Liping Fang

Arsenic mobilization in flooded rice paddies is driven by microbial redox reactions, but how redox‐active organic matter coordinates arsenic‐gene‐bearing hosts and soil viromes remains unresolved. We examined the effects of fulvic acid (FA), humic acid (HA) and humin (HM) on arsenic‐mobilizing host–virome assemblages using sequential anoxic slurry‐transfer enrichments, genome‐resolved metagenomics and curated virome analysis. FA and HA produced greater late‐transfer arsenite accumulation than HM or unamended soil, while treatment‐associated host genomes carried contrasting arsenic redox and detoxification repertoires. We identified two large temperate phages (> 100 kb) carrying receiver‐only AioR‐like loci in the FA and HA enrichments, with host‐prediction signals converging on Bacillaceae . These loci were supported by hallmark‐rich viral scaffold context and intact‐locus read coverage and remained invariant despite genome‐wide polymorphism. Reanalysis of 49,649 soil‐derived viral genomes showed that arsenic‐associated viral genes were rare among the 9518 quality‐filtered genomes (0.29%) and occurred mainly as truncated regulatory architectures, particularly AioR‐like receiver and AioS‐like kinase‐core fragments, on putatively lytic 30–70 kb genomes. By contrast, arsenic‐associated viral‐gene carriers were more frequent in our enrichment viromes (3.7%). These findings link distinct humic fractions to arsenic‐mobilizing host–virome assemblages and reveal a candidate regulatory layer involving rare large temperate phages carrying receiver‐only AioR‐like loci.

The uptake of arsenic (As), cadmium (Cd), and mercury (Hg) in rice is a global health concern. The variable biogeochemical processes that govern contamination risk, along with increased anthropogenic pressures, present significant obstacles to implementing mitigation strategies. This perspective highlights the biogeochemical processes governing the mobility and rice uptake of metal(loid)s across the soil-rice continuum and provides recent insights into mitigation strategies. An overview of anthropogenic stressors that may further exacerbate rice contamination, particularly climate change, is also provided. Finally, in the context of historical knowledge, we identify and discuss a future roadmap for research priorities and mitigation strategies, including (1) addressing variability in soil-rice systems that alters metal(loid) uptake dynamics, (2) investigating practical applications and mitigation strategies for farmers, and (3) expanding research into the myriad effects climate change may have on metal(loid) cycling.

Anaerobic arsenic (As) methylation by fermentative microorganisms, particularly Clostridium-related populations, controls As speciation, mobility, and volatilization in flooded paddy soils, yet the mechanisms promoting this process remain poorly understood. Here, we reveal that phenazine- and phenoxazine-like redox mediators can enhance anaerobic As methylation via reshaping the intracellular electron allocation in a representative As-methylating fermentative bacterium. We integrated As speciation analysis, metabolite profiling, proteomics, and metabolic-flux modeling to determine how resazurin, as a represenative lipophilic redox mediator, reshapes fermentative metabolism and methylated As (MeAs) formation. The membrane-permeable redox mediator resazurin increased the apparent rate constant of MeAs formation by up to fourfold relative to the hydrophilic mediator anthraquinone-2,6-disulfonic acid (AQDS). Unlike AQDS, resazurin enhanced dimethylarsine formation while establishing a more reducing intracellular environment by diverting electrons from hydrogen evolution, indicating altered intracellular electron disposal. At the proteomic level, resazurin induced coordinated increases in As(III) methyltransferase (ArsM) and proteins involved in S-adenosylmethionine (SAM) biosynthesis, representing the primary molecular responses associated with enhanced As methylation. Proteins involved in amino-acid-fueled energy conservation and redox homeostasis were also enriched, potentially creating favorable cellular conditions for SAM-dependent As methylation. In a paddy-soil-derived fermentative consortium, resazurin likewise enhanced MeAs production and increased transcript levels of Clostridium-associated arsM and the SAM synthetase gene (metK). These findings identify lipophilicity-dependent, redox-compound-mediated intracellular electron flow reprogramming as a previously underappreciated control on anaerobic As methylation and provide a mechanistic basis for predicting MeAs formation in flooded soil environments.

