Proteomic mechanism of decabromodiphenyl ether (BDE-209) biodegradation by Microbacterium Y2 and its potential in remediation of BDE-209 contaminated water-sediment system

Metabolic perturbation and oxidative damage induced by tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) and tris(2-ethylhexyl) phosphate (TEHP) on Escherichia coli through integrative analyses of metabolome

Organophosphate esters (OPEs) are one of the emerging environmental threats, causing the hazard to ecosystem safety and human health. Yet, the toxic effects and metabolic response mechanism after Escherichia coli (E.coli) exposed to TDCIPP and TEHP is inconclusive. Herein, the levels of SOD and CAT were elevated in a concentration-dependent manner, accompanied with the increase of MDA contents, signifying the activation of antioxidant response and occurrence of lipid peroxidation. Oxidative damage mediated by excessive accumulation of ROS decreased membrane potential and inhibited membrane protein synthesis, causing membrane protein dysfunction. Integrative analyses of GC-MS and LC-MS based metabolomics evinced that significant perturbation to the carbohydrate metabolism, nucleotide metabolism, lipids metabolism, amino acid metabolism, organic acids metabolism were induced following exposure to TDCIPP and TEHP in E.coli, resulting in metabolic reprogramming. Additionally, metabolites including PE(16:1(5Z)/15:0), PA(17:0/15:1(9Z)), PC(20:2(11Z,14Z)/12:0), LysoPC(18:3(6Z,9Z,12Z)/0:0) were significantly upregulated, manifesting that cell membrane protective molecule was afforded by these differential metabolites to improve permeability and fluidity. Overall, current findings generate new insights into the molecular toxicity mechanism by which E.coli respond to TDCIPP and TEHP stress and supply valuable information for potential ecological risks of OPEs on aquatic ecosystems.

Global responses to tris(1-chloro-2-propyl) phosphate and tris(2-butoxyethyl) phosphate in Escherichia coli: Evidences from biomarkers, and metabolic disturbance using GC-MS and LC-MS metabolomics analyses

Tris(1-chloro-2-propyl) phosphate (TCPP) and tris(2-butoxyethyl) phosphate (TBEP) as pollutants of emerging concern have aroused the rising attention due to their potential risks on aquatic ecosystem and public health. Nevertheless, there is a lack of toxicological mechanisms exploration of TCPP and TBEP at molecular levels. Herein, the toxicity effects and molecular mechanism of them were fully researched and summarized on Escherichia coli (E.coli). Acute exposure to them significantly activated antioxidant defense system and caused lipid peroxidation, as proved by the changes of antioxidant enzymes and MDA. The ROS overload resulted in the drop of membrane potential as well as the downregulated synthesis of ATPase, endorsing that E. coli cytotoxicity was ascribed to oxidative stress damage induced by TCPP and TBEP. The combination of GC-MS and LC-MS based metabolomics validated that TCPP and TBEP induced metabolic reprogramming in E.coli. More specifically, the responsive metabolites in carbohydrate metabolism, lipids metabolism, nucleotide metabolism, amino acid metabolism, and organic acids metabolism were significantly disturbed by TCPP and TBEP, confirming the negative effects on metabolic functions and key bioprocesses. Additionally, several biomarkers including PE(16:1(5Z)/15:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(19:1(9Z)/0:0), and LysoPE(0:0/18:1(11Z)) were remarkably upregulated, verifying that the protection of cellular membrane was conducted by regulating the expression of lipids-associated metabolites. Collectively, this work sheds new light on the potential molecular toxicity mechanism of TCPP and TBEP on aquatic organisms, and these findings using GC-MS and LC-MS metabolomics generate a fresh insight into assessing the effects of OPFRs on target and non-target aquatic organisms.

Modified nano zero-valent iron coupling microorganisms to degrade BDE-209: Degradation pathways and microbial responses

Polybrominated diphenyl ethers (PBDEs) in soil and groundwater have garnered considerable attention owing to the significant bioaccumulation potential and toxicity. Currently, the coupling treatment method of nano zero-valent iron (nZVI) with dehalogenation microorganisms is a research hotspot in the field of PBDE degradation. In this study, various systems were established within anaerobic environments, including the nZVI-only system, microorganism-only system, and the nZVI + microorganisms system. The aim was to investigate the degradation pathway of BDE-209 and elucidate the degradation mechanism within the coupled system. The results indicated that the degradation efficiency of the coupled system was better than that of the nZVI-only or microorganism-only system. Two modified nZVI (carboxymethyl cellulose and polyacrylamide) were prepared to improve the coupling degradation efficiency. CMC-nZVI showed the highest stability, and the coupled system consisting of microorganisms and CMC-nZVI showed the best degradation effect among all of the systems in this study, reaching 89.53% within 30 days. Furthermore, 22 intermediate products were detected in the coupling systems. Notably, changing the inoculation time did not significantly improve the degradation effect. The expression changes of the two reductive dehalogenase genes, e.g. TceA and Vcr, reflected the stress response and self-recovery ability of the dehalogenating bacteria, indicating such genes can be used as biomarker for evaluating the degradation performance of the coupling system. These findings provide a better understanding about the mechanism of coupling debromination process and the direction for the optimization and on-site repair of coupled systems.

