Coupling between Nitrogen Fixation and Tetrachlorobiphenyl Dechlorination in a Rhizobium-Legume Symbiosis

Applying cross-scale regulations to Sedum plumbizincicola for strengthening the bioremediation of the agricultural soil that contaminated by electronic waste dismantling and revealing the underlying mechanisms by multi-omics

Electronic waste dismantling has induced the surrounding agricultural soils suffered from combined contamination of heavy metals and organic pollutants. Lower efficiency and complex mechanisms of bioremediation remain to be resolved. Here, we adopted regulations to Sedum plumbizincicola cross aboveground and belowground scales to strengthen the bioremediation efficiency. Results showed that the S. plumbizincicola intercropping with the Astragalus sinicusL. that inoculated with Rhizobium had the highest performance in reductions of Cd, PBDEs and PCBs from soils by 0.11 mg/kg, 67.93 μg/kg and 38.91 μg/kg, respectively. Rhizosphere soil metabolomics analysis demonstrated that reductions in Cd and PBDEs significantly associated with 2-Methylhippuric acid and L-Saccharopine, which were involved in phenylalanine metabolism, biosynthesis of amino acids and lysine. Metagenomics analysis revealed that these functional pathways were mediated by Frankia, Mycobacterium, Blastococcus, etc. microbial taxa, which were also significantly altered by regulations. Moreover, regulation regimes significantly affected transcription genes of S. plumbizincicola. Functional annotation revealed that cross-scale regulations significantly improved bioremediation efficiency through microorganisms and metabolites in the rhizosphere and transcription genes of S. plumbizincicola, which were illustrated to promote plant growth and tolerance to environmental stress. Our integration of multi-omics provides comprehensive and deep insights into molecular mechanisms in the cross-scale regulations of S. plumbizincicola, which would favor remediation techniques advances for the soil contaminated by electronic waste dismantling.

Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil

Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). 15N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5-13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.

Biohydrogen utilization in legume-rhizobium symbiosis reveals a novel mechanism of accelerated tetrachlorobiphenyl transformation

Symbiosis between Glycine max and Bradyrhizobium diazoefficiens were used as a model system to investigate whether biohydrogen utilization promotes the transformation of the tetrachlorobiphenyl PCB77. Both a H2 uptake-positive (Hup+) strain (wild type) and a Hup- strain (a hupL deletion mutant) were inoculated into soybean nodules. Compared with Hup- nodules, Hup+ nodules increased dechlorination significantly by 61.1 % and reduced the accumulation of PCB77 in nodules by 37.7 % (p < 0.05). After exposure to nickel, an enhancer of uptake hydrogenase, dechlorination increased significantly by 2.2-fold, and the accumulation of PCB77 in nodules decreased by 54.4 % (p < 0.05). Furthermore, the tetrachlorobiphenyl transformation in the soybean root nodules was mainly testified to be mediated by nitrate reductase (encoded by the gene NR) for tetrachlorobiphenyl dechlorination and biphenyl-2,3-diol 1,2-dioxygenase (bphC) for biphenyl degradation. This study demonstrates for the first time that biohydrogen utilization has a beneficial effect on tetrachlorobiphenyl biotransformation in a legume-rhizobium symbiosis.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil

Endogenous hydrogen (H₂) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H₂ leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H₂ from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H₂. Based on metagenomes of ¹³C-enriched DNA fractions, endogenous H₂ selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H₂ of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H₂ is a significant energy source for active PCB-degrading communities and suggests that elevated H₂ can influence the microbial ecology and biogeochemistry of the legume rhizosphere.

