Characterization of Nitrate-Dependent As(III)-Oxidizing Communities in Arsenic-Contaminated Soil and Investigation of Their Metabolic Potentials by the Combination of DNA-Stable Isotope Probing and Metagenomics

Explainable machine learning for arsenic remobilization potential in the vadose zone: Leveraging readily available soil properties

The vadose zone acts as a natural buffer that prevents contaminants such as arsenic (As) from contaminating groundwater resources. Despite its capability to retain As, our previous studies revealed that a substantial amount of As could be remobilized from soil under repeated wet-dry conditions. Overlooking this might underestimate the potential risk of groundwater contamination. This study quantified the remobilization of As in the vadose zone and developed a prediction model based on soil properties. 22 unsaturated soil columns were used to simulate vadose zones with varying soil properties. Repeated wet-dry cycles were conducted upon the As-retaining soil columns. Consequently, 13.9-150.6 mg/kg of As was remobilized from the columns, which corresponds to 37.0-74.6 % of initially retained As. From the experimental results, a machine learning model using a random forest algorithm was established to predict the potential for As remobilization based on readily accessible soil properties, including organic matter (OM) content, iron (Fe) content, uniformity coefficient, D30, and bulk density. Shapley additive explanation analyses revealed the interrelated effects of multiple soil properties. D30, which is inter-related with Fe content, exhibited the highest contribution to As remobilization, followed by OM content, which was partially mediated by bulk density.

Increased temperature enhances microbial-mediated lignin decomposition in river sediment

BACKGROUND

Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using 13C-lignin and 13C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS

We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The 13C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS

Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.

Novel arsenate-respiring bacteria drive arsenic biogeochemical cycling in Tibetan geothermal springs revealed by DNA-SIP based metagenomics

Arsenic (As) is a toxic element posing health risks globally, with geothermal environment as one of the hotspots. Arsenic biotransformation is mainly mediated by microorganisms which often employ diverse metabolic strategies for survival. However, the microorganisms responsible for As cycling and their survival strategies in geothermal environment in Tibet, the Third Pole, remain unclear. To address this knowledge gap, we investigated As biotransformation in representative geothermal springs using DNA-stable isotope probing (DNA-SIP) combined with metagenomic sequencing. As(V) reduction to the more toxic As(III) was found to be prevalent. Pseudomonas and Thermincola were identified as the dominant As(V)-reducing bacteria (AsRB). Metagenome-assembled genomes (MAGs) affiliated with AsRB contained abundant genes encoding As(V)-respiratory reductase (arrA, 1044.34 transcripts per million (TPM)), nitrate reduction pathway (e.g., narG), and Wood-Ljungdahl pathway (e.g., acsA), indicating their role as dissimilatory As(V)-reducing prokaryotes (DARPs) with diverse metabolic strategies. Here, Thermincola's potential of As(V) reduction via arrA and carbon fixation via Wood-Ljungdahl pathway was observed for the first time, which was found to be widespread in various ecosystems. Our study unravels the key players driving As biogeochemical cycle in Tibetan geothermal springs and provides insights into the genetic mechanisms enabling their survival in extreme environments.

Key active mercury methylating microorganisms and their synergistic effects on methylmercury production in paddy soils

Rice contamination with neurotoxic methylmercury (MeHg) from paddy soils is an escalating global concern. Identifying the microorganisms responsible for mercury (Hg) methylation in these soils is essential for controlling Hg contamination in the food chain and mitigating health impacts. Current research often focuses on total Hg-methylating microorganisms, overlooking the contributions of active ones, which can lead to either overestimating or neglecting the specific roles of microorganisms in Hg methylation within paddy soils. In this study, active Hg-methylating microorganisms in paddy soils were identified using a combination of DNA-SIP, Hg isotope labelling, and Hg methylation gene sequencing techniques. Our findings revealed that Geobacter and Anaerolinea are pivotal active Hg-methylating microorganisms across a contamination gradient in paddy soils. Transcriptomic analysis of soils from major rice-producing provinces in China confirmed the widespread and synergistic involvement of these microorganisms. Microbial incubation further validated their interaction significantly enhances Hg methylation, with Me198Hg concentrations increasing 2.8-fold compared to Geobacter alone and 5.2-fold compared to Anaerolinea alone. These findings enhance our understanding of microbial Hg methylation in paddy soils, providing critical insights for accurately predicting soil MeHg load, rice grain MeHg contamination, and human MeHg exposure risks.

Assessing the combined impacts of microplastics and nickel oxide nanomaterials on soybean growth and nitrogen fixation potential

The excessive presence of polystyrene microplastic (PS-MPx) and nickel oxide nanomaterials (NiO-NPs) in agriculture ecosystem have gained serious attention about their effect on the legume root-nodule symbiosis and biological nitrogen fixation (BNF). However, the impact of these contaminants on the root-nodule symbiosis and biological N2-fixation have been largely overlooked. The current findings highlighted that NiO-NMs at 50 mg kg-1 improved nodule formation and N2-fixation potential, leading to enhanced N2 uptake by both roots and shoots, resulting in increased plant growth and development. While single exposure of PS-MPx (500 mg kg-1) significantly reduced the photosynthetic pigment (8-14 %), phytohormones (9-25 %), nodules biomass (24 %), N2-related enzymes (12-17 %) that ultimately affected the N2-fixation potential. Besides, co-exposure of MPx and NiO at 100 mg kg-1 altered the nodule morphology. Additionally, single and co-exposure of MPx and NiO-NMs at 100 mg kg-1 reduced the relative abundance of Proteobacteria, Gemmatimonadota, Actinobacteria, Firmicutes, and Bacteroidetes is associated with N2-cycling and N2-fixation potential. The findings of this study will contribute to understanding the potential risks posed by MPx and NiO-NMs to leguminous crops in the soil environment and provide scientific insights into the soybean N2-fixation potential.