Investigation of the effects of different substrates on the promotion of the soil microbial consortium, encompassing bacteria and fungi, in the bioremediation of decabromodiphenyl ether (BDE-209)

Decabromodiphenyl ether (BDE-209) is recognized as an emerging and hazardous pollutant in numerous ecosystems. Despite this, only a few studies have concurrently investigated the biodegradation of BDE-209 by a microbial consortium comprising both bacteria and fungi. Consequently, the interactions between bacterial and fungal populations and their mutual effects on BDE-209 degradation remain unclear. Our main objective was to concurrently assess the changes and activity of bacterial and fungal communities during the biodegradation of BDE-209 in a real soil matrix. In the present study, various organic substrates were employed to promote soil biomass for the biodegradation of BDE-209. Soil respiration and molecular analysis were utilized to monitor biological activity and biomass community structure, respectively. The findings revealed that the use of wheat straw in the soil matrix resulted in the highest soil respiration and microbial activity among the treatments. This approach obviously provided suitable habitats for the soil microflora, which led to a significant increase in the biodegradability of BDE-209 (49%). Biomass survival efforts and the metabolic pathway of lignin degradation through co-metabolism contributed to the biodegradation of BDE-209. Microbial community analysis identified Proteobacteria (Alphaproteobacteria-Betaproteobacteria), Firmicutes, Bacteroides (bacterial phyla), as well as Ascomycota and Basidiomycota (fungal phyla) as the key microorganisms in the biological community involved in the biodegradation of BDE-209. This study demonstrated that applying wheat straw can improve both the biological activity and the biodegradation of BDE-209 in the soil of polluted sites.

Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis

Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as 'plastisphere'. Previous metagenomic investigations of the 'plastisphere' indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine 'plastisphere' to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10-200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine 'plastisphere' to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.

A critical review on BDE-209: Source, distribution, influencing factors, toxicity, and degradation

As the most widely used polybrominated diphenyl ether, BDE-209 is commonly used in polymer-based commercial and household products. Due to its unique physicochemical properties, BDE-209 is ubiquitous in a variety of environmental compartments and can be exposed to organisms in various ways and cause toxic effects. The present review outlines the current state of knowledge on the occurrence of BDE-209 in the environment, influencing factors, toxicity, and degradation. BDE-209 has been detected in various environmental matrices including air, soil, water, and sediment. Additionally, environmental factors such as organic matter, total suspended particulate, hydrodynamic, wind, and temperature affecting BDE-209 are specifically discussed. Toxicity studies suggest BDE-209 may cause systemic toxic effects on living organisms, reproductive toxicity, embryo-fetal toxicity, genetic toxicity, endocrine toxicity, neurotoxicity, immunotoxicity, and developmental toxicity, or even be carcinogenic. BDE-209 has toxic effects on organisms mainly through epigenetic regulation and induction of oxidative stress. Evidence regarding the degradation of BDE-209, including biodegradation, photodegradation, Fenton degradation, zero-valent iron degradation, chemical oxidative degradation, and microwave radiation degradation is summarized. This review may contribute to assessing the environmental risks of BDE-209 to help develop rational management plans.

Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species

Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.

Metagenomic insights into the mechanisms of triphenyl phosphate degradation by bioaugmentation with Sphingopyxis sp. GY

Biodegradation of triphenyl phosphate (TPHP) by Sphingopyxis sp. GY was investigated, and results demonstrated that TPHP could be completely degraded in 36 h with intracellular enzymes playing a leading role. This study, for the first time, systematically explores the effects of the typical brominated flame retardants, organophosphorus flame retardants, and heavy metals on TPHP degradation. Our findings reveal that TCPs, BDE-47, HBCD, Cd and Cu exhibit inhibitory effects on TPHP degradation. The hydrolysis-, hydroxylated-, monoglucosylated-, methylated products and glutathione (GSH) conjugated derivative were identified and new degradation pathway of TPHP mediated by microorganism was proposed. Moreover, toxicity evaluation experiments indicate a significant reduction in toxicity following treatment with Sphingopyxis sp. GY. To evaluate its potential for environmental remediation, we conducted bioaugmentation experiments using Sphingopyxis sp. GY in a TPHP contaminated water-sediment system, which resulted in excellent remediation efficacy. Twelve intermediate products were detected in the water-sediment system, including the observation of the glutathione (GSH) conjugated derivative, monoglucosylated product, (OH)2-DPHP and CH3-O-DPHP for the first time in microorganism-mediated TPHP transformation. We further identify the active microbial members involved in TPHP degradation within the water-sediment system using metagenomic analysis. Notably, most of these members were found to possess genes related to TPHP degradation. These findings highlight the significant reduction of TPHP achieved through beneficial interactions and cooperation established between the introduced Sphingopyxis sp. GY and the indigenous microbial populations stimulated by the introduced bacteria. Thus, our study provides valuable insights into the mechanisms, co-existed pollutants, transformation pathways, and remediation potential associated with TPHP biodegradation, paving the way for future research and applications in environmental remediation strategies.