Electrocatalytic hydro-dehalogenation of halogenated organic pollutants from wastewater: A critical review

Halogenated organic pollutants are often found in wastewater effluent although it has been usually treated by advanced oxidation processes. Atomic hydrogen (H*)-mediated electrocatalytic dehalogenation, with an outperformed performance for breaking the strong carbon-halogen bonds, is of increasing significance for the efficient removal of halogenated organic compounds from water and wastewater. This review consolidates the recent advances in the electrocatalytic hydro-dehalogenation of toxic halogenated organic pollutants from contaminated water. The effect of the molecular structure (e.g., the number and type of halogens, electron-donating or electron-withdrawing groups) on dehalogenation reactivity is firstly predicted, revealing the nucleophilic properties of the existing halogenated organic pollutants. The specific contribution of the direct electron transfer and atomic hydrogen (H*)-mediated indirect electron transfer to dehalogenation efficiency has been established, aiming to better understand the dehalogenation mechanisms. The analyses of entropy and enthalpy illustrate that low pH has a lower energy barrier than that of high pH, facilitating the transformation from proton to H*. Furthermore, the quantitative relationship between dehalogenation efficiency and energy consumption shows an exponential increase of energy consumption for dehalogenation efficiency increasing from 90% to 100%. Lastly, challenges and perspectives are discussed for efficient dehalogenation and practical applications.

Removal of cadmium and polychlorinated biphenyls by clover and the associated microbial community in a long-term co-contaminated soil

Legumes such as clover are cost-effective and environmentally friendly components of strategies for remediating soils contaminated with heavy metals or organic pollutants. However, the mechanisms by which clover remediates co-contaminated soils are unclear. The present study explored the effects of phytoremediation by clover on pollutant removal and the microbial community in soil co-contaminated with cadmium (Cd) and polychlorinated biphenyls (PCBs). After 18 months of phytoremediation, Cd removal increased from 20.25 % in the control to 40.65 % in soil planted with clover, while PCB removal increased from 29.81 % to 60.02 %. High-throughput sequencing analysis showed that the relative abundances of the bacterial phylum Proteobacteria and the diazotrophic genus Rhizobium increased significantly after phytoremediation. Random forest analysis showed that bacterial and diazotrophic diversity significantly influenced Cd and PCB removal. Furthermore, co-occurrence network and correlation analyses revealed that Rhizobiales and Micromonosporales were the main bacteria associated with Cd removal, while Rhizobiales, Burkholderiales, and Xanthomonadales were identified as the main degraders of PCBs. PICRUSt functional prediction demonstrated that the gene bphC, which is related to PCB degradation, was significantly increased in the rhizosphere soil in the presence of clover. These results provide a better understanding for further studies of remediation efficiency by clover, rhizosphere microbial response and remediation mechanisms of co-contaminated soils under in situ conditions in the field.

Enhancement of nitrogen fixation and diazotrophs by long-term polychlorinated biphenyl contamination in paddy soil

Biological nitrogen fixation (BNF) driven by diazotrophs is a major means of increasing available nitrogen (N) in paddy soil, in addition to anthropogenic fertilization. However, the influence of long-term polychlorinated biphenyl (PCB) contamination on the diazotrophic community and nitrogen fixation in paddy soil is poorly understood. In this study, samples were collected from paddy soil subjected to > 30 years of PCB contamination, and the soil diazotrophic community and N₂ fixation rate were evaluated by Illumina MiSeq sequencing and acetylene reduction assays, respectively. The results indicated that high PCB contamination increased diazotrophic abundance and the N₂ fixation rate, and altered diazotrophic community structure in the paddy soil. The random forest model demonstrated that the β-diversity of the diazotrophic community was the most significant predictor of the N₂ fixation rate. Structure equation modeling identified a specialized keystone diazotrophic ecological cluster, predominated by Bradyrhizobium, Desulfomonile, and Cyanobacteria, as the key driver of N₂ fixation. Overall, our findings indicated that long-term PCB contamination enhanced the N₂ fixation rate by altering diazotrophic community abundance and structure, which may deepen our understanding of the ecological function of diazotrophs in organic-contaminated soil.

