Characterization of the simultaneous degradation of pyrene and removal of Cr(VI) by a bacteria consortium YH

Biodegradation of phenanthrene-Cr (VI) co-contamination by Pseudomonas aeruginosa AO-4 and characterization of enhanced degradation of phenanthrene

Microorganisms capable of simultaneously remediating heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) pollution hold significant importance in bioremediation efforts. In this study, we investigated the ability of Pseudomonas aeruginosa AO-4 to simultaneously degrade phenanthrene (PHE) and reduce Cr (VI). Specifically, it has the ability to reduce 100 % of Cr (VI) (30 mg/L) while degrading 43.8 % of PHE (50 mg/L). In batch experiments, it was observed that the presence of Cr (VI) can enhance the degradation of PHE by strain AO-4. The solubility of PHE in soluble extracellular polymeric substances (S-EPS) was found to be related to the initial concentration of Cr (VI), which could explain why Cr (VI) promotes the degradation of PHE. Additionally, XPS analysis confirmed that Cr (VI) was reduced to Cr (III) with S-EPS produced by Pseudomonas aeruginosa AO-4. GC-MS analysis was conducted to analyze the degradation metabolites of phenanthrene, di(2-ethylhexyl) phthalate and 2TMS derivatives of salicylic acid were detected, indicating that Pseudomonas aeruginosa AO-4 is capable of degrading phenanthrene through two distinct pathways. These findings demonstrate the potential of Pseudomonas aeruginosa AO-4 in the treatment of co-contamination scenarios involving PAHs and HMs.

Application of bacterial agent YH for remediation of pyrene-heavy metal co-pollution system: Efficiency, mechanism, and microbial response

The combination of organic and heavy metal pollutants can be effectively and sustainably remediated using bioremediation, which is acknowledged as an environmentally friendly and economical approach. In this study, bacterial agent YH was used as the research object to explore its potential and mechanism for bioremediation of pyrene-heavy metal co-contaminated system. Under the optimal conditions (pH 7.0, temperature 35°C), it was observed that pyrene (PYR), Pb(II), and Cu(II) were effectively eliminated in liquid medium, with removal rates of 43.46%, 97.73% and 81.60%, respectively. The microscopic characterization (SEM/TEM-EDS, XPS, XRD and FTIR) results showed that Pb(II) and Cu(II) were eliminated by extracellular adsorption and intracellular accumulation of YH. Furthermore, the presence of resistance gene clusters (cop, pco, cus and pbr) plays an important role in the detoxification of Pb(II) and Cu(II) by strains YH. The degradation rate of PYR reached 72.51% in composite contaminated soil, which was 4.33 times that of the control group, suggesting that YH promoted the dissipation of pyrene. Simultaneously, the content of Cu, Pb and Cr in the form of F4 (residual state) increased by 25.17%, 6.34% and 36.88%, respectively, indicating a decrease in the bioavailability of heavy metals. Furthermore, YH reorganized the microbial community structure and enriched the abundance of hydrocarbon degradation pathways and enzyme-related functions. This study would provide an effective microbial agent and new insights for the remediation of soil and water contaminated with organic pollutants and heavy metals.

Characteristic microbiome and synergistic mechanism by engineering agent MAB-1 to evaluate oil-contaminated soil biodegradation in different layer soil

Bioremediation is a sustainable and pollution-free technology for crude oil-contaminated soil. However, most studies are limited to the remediation of shallow crude oil-contaminated soil, while ignoring the deeper soil. Here, a high-efficiency composite microbial agent MAB-1 was provided containing Bacillus (naphthalene and pyrene), Acinetobacter (cyclohexane), and Microbacterium (xylene) to be synergism degradation of crude oil components combined with other treatments. According to the crude oil degradation rate, the up-layer (63.64%), middle-layer (50.84%), and underlying-layer (54.21%) crude oil-contaminated soil are suitable for bioaugmentation (BA), biostimulation (BS), and biostimulation+bioventing (BS+BV), respectively. Combined with GC-MS and carbon number distribution analysis, under the optimal biotreatment, the degradation rates of 2-ring and 3-ring PAHs in layers soil were about 70% and 45%, respectively, and the medium and long-chain alkanes were reduced during the remediation. More importantly, the relative abundance of bacteria associated with crude oil degradation increased in each layer after the optimal treatment, such as Microbacterium (2.10-14%), Bacillus (2.56-12.1%), and Acinetobacter (0.95-12.15%) in the up-layer soil; Rhodococcus (1.5-6.9%) in the middle-layer soil; and Pseudomonas (3-5.4%) and Rhodococcus (1.3-13.2%) in the underlying-layer soil. Our evaluation results demonstrated that crude oil removal can be accelerated by adopting appropriate bioremediation approach for different depths of soil, providing a new perspective for the remediation of actual crude oil-contaminated sites.

