested soils. Our study revealed the overlooked high N2 emissions, mainly derived from native soil-N and strengthened by increasing soil pH, under relatively real-world conditions with continuous root C exudation. This highlights the important role of N2O and N2 production from native soil-N in terrestrial N cycling when there is a continuous C supply (e.g., plant-root exudate) and helps mitigate emissions and constrain global budgets of the two concerned nitrogenous gases.

Coastal blue carbon in China as a nature-based solution toward carbon neutrality

To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year-1, of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year-1 along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha-1 year-1. The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.

Coprecipitation with Ferrihydrite Inhibits Mineralization of Glucuronic Acid in Anoxic Soils

It is known that the association of soil organic matter (SOM) with iron minerals limits carbon mobilization and degradation in aerobic soils and sediments. However, the efficacy of iron mineral protection mechanisms under reducing soil conditions, where Fe(III)-bearing minerals may be used as terminal electron acceptors, is poorly understood. Here, we quantified the extent to which iron mineral protection inhibits mineralization of organic carbon in reduced soils by adding dissolved ¹³C-glucuronic acid, a ⁵⁷Fe-ferrihydrite-¹³C-glucuronic acid coprecipitate, or pure ⁵⁷Fe-ferrihydrite to anoxic soil slurries. In tracking the re-partitioning and transformation of ¹³C-glucuronic acid and native SOM, we find that coprecipitation suppresses mineralization of ¹³C-glucuronic acid by 56% after 2 weeks (at 25 °C) and decreases to 27% after 6 weeks, owing to ongoing reductive dissolution of the coprecipitated ⁵⁷Fe-ferrihydrite. Addition of both dissolved and coprecipitated ¹³C-glucuronic acid resulted in increased native SOM mineralization, but the reduced bioavailability of the coprecipitated versus dissolved ¹³C-glucuronic acid decreased the priming effect by 35%. In contrast, the addition of pure ⁵⁷Fe-ferrihydrite resulted in negligible changes in native SOM mineralization. Our results show that iron mineral protection mechanisms are relevant for understanding the mobilization and degradation of SOM under reducing soil conditions.

Reductive Sequestration of Cr(VI) and Immobilization of C during the Microbially Mediated Transformation of Ferrihydrite-Cr(VI)-Fulvic Acid Coprecipitates

Cr(VI) detoxification and organic matter (OM) stabilization are usually influenced by the biological transformation of iron (Fe) minerals; however, the underlying mechanisms of metal-reducing bacteria on the coupled kinetics of Fe minerals, Cr, and OM remain unclear. Here, the reductive sequestration of Cr(VI) and immobilization of fulvic acid (FA) during the microbially mediated phase transformation of ferrihydrite with varying Cr/Fe ratios were investigated. No phase transformation occurred until Cr(VI) was completely reduced, and the ferrihydrite transformation rate decreased as the Cr/Fe ratio increased. Microscopic analysis was uncovered, which revealed that the resulting Cr(III) was incorporated into the lattice structure of magnetite and goethite, whereas OM was mainly adsorbed on goethite and magnetite surfaces and located within pore spaces. Fine line scan profiles showed that OM adsorbed on the Fe mineral surface had a lower oxidation state than that within nanopores, and C adsorbed on the magnetite surface had the highest oxidation state. During reductive transformation, the immobilization of FA by Fe minerals was predominantly via surface complexation, and OM with highly aromatic and unsaturated structures and low H/C ratios was easily adsorbed by Fe minerals or decomposed by bacteria, whereas Cr/Fe ratios had little effect on the binding of Fe minerals and OM and the variations in OM components. Owing to the inhibition of crystalline Fe minerals and nanopore formation in the presence of Cr, Cr sequestration and C immobilization can be synchronously favored at low Cr/Fe ratios. These findings provide a profound theoretical basis for Cr detoxification and synchronous sequestration of Cr and C in anoxic soils and sediments.