A systematic analysis of residue and risk of cyantraniliprole in the water-sediment system: Does metabolism reduce its environmental risk?

As a representative variety of diamide insecticides, cyantraniliprole has broad application prospects. In this study, the fate and risk of cyantraniliprole and its main metabolite J9Z38 in a water-sediment system were investigated. The present result showed that more J9Z38 was adsorbed in the sediment at the end of exposure. However, the bioaccumulation capacity of cyantraniliprole in zebrafish was higher than that of J9Z38. Cyantraniliprole had stronger influence on the antioxidant system and detoxification system of zebrafish than J9Z38. Moreover, cyantraniliprole induced more significant oxidative stress effect and more differentially expressed genes (DEGs) in zebrafish. Cyantraniliprole had significantly influence on the expression of RyR-receptor-related genes, which was confirmed by resolving their binding modes with key receptor proteins using AlphaFold2 and molecular docking techniques. In the sediment, both cyantraniliprole and J9Z38 had inhibitory effects on microbial community structure diversity and metabolic function, especially cyantraniliprole. The methane metabolism pathway, mediated by methanogens such as Methanolinea, Methanoregula, and Methanosaeta, may be the main pathway of degradation of cyantraniliprole and J9Z38 in sediments. The present results demonstrated that metabolism can reduce the environmental risk of cyantraniliprole in water-sediment system to a certain extent.

Mitochondrial Dysfunction Was Involved in Decabromodiphenyl Ethane-Induced Glucolipid Metabolism Disorders and Neurotoxicity in Zebrafish Larvae

Decabromodiphenyl ethane (DBDPE), a novel brominated flame retardant, is becoming increasingly prevalent in environmental and biota samples. While DBDPE has been shown to cause various biological adverse effects, the molecular mechanism behind these effects is still unclear. In this research, zebrafish embryos were exposed to DBDPE (50-400 μg/L) until 120 h post fertilization (hpf). The results confirmed the neurotoxicity by increased average swimming speed, interfered neurotransmitter contents, and transcription of neurodevelopment-related genes in zebrafish larvae. Metabolomics analysis revealed changes of metabolites primarily involved in glycolipid metabolism, oxidative phosphorylation, and oxidative stress, which were validated through the alterations of multiple biomarkers at various levels. We further evaluated the mitochondrial performance upon DBDPE exposure and found inhibited mitochondrial oxidative respiration accompanied by decreased mitochondrial respiratory chain complex activities, mitochondrial membrane potential, and ATP contents. However, addition of nicotinamide riboside could effectively restore DBDPE-induced mitochondrial impairments and resultant neurotoxicity, oxidative stress as well as glycolipid metabolism in zebrafish larvae. Taken together, our data suggest that mitochondrial dysfunction was involved in DBDPE-induced toxicity, providing novel insight into the toxic mechanisms of DBDPE as well as other emerging pollutants.

N-acetylcysteine rescues meiotic arrest during spermatogenesis in mice exposed to BDE-209

Deca-bromodiphenyl ethers (BDE-209) has been widely used in electronic devices and textiles as additives to flame retardants. Growing evidence showed that BDE-209 exposure leads to poorer sperm quality and male reproductive dysfunction. However, the underlying mechanisms of BDE-209 exposure caused a decline in sperm quality remains unclear. This study aimed to evaluate the protective effects of N-acetylcysteine (NAC) on meiotic arrest in spermatocytes and decreased sperm quality in BDE-209-exposed mice. In the study, mice were treated with NAC (150 mg/kg BW) 2 h before administrated with BDE-209 (80 mg/kg BW) for 2 weeks. For the in vitro studies, spermatocyte cell line GC-2spd cells were pretreated with NAC (5 mM) 2 h before treated with BDE-209 (50 μM) for 24 h. We found that pretreatment with NAC attenuated the oxidative stress status induced by BDE-209 in vivo and in vitro. Moreover, pretreatment with NAC rescued the testicular histology impairment and decreased the testicular organ coefficient in BDE-209-exposed mice. In addition, NAC supplement partially promoted meiotic prophase and improved sperm quality in BDE-209-exposed mice. Furthermore, NAC pretreatment effectively improved DNA damage repair by recovering DMC1, RAD51, and MLH1. In conclusion, BDE-209 caused spermatogenesis dysfunction related to the meiotic arrest medicated by oxidative stress, decreasing sperm quality.

