Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community

New insights into autochthonous fungal bioaugmentation mechanisms for recalcitrant petroleum hydrocarbon components using stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is a promising strategy for the microbial remediation of petroleum hydrocarbon (PH)-contaminated soils. However, the mechanisms underlying AFB, particularly for degrading recalcitrant PH components, are not fully understood. This study employed stable isotope probing (SIP) and high-throughput sequencing to investigate the AFB mechanisms of two hydrocarbon-degrading fungi, Fusarium solani LJD-11 and Aspergillus fumigatus LJD-29, focusing on three challenging PH components: n-Hexadecane (n-Hex), Benzo[a]pyrene (BaP), and Dibenzothiophene (DBT). Our findings indicate that both fungal strains significantly enhanced pollutant removal rates, with combined application yielding optimal results. AFB treatment reduced the microbial diversity index and altered the soil microbial community, especially affecting fungal populations. A significant correlation between the microbial diversity index and degradation efficiency suggests that greater diversity enhances pollutant removal. SIP analysis showed that LJD-11 and LJD-29 could directly assimilate n-Hex and DBT, but not BaP. Correlation analyses between functional microorganisms and other biological indicators suggest that the removal of pollutants is also attributable to indigenous functional bacteria. Additionally, non-inoculated functional fungi present in the soil play a crucial role in BaP degradation. These findings reveal distinct degradation pathways for the three pollutants. The addition of carrier substrate reduced the complexity of the network, while AFB treatment restored it. In addition, the combined fungal treatment resulted in higher network parameters, leading to a more complex and stable network structure. These results provide insights into the mechanisms of AFB for degrading recalcitrant PH components, underscoring its potential for in situ bioremediation of petroleum-contaminated soils.

Rapid screening of indigenous degrading microorganisms for enhancing in-situ bioremediation of organic pollutants-contaminated soil

Organic pollutants (OPs) have caused severe environmental contaminations in the world and aroused wide public concern. Autochthonous bioaugmentation (ABA) is considered a reliable bioremediation approach for OPs contamination. However, the rapid screening of indigenous degrading strains from in-situ environments remains a primary challenge for the practical application of ABA. In this study, 3,5,6-Trichloro-2-pyridinol (TCP, an important intermediate in the synthesis of various pesticides) was selected as the target OPs, and DNA stable isotope probing (DNA-SIP) combined with high-throughput sequencing was employed to explore the rapid screening of indigenous degrading microorganisms. The results of DNA-SIP revealed a significant enrichment of OTU557 (Cupriavidus sp.) in the 13C-TCP-labeled heavy DNA fractions, indicating that it is the key strain involved in TCP metabolism. Subsequently, an indigenous TCP degrader, Cupriavidus sp. JL-1, was rapidly isolated from native soil based on the analysis of the metabolic substrate spectrum of Cupriavidus sp. Furthermore, ABA of strain JL-1 demonstrated higher remediation efficacy and stable survival compared to the exogenous TCP-degrading strain Cupriavidus sp. P2 in in-situ TCP-contaminated soil. This study presents a successful case for the rapid acquisition of indigenous TCP-degrading microorganisms to support ABA as a promising strategy for the in-situ bioremediation of TCP-contaminated soil.

Biodegradation of phenolic pollutants and bioaugmentation strategies: A review of current knowledge and future perspectives

The widespread use of phenolic compounds renders their occurrence in various environmental matrices, posing ecological risks especially the endocrine disruption effects. Biodegradation-based techniques are efficient and cost-effective in degrading phenolic pollutants with less production of secondary pollution. This review focuses on phenol, 4-nonylphenol, 4-nitrophenol, bisphenol A and tetrabromobisphenol A as the representatives, and summarizes the current knowledge and future perspectives of their biodegradation and the enhancement strategy of bioaugmentation. Biodegradation and isolation of degrading microorganisms were mainly investigated under oxic conditions, where phenolic pollutants are typically hydroxylated to 4-hydroxybenzoate or hydroquinone prior to ring opening. Bioaugmentation efficiencies of phenolic pollutants significantly vary under different application conditions (e.g., increased degradation by 10-95% in soil and sediment). To optimize degradation of phenolic pollutants in different matrices, the factors that influence biodegradation capacity of microorganisms and performance of bioaugmentation are discussed. The use of immobilization strategy, indigenous degrading bacteria, and highly competent exogenous bacteria are proposed to facilitate the bioaugmentation process. Further studies are suggested to illustrate 1) biodegradation of phenolic pollutants under anoxic conditions, 2) application of microbial consortia with synergistic effects for phenolic pollutant degradation, and 3) assessment on the uncertain ecological risks associated with bioaugmentation, resulting from changes in degradation pathway of phenolic pollutants and alterations in structure and function of indigenous microbial community.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions

Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.