Fe(III) stabilizing soil organic matter and reducing methane emissions in paddy fields under varying flooding conditions

The role of iron (Fe) in soil organic matter (SOM) stabilization and decomposition in paddy soils has recently gained attention, but the underlying mechanisms during flooding and drying periods remain elusive. As the depth water layer is maintained in the fallow season, there will be more soluble Fe than during the wet and drainage seasons and the availability of oxygen (O₂) will be different. To assess the influence of soluble Fe on SOM mineralization during flooding, an incubation experiment was designed under oxic and anoxic flooding conditions, with and without Fe(III) addition. The results showed that Fe(III) addition significantly (p < 0.05) decreased SOM mineralization by 14.4 % under oxic flooding conditions over 16 days. Under anoxic flooding incubation, Fe(III) addition significantly (p < 0.05) decreased 10.8 % SOM decomposition, mainly by 43.6 % methane (CH₄) emission, while no difference in carbon dioxide (CO₂) emission was noticed. These findings suggest that implementing appropriate water management strategies in paddy soils, considering the roles of Fe under both oxic and anoxic flooding conditions, can contribute to SOM preservation and mitigation of CH₄ emissions.

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

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

Interactions between organic matter and Fe oxides at soil micro-interfaces: Quantification, associations, and influencing factors

Iron (Fe) oxides are widely recognized to prevent the degradation of organic matter (OM) in environments, thereby promoting the persistence of organic carbon (OC) in soils. Thus, discerning the association mechanisms of Fe oxides and OC interactions is key to effectively influencing the dynamics and extent of organic C cycling in soils. Previous studies have focused on i) quantifying Fe oxide-bound organic carbon (Fe-OC) in individual environments, ii) investigating the distribution and adsorption capacity of Fe-OC, and iii) assessing the redox cycling and transformation of Fe-OC. Furthermore, the widespread application of high-tech instrumentation and methods has greatly contributed to a better understanding of the mechanism of organic mineral assemblages in the past few decades. However, few literature reviews have comprehensively summarized Fe-OC distributions, associations, and characteristics in soil-plant systems. Here, studies investigating the Fe-OC contents among different environments are reviewed. In addition, the mechanisms and processes related to OM transformation dynamics occurring at mineral-organic interfaces are also described. Recent studies have highlighted that diverse interactions occur between Fe oxides and OC, with organic compounds adhering to Fe oxides due to their huge specific surfaces area and active reaction sites. Moreover, we also review methods for understanding Fe-OC interactions at micro-interfaces. Lastly, developmental prospects for understanding coupled Fe-OC geochemical processes in soil environments at molecular- and nano-scales are outlined. The summary suggests that combined advanced techniques and methods should be used in future research to explore micro-interfaces and in situ descriptions of organic mineral assemblages. This review also suggests that future studies need to consider the functional and spatial complexity that is typical of soil/sediment environments where Fe-OC interactions occur.

Effects of exogenous Fe addition on soil respiration rate and dissolved organic carbon structure in temperate forest swamps of northeastern China

Fe as an important redox-active transition metal plays a key role in the carbon cycle of ecosystems. To date, the mechanisms by which Fe affects organic carbon (soil respiration rate [Rs] and dissolved organic carbon [DOC] structure) remain unclear, because most studies only focused on the effect of Fe on soil organic carbon content. To understand these effects, a 30-day laboratory incubation experiment was conducted using forest swamp soils from northeastern China amended with different concentrations of exogenous Fe (no exogenous Fe added [L0], add exogenous Fe at 1 time the soil background value [L1], add exogenous Fe at 2 times the soil background value [L2]). Our results showed that exogenous Fe addition reduced the soil respiration rate by 54.8% during the incubation time. The DOC concentration decreased by 40.5% with exogenous Fe addition during the incubation time. The dissolved organic matter (DOM) characteristic parameters showed apparent variations (p < 0.05), including significant increases in the fluorescence and biological index and significant decreases in the humification index, which indicate that exogenous Fe addition reduced humification, which may lead to the increased fixation of dissolved organic carbon. In addition significant increases in tryptophan-like DOM was observed when exogenous Fe addition resulted in a soil Fe concentration of twice the background value (p < 0.05). These findings indicate that exogenous Fe addition promotes the production of endogenous soil DOC by microorganisms. Overall, Our study uses three-dimensional fluorescence spectroscopy techniques combined with the parallel factor analysis (PARAFAC) to characterize the dissolved organic matter components in soil samples under exogenous Fe addition conditions, with a view to exploring the differences in the effects of Fe on the DOC concentration and structure of wetland soils, providing a theoretical basis for the mechanisms of soil carbon fixation and soil organic matter transformation in wetland soils.