Transcriptome profiling of Microbacterium resistens MZT7 reveals mechanisms of 17β-estradiol response and biotransformation

17β-estradiol (E2) pollution has attracted much attention, and the existence of E2 poses certain risks to the environment and human health. However, the mechanism of microbial degradation of E2 remains unclear. In this study, the location of E2-degrading enzymes was investigated, and transcriptome analysis of Microbacterium resistens MZT7 (M. resistens MZT7) exposed to E2. The degradation of E2 by M. resistens MZT7 was via the biological action of E2-induced intracellular enzymes. With the RNA sequencing, we found 1109 differentially expressed genes (DEGs). Among them, 773 genes were up-regulated and 336 genes were down-regulated. The results of the RNA sequencing indicated the DEGs were related to transport, metabolism, and stress response. Genes for transport, transmembrane transport, oxidoreductase activity, ATPase activity, transporter activity and quorum sensing were up-regulated. Genes for the tricarboxylic acid cycle, ribosome, oxidative phosphorylation and carbon metabolism were down-regulated. In addition, heterologous expression of one enzymes efficiently degraded E2. These findings provide some new insights into the molecular mechanism of biotransformation of E2 by M. resistens MZT7.

Aerobic Degradation Characteristics and Mechanism of Decabromodiphenyl Ether (BDE-209) Using Complex Bacteria Communities

Complex bacteria communities that comprised Brevibacillus sp. (M1) and Achromobacter sp. (M2) with effective abilities of degrading decabromodiphenyl ether (BDE-209) were investigated for their degradation characteristics and mechanisms under aerobic conditions. The experimental results indicated that 88.4% of 10 mg L^-1 BDE-209 could be degraded after incubation for 120 h under the optimum conditions of pH 7.0, 30 °C and 15% of the inoculation volume, and the addition ratio of two bacterial suspensions was 1:1. Based on the identification of BDE-209 degradation products via liquid chromatography-mass spectrometry (LC-MS) analysis, the biodegradation pathway of BDE-209 was proposed. The debromination, hydroxylation, deprotonation, breakage of ether bonds and ring-opening processes were included in the degradation process. Furthermore, intracellular enzymes had the greatest contribution to BDE-209 biodegradation, and the inhibition of piperyl butoxide (PB) for BDE-209 degradation revealed that the cytochrome P450 (CYP) enzyme was likely the key enzyme during BDE-209 degradation by bacteria M (1+2). Our study provided alternative ideas for the microbial degradation of BDE-209 by aerobic complex bacteria communities in a water system.

Extraction, Purification, Characterization and Application in Livestock Wastewater of S Sulfur Convertase

Sulfide is a toxic pollutant in the farming environment. Microbial removal of sulfide always faces various biochemical challenges, and the application of enzymes for agricultural environmental remediation has promising prospects. In this study, a strain of Cellulosimicrobium sp. was isolated: numbered strain L1. Strain L1 can transform S^2-, extracellular enzymes play a major role in this process. Next, the extracellular enzyme was purified, and the molecular weight of the purified sulfur convertase was about 70 kDa. The sulfur convertase is an oxidase with thermal and storage stability, and the inhibitor and organic solvent have little effect on its activity. In livestock wastewater, the sulfur convertase can completely remove S^2-. In summary, this study developed a sulfur convertase and provides a basis for the application in environmental remediation.

Integration of transcriptomic and proteomic reveals the toxicological molecular mechanisms of decabromodiphenyl ethane (DBDPE) on Pleurotus ostreatus

Decabromodiphenyl ethane (DBDPE), as one of the most widely used new brominated flame retardants (NBFRs), can pose a potential threat to human health and the environment. An integrated transcriptome and proteome was performed for investigating the toxicological molecular mechanisms of Pleurotus ostreatus (P. ostreatus) during the biodegradation of DBDPE at the concentrations of 5 and 20 mg/L. A total of 1193/1018 and 92/126 differentially expressed genes/proteins (DEGs/DEPs) were found, respectively, with DBDPE exposure at 5 and 20 mg/L. These DEGs and DEPs were mainly involved in the cellular process as well as metabolic process. DEPs for oxidation-reduction process and hydrolase activity were up-regulated, and those for membrane, lipid metabolic process and transmembrane transport were down-regulated. The DEGs and DEPs related to some key enzymes were down-regulated, such as NADH dehydrogenase/oxidoreductase, succinate dehydrogenase, cytochrome C1 protein, cytochrome-c oxidase/reductase and ATP synthase, which indicated that DBDPE affected the oxidative phosphorylation as well as tricarboxylic acid (TCA) cycle. Cytochrome P450 enzymes (CYPs) might be involved in DBDPE degradation through hydroxylation and oxidation. Some stress proteins were induced to resist DBDPE toxicity, including major facilitator superfamily (MFS) transporter, superoxide dismutase (SOD), molecular chaperones, heat shock proteins (HSP20, HSP26, HSP42), 60S ribosomal protein and histone H4. The findings help revealing the toxicological molecular mechanisms of DBDPE on P. ostreatus, aiming to improve the removal of DBDPE.