Microbial respiration-triggered reductive transformation of dissolved organic matter (DOM) plays a central role in O2 activation and, consequently, As(III) oxidation under fluctuating hydrological conditions. However, the key DOM components and their molecular transformations associated with this electron-transfer process remain poorly resolved. Here, by integrating Fourier transform ion cyclotron resonance mass spectrometry with machine learning, we reveal that fulvic acid (FA), the predominant DOM fraction, undergoes selective molecular transformation by Geobacter sulfurreducens PCA, forming a reactive subpool that drives O2 activation and thereby enhances As(III) oxidation by approximately 2–10 fold. Reaction network analysis reveals that oxygen-rich aromatic precursors are preferentially transformed into more reduced intermediates through decarboxylation, dehydrogenation, and partial reduction pathways. These transformations collectively shift the molecular composition toward lower oxidation states and enhanced redox reactivity. Machine-learning analysis further identifies nitrogen- and sulfur-containing molecules with low oxidation states as the key components governing the overall redox activity of the system. These species represent a functionally distinct fraction of microbially transformed FA with enhanced electron-donating capacity. This study provides molecular-level insights into how microbial DOM transformation regulates O2 activation and As(III) oxidation, offering a mechanistic basis for predicting and manipulating redox reactivity in dynamic soil and sediment systems.

Nanoplastics (NPs) have emerged as ubiquitous environmental contaminants, raising increasing concerns over their ecological impacts and potential risks to human health. However, accurate quantification of NPs in aquatic environments remain analytically challenging due to the lack of effective enrichment techniques capable of operating at trace concentrations. Herein, we developed a robust, rapid, and organic-free flocculation-based preconcentration strategy for NP quantification in water samples. Utilizing polymerized ferrous sulfate (PFS) as an flocculant, diverse NPs, including polystyrene (PS), poly(methyl methacrylate) (PMMA), poly(vinyl chloride) (PVC), polypropylene (PP), and poly(ethylene terephthalate) (PET), were efficiently coprecipitated with ferrihydrite (FeOOH) and subsequently isolated by centrifugation. The enriched NPs were analyzed by pyrolysis gas chromatography/mass spectrometry (Py-GC/MS), achieving high recoveries (≥92.8%) and low detection limits (0.01-0.02 μg/L). Field application revealed PS NP concentrations ranging from 0.11 to 0.36 μg/L, while recovery experiments in representative natural waters yielded consistent results (81.3-97.3%), confirming the method's accuracy and matrix tolerance. Compared with conventional extraction approaches (e.g., cloud point extraction), this protocol avoids the introduction of organic additives that may interfere with pyrolysis, thereby improving analytical sensitivity and reducing background complexity. Overall, the proposed method provides a reliable and practical platform for monitoring NP pollution in diverse aquatic systems.

Iron plaques serve as the final barrier for the catalytic transformation and sequestration of pollutants, such as arsenic, on rice roots, yet the role of surface structural properties in their performance remains largely unknown. Here, we demonstrate that the presence of oxygen vacancies (OVs) on iron plaques plays a dual role in augmenting the molecular O₂ activation and sequestration of arsenic. The incorporation of copper (Cu) atoms into lattices increases the OV density, boosting extracellular reactive oxygen species (ROS) generation by enhancing the radial oxygen loss and facilitating electron transfer from Fe(II) that activates O₂ on the plaque surface. This process leads to an elevated H₂O₂ flux and higher yields of ^•O₂^- and ^•OH on rice roots. Notably, the stimulation of extracellular ROS imposes no detectable adverse effects on rice growth. The increase in OVs also significantly enhances the adsorption capacity of rice iron plaques for arsenic sequestration, attributed to the improved surface binding free energy between arsenic and iron plaques. The findings of this study underscore the crucial but previously overlooked role of OVs in regulating arsenic uptake by iron plaques, offering new insights into biogeochemical chemistry of iron coupled to arsenic in the rice rhizospheres.

Dissolved organic matter (DOM) plays an important role in microbial electron transfer, influencing elemental biogeochemical cycles and pollutant fate. However, its electron exchange capacity (EEC) can be strongly altered by ferrous {Fe(II)} oxidation-driven adsorptive fractionation and chemical transformations under long-term periodic hydrological fluctuations, which remain largely unexplored. Here, we demonstrate that periodic Fe(II) oxidation progressively increases DOM's EEC by up to 6.2-fold. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis revealed that Fe(II) oxidation increased the low-molecular-weight polyphenolic and highly unsaturated phenolic fractions of DOM by 26.3 and 24.4%, respectively, and enriched quinone and phenolic groups that can mediate electron transfer. Meanwhile, integration of FT-ICR MS data with machine learning identified the changes in molecular weight and O/C ratio as the critical characteristics determining the enhanced EEC of DOM, with newly produced sulfur-containing groups contributing thereafter. Both adsorptive fractionation and reactive oxygen species-triggered oxidative transformation during Fe(II) oxidation determined the increased EEC of DOM, with adsorptive fractionation playing the dominant role. These dynamic DOM changes significantly promoted microbial electron transfer, continuously stimulating iron reduction and concurrent arsenic release in paddy soils, thereby potentially exacerbating toxic metal bioavailability and posing risks to food safety.

Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.