Oxygen availability regulates the quality of soil dissolved organic matter by mediating microbial metabolism and iron oxidation

Dissolved organic matter (DOM) plays a vital role in biogeochemical processes and in determining the responses of soil organic matter (SOM) to global change. Although the quantity of soil DOM has been inventoried across diverse spatio-temporal scales, the underlying mechanisms accounting for variability in DOM dynamics remain unclear especially in upland ecosystems. Here, a gradient of SOM storage across 12 croplands in northeast China was used to understand links between DOM dynamics, microbial metabolism, and abiotic conditions. We assessed the composition, biodegradability, and key biodegradable components of DOM. In addition, SOM and mineral-associated organic matter (MAOM) composition, soil enzyme activities, oxygen availability, soil texture, and iron (Fe), Fe-bound organic matter, and nutrient concentrations were quantified to clarify the drivers of DOM quality (composition and biodegradability). The proportion of biodegradable DOM increased exponentially with decreasing initial DOM concentration due to larger fractions of depolymerized DOM that was rich in small-molecular phenols and proteinaceous components. Unexpectedly, the composition of DOM was decoupled from that of SOM or MAOM, but significantly related to enzymatic properties. These results indicate that microbial metabolism exhibited a dominant role in DOM generation. As DOM concentration declined, increased soil oxygen availability regulated DOM composition and enhanced its biodegradability mainly through mediating microbial metabolism and Fe oxidation. The oxygen-induced oxidation of Fe(II) to Fe(III) removed complex DOM compounds with large molecular weight. Moreover, increased oxygen availability stimulated oxidase-catalyzed depolymerization of aromatic substances, and promoted production of protein-like DOM components due to lower enzymatic C/N acquisition ratio. As global changes in temperature and moisture will have large impacts on soil oxygen availability, the role of oxygen in regulating DOM dynamics highlights the importance of integrating soil oxygen supply with microbial metabolism and Fe redox status to improve model predictions of soil carbon under climate change.

Structure and core taxa of bacterial communities involved in extracellular electron transfer in paddy soils across China

Microbial communities with extracellular electron transfer (EET) activity are capable of driving geochemical changes and cycles, but a comprehensive understanding of the key microbiota responsible for EET in complex soil matrices is still lacking. Herein, the EET activities, in terms of maximum current density (j_max) and accumulated charge output (C_out), of 41 paddy soils across China were evaluated from the exoelectrogenic properties with a conventional bioelectrochemical system (BES). The j_max with a range of 8.85 × 10^-4 to 0.41 A/m² and C_out with a range of 0.27 to 172.21C were obtained from these soil-based BESs. The bacterial community analyses revealed that the most abundant phylum, order, and genus were Firmicutes, Clostridiales, and Clostridum-sensus-stricto 10, respectively. Bacterial network analysis displayed the positive correlations between the majority of electroactive bacteria-containing genera and multiple other genera, indicating their underlying cooperation for the EET. Partial least squares regression (PLSR) model showed remarkable performance in describing the EET activity with 75 most abundant genera as input variables, identified that 32 genera were very important for governing the EET activities. Multiple linear regression (MLR) analyses further prioritized that the genera norank-c-Berkelbacteria and Fonticella were the key contributors, while the genus Paenibacillus was the key competitor against bacterial exoelectrogenesis in paddy soils. Moreover, the spearman analysis showed that the abundance of these keystone taxa was mainly influenced by the carbon content and pH. This approach provides a promising avenue to monitor the microbial activities in paddy soils as well as the links between microbial community composition and ecological function.

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.