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.

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BACKGROUND

Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS

Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS

Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.

Arsenic Enhances the Degradation of Middle-Chain Petroleum Hydrocarbons by Rhodococcus sp. 2021 Under Their Combined Pollution

The efficient and green remediation of petroleum hydrocarbon (PH) contamination has emerged as a viable strategy for environmental management. Here, we investigated the interaction between arsenic and PH degradation by Rhodococcus sp. 2021 under their combined pollution. The strain exhibited disparate responses to varying concentrations and valences of arsenic. The elevated concentration of arsenic (>100 mg/L) facilitated the degradation of PHs, and there was a positive correlation between arsenic-promoted degradation of PHs and their carbon-chain length. The degradation of PHs changed with arsenic conditions as follows: trivalent arsenic groups > pentavalent arsenic groups > arsenic-free groups (control). Arsenite and arsenate significantly promoted the gene expression of arsenic metabolism and alkane degrading. But unlike arsenite, arsenate also significantly promoted the gene expression of phosphate metabolism. And arsenite promoted the up-regulation of the expression of genes involved in the process of PHs oxidation and fatty acid oxidation. These results highlight the potential of Rhodococcus sp. 2021 in the remediation of combined total petroleum hydrocarbon (TPH) and heavy metal pollution, providing new insights into the green and sustainable bioremediation of combined pollution of organic matters such as PHs and heavy metals/heavy metal-like elements such as arsenic.

Enhanced oxidation of Mn(II) and As(III) by aerobic granular sludge via ferrous citrate: Key roles of colloidal iron and extracellular superoxide radical

Microbial manganese (Mn) oxidation plays a crucial role in shaping the fate of various elements, including arsenic (As). However, this process faces challenges in wastewater environments due to its inherent inefficiency and instability. In our initial research, a serendipitous discovery occurred: the addition of citrate to Fe(II)-containing wastewater stimulated the oxidation of Mn(II) by aerobic granular sludge (AGS). Subsequent experiments in four sequencing batch reactors (SBRs) over a 67-day period confirmed this stimulatory effect. The presence of Fe(II)-citrate led to a remarkable twofold increase in the oxidation of Mn(II) and As(III). The removal efficiency improved from 21±4 % to 87±7 % for Mn(II) and from 77.1 ± 1.8 % to 93.6 ± 0.2 % for As(III). The verification experiments demonstrated that the simultaneous addition of manganese-oxidizing bacteria (MnOB) and Fe(II)-citrate is an effective strategy for enhancing the oxidation and removal of Mn(II) and As(III) by AGS. Through a combination of genomic analysis, cell-free filtrate incubation, and bacterial batch cultivations (including monitoring the time-course changes of 17 substances and 2 free radicals), we elucidated a novel Mn(II) oxidation pathway in Pseudomonas, along with its stimulation method and mechanism. First, bacteria rapidly degrade citrate possibly via the citrate-Mg2+:H+ symporter (CitMHS) and the tricarboxylic acid (TCA) cycle, resulting in the formation of colloidal Fe(II), colloidal Fe(III), and biogenic iron (hydr)oxides (FeOx). Then, colloidal Fe(II) and colloidal Fe(III) stimulated extracellular proteins to produce superoxide radicals (·O2-). These radicals were responsible for oxidizing Mn(II) into Mn(III), ultimately forming biogenic manganese oxides (MnOx). Finally, MnOx effectively oxidized As(III) to the less toxic As(V). This innovative approach for bacterial Mn(II) oxidation holds promise for treating Mn(II) and As(III) in water and wastewater. Furthermore, the mechanism by which colloidal iron stimulates extracellular proteins to produce ·O2-, thereby facilitating Mn(II) oxidation, may widely occur across various engineering and natural ecosystems.

Arsenic behavior in soil-plant system under the manure application with the combination of antibiotic and roxarsone

Limited attention has been given to the interaction between antibiotics and arsenic in the soil-plant system. In this investigation, Medicago sativa seedlings were grown in soil treated with cow manure containing oxytetracycline (OTC) or sulfadiazine (SD), as well as arsenic (introduced through roxarsone, referred to as ROX treatment). The study revealed a notable increase in As(III) and dimethylarsinic acid (DMA(V)) levels in rhizosphere soils and plant root tissues as arsenic contamination intensified in the presence of antibiotics, while concentrations of As(V) and monomethylarsonic acid (MMA(V)) decreased. Conversely, elevated antibiotic presence resulted in higher levels of As(V) but reduced DMA concentrations in both rhizosphere soils and plant root tissues in the presence of arsenic. The arsenic biotransformation gene aioA was inhibited by arsenic contamination when antibiotics were present, and suppressed by antibiotic contamination in the presence of arsenic, especially in SD treatments, resulting in reduced expression levels at higher SD concentrations. Conversely, the arsM gene exhibited consistent upregulation under all conditions. However, its expression was found to increase with higher concentrations of ROX in the presence of antibiotics, decrease with increasing SD concentrations, and initially rise before declining with higher levels of OTC in the presence of arsenic. Bacterial genera within the Proteobacteria phylum, such as Geobacter, Lusitaniella, Mesorhizobium, and Methylovirgula, showed significant co-occurrence with both aioA and arsM genes. Correlation analysis demonstrated associations between the four arsenic species and the two arsenic biotransformation genes, emphasizing pH as a critical factor influencing the transformation and uptake of different arsenic species in the soil-plant system. The combined stress of antibiotics and arsenic has the potential to modify arsenic behavior and associated risks in soil-plant systems, highlighting the necessity of considering this interaction in future research endeavors.