Cometabolic degradation of pyrene with phenanthrene as substrate: assisted by halophilic Pseudomonas stutzeri DJP1

At present, cometabolic degradation is an extensive method for the biological removal of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) in the marine environment. However, due to the refractory to degradation and high toxicity, there are few studies on pyrene (PYR) cometabolic degradation with phenanthrene (PHE) as substrate. In this study, a Pseudomonas stutzeri DJP1 strain isolated from sediments was used in the cometabolic system of PHE and PYR. The biomass and the activity of key enzymes such as dehydrogenase and catechol 12 dioxygenase of strain were improved, but the enhancement of biotoxicity resulted in the inhibition of cometabolism simultaneously. Seven metabolites were identified respectively in PYR, PHE degradation cultures. It was speculated that the cometabolism of PHE and PYR had a common phthalic acid pathway, and the degradation pathway of PHE was included in the downstream pathway of PYR. The functional genes such as PhdF, NidD and CatA involved in DJP1 degradation were revealed by Genome analysis. This study provides a reference for the biodegradation of PYR and PHE in real marine environment.

Mechanism of Cr(VI) removal by efficient Cr(VI)-resistant Bacillus mobilis CR3

Cr(VI) is a hazardous environmental pollutant that poses significant risks to ecosystems and human health. We successfully isolated a novel strain of Bacillus mobilis, strain CR3, from Cr(VI)-contaminated soil. Strain CR3 showed 86.70% removal capacity at 200 mg/L Cr(VI), and a good Cr(VI) removal capacity at different pH, temperature, coexisting ions, and electron donor conditions. Different concentrations of Cr(VI) affected the activity of CR3 cells and the removal rate of Cr(VI), and approximately 3.46% of total Cr was immobilized at the end of the reaction. The combination of SEM-EDS and TEM-EDS analysis showed that Cr accumulated both on the cell surface and inside the cells after treatment with Cr(VI). XPS analysis showed that both Cr(III) and Cr(VI) were present on the cell surface, and FTIR results indicated that the presence of Cr on the cell surface was mainly related to functional groups, such as O-H, phosphate, and -COOH. The removal of Cr(VI) was mainly achieved through bioreduction, which primarily occurred outside the cell. Metabolomics analysis revealed the upregulation of five metabolites, including phenol and L-carnosine, was closely associated with Cr(VI) reduction, heavy metal chelation, and detoxification mechanisms. In addition, numerous metabolites were linked to cellular homeostasis exhibited differential expression. Cr(VI) exerted inhibitory effects on the division rate and influenced critical pathways, including energy metabolism, nucleotide metabolism, and amino acid synthesis and catabolism. These findings reveal the molecular mechanism of Cr(VI) removal by strain CR3 and provide valuable insights to guide the remediation of Cr(VI)-contaminated sites.

Artificial mixed microbial system for polycyclic aromatic hydrocarbons degradation

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants with major risks to human health. Biological degradation is environmentally friendly and the most appealing remediation method for a wide range of persistent pollutants. Meanwhile, due to the large microbial strain collection and multiple metabolic pathways, PAH degradation via an artificial mixed microbial system (MMS) has emerged and is regarded as a promising bioremediation approach. The artificial MMS construction by simplifying the community structure, clarifying the labor division, and streamlining the metabolic flux has shown tremendous efficiency. This review describes the construction principles, influencing factors, and enhancement strategies of artificial MMS for PAH degradation. In addition, we identify the challenges and future opportunities for the development of MMS toward new or upgraded high-performance applications.

Synergistic remediation of phenanthrene-cadmium co-contaminants by an immobilized acclimated bacterial-fungal consortium and its community response

Bioremediation has tremendous potential to mitigate the serious threats posed by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). In the present study, nine bacterial-fungal consortia were progressively acclimated under different culture conditions. Among them, a microbial consortium 1, originating from activated sludge and copper mine sludge microorganisms, was developed through the acclimation of a multi-substrate intermediate (catechol)-target contaminant (Cd²⁺, phenanthrene (PHE)). Consortium 1 exhibited the best PHE degradation, with an efficiency of 95.6% after 7 d of inoculation, and its tolerance concentration for Cd²⁺ was up to 1800 mg/L within 48 h. Bacteria Pandoraea and Burkholderia-Caballeronia-Paraburkholderia, as well as fungi Ascomycota and Basidiomycota predominated in the consortium 1. Furthermore, a biochar-loaded consortium was constructed to better cope with the co-contamination behavior, which exhibited excellent adaptation to Cd²⁺ ranging of 50-200 mg/L. Immobilized consortium efficiently degraded 92.02-97.77% of 50 mg/L PHE within 7 d while removing 93.67-99.04% of Cd²⁺. In remediation of co-pollution, immobilization technology improved the bioavailability of PHE and dehydrogenase activity of the consortium to enhance PHE degradation, and the phthalic acid pathway was the main metabolic pathway. As for Cd²⁺ removal, oxygen-containing functional groups (-OH, C=O, and C-O) of biochar or microbial cell walls and EPS components, fulvic acid and aromatic proteins, participated through chemical complexation and precipitation. Furthermore, immobilization led to more active consortium metabolic activity during the reaction, and the community structure developed in a more favorable direction. The dominant species were Proteobacteria, Bacteroidota, and Fusarium, and the predictive expression of functional genes corresponding to key enzymes was elevated. This study provides a basis for combining biochar and acclimated bacterial-fungal consortia for co-contaminated site remediation.