Feammox process driven anaerobic ammonium removal of wastewater treatment under supplementing Fe(III) compounds

Ammonium removal in wastewater treatment plants demands large quantities energy input, such as aeration for wastewater and the addition of organics for nitrate reduction. Anaerobic ammonium oxidation coupled to Fe(III) reduction, called Feammox process play a crucial role in natural nitrogen cycle, which has been rarely investigated in the field of wastewater treatment. Besides, Iron-reducing bacteria (FeRB) as function bacteria of Feammox could transfer electrons to iron oxide by oxidizing organics. The possibility of anaerobic ammonium removal coupled with organics should be investigated to assess the potential of Feammox process for conventional wastewater treatment. In this study, five Fe(III) compounds, Fe₂O₃, Fe₃O₄, Fe(OH)₃, Citrate-Fe and pyrite were supplemented to investigate the effect of iron oxides on ammonium removal in serum bottles with working volume of 100 mL. It was found that ammonium removal efficiency of the Fe₂O₃ group was the highest. To simulate wastewater treatment process in sewage treatment plant, three Up-flow anaerobic sludge blanket reactors with volume of 250 mL adding Fe₂O₃ were applied with influent of ammonium and carbon sources. It was found that the organics significantly inhibited the ammonium removal by Feammox process. This was attributed to that carbon sources and ammonium could be used as electron donors for Fe(III) reduction. In addition, this nitrogen removal was also likely related with the iron cycle, i.e., Fe(III) reduction with ammonium oxidation and Fe(II) oxidation with nitrate/nitrite reduction. This study provides a promising alternative technology for anaerobic ammonium removal in wastewater treatment. Optimizing nitrogen removal and carbon sources applied in conventional wastewater plants are required in future.

Influence mechanisms of iron, aluminum and manganese oxides on the mineralization of organic matter in paddy soil

The mineralization of soil organic matter (SOM) is closely related to the emission of greenhouse gas into atmosphere and the stability of organic carbon in soil. The influence of minerals on SOM mineralization in the specific soil received very few attentions. The influence characteristics and potential mechanisms of oxides on the mineralization of SOM in the paddy soil were observed in this study by incubating soil with the addition (dosage: 10 g kg^-1) of prepared gibbsite, goethite, ferrihydrite or birnessite for 60 days. A sequence control treatment (753 mg CO₂-C kg^-1) > goethite treatment (656 mg CO₂-C kg^-1) ≈ gibbsite treatment (649 mg CO₂-C kg^-1) > birnessite treatment (529 mg CO₂-C kg^-1) > ferrihydrite treatment (441 mg CO₂-C kg ^-1) was found in the cumulative amount of released CO₂ in 60 days of incubation. Oxides especially ferrihydrite significantly decreased the content of dissolved organic matter (DOM) but tended to increase the content of microbial biomass carbon (MBC). The molecular structure of DOM in the paddy soil was simplified by gibbsite, ferrihydrite and birnessite after the incubation. Oxides especially birnessite and ferrihydrite reduced soil pH and the content of soil available N but increased soil redox potential (Eh). All examined oxides especially Fe oxides enhanced soil bacterial abundance but only birnessite significantly affected bacterial composition at phyla level. The stimulation on the immobilization and/or microbial assimilation of labile organic carbon, the modulation on soil basic properties (available N, pH, Eh), and the decrease of the relative abundance of some decomposing bacteria phyla such as Actinobacteria were the potential pathways of oxides in decreasing SOM mineralization.

Extensive production of hydroxyl radicals during oxygenation of anoxic paddy soils: Implications to imidacloprid degradation

Hydroxyl radical (^•OH) plays a critical role in driving organic pollutants degradation during redox fluctuations. Such processes have been frequently investigated in sedimentary environments, but rarely referred to the agricultural fields, such as paddy soils with frequent occurrence of redox fluctuations. Our findings demonstrated that extensive ^•OH (40.3-1061.4 μmol kg^-1) was produced during oxygenation of anoxic paddy slurries under circumstance conditions. Wet chemical sequential extractions, Mössbauer spectra, and X-ray photoelectron spectroscopy characterizations collectively corroborated that 0.5 M HCl-extracted Fe(II) (i.e., surface-bound Fe and Fe in low-crystalline minerals) contributed to more ^•OH production than aqueous Fe²⁺. The produced ^•OH can efficiently induce the oxidative transformation of organic carbon and the degradation of imidacloprid (IMP), which in turn produced the by-products, such as IMP-urea, IMP-olefin, and 6-chloronicontinic acid, via ^•OH-attacking mechanisms. Quenching experiments showed that hydrogen peroxide (H₂O₂) was the important intermediate for ^•OH formation via Haber-Weiss mechanisms during oxygenation processes. These findings indicate that abundant ^•OH can be produced during the redox fluctuations of paddy soil, which might be of great significance to predict the removal of organic contaminants and the mineralization of organic carbon in paddy fields.