Untargeted Metabolomics and Soil Community Metagenomics Analyses Combined with Machine Learning Evaluation Uncover Geographic Differences in Ginseng from Different Locations

Panax ginseng C.A. Meyer, known as the "King of Herbs," has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environments of different geographical origins lead to obvious differences in the quality of ginseng, but the potential mechanism of the differences remains unclear. In this study, 20 key differential metabolites, including ginsenoside Rb1, glucose 6-phosphate, etc., were found in ginseng from 10 locations in China using an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-untargeted metabolomics approach. The soil properties were analyzed and combined with metagenomics technology to explore the possible relationships among microbial elements in planting soil. Through Spearman correlation analysis, it was found that the top 10 microbial colonies with the highest abundance in the soil were significantly correlated with key metabolites. In addition, the relationship model established by the random forest algorithm and the quantitative relationship between soil microbial abundance and ginseng metabolites were successfully predicted. The XGboost model was used to determine 20(R)-ginseng Rg2 and 2'(R)-ginseng Rg3 as feature labeled metabolites, and the optimal ginseng production area was discovered. These results prove that the accumulation of metabolites in ginseng was influenced by microorganisms in the planting soil, which led to geographical differences in ginseng quality.

Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue

Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

Increase in potato yield by the combined application of biochar and organic fertilizer: key role of rhizosphere microbial diversity

Purpose

The large-scale planting of potatoes leads to soil degradation, thus limiting the potato yield. An effective method of improving soil quality involves the combined application of biochar and organic fertilizer. However, the proportion of biochar and organic fertilizer at which potato yield can be improved, as well as the improvement mechanism, remain unclear.

Methods

A combined application experiment involving biochar (B) and organic fertilizer (O) with four concentration gradients was conducted using the equal carbon ratio method. On this basis, rhizosphere soil fertility, bacterial community composition, and bacterial diversity in potato crops, as well as the potato yield difference under different combined application ratios, were investigated. Then, the direct and indirect effects of these factors on potato yield were analyzed.

Results

The results suggest that soil fertility was improved by the combined application of biochar and organic fertilizer, with the best effect being achieved at a ratio of B:O=1:2. The dominant bacterial communities in the potato rhizosphere included Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes. When compared to the control, the relative abundance and diversity index of soil bacteria were significantly improved by the treatment at B:O=1:2, which exerted a stronger effect on improving the relative abundance of beneficial bacteria. Soil available phosphorus (AP), soil pH (SpH), and soil organic carbon (SOC) explained 47.52% of the variation in bacterial composition. Among them, the main factor was the content of soil available nutrients, while SpH generated the weakest effect. The bacterial diversity index showed a significant positive correlation with soil AP, SOC, available potassium (AK), total nitrogen (TN), and C/N ratio, and a significant negative correlation with SpH. Bacterial diversity directly affected the potato yield, while soil fertility indirectly affected potato yield by influencing the soil bacterial diversity.

Conclusion

The combined application of biochar and organic fertilizer elevates potato yield mainly by improving the diversity of bacterial communities in potato rhizosphere soil, especially the combined application of biochar and organic fertilizer at a 1:2 ratio (biochar 0.66 t ha-1+organic fertilizer 4.46 t ha-1), which made the largest contribution to increasing potato yield.

Arsenic stress on soil microbial nutrient metabolism interpreted by microbial utilization of dissolved organic carbon

In a 120-day microcosm incubation experiment, we investigated the impact of arsenic contamination on soil microbial nutrient metabolism, focusing on carbon cycling processes. Our study encompassed soil basal respiration, key enzyme activities (particularly, β-1,4-N-acetylglucosaminidase and phosphatases), microbial biomass, and community structure. Results revealed a substantial increase (1.21-2.81 times) in β-1,4-N-acetylglucosaminidase activities under arsenic stress, accompanied by a significant decrease (9.86%-45.20%) in phosphatase activities (sum of acid and alkaline phosphatases). Enzymatic stoichiometry analysis demonstrated the mitigation of microbial C and P requirements in response to arsenic stress. The addition of C-sources alleviated microbial C requirements but exacerbated P requirements, with the interference amplitude increasing with the complexity of the C-source. Network analysis unveiled altered microbial nutrient requirements and an increased resistance process of microbes under arsenic stress. Microbial carbon use efficiency (CUE) and basal respiration significantly increased (1.17-1.59 and 1.18-3.56 times, respectively) under heavy arsenic stress (500 mg kg-1). Arsenic stress influenced the relative abundances of microbial taxa, with Gemmatimonadota increasing (5.5-50.5%) and Bacteroidota/ Nitrospirota decreasing (31.4-47.9% and 31.2-63.7%). Application of C-sources enhanced microbial resistance to arsenic, promoting cohesion among microorganisms. These findings deepen our understanding of microbial nutrient dynamics in arsenic-contaminated areas, which is crucial for developing enzyme-based toxicity assessment systems for soil arsenic contamination.