Nontargeted metabolomic analysis to unravel alleviation mechanisms of carbon nanotubes on inhibition of alfalfa growth under pyrene stress

Carbon nanotubes have displayed great potential in enhancing phytoremediation of PAHs polluted soils. However, the response of plants to the coexistence of carbon nanotubes and PAHs and the associated influencing mechanisms remain largely unknown. Here, the effect of carbon nanotubes on alfalfa growth and pyrene uptake under exposure to pyrene was evaluated through sand culture experiment and gas chromatography time-of-flight mass spectrometer (GC-TOF-MS) based metabolomics. Results showed that pyrene at 10 mg kg^-1 obviously reduced the shoot fresh weight of alfalfa by 18.3 %. Multiwall carbon nanotubes (MWCNTs) at 25 and 50 mg kg^-1 significantly enhanced the shoot fresh weight in a dose-dependent manner, nearly by 80 % at 50 mg kg^-1. Pyrene was mainly accumulated in alfalfa roots, in which the concentration was 35 times as much as that in shoots. MWCNTs greatly enhanced the accumulation of pyrene in alfalfa roots, almost by two times at 50 mg kg^-1, while decreased pyrene concentration in shoots, from 0.11 mg kg^-1 to 0.044 mg kg^-1 at MWCNTs concentration of 50 mg kg^-1. Metabolomics data revealed that pyrene at 10 mg kg^-1 trigged significant metabolic changes in alfalfa root exudates, downregulating 27 metabolites. MWCNTs generated an increase in the contents of some downregulated metabolites caused by pyrene stress, which were restored to the original level or even higher, mainly including organic acids and amino acids. MWNCTs significantly enriched some metabolic pathways positively correlated with shoot growth and pyrene accumulation in shoots under exposure to pyrene, including TCA cycle, glyoxylate and dicarboxylate metabolism, cysteine and methione metabolism as well as alanine, aspartate and glutamate metabolism. This work highlights the regulation effect of MWCNTs on the metabolism of root exudates, which are helpful for alfalfa to alleviate the stress from pyrene contamination.

Enhanced rhizoremediation of polychlorinated biphenyls by resuscitation-promoting factor stimulation linked to plant growth promotion and response of functional microbial populations

Rhizoremediation is acknowledged as a green technology for removing polychlorinated biphenyls (PCBs) in soil. However, rhizoremediation is limited because most soil microorganisms enter into a viable but non-culturable (VBNC) state under PCBs stress. This work was to study the effect of resuscitation-promoting factor (Rpf) on rhizoremediation efficiency of PCBs in alfalfa and rhizosphere microbiological communities. Results suggested that Rpf promoted alfalfa growth in PCB-contaminated soil by improving antioxidant enzymes and detoxification metabolites in alfalfa. After 40 d Rpf treatment, removal rate for five selected PCBs significantly increased by 0.5-2.2 times. Rpf enhanced relative abundances of bphA and bphC responsible for degrading PCBs, and enzymatic activities of metabolizing exogenous compounds in rhizosphere soil. High-throughput sequencing showed that Rpf did not change the dominant microbial population at phyla and genera levels, but caused variation of the bacterial community structures. The promoting function of Rpf was linked to the shift of various key populations having different functions depending on Rpf concentrations. Pseudomonas and Rhizobium spp. enrichment might stimulate PCB degradation and Streptomyces and Bacillus spp. primarily contributed to alfalfa growth. Predicted functions in rhizosphere soil bacterial community indicated Rpf facilitated soil nutrient cycling and environmental adaptation. This study indicated that Rpf was an active additive for strengthening rhizoremediation efficiency of PCB-contaminated soil and enhancing their in-situ remediation.

Oxidative dehalogenation and mineralization of polychlorinated biphenyls by a resuscitated strain Streptococcus sp. SPC0

Most functional microorganisms cannot be cultivated due to entering a viable but non-culturable (VBNC) state, which limits the characterization and application of polychlorinated biphenyl (PCB)-degrading strains. Resuscitating VBNC bacteria could provide huge candidates for obtaining high-efficient PCB degraders. However, limited studies have focused on the ability of resuscitated strains for PCBs degradation. In the present study, whole-genome analysis of a resuscitated strain SPC0, and its performances in degradation of three prevalent PCB congeners (PCBs 18, 52 and 77) were investigated. The results indicate that the strain SPC0 belonged to the genus Streptococcus, possessed the degradation potential for aromatic xenobiotics. The SPC0 could effectively degrade PCBs 18 and 52, but exhibited lower degradation efficiency of PCB 77. Degradation of PCBs 18 and 52 could be fitted well by zero-order model, whereas the fittest model for PCB 77 degradation was pseudo second-order kinetics. The bph genes expression, chloride ions release and degradation metabolites identification, suggest that SPC0 possessed the capability of oxidative dehalogenation and mineralization of PCBs. Interestingly, SPC0 can degrade PCBs via the bph-encoded biphenyl pathway, and further mineralize metabolite dichlorobenzoate via protocatechuate pathway. This study is the first to show that a strain belonging to genus Streptococcus possessed PCB-degrading capability, which uncovered the powerful potential of resuscitated strains for bioremediation of PCB-contaminated sites.