Enhanced crude oil degradation by remodeling of crude oil-contaminated soil microbial community structure using sodium alginate/graphene oxide/Bacillus C5 immobilized pellets

Bioaugmentation (BA) of oil-contaminated soil by immobilized microorganisms is considered to be a promising technology. However, available high-efficiency microbial agents remain very limited. Therefore, we prepared a SA/GO/C5 immobilized gel pellets by embedding the highly efficient crude oil degrading bacteria Bacillus C5 in the SA/GO composite material. The optimum preparation conditions of SA/GO/C5 immobilized gel pellets were: SA 3.0%, GO 25.0 μg/mL, embedding amount of C5 6%, water bath temperature of 50°C, CaCl₂ solution concentration 3% and cross-linking time 20 h. BA experiments were carried out on crude oil contaminated soil to explore the removal effect of SA/GO/C5 immobilized pellets. The results showed that the SA/GO/C5 pellets exhibited excellent mechanical strength and specific surface area, which facilitated the attachment and growth of the Bacillus C5. Compared with free bacteria C5, the addition of SA/GO/C5 significantly promoted the removal of crude oil in soil, reaching 64.92% after 30 d, which was 2.1 times the removal rate of C5. The addition of SA/GO/C5 promoted the abundance of soil exogenous Bacillus C5 and indigenous crude oil degrading bacteria Alcanivorax and Marinobacter. In addition, the enrichment of hydrocarbon degradation-related functional abundance was predicted by PICRUSt2 in the SA/GO/C5 treatment group. This study demonstrated that SA/GO/C5 is an effective method for remediating crude oil-contaminated soil, providing a basis and option for immobilized microorganisms bioaugmentation to remediate organic contaminated soil.

Reconstruction of microbiome and functionality accelerated crude oil biodegradation of 2,4-DCP-oil-contaminated soil systems using composite microbial agent B-Cl

Biodegradation is one of the safest and most economical methods for the elimination of toxic chlorophenols and crude oil from the environment. In this study, aerobic degradation of the aforementioned compounds by composite microbial agent B-Cl, which consisted of Bacillus B1 and B2 in a 3:2 ratio, was analyzed. The biodegradation mechanism of B-Cl was assessed based on whole genome sequencing, Fourier transform infrared spectroscopy and gas chromatographic analyses. B-Cl was most effective at reducing Cl^- concentrations (65.17%) and crude oil biodegradation (59.18%) at 7 d, which was when the content of alkanes ≤ C₃₀ showed the greatest decrease. Furthermore, adding B-Cl solution to soil significantly decreased the 2,4-DCP and oil content to below the detection limit and by 80.68%, respectively, and reconstructed of the soil microbial into a system containing more CPs-degrading (exaA, frmA, L-2-HAD, dehH, ALDH, catABE), aromatic compounds-degrading (pcaGH, catAE, benA-xylX, paaHF) and alkane- and fatty acid-degrading (alkB, atoB, fadANJ) microorganisms. Moreover, the presence of 2,4-DCP was the main hinder of the observed effects. This study demonstrates the importance of adding B-Cl solution to determine the interplay of CPs with microbes and accelerating oil degradation, which can be used for in-situ bioremediation of CPs and oil-contaminated soil.

A novel dehydrocoenzyme activator combined with a composite microbial agent TY for enhanced bioremediation of crude oil-contaminated soil

Bioaugmentation (BA) and biostimulation (BS) synergistic remediation is an effective remediation strategy for oil-contaminated soil. In this study, the optimal combination system of composite microbial agent TY (Achromobacter: Pseudomona = 2:1) and dehydrocoenzyme activator (NaNO₃ (7.0 g/L), (NH₄)₂HPO₄ (1.0 g/L), riboflavin (6.0 mg/L)) was screened. Under the best combination system, the degradation rate of crude oil in oil-contaminated soil reached 79.44% after 60 d, which was 1.74 times and 1.23 times higher than that of compound microbial agent TY treatment and dehydrogenase activator treatment, respectively. In addition, a highly efficient combination system was found to target the degradation of oil C₁₀-C₂₈ fractions by gas chromatography (GC). The increased abundance of dehydrogenase coenzymes such as flavin nucleotides (FAD and FMN), coenzyme I (NAD⁺, Co I) and coenzyme II (NADP⁺, Co II) as well as dioxygenases and monooxygenases promote the degradation of crude oil. Furthermore, the dominant genera at the genus level in soil were analyzed by high-throughput sequencing, which were Nocardioides (46.48%-56.07%), Gordonia (11.40%-14.61%), Intrasporangiaceae (5.05%-10.58%), Pseudomonas (1.39%-1.92%) and Dietzia (0.64%-2.77%). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis showed that the abundance of genes associated with crude oil degradation such as ABC transporters (2.89%), fatty acid (1.04%), carbon metabolism (4.5%) and aromatic compound (0.92%) was assigned enhanced after 60 d of remediation. These results indicated that the combination system of the compound bacterium TY and the dehydrocoenzyme activator is a propective option for the bioremediation of oil-contaminated soil.