Functional bacterial consortium responses to biochar and implications for BDE-47 transformation: Performance, metabolism, community assembly and microbial interaction

The influence of biochar on the biodegradation of persistent organic pollutants (POPs) has been extensively studied. However, the underlying mechanisms behind the response of functional microbial consortia to biochar remain poorly understood. Herein, we systematically explored the effect of biochar on 2,2',4,4'-tetrabrominated ether (BDE-47) biodegradation, and investigated the interaction and assembly mechanism of the functional bacterial consortium QY2. The results revealed that the biodegradation efficiency of QY2 for BDE-47 increased from 53.85% to 94.11% after the addition of biochar. Fluorescence excitation-emission matrix and electrochemical analysis showed that biochar-attached biofilms were rich in redox-active extracellular polymeric substances (EPS, 3.03-fold higher than free cell), whose strong interaction with biochar facilitated the electron transfer of the biofilm, thus enhancing the debromination degradation of BDE-47. Meanwhile, the assembly model and molecular ecological networks analysis indicated that bacterial community assembly in biofilms was more driven by deterministic processes (environmental selection >75.00%) upon biochar stimulation and exhibited closer interspecific cooperative interactions, leading to higher biodiversity and broader habitat niche breadth for QY2 in response to BDE-47 disturbance. Potential degraders (Methylobacterium, Sphingomonas, Microbacterium) and electrochemical bacteria (Ochrobactrum) were selectively enriched, whose role as keystone bacteria may be participated in biofilm formation and redox-active EPS secretion (r > 0.5, P < 0.05). These findings deepen the understanding of the mechanisms by which biochar promotes microbial degradation of PBDEs and provided a theoretical basis for better regulation of functional bacterial communities during environmental remediation.

Molecular response of Anoxybacillus sp. PDR2 under azo dye stress: An integrated analysis of proteomics and metabolomics

Treating azo dye wastewater using thermophilic bacteria is considered a more efficient bioremediation strategy. In this study, a thermophilic bacterial strain, Anoxybacillus sp. PDR2, was regarded as the research target. This strain was characterized at different stages of azo dye degradation by using TMT quantitative proteomic and non-targeted metabolome technology. A total of 165 differentially expressed proteins (DEPs) and 439 differentially metabolites (DMs) were detected in comparisons between bacteria with and without azo dye. It was found that Anoxybacillus sp. PDR2 can degrade azo dye Direct Black G (DBG) through extracellular electron transfer with glucose serving as electron donors. Most proteins related to carbohydrate metabolism, including acetoacetate synthase, and malate synthase G, were overexpressed to provide energy. The bacterium can also self-synthesize riboflavin as a redox mediator of in vitro electron transport. These results lay a theoretical basis for industrial bioremediation of azo dye wastewater.

Analysis of the functional gene of degrading BDE-47 by Acinetobacter pittii GB-2 based on transcriptome sequencing

2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) is one of the most widely distributed PBDEs. BDE-47 is also the most abundant in organisms and the most toxic to humans and animals. Herein, we have studied the pathway of BDE-47 degradation and gene involvement in Acinetobacter pittii GB-2. This degradation is dominated by hydroxylation, resulting in hydroxylated products 6-OH-BDE-47, 5-OH-BDE-47 and 2'-OH-BDE-28, and bromophenol products 2,4-DBP and 4-BP. Transcriptome sequencing results showed 359 differentially expressed genes (DEGs) induced by BDE-47, of which 159 were up-regulated and 200 were down-regulated. The up-regulated ones were mainly related to substance transport, degradation and cell stress. From these results, we suggest that 1,2-dioxygenase, phenol hydroxylase and monooxygenase are involved in BDE-47 degradation. The function of AntA gene was identified by constructing a prokaryotic expression vector. Our study contributes to understanding how the metabolism of strain GB-2 changes under BDE-47 stress conditions, and sheds light on the mechanism of BDE-47 degradation.

Aerobic Degradation Characteristics of Decabromodiphenyl ether through Rhodococcus ruber TAW-CT127 and Its Preliminary Genome Analysis

Decabromodiphenyl ether (BDE-209), a polybrominated diphenyl ether (PBDE) homolog, seriously threatens human health. In this study, a Rhodococcus ruber strain with high BDE-209 degradation activity, named TAW-CT127, was isolated from Tong’an Bay, Xiamen. Under laboratory conditions, the strain’s optimal growth temperature, pH, and salinity are 45 °C, 7.0, and 0–2.5%, respectively. Scanning electron microscopy (SEM) analysis shows that TAW-CT127 is damaged when grown in manual marine culture (MMC) medium with BDE-209 as the sole carbon source instead of eutrophic conditions. In the dark, under the conditions of 28 °C, 160 rpm, and 3 g/L (wet weight) TAW-CT127, the degradation rate of 50 mg/L BDE-209 is 81.07%. The intermediate metabolites are hexabromo-, octabromo-, and nonabromo-diphenyl ethers. Through whole-genome sequencing, multiple dehalogenases were found in the genome of TAW-CT127; these may be involved in the production of lower-brominated diphenyl ethers. Additionally, biphenyl-2,3-dioxygenase (BDO) in TAW-CT127 may catalyze the debromination reaction of BDE-209. Our research provides a new high-efficiency strain for bioremediation of BDE-209 pollution, and lays the foundation for the preliminary exploration of genes associated with BDE-209 degradation.