Catalytic electrodes' characterization study serving polluted water treatment: environmental healthcare and ecological risk assessment

Pesticide residues in the environment have irreparable effects on human health and other organisms. Hence, it is necessary to treat and degrade them from polluted water. In the current work, the electrochemical removal of the fenitrothion (FT), trifluralin (TF), and chlorothalonil (CT) pesticides were performed by catalytic electrode. The characteristics of SnO2-Sb2O3, PbO2, and Bi-PbO2 electrodes were described by FE-SEM and XRD. Dynamic electrochemical techniques including cyclic voltammetry, electrochemical impedance spectroscopy, accelerated life, and linear polarization were employed to investigate the electrochemical performance of fabricated electrodes. Moreover, evaluate the risk of toxic metals release from the catalytic electrode during treatment process was investigated. The maximum degradation efficiency of 99.8, 100, and 100% for FT, TF, and CT was found under the optimal condition of FT, TF, and CT concentration 15.0 mg L-1, pH 7.0, current density 7.0 mA cm-2, and electrolysis time of 120 min. The Bi-PbO2, PbO2, and SnO2-Sb2O3 electrodes revealed the oxygen evolution potential of 2.089, 1.983, 1.914 V, and the service lifetime of 82, 144, and 323 h, respectively. The results showed that after 5.0 h of electrolysis, none of the heavy metals such as Bi, Pb, Sb, Sn, and Ti were detected in the treated solution.

Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5

The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had k_cat and K_m values of 5.7 s^-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.

Fusarium equiseti-inoculation altered rhizosphere soil microbial community, potentially driving perennial ryegrass growth and salt tolerance

Fusarium equiseti is an effective plant growth-promoting fungi that induce systemic disease resistance in plants. However, the role of F. equiseti in regulating salt stress response and the underlying mechanisms remain largely unknown. Here, we investigated the effect of F. equiseti Z7 strain on the growth and salt stress response in perennial ryegrass. Additionally, the role of Z7 in regulating the abundance, composition, and structure of native microbial communities in the rhizosphere soil was determined. We observed that Z7 could produce indole-3-acetic acid (IAA) and siderophores. Hence, Z7 inoculation further enhanced plant growth and salt tolerance in perennial ryegrass. Inoculating Z7 increased K⁺ and decreased Na⁺ in plant tissues. Z7 inoculation also enhanced soil quality by reducing soluble salt and increasing available phosphorus. Moreover, inoculating Z7 altered the compositions of bacterial and fungal communities in the rhizosphere soil. For instance, beneficial bacterial genera, such as Flavobacterium, Enterobacter, Agrobacterium, and Burkholderiales were dominantly enriched in Z7-inoculated soil. Interestingly, the relative abundance of these genera showed significantly positive correlations with the fresh weight of perennial ryegrass. Our results demonstrate that Z7 could remarkably promote plant growth and salt tolerance by regulating ion homeostasis in plant tissues and microbial communities in the rhizosphere soil. This study provides a scientific foundation for applying microbes to improve plant growth under extreme salt stress conditions.

Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress

A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO₃-N production, and N₂O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.

Genetic bioaugmentation with triclocarban-catabolic plasmid effectively removes triclocarban from wastewater

Triclocarban, one of the emerging pollutants, has been accumulating, and it is frequently detected in wastewater. Due to its toxicity and persistence, the efficient removal of triclocarban from wastewater systems is challenging. Genetic bioaugmentation with transferable catabolic plasmids has been considered to be a long-lasting method to clean up pollutants in continuous flow wastewater treatment systems. In this study, bioaugmentation with Pseudomonas putida KT2440, harboring the transferrable triclocarban-catabolic plasmid pDCA-1-gfp-tccA2, rapidly converted 50 μM triclocarban in wastewater into 3,4-dichloroaniline and 4-chloroaniline, which are further mineralized more easily. RT-qPCR results showed that the ratio of the copy number of pDCA-1-gfp-tccA2 to the cell number of strain KT2440 gradually increased during genetic bioaugmentation, suggesting horizontal transfer and proliferation of the plasmid. By using DNA stable isotope probing (SIP) and amplicon sequencing, OTU86 (Escherichia-Shigella), OTU155 (Citrobacter), OTU5 (Brucella), and OTU15 (Enterobacteriaceae) were found to be the potential recipients of the plasmid pDCA-1-gfp-tccA2 in the wastewater bacterial community. Furthermore, three transconjugants in the genera of Escherichia, Citrobacter, and Brucella showing triclocarban-degrading abilities were isolated from the wastewater. This study develops a new method for removing triclocarban from wastewater and provides insights into the environmental behavior of transferrable catabolic plasmids in bacterial community in wastewater systems.