Arsenic and cadmium load in rice tissues cultivated in calcium enriched biochar amended paddy soil

Arsenic (As) and cadmium (Cd) are unnecessary metal(loids) toxic at high concentration to plants and humans, hence lessening their rice grain accumulation is crucial for food security and human healthiness. Charred eggshell (EB), corncob biochar (CB), and eggshell-corncob biochar (ECB) were produced and amended to As and Cd co-polluted paddy soil at 1% and 2% application rates to alleviate the metal(loids) contents in rice grains using pot experiments. All the amendments increased paddy yields at 1%, while EB at 2% significantly reduced the yields compared to untreated control. The resulting yield loss in 2%EB was from the combined effects of its high CaCO₃ supplementation, and the increment of rhizosphere soil pH which could insolubilize plant nutrients. The amendments were inefficient in decreasing rice grain As (As_Grain), but all the treatments significantly reduced the rice grain Cd (Cd_Grain) at both 1% (44.4-77.1%) and 2% (79.8-91.5%) application rates compared to that of control. Regression analysis for contribution weights of control factors revealed that rhizosphere soil Eh and pH were vital influential factors regulating the As_Grain, whereas porewater Cd was main factor controlling Cd_Grain accumulation. These investigations indicated that the Ca-enriched eggshell-corncob biochar even at high application rate (i.e., 2%ECB) could be a potential tactic for grain accumulation remediation of the cationic pollutant (i.e., Cd) from the paddy soil to rice grain scheme with concurrent increase in rice yields.

Orbitrap ESI-MS evaluation of solvent extractable organics from a crude oil release site

The concentrations of oxygen-containing organic compounds (OCOC), measured as dissolved organic carbon (DOC), in groundwater exceeds those of dissolved hydrocarbons, measured as total petroleum hydrocarbons (TPH), at a crude oil release site. Orbitrap mass spectrometry was used to characterize OCOC in samples of the oil, water from upgradient of the release, source area, and downgradient wells, and a local lake. Chemical characterization factors included carbon number, oxygen number, formulae similarity, double bond equivalents (DBE) and radiocarbon dating. Oil samples were dominated by formulae with less than 30 carbons, four or fewer oxygens, and a DBE of less than four. In water samples, formulae were identified with more than 30 carbons, more than 10 oxygens, and a DBE exceeding 30. These characteristics are consistent with DOC found in unimpacted water. Between 65% and 92% of the formulae found in samples collected within the elevated OCOC plume were also found in the upgradient or surface water samples. Evidence suggests that many of the OCOC are not petroleum degradation intermediates, but microbial products generated as a result of de novo synthesis by organisms growing on carbon supplied by the oil. Implications of these results for understanding the fate and managing the risk of hydrocarbons in the subsurface are discussed.

The anaerobic oxidation of methane in paddy soil by ferric iron and nitrate, and the microbial communities involved