Understanding the role of biochar in affecting BDE-47 biodegradation by Pseudomonas plecoglossicida: An integrated analysis using chemical, biological, and metabolomic approaches

Biochar-assisted microbial degradation technology is considered as an important strategy to eliminate organic pollutants, but the mechanism of biochar in affecting biodegradation has not been systematically studied. To address this knowledge gap, the effect of various biochars on biodegradation of different initial concentrations of BDE-47 by Pseudomonas plecoglossicida was investigated. The results showed that biochar exhibited significant promotion to the biodegradation of BDE-47, especially at concentrations of BDE-47 above 100 μg/L. The promotion effect was negatively influenced by the aromaticity and micropore volume of biochar. Biochar alleviated the cytotoxicity of BDE-47 to P. plecoglossicida and promoted cell proliferation based on toxicity assays. Additionally, biochar acted as shelter and stimulated the secretion of extracellular polymeric substances, which might support P. plecoglossicida to struggle with extreme conditions. Metabolomic analysis indicated that biochar resulted in upregulation expression of 38 metabolites in P. plecoglossicida. These upregulated metabolites were mainly related to glyoxylate and dicarboxylate metabolism, citrate cycle, and serial amino acid metabolism, suggesting that biochar could improve the BDE-47 biodegradation via enhancing oxidative metabolism and energy supply of the bacterial cells. This work elucidates how biochar can affect BDE-47 biodegradation and provides insights for the application prospect of biochar-assisted microbial degradation technology in the environment.

Microbial diversity drives pyrene dissipation in soil

Soil microbial diversity is an essential driver of multiple ecosystem functions and services. However, the role and mechanisms of microbial diversity in the dissipation of persistent organic pollutants in soil are largely unexplored. Here, a gradient of soil microbial diversity was constructed artificially by a dilution-to-extinction approach to assess the role of soil microbial diversity in the dissipation of pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), in a 42-day microcosm experiment. The results showed that pyrene dissipation (98.1%) and the abundances of pyrene degradation genes (the pyrene dioxygenase gene nidA and the gram-positive PAH-ring hydroxylating dioxygenase gene PAH-RHDα GP) were highest in soils with high microbial diversity. Random-forest machine learning was combined with linear regression analysis to identify a range of keystone taxa (order level) associated with pyrene dissipation, including Sphingobacteriales, Vampirovibrionales, Blastocatellales, Myxococcales, Micrococcales and Rhodobacterales. The diversity of these keystone taxa was significantly and positively correlated with the abundance of pyrene degradation genes and the removal rate of pyrene. According to (partial) Mantel tests, keystone taxa diversity was the dominant factor determining pyrene dissipation compared with total microbial diversity. Moreover, co-occurrence network analysis revealed that diverse keystone taxa may drive pyrene dissipation via more positive interactions between keystone species and with other species in soil. Taken together, these findings provide new insights on the regulation of keystone taxa diversity to promote the dissipation of PAH in soil.

Laccases—Versatile Enzymes Used to Reduce Environmental Pollution

The accumulation of waste and toxic compounds has become increasingly harmful to the environment and human health. In this context, the use of laccases has become a focus of interest, due to the properties of these versatile enzymes: low substrate specificity, and water formation as a non-toxic end product. Thus, we begin our study with a general overview of the importance of laccase for the environment and industry, starting with the sources of laccases (plant, bacterial and fungal laccases), the structure and mechanism of laccases, microbial biosynthesis, and the immobilization of laccases. Then, we continue with an overview of agro-waste treatment by laccases wherein we observe the importance of laccases for the biodisponibilization of substrates and the biodegradation of agro-industrial byproducts; we then show some aspects regarding the degradation of xenobiotic compounds, dyes, and pharmaceutical products. The objective of this research is to emphasize and fully investigate the effects of laccase action on the decomposition of lignocellulosic materials and on the removal of harmful compounds from soil and water, in order to provide a sustainable solution to reducing environmental pollution.

Metabolomic analysis and oxidative stress response reveals the toxicity in Escherichia coli induced by organophosphate flame retardants tris(2-chloroethyl) phosphate and triphenyl phosphate