Determination of chlorothalonil levels through inhibitory effect on papain activity at protein-decorated liquid crystal interfaces

A liquid crystal (LC)-based assay was developed to detect chlorothalonil (CHL). The detection principle is based on (i) the electrostatic interaction between the positively charged protein protamine (PRO) with the negatively charged phospholipid dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DOPG) and (ii) the CHL-mediated inhibition of papain (PAP) activity. The aqueous/LC interface was decorated with a monolayer of DOPG and PRO that self-assembled via electrostatic interactions. PAP can hydrolyze PRO, resulting in the realignment of an LC by DOPG, inducing a shift in the LC response from bright to dark. The addition of CHL can inhibit the activity of PAP, leading to the attraction of PRO to DOPG and the consequent disruption of the LC orientation. The orientation change of the LC in the presence or absence of CHL can be observed from the changes in its optical appearance using a polarized light microscope. Under optimal conditions, the developed assay achieved a detection limit of 0.196 pg mL-1 within a range of determination of 0.65-200 pg mL-1. The selectivity of the assay was verified in the presence of carbendazim and imidacloprid. The practical application of the proposed assay was demonstrated by its use to determine the levels of CHL in food extracts and environmental samples, which yielded recoveries and relative standard deviations (RSD) in the ranges of 87.39-99.663% and 1.03-6.32%, respectively.

The efficient persistence and migration of Cupriavidus gilardii T1 contribute to the removal of MCPA in laboratory and field soils

The application of exogenous biodegradation strains in pesticide-polluted soils encounters the challenges of migration and persistence of inoculants. In this study, the degradation characteristics, vertical migration capacity, and microbial ecological risk assessment of an enhanced green fluorescent protein (EGFP)-tagged 2-Methyl-4-chlorophenoxyacetic acid (MCPA)-degrading strain Cupriavidus gilardii T1 (EGFP) were investigated in the laboratory and field soils. The optimum remediation conditions for T1 (EGFP) was characterized in soils. Meanwhile, leaching experiments showed that T1 (EGFP) migrated vertically downwards in soil and contribute to the degradation of MCPA at different depths. After inoculation with T1 (EGFP), a high expression levels of EGFP gene was observed at 28 d in the laboratory soil and at 45 d in the field soil. The degradation rates of MCPA were ≥ 60% in the laboratory soil and ≥ 48% in the field soil, indicating that T1 (EGFP) can efficiently and continuously remove MCPA in both laboratory and field conditions. In addition, the inoculation of T1 (EGFP) not only showed no significant impact on the soil microbial community structure but also can alleviate the negative effects induced by MCPA to some extent. Overall, our findings suggested that T1 (EGFP) strain is an ecologically safe resource for the in situ bioremediation of MCPA-contaminated soils.

The fate of erythromycin in soils and its effect on soil microbial community structure

Erythromycin is one of the most commonly used macrolide antibiotics. However, little is known currently about the environmental behavior and fate of erythromycin in soils. Here erythromycin was ¹⁴C-labeled to investigate its degradation, mineralization and bound residues (BRs) in three typical agricultural soils. Results indicated the fate of ¹⁴C-erythromycin in soils varied greatly with soils types. Erythromycin was rapidly mineralized in black soil (BS) and fluvo-aquic soil (FS), whereas it rapidly formed large amounts of BRs in red soil (RS) with slow mineralization. At 120 d, about 90% of the introduced ¹⁴C-erythromycin was mineralized as ¹⁴CO₂ in BS and FS, but only 30% in RS. There was still a certain proportion of BRs in all soils, especially in RS, up to 50%. Erythromycin residues (ERs) may be underestimated if its residues are only assessed by extractable residues. We recommend to include a practical silylation procedure to quantify Type I BRs in regular erythromycin residue monitoring, which can be used as signal of the need to initiate further laboratory BRs experiments. The degradation of erythromycin was mainly attributed to soil microorganisms, which promote erythromycin mineralization and lead to the re-release of BRs. Microbial analysis showed that erythromycin persisted longer in soils with lower microbial diversity and richness. Erythromycin at 2.5 mg kg^-1 showed no significant impact on soil microbial diversity in all treatments, but caused changes in soil community composition. This study provides a reference for scientific evaluation and pollution remediation of erythromycin in soils.