The anaerobic oxidation of methane (AOM) mediated by microorganisms is a key process in the reduction of methane emissions, and AOM-coupled electron acceptors have been shown to regulate methane emissions into the atmosphere in marine systems. Paddy fields are a significant source of methane and account for 20% of global methane emissions, but the effect of electron acceptors on the methane emission process in flooded paddy fields has been poorly characterized. This study aimed to determine whether the electron acceptors ferric iron and nitrate, and biochar, acting as an electron shuttle, can regulate the AOM process in paddy soil, with or without interaction between biochar and these two electron acceptors. We also aimed to characterize which microorganisms are actively involved. Here, we added ¹³C-labeled CH₄ (¹³CH₄) into anaerobic microcosms to evaluate the role of electron acceptors by measuring the methane oxidation rate and the enrichment of ¹³C-labeled CO₂ (¹³CO₂). We then combined DNA-stable isotope probing with amplicon sequencing to study the active microorganisms. We found for the first time that, in addition to nitrate, ferric iron can also effectively promote AOM in paddy soil. However, there was no significant effect of biochar. Ferric iron-dependent AOM was mainly carried out by iron-reducing bacteria (Geobacter, Ammoniphilus and Clostridium), and nitrate-dependent AOM was mainly by nitrate-reducing bacteria (Rhodanobacter, Paenibacillus and Planococcus). Our results demonstrate that the AOM process, regulated by the electron acceptors ferric iron and nitrate, can alleviate methane emission from paddy soil. The potentially active microorganisms related to electron acceptor reduction may be crucial for this methane sink and deserve further research.

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.

Evaluation of Microbe-Driven Soil Organic Matter Quantity and Quality by Thermodynamic Theory

Microbial communities, coupled with substrate quality and availability, regulate the stock (formation versus mineralization) of soil organic matter (SOM) in terrestrial ecosystems. However, our understanding of how soil microbes interact with contrasting substrates influencing SOM quantity and quality is still very superficial. Here, we used thermodynamic theory principles and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the linkages between dissolved organic matter (DOM [organic substrates in soil that are readily available]), thermodynamic quality, and microbial communities. We investigated soils from subtropical paddy ecosystems across a 1,000-km gradient and comprising contrasting levels of SOM content and nutrient availability. Our region-scale study suggested that soils with a larger abundance of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and higher SOM content. We further advocated a novel phylotype-level microbial classification based on their associations with OM quantities and qualities and identified two contrasting clusters of bacterial taxa: phylotypes that are highly positively correlated with thermodynamically favorable DOM and larger SOM content versus those which are associated with less-favorable DOM and lower SOM content. Both groups are expected to play critical roles in regulating SOM contents in the soil. By identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities and should be considered in models of soil organic matter preservation.IMPORTANCE Microbial communities are known to be important drivers of organic matter (OM) accumulation in terrestrial ecosystems. However, despite the importance of these soil microbes and processes, the mechanisms behind these microbial-SOM associations remain poorly understood. Here, we used the principles of thermodynamic theory and novel Fourier transform ion cyclotron resonance mass spectrometry techniques to investigate the links between microbial communities and dissolved OM (DOM) thermodynamic quality in soils across a 1,000-km gradient and comprising contrasting nutrient and C contents. Our region-scale study provided evidence that soils with a larger amount of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and larger SOM content. Moreover, we created a novel phylotype-level microbial classification based on the associations between microbial taxa and DOM quantities and qualities. We found two contrasting clusters of bacterial taxa based on their level of association with thermodynamically favorable DOM and SOM content. Our study advances our knowledge on the important links between microbial communities and SOM. Moreover, by identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities. Together, our findings support that the association between microbial species taxa and substrate thermodynamic quality constituted an important complement explanation for soil organic matter preservation.

Iron Stable Isotopes in Bulk Soil and Sequential Extracted Fractions Trace Fe Redox Cycling in Paddy Soils

In paddy soils, iron (Fe) forms are highly influenced by the seasonal redox changes and leave detectable isotope signals because of fractionation between different Fe forms. Here, we present Fe concentrations and Fe isotope compositions (expressed as δ⁵⁶Fe values) in a paddy soil profile from Suzhou, China. Light Fe isotopes were enriched in two iron-accumulation layers (Br3 and G1) with high Fe concentrations. In particular, large shifts in both Fe concentrations and δ⁵⁶Fe values were found at the Br2 and Br3 boundaries, showing fast and efficient transformation between these horizons. With sequential extraction, we show that Fe isotopes in the short-range-ordered Fe minerals and crystalline Fe oxides were lighter than those in the residual silicate minerals. Iron enriched in light isotopes was leached from the Ap horizon and subsequently moved to Br horizon, quickly precipitating there as Fe oxides.