Organophosphate flame retardants (OPFRs) are emerging environmental pollutants that are increasingly being used in consumer commodities. The adverse effects on biota induced by tris(2-chloroethyl) phosphate (TCEP) and triphenyl phosphate (TPHP) have become a growing concern. Unfortunately, toxic mechanisms at the molecular level for OPFRs in organisms are still lacking. Herein, Escherichia coli (E.coli) was exposed to TCEP and TPHP for 24 and 48 h to reveal oxidative stress response and molecular toxicity mechanisms. The results indicated that promotion of ROS overload occurred at higher dosages groups. The levels of SOD and CAT were significantly elevated along with the increase of MDA attributed to lipid peroxidation. Additionally, apoptosis rates increased, accompanied by a decline in membrane potential and Na⁺/K⁺-ATPase and Ca²⁺/Mg²⁺-ATPase contents, signifying that E. coli cytotoxicity induced by TCEP and TPHP was mediated by oxidative stress. Based on metabolomic analysis, different metabolic pathways were disrupted, including glycolysis/gluconeogenesis, pentose phosphate metabolism, purine metabolism, glutathione metabolism, amino acid biosynthesis, butanoate metabolism, alanine and aspartate metabolism. Most differentially expressed metabolites were downregulated, indicating an inhibitory effect on metabolic functions and key metabolic pathways. These findings generated new insights into the potential environmental risks of OPFRs in aquatic organisms.

Insights into biodegradation mechanisms of triphenyl phosphate by a novel fungal isolate and its potential in bioremediation of contaminated river sediment

In this study, Aspergillus sydowii FJH-1 isolated from soil was verified to be a novel triphenyl phosphate (TPhP) degrader. Biodegradation efficiency of TPhP by Aspergillus sydowii FJH-1 exceeded 90% within 6 days under the optimal conditions (pH 4-9, 30 ℃, initial concentration less than 20 mg/L). Proteomics analysis uncovered the proteins perhaps involved in hydrolysis, hydroxylation, methylation and sulfonation of TPhP and the primary intracellular adaptive responses of Aspergillus sydowii FJH-1 to TPhP stress. The expression of carboxylic ester hydrolase along with several thioredoxin- and glutathione-dependent oxidoreductases were induced to withstand the toxicity of TPhP. The presence of TPhP also caused obvious upregulation of proteins concerned with glycolysis, pentose phosphate pathway and tricarboxylic acid cycle. Data from toxicological tests confirmed that the cytotoxicity and phytotoxicity of TPhP was effectively decreased after treatment with Aspergillus sydowii FJH-1. Additionally, bioaugmentation with Aspergillus sydowii FJH-1 was available for promoting TPhP removal in real water and water-sediment system. Collectively, the present study offered a deeper insight into the biodegradation mechanism and pathway of TPhP by a newly screened fungal strain Aspergillus sydowii FJH-1 and validated the feasibility of applying this novel degrader in the bioremediation of TPhP-polluted matrices.

Biodegradation of poly (vinyl alcohol) by an orychophragmus rhizosphere-associated fungus Penicillium brevicompactum OVR-5, and its proposed PVA biodegradation pathway

In recent years, the utilisation of endophytes has emerged as a promising biological treatment technology for the degradation of plastic wastes such as biodegradation of synthetic plastics. This study, therefore, aimed to explore and extensively screen endophytic fungi (from selected plants) for efficient in vitro polyvinyl alcohol (PVA) biodegradation. In total, 76 endophytic fungi were isolated and cultivated on a PVA screening agar medium. Among these fungi, 10 isolates showed potential and were subsequently identified based on phenotypical characteristics, ITS ribosomal gene sequences, and phylogenetic analyses. Four strains exhibited a maximum level of PVA-degradation in the liquid medium when cultivated for 10 days at 28 °C and 150 rpm. These strains showed varied PVA removal rates of 81% (Penicillium brevicompactum OVR-5), 67% (Talaromyces verruculosus PRL-2), 52% (P. polonicum BJL-9), and 41% (Aspergillus tubingensis BJR-6) respectively. The most promising PVA biodegradation isolate 'OVR-5', with an optimal pH at 7.0 and optimal temperature at 30 °C, produced lipase, manganese peroxidase, and laccase enzymes. Based on analyses of its metabolic intermediates, as identified with GC-MS, we proposed the potential PVA degradation pathway of OVR-5. Biodegradation results were confirmed through scanning electron microscopy and Fourier transform infrared spectroscopy. This study provides the first report on an endophytic P. brevicompactum strain (associated with Orychophragmus violaceus) that has a great ability for PVA degradation providing more insight on potential fungus-based applications in plastic waste degradation.

Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y

A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.

Effects of methanol on the performance of a novel BDE-47 degrading bacterial consortium QY2 in the co-metabolism process

2,2',4,4'-tetrabrominated diphenyl ether (BDE-47), frequently detected in the environment, is arduous to be removed by conventional biological treatments due to its persistence and toxicity. Herein effects of methanol as a co-metabolic substrate on the biodegradation of BDE-47 was systematically studied by a functional bacterial consortium QY2, constructed through long-term and successive acclimation from indigenous microorganisms. The results revealed that BDE-47 (0.25 mg/L) was completely removed within 7 days in the 2.5 mM methanol treatment group, and its degradation efficiency was 3.26 times higher than that without methanol treatment. The addition of methanol dramatically accelerated the debromination, hydroxylation and phenyl ether bond breakage of BDE-47 by QY2. However, excessive methanol (>5 mM) combined with BDE-47 had strong stress on microbial cells, including significant (p < 0.05) increase of reactive oxygen species level, superoxide dismutase activity, catalase activity and malondialdehyde content, even causing 20.65% cell apoptosis and 11.27% death. It was worth noting that the changes of QY2 community structure remained relatively stable after adding methanol, presumably attributed to the important role of the genus Methylobacterium in maintaining the functional and structural stability of QY2. This study deepened our understanding of how methanol as co-metabolite substances stimulated the biodegradation of BDE-47 by microbial consortium.