Fe-based nanomaterial transformation to amorphous Fe: Enhanced alfalfa rhizoremediation of PCBs-contaminated soil

Nano-enabled phytoremediation is an emerging remediation strategy for soils that are moderately contaminated with persistent organic contaminants, and there is a significant need for increased mechanistic understanding and for case studies. Herein, we evaluated the remediation of PCB28-contaminated soil using combined alfalfa and Fe-based materials, including zero-valent iron at 20 nm, 100 nm, and 5 µm, and also iron oxide nanomaterials including α-Fe₂O₃, γ-Fe₂O₃, and Fe₃O₄ around 20-30 nm. Compared with alfalfa remediation alone (63.2%), Fe-based nanomaterials increased PCB28 removal values to 72.4-93.5% in planted soil, with α-Fe₂O₃ treatment promoting the most effective pollutant removal. Mechanistically, the crystalline Fe-based nanoparticles were transformed into amorphous forms in the plant rhizosphere, resulting in greater availability and enhanced iron nutrition. This nutritional shift induced root metabolic reprogramming of amino acid and carbohydrate cycling, and related functional bacterial enrichment of Ramlibacter, Dyella, Bacillus, and Paraburkholderia in rhizosphere. A significant positive correlation between amorphous iron and root metabolites-associated microbes with PCB28 removal was evident, implying that iron supplementation selected for rhizospheric microorganisms favored PCBs degradation. Overall, this rhizoremediation promotion strategy of Fe species-metabolites-microbes highlights the potential for the hybrid application of nano-enabled phytotechnology in the remediation of soils contaminated with persistent organic xenobiotics.

Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

Nitrogen addition facilitates phytoremediation of PAH-Cd cocontaminated dumpsite soil by altering alfalfa growth and rhizosphere communities

Thousands of unlined landfills and open dumpsites seriously threatened the safety of soil and groundwater due to leachate leakage with a mass of pollutants, particularly heavy metals, organic contaminants and ammonia. Phytoremediation is widely used in the treatment of cocontaminated soils because it is cost-effective and environmentally friendly. However, the extent to which phytoremediation efficiency and plant physiological responses are affected by the high nitrogen (N) content in such cocontaminated soil is still uncertain. Here, pot experiments were conducted to investigate the effects of N addition on the applicability of legume alfalfa remediation for polycyclic aromatic hydrocarbon‑cadmium (PAHCd) co-/contaminated soil and the corresponding microbial regulation mechanism. The results showed that the PAH dissipation rates and Cd removal rates in the high-contamination groups increased with the external N supply, among which the pyrene dissipation rates in the cocontaminated soil was elevated most significantly, from 78.10% to 87.25%. However, the phytoremediation efficiency weakened in low cocontaminated soil, possibly because the excessive N content had inhibitory effects on the rhizobium Ensifer and restrained alfalfa growth. Furthermore, the relative abundance of PAH-degrading bacteria in the rhizosphere dominated PAH dissipation. As reflected by principal coordinate analysis (PCoA) analysis and hierarchical dendrograms, the microbial community composition changed with N addition, and a more pronounced shift was found in the rhizosphere relative to the endosphere or shoots of alfalfa. This study will provide a theoretical basis for legume plant remediation of dumpsites as well as soil contaminated with multiple pollutants.

Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production

Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO^•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.