Bacteria associated with Comamonadaceae are key arsenite oxidizer associated with Pteris vittata root

Pteris vittata (P. vittata), an arsenic (As) hyperaccumulator commonly used in the phytoremediation of As-contaminated soils, contains root-associated bacteria (RAB) including those that colonize the root rhizosphere and endosphere, which can adapt to As contamination and improve plant health. As(III)-oxidizing RAB can convert the more toxic arsenite (As(III)) to less toxic arsenate (As(V)) under As-rich conditions, which may promote plant survial. Previous studies have shown that microbial As(III) oxidation occurs in the rhizospheres and endospheres of P. vittata. However, knowledge of RAB of P. vittata responsible for As(III) oxidation remained limited. In this study, members of the Comamonadaceae family were identified as putative As(III) oxidizers, and the core microbiome associated with P. vittata roots using DNA-stable isotope probing (SIP), amplicon sequencing and metagenomic analysis. Metagenomic binning revealed that metagenome assembled genomes (MAGs) associated with Comamonadaceae contained several functional genes related to carbon fixation, arsenic resistance, plant growth promotion and bacterial colonization. As(III) oxidation and plant growth promotion may be key features of RAB in promoting P. vittata growth. These results extend the current knowledge of the diversity of As(III)-oxidizing RAB and provide new insights into improving the efficiency of arsenic phytoremediation.

Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings?

Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.

Simultaneous suppression of As mobilization and N2O emission from NH4+/As-rich paddy soils by combined nitrate and birnessite amendment

The environmental impacts of As mobilization and nitrous oxide (N2O) emission in flooded paddy soils are serious issues for food safety and agricultural greenhouse gas emissions. Several As immobilization strategies utilizing microbially-mediated nitrate reducing-As(III) oxidation (NRAO) and birnessite (δ-MnO2)-induced oxidation/adsorption have proven effective for mitigating As bioavailability in flooded paddy soils. However, several inefficiency and unsustainability issues still exist in these remediation approaches. In this study, the effects of a combined treatment of nitrate and birnessite were assessed for the simultaneous suppression of As(III) mobilization and N2O emission from flooded paddy soils. Microcosm incubations confirmed that the combined treatment achieved an effective suppression of As(III) mobilization and N2O emission, with virtually no As(T) released and at least a 87% decrease in N2O emission compared to nitrate treatment alone after incubating for 8 days. When nitrate and birnessite are co-amended to flooded paddy soils, the activities of denitrifying enzymes within the denitrification electron transport pathway were suppressed by MnO2. As a result, the majority of applied nitrate participated in nitrate-dependent microbial Mn(II) oxidation. The regenerated biogenetic MnO2 was available to facilitate subsequent cycles of As(III) immobilization and concomitant N2O emission suppression, sustainable remediation strategy. Moreover, the combined nitrate-birnessite amendment promoted the enrichment of Pseudomonas, Achromobacter and Cupriavidu, which are known to participate in the oxidation of As(III)/Mn(II). Our findings document strong efficacy for the combined nitrate/birnessite treatment as a remediation strategy to simultaneously mitigate As-pollution and N2O emission, thereby improving food safety and reducing greenhouse gas emissions from flooded paddy soils enriched with NH4+ and As.

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC)

High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.

Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation

The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.

Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.

Illuminated fulvic acid stimulates denitrification and As(III) immobilization in flooded paddy soils via an enhanced biophotoelectrochemical pathway

Fulvic acid (FA) is a representative photosensitive dissolved organic matter (DOM) compound that occurs naturally in paddy soils. In this study, the effect of a FA + nitrate treatment (0, 4 and 8 mg/L FA + 20 mmol/L nitrate) on denitrification and As(III) immobilization in flooded paddy soils was assessed under dark and intermittently illuminated conditions (12 h light+12 h dark). The FA input stimulated denitrification in illuminated soils (~100 % of nitrate removal within 6 days) compared to dark conditions (~92 % nitrate removal after 6 days). Meanwhile, As(III) (initial concentration of 0.1 mmol/L) was nearly completely immobilized (~100 %) under illuminated conditions after 4 days for the FA + nitrate treatment compared to 90- 93 % retention in the dark. Denitrification and As immobilization were positively related to the FA dosage in the illuminated assays. The stronger denitrification in illuminated soils was ascribed to denitrifiers harvesting photoelectrons from photosensitive substrates/semiconducting minerals. FA addition also increased the activities of denitrifying enzymes (e.g., NAR, NIR and NOR) and the denitrification electron transport system by nearly 0.6-0.7 and 1.5-1.8 times that of the nitrate-alone treatment under illuminated and dark conditions, thereby fostering stronger denitrification. Upon irradiation, As(III) immobilization was not only stimulated by the interactions with the denitrification pathway whereby As(III) acts as an electron donor for denitrifiers, but was also modulated by Fe(III)/oxidative reactive species-derived photooxidation of As(III). Moreover, the FA + nitrate treatment promoted the enrichment of metal-oxidizing bacteria (e.g., Stenotrophomonas and Acidovorax) that are responsible for nitrate-dependent As(III)/Fe(II) oxidation. The results of this study enhance our understanding of interactions among the biogeochemical cycles of As, Fe, N and C, which are intricately linked by a biophotoelectrochemical pathway in flooded paddy soils.

Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments

Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.

Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure

Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.

Leptolyngbya sp. XZMQ and Bacillus XZM co-inoculation reduced sunflower arsenic toxicity by regulating rhizosphere microbial structure and enzyme activity

Microorganisms are of great significance for arsenic (As) toxicity amelioration in plants as soil fertility is directly affected by microbes. In this study, we innovatively explored the effects of indigenous cyanobacteria (Leptolyngbya sp. XZMQ) and plant growth-promoting bacteria (PGPB) (Bacillus XZM) on the growth and As absorption of sunflower plants from As-contaminated soil. Results showed that single inoculation and co-inoculation stimulated the growth of sunflower plants (Helianthus annuus L.), enhanced enzyme activities, and reduced As contents. In comparison to the control group, single innoculation of microalgae and bacteria in the rhizosphere increased extracellular polymeric substances (EPS) by 21.99% and 14.36%, respectively, whereas co-inoculation increased them by 35%. Compared with the non-inoculated group, As concentration in the roots, stems and leaves of sunflower plants decreased by 38%, 70% and 41%, respectively, under co-inoculation conditions. Inoculation of Leptolyngbya sp. XZMQ significantly increased the abundance of nifH in soil, while co-inoculation of cyanobacteria and Bacillus XZM significantly increased the abundance of cbbL, indicating that the coupling of Leptolyngbya sp. XZMQ and Bacillus XZM could stimulate the activity of nitrogen-fixing and carbon-fixing microorganisms and increased soil fertility. Moreover, this co-inoculation increased the enzyme activities (catalase, sucrase, urease) in the rhizosphere soil of sunflower and reduced the toxic effect of As on plant. Among these, the activities of catalase, peroxidase, and superoxide dismutase decreased. Meanwhile, co-inoculation enables cyanobacteria and bacteria to attach and entangle in the root area of the plant and develop as symbiotic association, which reduced As toxicity. Co-inoculation increased the abundance of aioA, arrA, arsC, and arsM genes in soil, especially the abundance of microorganisms with aioA and arsM, which reduced the mobility and bioavailability of As in soil, hence, reduced the absorption of As by plants. This study provides a theoretical basis for soil microbial remediation in mining areas.

Insight into microbial functional genes' role in geochemical distribution and cycling of uranium: The evidence from covering soils of uranium tailings dam

There exists a research gap on microbial functional genes' role in U geochemical behavior and cycling in U contaminated soils, which has been poorly understood. Herein, 16S rRNA sequencing gene amplifiers and metagenome analysis were applied to probe microbial community structure and functional metabolism of different depth layers of covering soils in U tailings dam. Results showed that the soils were highly enriched with U (47.5-123.3 mg/kg) and a remarkable portion of 35-70% was associated with the labile fractions. It was found that U geochemical distribution was notably interacted with functional genes from N, S, Fe and P related microbes. Importantly, diminution in gene NirK and amplification in nrfH involving in nitrate reduction could induce microbial tolerance to U. Moreover, gene Sat in microbial sulfate reduction, NosZ and NorB in nitrate reduction, phnD, upgA and upgC in P transportation and phnI, phnK, phoA and opd in microbial organic P mineralization, were all closely linked to U geochemical distribution, species and cycling. All these findings disclose the functional genes that may control the transfer and transformation behavior of U in soil environment, which provides important and novel indications for the bio-remediation strategies towards U polluted sites.

A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China

The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.

Brevibacterium sp. strain CS2: A potential candidate for arsenic bioremediation from industrial wastewater

A multiple metal-resistant Brevibacterium sp. strain CS2, isolated from an industrial wastewater, resisted arsenate and arsenate upto 280 and 40 mM. The order of resistance against multiple metals was Arsenate > Arsenite > Selenium = Cobalt > Lead = Nickel > Cadmium = Chromium = Mercury. The bacterium was characterized as per morphological and biochemical characteristics at optimum conditions (37 ℃ and 7 pH). The appearance of brownish color precipitation was due to the interaction of silver nitrate confirming its oxidizing ability against arsenic. The strain showed arsenic processing ability at different temperatures, pH, and initial arsenic concentration which was 37% after 72 h and 48% after 96 h of incubation at optimum conditions with arsenite 250 mM/L (initial arsenic concentration). The maximum arsenic removal ability of strain CS2 was determined for 8 days, which was 32 and 46% in wastewater and distilled water, respectively. The heat-inactivated cells of the isolated strain showed a bioremediation efficiency (E) of 96% after 10 h. Genes cluster (9.6 kb) related to arsenite oxidation was found in Brevibacterium sp. strain CS2 after the genome analysis of isolated bacteria through illumine and nanopore sequencing technology. The arsenite oxidizing gene smaller subunit (aioB) on chromosomal DNA locus (Prokka_01508) was identified which plays a role in arsenite oxidation for energy metabolism. The presence of arsenic oxidizing genes and an efficient arsenic oxidizing potential of Brevibacterium sp. strain CS2 make it a potential candidate for green chemistry to eradicate arsenic from arsenic-contaminated wastewater.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Arsenic removal in flue gas through anaerobic denitrification and sulfate reduction cocoupled arsenic oxidation