Aerobic degradation of decabrominated diphenyl ether through a novel bacterium isolated from municipal waste dumping site: Identification, degradation and metabolic pathway

In the present study, a novel bacterium capable of degrading BDE-209 aerobically was isolated from a municipal waste dumping site and identified as Bacillus tequilensis strain BDE-S1 through 16S rRNA gene sequencing. A correlation between BDE-209 and bromide concentration, COD, TOC, and cell biomass was established. 65% of 50 mg/L initial concentration of BDE-209 was degraded within eight days of incubation by BDE-S1 strain. Two hexa, two penta, one tetra-BDE congener, and benzamide were detected as metabolites. The bromide release, COD, TOC and cell biomass were found to be significantly correlated parameters with BDE-209 degradation. Based on the metabolite analysis, ortho and meta debromination, cleavage of diphenyl ether bond and ring-opening were suggested as possible degradation pathways. This is the first study demonstrating the use of indigenously isolated Bacillus tequilensis strain BDE-S1 for aerobic degradation of BDE-209, which could provide new comprehension for bioremediation of PBDEs from contaminated environments.

Removal of heavy metal ions and polybrominated biphenyl ethers by sulfurized nanoscale zerovalent iron: Compound effects and removal mechanism

Sulfurized nanoscale zerovalent iron (S-nZVI) has been widely reported to be able to quickly remove heavy metals/persistent organic pollutants, but the limited understanding of the complicated removal process of heavy metals-organic combined pollutants restricts the application of S-nZVI. Here, we demonstrate that there is significant difference in the effectiveness of S-nZVI for removing single pollutant and complex pollutants. The removal kinetic constant (k_obs) of heavy metals by S-nZVI followed a sequence of Cr(VI)>Pb(II)>Ni(II)>Cd(II) with or without polybrominated diphenyl ethers (PBDEs). While the capacity of co-existing cations increasing the k_obs of PBDEs followed the order: Ni(II)>Pb(II)>Cd(II), and the co-existence of Cr(VI) anion inhibited the reduction of PBDE by S-nZVI because the generated Cr-Fe precipitate hindered the electron transfer. The de-passivation process on S-nZVI surface by Cd(II) ions slightly accelerated the transformation rate of electron. Nevertheless, the co-existing Pb(II) significantly accelerated the transformation of BDE-209 via the galvanic effect from the generated Pb⁰/Fe⁰ bimetal. Interestingly, the k_obs of BDE-47 in Ni(II)/S-nZVI system was 5.51 times higher than that of Pb(II)/S-nZVI system, implying that an atomic hydrogen mechanism dominated the reduction of BDE-47 by Ni(II)/S-nZVI. In conclusion, the results provided a deep comprehending of removal mechanism of heavy metal-organic complex pollutants by S-nZVI.

Effects of iron plaque and fatty acids on the transfer of BDE-209 from soil to rice under iron mineral Fenton-like oxidation condition

To understand the effect mechanisms of iron plaque and fatty acids on the migration of PBDEs from soil to rice (Oryza sativa), pot experiments were conducted in the soil spiked with decabromodiphenyl ether (BDE-209) under the conditions of tourmaline and nano-goethite Fenton-like treatments. The results showed that iron mineral Fenton-like oxidation could effectively remove BDE-209 from rhizosphere soil, the highest removal rate obtained 89.29% with the addition of 0.4 mmol/L H₂O₂ and 8 g nano-goethite (G + 3H group). Iron mineral Fenton-like oxidation could produce iron plaque (IP) on rice roots and accumulate a part of contaminants on the surface of IP, further weakening BDE-209 uptake in the plants. Additionally, the occurrence of fatty acid variation induced by BDE-209 stress, iron mineral Fenton-like oxidation at high concentrations of H₂O₂ with 0.4 mmol/L affected the distribution of fatty acids in plant tissues, especially for C_18:0 fatty acid. While the IP on rice roots prevented the BDE-209 into plant, it was also closely related to the distribution of fatty acids in rice, altering BDE-209 accumulation in the rice. To safely use the iron mineral Fenton-like oxidation in the agricultural soil remediation, the safety of plant cells treated by mineral Fenton-like oxidation was evaluated using the transmission electron microscopy (TEM) and enzyme activity determination, which indicated that iron mineral Fenton-like oxidation would destroy the inner structures of plant cells, especially for G + 3H group.

Proteomics in systems toxicology

Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

Can proteomics contribute to biomonitoring of aquatic pollution? A critical review

Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.