Designing an Electron-Deficient Pd/NiCo2O4 Bifunctional Electrocatalyst with an Enhanced Hydrodechlorination Activity to Reduce the Consumption of Pd

Reducing the Pd loading on electrodes is critical in the electrocatalytic hydrodechlorination (EHDC) of chlorinated organic compounds (COCs). The EHDC reaction of COCs on Pd involves three steps: H* formation, H* adsorption, and dechlorination. It has been established that the initial hydrogen evolution reaction (HER) occurs on Pd⁰ and the dechlorination steps occur on Pd²⁺. A strategy is proposed to design new electrodes by adding a reducible HER-active interlayer to replace Pd⁰, fulfilling the responsibility of producing hydrogen, and to facilitate the formation of more Pd²⁺ for following C-Cl bond cleavage. Keeping the atomic hydrogen adsorption energy on the Pd/interlayer similar to that on pure Pd is also necessary for H* adsorption as well as to maintain a high EHDC activity. For the first time, the NiCo₂O₄-interlayer-modified Pd/Ni-foam electrode was applied in the EHDC of COCs, which enhanced the EHDC efficiency to 100% within 90 min and reduced 88.6% of Pd consumption. The Pd/NiCo₂O₄/Ni-foam electrode with enhanced EHDC activity was also observed with almost 100% product selectivity and good stability. A synergistic mechanism is proposed for the enhanced EHDC activity on the Pd/NiCo₂O₄/Ni-foam. This work offers a simple and useful strategy to design robust electrocatalysts for the EHDC of COCs.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Low Concentrations of Silver Nanoparticles and Silver Ions Perturb the Antioxidant Defense System and Nitrogen Metabolism in N2-Fixing Cyanobacteria

Although toxic effects of silver nanoparticles (AgNPs) on aquatic organisms have been extensively reported, responses of nitrogen-fixing cyanobacteria to AgNPs/Ag⁺ under environmentally relevant concentrations are largely unknown. Here, cyanobacteria were exposed to different concentrations of AgNPs (0.01, 0.1, and 1 mg/L) or Ag⁺ (0.1, 1, and 10 μg/L) for 96 h. The impacts of AgNPs and Ag⁺ on photosynthesis and N₂ fixation in cyanobacteria (Nostoc sphaeroides) were evaluated. In addition, gas chromatography-mass spectrometry (GC-MS)-based metabolomics was employed to give an instantaneous snapshot of the physiological status of the cells under AgNP/Ag⁺ exposure. Exposure to high doses of AgNPs (1 mg/L) or Ag⁺ (10 μg/L) caused growth inhibition, reactive oxygen species overproduction, malondialdehyde accumulation, and decreased N₂ fixation. In contrast, low doses of AgNPs (0.01 and 0.1 mg/L) and Ag⁺ (0.1 and 1 μg/L) did not induce observable responses. However, metabolomics revealed that metabolic reprogramming occurred even at low concentrations of AgNP and Ag⁺ exposure. Levels of a number of antioxidant defense-related metabolites, especially phenolic acid and polyphenols (gallic acid, resveratrol, isochlorogenic acid, chlorogenic acid, cinnamic acid, 3-hydroxybenzoic acid, epicatechin, catechin, and ferulic acid), significantly decreased in response to AgNPs or Ag⁺. This indicates that AgNPs and Ag⁺ can disrupt the antioxidant defense system and disturb nitrogen metabolism even at low-dose exposure. Metabolomics was shown to be a powerful tool to detect "invisible" changes, not observable by typical phenotypic-based endpoints.

Exploring bacterial community structure and function associated with polychlorinated biphenyl biodegradation in two hydrogen-amended soils