Long-term effect of epigenetic modification in plant-microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process

BACKGROUND

Soil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms from discovery to agricultural application remains challenging, as the mechanisms underlying the interactions between beneficial strains and plants in native soils are still largely unknown. Increasing numbers of studies have indicated that strains introduced to manipulate microbiomes are usually eliminated in soils, while others have reported that application of PGPB as inocula significantly improves plant growth. This contradiction suggests the need for a deeper understanding of the mechanisms underlying microbe-induced growth promotion.

RESULTS

We showed PGPB-induced long-term plant growth promotion after elimination of the PGPB inoculum in soils and explored the three-way interactions among the exogenous inoculum, indigenous microbiome, and plant, which were key elements of the plant growth-promoting process. We found the rhizosphere microbiome assembly was mainly driven by plant development and root recruitments greatly attenuated the influence of inocula on the rhizosphere microbiome. Neither changes in the rhizosphere microbiome nor colonization of inocula in roots was necessary for plant growth promotion. In roots, modification of DNA methylation in response to inoculation affects gene expression related to PGPB-induced growth promotion, and disruptions of the inoculation-induced DNA methylation patterns greatly weakened the plant growth promotion. Together, our results showed PGPB-induced DNA methylation modifications in roots mediated the promotion process and these modifications remained functional after elimination of the inoculum from the microbiome.

CONCLUSION

This study suggests a new mechanism in which PGPB affect DNA methylation in roots to promote plant growth, which provides important insights into microbiome-plant interactions and offers new strategies for plant microbiome engineering beyond the perspective of maintaining inoculum persistence in soils. Video abstract.

Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli

Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a ¹³C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.

Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community

Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.

Cyanobacterial bloom induces structural and functional succession of microbial communities in eutrophic lake sediments

Cyanobacterial blooms have considerable effects on lacustrine microbial communities. The current study explored the temporal pattern of sedimentary archaea and bacteria during cyanobacterial bloom in a eutrophic lake. With the sampling period divided into bloom phase, interval phase and end phase according to the variation of physicochemical parameters, the structures and functions of both kingdoms presented a significant difference among phases. Bloom phases could be characterized with the lowest diversity and up-regulated functions in biodegradation of cyanobacterial metabolites driven by bacteria. Archaeal community showed an increased metabolic function during interval phases, including active methanogenesis sensitive to carbon input. The highest diversity and an enrichment of hub genera in microbial network were both observed in end phase, allowing for closer cooperation among groups involved in cyanobacteria-derived organic matter transformation. Although the archaeal community was less variable or diverse than bacteria, methanogenic functions dramatically fluctuated with cyanobacterial dynamics. And microbial groups related to methane cycling played an important role in microbial network. The results provided new insights into temporal dynamics of lacustrine microbial communities and microbial co-occurrence, and highlighted the significant ecological role of methane cycling-related microbes in lake sediments under the influence of cyanobacterial blooms.

Rapid Surface-Enhanced Raman Spectroscopy Detection of Chlorothalonil in Standard Solution and Orange Peels with Pretreatment of Ultraviolet Irradiation