Arsenic in flue gas from municipal solid waste incineration can damage to human health and ecological environment. A sulfate-nitrate-reducing bioreactor (SNRBR) for flue gas arsenic removal was investigated. Arsenic removal efficiency attained 89.4%. An integrated metagenomic and metaproteomic investigation showed that three nitrate reductases (NapA, NapB and NarG), three sulfate reductases (Sat, AprAB and DsrAB), and arsenite oxidase (ArxA) regulated nitrate reduction, sulfate reduction and bacterial As(III)-oxidation, respectively. Citrobacter and Desulfobulbus could synthetically regulate the expression of arsenite-oxidizing gene, nitrate reductases and sulfate reducatases, which involved in As(III) oxidation, nitrate and sulfate reduction. A bacterial consortium containing Citrobacter, UG_Enterobacteriaceas, Desulfobulbus and Desulfovibrio could capable of simultaneously arsenic oxidation, sulfate reduction and denitrification. Anaerobic denitrification and sulfate reduction were cocoupled to arsenic oxidation. The biofilm was characterized by FTIR, XPS, XRD, EEM, and SEM. XRD and XPS spectra verified the formation of aarsenic species (As(V)) from flue gas As(III) conversion. Arsenic speciation in biofilms of SNRBR consisted of 77% residual arsenic, 15.9% organic matter-bound arsenic, and 4.3% strongly absorbed arsenic. Flue gas arsenic was bio-stabilized in the form of Fe-As-S and As-EPS through biodeposition, biosorption and biocomplexation. This provides a new way of flue gas arsenic removal using the sulfate-nitrate-reducing bioreactor.

Effects of microplastics and nitrogen deposition on soil multifunctionality, particularly C and N cycling

Both nitrogen deposition (ND) and microplastics (MPs) pose global change challenges. The effects of MPs co-existing with ND on ecosystem functions are still largely unknown. Herein, we conducted a 10-month soil incubation experiment to explore the effects of polyethylene (PE) and polylactic acid (PLA) MPs on soil multifunctionality under different ND scenarios. We found that the interactions between ND and MPs affected soil multifucntionality. FAPROTAX function prediction indicated that both ND and MPs affected C and N cycling. ND increased some C-cycling processes, such as cellulolysis, ligninolysis, and plastic degradation. MPs also showed stimulating effects on these processes, particularly in the soil with ND. ND significantly decreased the abundance of functional genes NifH, amoA, and NirK, leading to inhibited N-fixation, nitrification, and denitrification. The addition of MPs also modified N-cycling processes: 0.1% PE enriched the bacterial groups for nitrate reduction, nitrate respiration, nitrite respiration, and nitrate ammonification, and 1% PLA MPs enriched N-fixation bacteria at all ND levels. We found that ND caused lower soil pH but higher soil N, decreased bacterial diversity and richness, and changed the composition and activity of functional bacteria, which explains why ND changed soil functions and regulated the impact of MPs.

Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments

Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.

Arsenic pollution remediation mechanism and preliminary application of arsenic-oxidizing bacteria isolated from industrial wastewater

Microbial remediation is vital for improving heavy metal-polluted water. In this work, two bacterial strains, K1 (Acinetobacter gandensis) and K7 (Delftiatsuruhatensis), with high tolerance to and strong oxidation of arsenite [As(III)], were screened from industrial wastewater samples. These strains tolerated 6800 mg/L As(III) in a solid medium and 3000 mg/L (K1) and 2000 mg/L (K7) As(III) in a liquid medium; arsenic (As) pollution was repaired through oxidation and adsorption. The As(III) oxidation rates of K1 and K7 were the highest at 24 h (85.00 ± 0.86%) and 12 h (92.40 ± 0.78%), respectively, and the maximum gene expression levels of As oxidase in these strains were observed at 24 and 12 h. The As(III) adsorption efficiencies of K1 and K7 were 30.70 ± 0.93% and 43.40 ± 1.10% at 24 h, respectively. The strains exchanged and formed a complex with As(III) through the -OH, -CH3, and C]O groups, amide bonds, and carboxyl groups on the cell surfaces. When the two strains were co-immobilized with Chlorella, the adsorption efficiency of As(III) improved (76.46 ± 0.96%) within 180 min, thereby exhibiting good adsorption and removal effects of other heavy metals and pollutants. These results outlined an efficient and environmentally friendly method for the cleaner production of industrial wastewater.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Accumulation and speciation of arsenic in Eisenia fetida in sodium arsenite spiked soils - A dynamic interaction between soil and earthworms

Arsenic (As) is a toxic metalloid that is a significant global pollutant of the environment and a persistent bioaccumulation carcinogen. Earthworms are frequently employed as sentinel organisms to investigate the bioavailability of As in contaminated soils. However, the process of As accumulation in earthworms and the mechanism of transformation of As species in their bodies are not well understood. The accumulation of As and variation of As species in the earthworms (Eisenia fetida) exposed to sodium arsenite (0, 20, and 80 mg kg^-1 As) were investigated in this study. The total As concentration of earthworms in the three treatments at various sample times was dose-dependent on soil As content. After 56 days of exposure, the high concentration treatment had the highest total As content (772 ± 21 mg kg^-1) in earthworms, followed by the low concentration treatment (579 ± 42 mg kg^-1) and control (31 ± 1 mg kg^-1). During 56 days, the proportion of trivalent As in earthworms increased from 70% to more than 90%, while pentavalent As decreased by 11-18%. On day 28, the sum of the four organic As species reached a maximum (<1%). Changes in soil As species and an increase in bioavailable As cause earthworms to accumulate more As. The total As in soil after 56 days of exposure was 9.51 ± 0.50, 25.6 ± 0.60, and 82.8 ± 0.28 mg kg^-1, which was not significantly different from the total As in soil before the experiment. These findings are useful in assessing the risk of earthworm exposure to sodium arsenite in the soil.

Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils

Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.

Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO₂ fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).

Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats

Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N₂. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N₂ fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.

Characterization of keystone taxa and microbial metabolic potentials in copper tailing soils

Copper mining has caused serious soil contamination and threaten the balance of underground ecosystem. Effects of metal contamination on the soil microbial community assembly and their multifunctionality are still unclear. In this study, the keystone taxa and microbial metabolic potential of soil microorganisms surrounding a typical copper tailing were investigated. Results showed that pH and metal contents of adjacent soil in copper tailing increased, which largely reduced soil microbial communities' diversity. Metal contaminated soils enriched a group of keystone taxa with metal-tolerance such as Bacteroidota (20-54%) and Firmicutes (24-48%), which were distinct from the uncontaminated background soils that dominated by Proteobacteria (19-24%) and Actinobacteria (13-24%). In the contaminated soils, these keystone taxa were identified as Alistipes, Bacteroides, and Faecalibacterium, suggesting their adaptation to the metal-rich environment. Co-occurrence network analysis showed that the microbial community was loosely connected in the metal contaminated soils with a lower number of nodes and links. Co-occurrence networks further revealed that the dynamics of keystone taxa significantly correlated with copper content. Functional gene analysis of soil microorganisms indicated that metal contamination might inhibit important microbial metabolic potentials, such as secondary metabolites biosynthesis, carbon fixation, and nitrogen fixation. Results also found the flexible adaptation strategies of soil microbial communities to metal-rich environments with metal-resistance or bio-transformation, such as efflux (CusB/CusF/CzsB and pcoB/copB) and oxidation (aoxAB). These findings provide insight into the interaction between keystone taxa and soil environment, which is helpful to reveal the microbial metabolic potential and physiological characteristics in tailing contaminated soils.

Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin

High arsenic (As) in groundwater is an environmental issue of global concern, which is closely related to microbe-mediated As biogeochemical cycling. However, the distribution of genes related to As cycling and underlying microbial As biogeochemical processes in high As groundwater remain elusive. Hence, we profiled the As cycling genes (arsC, arrA, and aioA genes) and indigenous microbial communities in groundwater from a typical high As area, the Hetao Basin from China, using amplicon sequencing and qPCR techniques. Here, we revealed the significant difference in microbial community structure between low As groundwater samples (LG) and high As groundwater samples (HG). Acinetobacter, Thiovirga, Hydrogenophaga, and Sulfurimonas were dominant in LG, while Aquabcterium, Acinetobacter, Sphingomonas, Pseudomonas, Desulfomicrobium, Hydrogenophaga, and Nitrospira were predominant in HG. Shannon and Chao indices of the microbial communities in HG were significantly higher than those of in LG. Alpha diversity and abundance of arsC and arrA genes were higher than those of aioA genes. The significant positive correlation was uncovered between the abundances of arsC and aioA genes, suggesting the cooccurrence of As functional genes in groundwater. Sphingopyxis, Agrobacterium, Klebsiella, Hoeflea, and Aeromonas represented the dominant taxa within the As (V) reducers communities. Distance-based redundancy analysis showed that ORP, pH, As_tot, Mn, and DOC were the key factors shaping the diverse microbial populations, while ORP, S^2-, As(III), Fe(II), NH₄⁺, pH, Mn, SO₄^2-, As(V), temperature, and P as the main drivers affecting arsenotrophic microbiota. This work provides an insight into microbial communities linked to As biogeochemical processes in high As groundwater, playing a fundamental role in groundwater As cycling.

Arsenic biotransformation genes and As transportation in soil-rice system affected by iron-oxidizing strain (Ochrobactrum sp.)

Arsenic (As) biotransformation in soil affects As biogeochemical cycling and is associated with As accumulation in rice. After inoculation with 1% iron-oxidizing bacteria (FeOB) in paddy soil, As speciation, As biotransformation genes in soil, As/Fe in Fe plaques, and As accumulation in rice were characterized. Compared with the control, the available As concentrations in soils decreased while amorphous and poorly crystalline Fe-Al oxidized As and crystalline Fe-Al oxidized As fractions increased of F (FeOB) and RF (rice and FeOB) treatments. Fe concentrations increased and positively correlated with As concentrations in Fe plaques on the rice root surface (***P < 0.001). Compared with R (rice), Monomethyl As (MMA), dimethyl As (DMA), arsenate (As(V)), and arsenite (As(III)) concentrations in rice plants showed a downwards trend of RF treatment. The As concentration in grains was below the National Standard for Food Safety (GB 2762-2017). A total of 16 As biotransformation genes in rhizosphere soils of different treatments (CK, F, R and RF were quantified by high-throughput qPCR (HT-qPCR). Compared with the control, the As(V) reduction and As transport genes abundance in other treatments increased respectively by 54.54%-69.17% and 54.63%-73.71%; the As(III) oxidation and As (de) methylation genes did not change significantly; however, several As(III) oxidation genes (aoxA, aoxB, aoxS, and arsH) increased. These results revealed that FeOB could reduce, transport As, and maybe also oxidize As. In addition, As(III) oxidation gene (aoxC) in rhizosphere soil was more abundant than in non-rhizosphere soil. It indicated that radial oxygen loss (ROL) promoted As(III) oxidation in rhizosphere soils. The results provide evidence for As biotransformation by ROL and FeOB in soil-rice system. ROL affects As oxidation and immobilization, and FeOB affects As reduction, transportation and may also affect As oxidation.