Hydrogen (H₂) is a universal energy source supplying survival energy for numerous microbial functions. Diffusive fluxes of H₂ released by rhizobacterial symbiont nodules in which H₂ is an obligate by-product of dinitrogen fixation may act as an additional energy input shaping microbial community structure and function in soils. However, the effects of H₂ at the soil-nodule interface on soil contaminant degradation processes are poorly understood. Here, we mimicked the hydrogen conditions present at the soil-nodule interface (10,000 ppmv) to test the impact of elevated H₂ concentrations on soil microbial removal of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) and examined the associated bacterial communities and their functions by conducting a microcosm experiment using two different soil types at three PCB contamination levels (0.5, 1.0 and 5.0 mg kg^-1). After incubation for 84 days the PCB77 removal rates in the elevated H₂ treatments in the Paddy soil were significantly promoted (by 4.88 to 6.41%) compared with the control (0.5 ppmv H₂) but no significant effect was observed in a Fluvo-aquic soil. This is consistent with changes in the abundance of functional genes for PCB-degraders as shown by quantitative real-time PCR (Q-PCR) and phylogenetic investigation of bacterial communities by reconstruction of unobserved states (PICRUSt). 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genera to potential PCB degradation. The abundance of a total of four potentially PCB-degrading bacterial genera (Bacillus, Streptomyces, Ramlibacter and Paenibacillus) increased with increasing H₂ level. In addition, the abundance of hydrogenase in the elevated H₂ treatments was higher than in the control across different contamination levels in both soil types. Thus, elevated H₂ stimulated soil PCB degradation with direct effects (aerobic PCB-degrading bacteria directly utilized H₂ as an energy source for growth and thus enhanced PCB degradation efficiency) and indirect effects (aerobic PCB-degrading bacteria acted synergistically with other hydrogenotrophs to enhance PCB degradation efficiency by exchange of substances and energy). These results help to further understand the role of elevated hydrogen amendment in the PCB biodegradation process and provide evidence that H₂ supports metabolic and energetic flexibility in microorganisms supplying a range of ecosystem services.

Contribution of autochthonous diazotrophs to polycyclic aromatic hydrocarbon dissipation in contaminated soils

Understanding the role played by autochthonous functional microbes involved in the biotransformation of pollutants would help optimize bioremediation performance at contaminated sites. However, our knowledge of the remediation potential of indigenous diazotrophs in contaminated soils remains inadequate. Using a microcosm experiment, soil nitrogen fixation activity was manipulated by molybdenum (Mo) and tungsten (W), and their effect on the removal of polycyclic aromatic hydrocarbons (PAHs) was determined in agricultural and industrial soils. Results showed that after 42 days of incubation, PAH dissipation efficiency was significantly enhanced by 1.06-fold in 600 μg kg^-1 Mo-treated agricultural soil, compared with that in the control. For the industrial soil, 1200 μg kg^-1 Mo treatment significantly promoted PAH removal by 90.76% in 21 days, whereas no significant change was observed between treatments and control at the end of the incubation period. W also exerted a similar effect on PAH dissipation. The activity and gene abundance of nitrogenase were also increased under Mo/W treatments in the two soils. Spearman's correlation analysis further indicated that removal of PAHs was positively correlated with nitrogenase activity in soil, which could be due to the elevated abundances of PAH-degrading genes (PAH-RHDα) in these treatments. Our results suggest the importance of autochthonous diazotrophs in PAH-contaminated soils, which indicates a feasible and environmentally friendly biostimulation strategy of manipulating nitrogen fixation capacity.

Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil

Bioremediation of organic pollutants has been identified as an economically efficient and environmentally friendly method. Here, a pot experiment was conducted to evaluate the bioremediation efficiency of dibutyl phthalate (DBP) by Gordonia phthalatica sp. nov. QH-11 in agricultural soils, along with the effect of this exogenous organism on the native microbial community and ecosystem functions during the bioremediation process. The results showed that inoculation with strain QH-11 accelerated DBP degradation in the soil and decreased DBP accumulation in plants, thereby reducing the health risks associated with vegetables grown in those soils. High-throughput sequencing demonstrated that both DBP contamination and the bioremediation process significantly altered prokaryotic community composition, structure, and network interactions; however, these effects were greatly reduced after 30 d. Dibutyl phthalate affected the prokaryotic community by influencing soil properties rather than directly impacting on microorganisms. In addition, ecosystem functions, like the nitrogen cycle, were significantly altered. Contamination with DBP promoted nitrogen fixation and the denitrification processes while inhibiting nitrification. Bioremediation may mitigate some of the changes to nitrogen cycling, helping to maintain the balance of prokaryotic community function. According to this study, bioremediation through highly efficient degradation bacteria may be a safe and promising method for reducing PAEs contamination in soil-vegetable systems.