At present, the detection of chlorothalonil is generally based on chromatography and immunoassay; both of which are time-consuming and costly. In this study, Surface-enhanced Raman Spectroscopy (SERS) has been successfully utilized in the detection of chlorothalonil coupled with photochemistry and meanwhile, gold nanoparticles were prepared to enhance the Raman signal. Two Raman peaks (2246 cm^- 1 and 2140 cm^- 1) of chlorothalonil were appeared after ultraviolet (UV) irradiation compared to the original solution. Chlorothalonil generated excited and weakened C≡N bonds in its structure by absorbing UV energy, thus leading to two kinds of corresponding peaks. These two kinds of peaks were both selected as analytical peaks in chlorothalonil detection. Different light sources and solvents were made different contributions to the final spectra. Chlorothalonil methanol solution under 302 nm wavelength irradiation was performed the best. The 2246 cm^- 1 sharp peak represented to the normal C≡N bond appeared at first, which overall trend was significantly increased followed by a gradual decrease. The 2140 cm^- 1 broad peak represented to the weakened C≡N bond appeared later, which overall trend was increased as the irradiation time passing by and then kept stable. Natural bond orbital (NBO) analysis indicates that the downshift of C≡N bond from 2246 cm^- 1 to 2140 cm^- 1 is due to the increase of electronic populations of π* orbital of C≡N bond transited from π orbital excited by UV irradiation. The positively charged C≡N bond had more chance to approach negatively charged gold nanoparticles. The detection limit of chlorothalonil was as low as 0.1 ppm in the standard solution. Orange peels spiked with chlorothalonil oil were also detected in this paper to confirm the practical operability of this method. The SERS method may be further developed as a rapid detection of pesticides that contains a triple bond by utilizing photochemistry.

Reducing the Environmental Risk of Chlorpyrifos Application through Appropriate Agricultural Management: Evidence from Carbon-14 Tracking

Chlorpyrifos (CPF) is one of the most critical insecticides in the world. However, many countries are gradually banning its use due to its reported hazardous impacts on humans. This study explored the possibility of reducing the environmental risk of CPF through appropriate agricultural management practices. Results showed that the environmental risk of CPF is lower under drainage conditions because there is more mineralization and less bound residues (BRs) than under submerged conditions. Bioaugmentation significantly enhanced the CPF mineralization and inhibited the formation of CPF-BRs. Biochar adsorbed CPF and thus reduced its bioavailability, but it could not completely eliminate the toxicity of CPF. In addition, bioaugmentation did not significantly affect the native microbial community of CPF-contaminated soil, suggesting its safety in reducing the environmental risk of CPF. The study indicated that the environmental risk of CPF could be reduced by appropriate agricultural management such as water management, bioaugmentation, soil biochar amendment, and selecting suitable soil types.

Waste activated sludge stimulates in situ microbial reductive dehalogenation of organohalide-contaminated soil

Due to its enriched organic matter, nutrients and growth cofactors, as well as a diverse range of microorganisms, waste activated sludge (WAS) might be an ideal additive to stimulate organohalide respiration for in situ bioremediation of organohalide-contaminated sites. In this study, we investigated the biostimulation and bioaugmentation impacts of WAS-amendment on the performance and microbiome in tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) dechlorinating microcosms. Results demonstrated that WAS-amendment increased PCE- and PCBs-dechlorination rate as much as 6.06 and 10.67 folds, respectively. The presence of WAS provided a favorable growth niche for organohalide-respiring bacteria (OHRB), including redox mediation and generation of electron donors and carbon sources. Particularly for the PCE dechlorination, indigenous Geobacter and WAS-derived Dehalococcoides were identified to play key roles in PCE-to-dichloroethene (DCE) and DCE-to-ethene dechlorination, respectively. Similar biostimulation and bioaugmentation effects of WAS-amendment were observed on both PCE- and PCBs-dechlorination in three different soils, i.e., laterite, brown loam and paddy soil. Risk assessment suggested low potential ecological risk of WAS amendment in remediation of organohalide-contaminated soil. Overall, this study provided an economic and efficient strategy to stimulate the organohalide respiration-based bioremediation in field applications.

Combined bioaugmentation with electro-biostimulation for improved bioremediation of antimicrobial triclocarban and PAHs complexly contaminated sediments

Haloaromatic antimicrobial triclocarban (TCC) is an emerging refractory contaminant that commonly coexisted with conventional contaminants such as polycyclic aromatic hydrocarbons (PAHs). TCC may negatively affect the metabolic activity of sediment microorganisms and persist in environment; however, remediation methods that relieve the TCC inhibitory effect in sediments remain unknown. Here, a novel electro-biostimulation and bioaugmentation combined remediation system was proposed by the simultaneous introduction of a TCC-degrading Ochrobactrum sp. TCC-2 and electrode into the TCC and PAHs co-contaminated sediments. Results indicated the PAHs and TCC degradation efficiencies of the combined system were 2.9-3.0 and 4.6 times respectively higher than those of the control group (no electro-biostimulation and no bioaugmentation treatments). The introduced strain TCC-2 and the enriched electroactive bacteria and PAHs degraders (e.g. Desulfobulbus, Clostridium, and Paenarthrobacter) synergistically contributed to the accelerated degradation of PAHs and TCC. The preferential elimination of the TCC inhibitory effect through bioaugmentation treatment could restore microbial functions by increasing the functional gene abundances related to various metabolic processes. This study offers new insights into the response of sediment functional communities to TCC stress, electro-biostimulation and bioaugmentation operations and provides a promising system for the enhanced bioremediation of the PAHs and TCC co-contaminated sediments.