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira

BACKGROUND

The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete.

RESULTS

In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification.

CONCLUSIONS

Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.

Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs

Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.

Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands

Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.

Characterization of arsenic-metabolizing bacteria in an alkaline soil

Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO₃^-, suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.

Stress response characteristics of indigenous microorganisms in aromatic-hydrocarbons-contaminated groundwater in the cold regions of Northeast China

The resistance mechanism of microbial communities in contaminated groundwater under combined stresses of aromatic hydrocarbons (AHs), NH₄⁺, and Fe-Mn exceeding standard levels was studied in an abandoned oil depot in Northeast China. The response of environmental parameters and microbial communities under different pollution levels in the study area was discussed, and microscopic experiments were conducted using background groundwater with different AHs concentrations. The results showed that indigenous microbial community were significantly affected by environmental factors, including pH, TH, COD_Mn, TFe, Cr (VI), NH₄⁺, NO₃^-, and SO₄^2-. AHs likely had a limited influence on microbial communities, mainly causing indirect changes in the microbial community structure by altering the electron donor/acceptor (mainly Fe, Mn, NO₃^-, NO₂^-, NH₄⁺, and SO₄^2-) content in groundwater, and there was no linear effect of AHs content on the microbial community. In low- and medium-AHs-contaminated groundwater, the microbial diversity increased, whereas high AHs contents decreased the diversity of the microbial community. The microbial community had the strongest ability to metabolize AHs in the medium-AHs-contaminated groundwater. In the high-AHs-contaminated groundwater, microbial communities mainly degraded AHs through a complex co-metabolic mechanism due to the inhibitory effect caused by the high concentration of AHs, whereas in low-AHs-contaminated groundwater, microbial communities mainly caused a mutual transformation of inorganic electron donors/acceptors (mainly including N, S), and the microbial community's ability to metabolize AHs was weak. In the high-AHs-contaminated groundwater, the microbial community resisted the inhibitory effect of AHs mainly via a series of resistance mechanisms, such as regulating their life processes, avoiding unfavorable environments, and enhancing their feedback to the external environment under high-AHs-contaminated conditions.

Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning

Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F₄₂₀H₂ dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

How different nitrogen fertilizers affect arsenic mobility in paddy soil after straw incorporation?

In straw return fields, nitrogen-fertilizers are added to mitigate microbial competition for nitrogen with plants. However, in arsenic (As)-contaminated paddy fields, the specific effects of different nitrogen fertilizers on As mobility after straw incorporation and the interactions among iron(Fe)/carbon(C)/nitrogen(N)/As are not well understood. In the reported microcosm experiment we monitored As-mobility as a function of different dosages of KNO₃, NH₄Cl and rice straw incorporation. Addition of both KNO₃ and NH₄Cl significantly inhibited the As mobilization induced by straw incorporation. Following the KNO₃ addition, the As concentration in porewater dropped by 51-66% after 2 days of the incubation by restraining Fe reduction and enhancing Fe oxidation. High-dose NH₄Cl addition reduced As in porewater by 22-43% throughout the incubation by decreasing porewater pH. High-throughput sequencing results demonstrated that KNO₃ addition enriches both the denitrifying and Fe-oxidizing bacteria, while diminishing Fe-reducing bacteria; NH₄Cl addition has the opposite effect on Fe-reducing bacteria. Network analysis revealed that As and Fe concentrations in porewater were positively correlated with the abundance of denitrifying and Fe-reducing bacteria. This study broadens our insight into the As biogeochemistry associated with the N/C/Fe balance in soil, which are of great significance for agronomic management and mitigation the risk of As-contaminated paddy fields.

Keystone taxa and functional analysis in arsenic and antimony co-contaminated rice terraces

Both arsenic (As) and antimony (Sb) are primary environmental contaminants that often co-exist at contaminated sites. Though the microbial community compositions of As- and Sb-contaminated sites have been previously described, the changes in microbial community interactions and community functions remain elusive. In the current study, several key metabolic processes, such as As/Sb detoxification and carbon fixation, were enriched under heavily contaminated conditions. Furthermore, the identified keystone taxa, which are associated with the families Nitrosomonadaceae, Pedosphaeraceae, Halieaceae, and Latescibacterota, demonstrated positive correlations with As and Sb concentrations, indicating that they may be resistant to As and Sb toxicities. Accordingly, arsenic resistance-related functions, along with several functions such as carbon fixation, were found to be enriched in heavily contaminated sites. The current study elucidated the key microbial populations in As- and Sb-contaminated rice terraces and may provide useful information for remediation purposes.