Evaluation use of bioaugmentation and biostimulation to improve degradation of sulfolane in artificial groundwater

Column systems were used to evaluate the effectiveness of different bioremediation methods (biostimulation (BS) and bioaugmentation (BA)) in treating sulfolane-contaminated groundwater. Batch test results confirmed that Cupriavidus sp. Y9 (Y9) was the most effective strain for BA. The optimal ratio of added native bacteria to Y9 was 10:3. The BA column adapted to a high sulfolane concentration (150 mg L^-1) more rapidly and had higher sulfolane removal efficiency (90%) than did the BS column. The change in the biotoxicity of sulfolane-contaminated groundwater upon bioremediation, according to a Microtox test, revealed decreases in the inhibition of the passing of light by the BS column and BS + BA column of 38% and 63%, respectively. These results reveal that combining BS with BA can reduce the biotoxicity of sulfolane. The column tests confirmed the most effective added bacterium in BA, the operating conditions for high-efficiency bioremediation, and possible problems in its future application. The results provide an important reference for the design of methods for the remediation of contaminated sites.

Bioaugmentation potential evaluation of a bacterial consortium composed of isolated Pseudomonas and Rhodococcus for degrading benzene, toluene and styrene in sludge and sewage

Bioaugmentation was conducted using a bacterial consortium of Pseudomonas putida SW-3 and Rhodococcus ruber SS-4, to test their ability to degrade benzene, toluene, and styrene (BTS). SW-3 and SS-4 were isolated from domestic sludge and sewage samples to establish a synthetic consortium with an optimized ratio of 2:1 to reach a degradation efficiency of 82.5-89.8% of BTS. The bacterial consortium was inoculated with sludge and sewage samples at a ratio of 2:1, resulting in a degradation efficiency of 97.9% and 92.7%, respectively, at a BTS concentration of 1800 mg·L^-1. Analysis of bacterial community structure following bioaugmentation indicated an increase in abundance of BTS-degrading bacteria, particularly Acinetobacter and Pseudoxanthomonas in sludge and Pseudomonas in sewage, enhancing the collective BTS degradation ability of the bacterial community. Principal component analysis demonstrated that a more balanced bacterial community structure was established following intervention. This indicated that the selected bacteria are excellent candidates for bioaugmentation.

Bioaugmentation of triclocarban and its dechlorinated congeners contaminated soil with functional degraders and the bacterial community response

Partial removal of haloaromatic antimicrobial triclocarban (TCC) during wastewater treatment caused the final introduction of residual TCC into soils. Bioaugmentation has been proposed for the biodegradation of TCC and its dechlorinated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) in soil. The isolated TCC-degrading strain Ochrobactrum sp. TCC-2 and chloroanilines-degrading strain Diaphorobacter sp. LD72 were used to study the removal efficiency of TCC, DCC and NCC mixture and their chloroanilines intermediates, respectively. The potential degradation competition between TCC and its dechlorinated congeners, and the response of bacterial community during the bioremediation were also investigated. The biodegradation of DCC and TCC was significantly enhanced for soil with inoculums compared with sterilized and natural soils. Chloroanilines products could also be effectively removed. For the degradation of combined substrates in the aqueous medium, NCC had negative effect on the degradation of TCC and DCC, while TCC and DCC negatively influenced each other. The bioaugmentation with two degraders obviously changed the phylogenetic composition and function of indigenous soil microbiome. Importantly, the inoculated degraders could be maintained, suggesting their adaptability and potential application in bioaugmentation for such recalcitrant contaminants. This study offers new insights into the enhanced bioremediation of TCC and its dechlorinated congeners contaminated soils by the bioaugmentation of functional degraders and the structure and function response of the indigenous soil microbiome to the bioremediation process.

Glutaredoxin S25 and its interacting TGACG motif-binding factor TGA2 mediate brassinosteroid-induced chlorothalonil metabolism in tomato plants

The presence of pesticide residues in fresh fruits and vegetables poses a serious threat to human health. Brassinosteroids (BRs) can reduce pesticide residues in plants, but the underlying mechanisms still remain unclear. Here, we identified a tomato glutaredoxin gene GRXS25 which was induced by 24-epibrassinolide (EBR) and chlorothalonil (CHT) in a way dependent on apoplastic reactive oxygen species (ROS). Silencing of GRXS25 in tomato abolished EBR-induced glutathione S-transferases (GSTs) gene expression and activity, leading to an increased CHT residue. Yeast two-hybrid and bimolecular fluorescence complementation assays showed protein-protein interaction between GRXS25 and a transcription factor TGA2. Electrophoretic mobility shift and chromatin immunoprecipitation assays indicated that TGA2 factor bound to the TGACG-motif in the GST3 promoter. While silencing of TGA2 strongly compromised, overexpression of TGA2 enhanced expression of GST genes and CHT residue metabolism. Our results suggest that BR-induced apoplastic ROS trigger metabolism of pesticide residue in tomato plants through activating TGA2 factor via GRXS25-dependent posttranslational redox modification. Activation of plant detoxification through physiological approaches has potential implication in improving the food safety of agricultural products.

Exploration on the bioreduction mechanism of Cr(Ⅵ) by a gram-positive bacterium: Pseudochrobactrum saccharolyticum W1

Bioremediation of chromium (Cr(Ⅵ)) contaminations has been widely reported, but the research on its removal mechanism is still scarce. Studies on Cr(Ⅵ) removal by strains affiliated to genus Pseudochobactrum revealed the Cr(Ⅵ) efficiency removal through the reduction of Cr(Ⅵ) to Cr(Ⅲ). However, the location of Cr(Ⅵ) reduction reaction and exact mechanism are still unspecified. In this work, a Gram-positive bacterial strain, Pseudochrobactrum saccharolyticum W1 (P. saccharolyticum W1) was isolated and tested to remove approximately 53.7% of Cr(Ⅵ) (initial concentration was 200 mg L^-1) from the MSM medium. Analysis of SEM-EDS and TEM-EDS indicated that chromium-containing particles precipitated both on the cell surface and in the cytoplasm. Batch experiments indicated that the heat-treated bacterial cells almost had no ability to remove Cr(Ⅵ) from solution, while the resting cells could remove 62.0% of Cr(Ⅵ) at the initial concentration of 10 mg L^-1. Additionally, at this concentration, 64.8% and 70.8% of Cr(Ⅵ) was reduced by cell envelope components and intracellular soluble substances after 6 h, respectively. These results suggested that the removal of Cr(Ⅵ) by P. saccharolyticum W1 was through direct reduction, which occurred on both cell envelop and cytoplasm. The results also showed that cytoplasm was the main site for Cr(Ⅵ) reduction compared to the cell envelop. Further analysis of FTIR and XPS verified that C-H, C-C, CO, C-OH and C-O-C groups of cells involved in correlation with chromium during Cr(Ⅵ) reduction. The study offered an insight into the Cr(VI) reduction mechanism of P. saccharolyticum W1.

Hazardous waste treatment technologies

This is a review of the literature published in 2018 on topics related to hazardous waste management in water, soils, sediments, and air. The review covers treatment technologies applying physical, chemical, and biological principles for contaminated water, soils, sediments, and air. PRACTITIONER POINTS: The management of waters, wastewaters, and soils contaminated by various hazardous chemicals including inorganic (e.g., oxyanions, salts, and heavy metals), organic (e.g., halogenated, pharmaceuticals and personal care products, pesticides, and persistent organic chemicals) was reviewed according to the technology applied, namely, physical, chemical and biological methods. Physical methods for the management of hazardous wastes including adsorption, coagulation (conventional and electrochemical), sand filtration, electrosorption (or CDI), electrodialysis, electrokinetics, membrane (RO, NF, MF), photocatalysis, photoelectrochemical oxidation, sonochemical, non-thermal plasma, supercritical fluid, electrochemical oxidation, and electrochemical reduction processes were reviewed. Chemical methods including ozone-based, hydrogen peroxide-based, persulfate-based, Fenton and Fenton-like, and potassium permanganate processes for the management of hazardous were reviewed. Biological methods such as aerobic, anaerobic, bioreactor, constructed wetlands, soil bioremediation and biofilter processes for the management of hazardous wastes, in mode of consortium and pure culture were reviewed.

Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems

Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.

Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies

Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.