Bioaugmentation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil with the nitrate-reducing bacterium PheN7 under anaerobic condition

Challenging the impact of consortium diversity on bioaugmentation efficiency and native bacterial community structure in an acutely PAH-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are priority pollutants. We studied the effect of bioaugmentation using three allochthonous bacterial consortia with increasing diversity: SC AMBk, SC1, and SC4, on the structure and functionality of an artificially and acutely PAH-contaminated soil microbiome. The PAH supplementation increased substrate availability, allowing the inocula to efficiently degrade the supplemented PAHs after 15 days of incubation, become temporarily established, and modify the number of total interactions with soil residents. Sphingobium and Burkholderia, both members of the inoculants, were the major contributors to functional KOs (KEGG orthologs) linked to degradation and were differentially abundant genera in inoculated microcosms, indicating their competitiveness in the soil. Hence, bioaugmentation efficiency relied on them, while further degradation could be carried out by native microorganisms. This is one of the first studies to apply three inocula, designed from naturally occurring bacteria, and to study their effect on the soil's native community through ANCOM-BC. We revealed that when a resource that can be used by the inoculant is added to the soil, a high-diversity inoculant is not necessary to interact with the native community and establish itself. This finding is crucial for the design of microbiome engineering in bioremediation processes.

The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions

Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.

The negative effects of the excessive nitrite accumulation raised by anaerobic bioaugmentation on bioremediation of PAH-contaminated soil

Nitrite accumulation in anaerobic bioaugmentation and its side effects on remediation efficiency of polycyclic aromatic hydrocarbon (PAH)-contaminated soil were investigated in this study. Four gradient doses of PAH-degrading inoculum (10^4, 10^5, 10^6 and 10^7 cells/g soil) were separately supplied to the actual PAH-contaminated soil combining with nitrate as the biostimulant. Although bioaugmented with higher dose of inoculum could effectively improve the biodegradation efficiencies in the initial stage than sole nitrate addition but also accelerated the accumulation of nitrite in soil. The inhibition effects of nitrite swiftly occurred following the rapid accumulation of nitrite in each experiment group, restraining the PAH-degrading functionality by inhibiting the growth of total biomass and denitrifying functions in soil. This study revealed the side effects of nitrite accumulation raised by bioaugmentation on soil microorganisms, contributing to further improving the biodegrading efficiencies in the actual site restoration.

The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.

Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation

Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.

Performance enhancement of white rot fungi extracellular enzymes via new hydrogel microenvironments for remediation of benzo[a]pyrene contaminated soil

Organic pollutants with low solubility and high ecotoxicity, mutagenicity, and carcinogenicity, are rapidly entering and accumulating in soil, resulting in soil pollution. Several methods have been investigated for remediation of organic contaminated soil, including enzymatic remediation approach. However, free enzymes are easily deactivated, which hinders their practical application in soil remediation. Immobilization of enzyme improves its stability and catalytic performance, but the immobilized material itself becomes secondary pollutants in soil. In this study, Trametes versicolor extracellular enzyme was immobilized on the degradable calcium alginate hydrogel microspheres. The laccase maintained a high activity. In addition, the addition of cellulose improved the strength of the carrier. Hydrogel microspheres solved the problems of easy inactivation of free enzyme and secondary contamination of immobilized materials. By a novel combination of extracellular enzymes and hydrogel microenvironments, immobilized enzymes not only demonstrate outstanding performance in thermal stability and pH adaptability, but also achieves a significant improvement in biocatalytic activity for benzo[a]pyrene contaminated soil. The thermal stability of immobilized enzyme was much higher than that of free enzyme. When the temperature increased to 50 °C, the activity of immobilized enzyme remained at 93.15% of the maximum enzyme activity, while the activity of free enzyme decreased to 63.76%. At pH 8, the immobilized enzyme activity maintained 74.84% of the maximum enzyme activity, while the free enzyme activity was only 11.86%. Immobilized enzymes can effectively remove 91.40% of benzo[a]pyrene from soil within 96 h. Furthermore, the catalytic oxidation of benzo[a]pyrene by enzymes that have been immobilized ultimately results in the production of 6,12-benzo[a]pyrene-dione. Molecular dynamics simulation showed that the catalytic degradation of benzo[a]pyrene was mainly through the interaction of amino acid residues PRO-391 with the Pi-alkyl of benzo[a]pyrene. This study presents an innovative strategy for designing and developing immobilized enzymes for use in biocatalytic applications related to eco-remediation of soil.

Microbial metabolism regulation on the efficient degradation of aromatic compounds for biochemical treatment process of coal chemical wastewater in pilot scale

At present, the common problems of biochemical treatment systems of coal chemical wastewater were the poor system stability and the difficulty in reaching COD discharge standards. Aromatic compounds were the main contributors to COD value. The effective removal of aromatic compounds was an urgent problem in the biochemical treatment systems of coal chemical wastewater. In this study, the dominant microbial strains that could degrade phenol, quinoline, and phenanthrene were isolated respectively and inoculated into the pilot scale biochemical tank of coal chemical wastewater. The regulation effect and mechanism of microbial metabolism on the efficient degradation of aromatic compounds were studied. The results indicated that the various aromatic compounds were significantly removed under the regulation of microbial metabolism, the removal efficiencies of COD, TOC, phenols, benzenes, N-CHs, and PAHs were increased by about 25%, 20%, 33%, 25%, 42%, and 45%, respectively, and their biotoxicity was also drastically reduced. Moreover, the abundance and diversity of microbial community, and the microbial activity were obviously improved, as well as the various functional strains were selectively enriched, suggesting that the regulation system could resist environmental stresses with high substrate concentration and toxicity, which could lead to more enhanced performance for aromatic compounds removal. In addition, the microbial EPS content was significantly increased, implying the formation of microbial hydrophobic cell surfaces, which could improve the bioavailability of aromatic compounds. Furthermore, the enzymatic activity analysis revealed that the relative abundance and activity of key enzymes were all obviously improved. In conclusion, multiple lines of evidence were provided to clarify the regulation mechanism of microbial metabolism on the efficient degradation of aromatic compounds for biochemical treatment process of coal chemical wastewater in pilot scale. The results laid a good foundation for realizing the harmless treatment of coal chemical wastewater.

Dissipation kinetics of chlorpyrifos and 3,5,6 trichloro-2-pyridinol under vegetation of different aromatic grasses: Linkage with enzyme kinetics and microbial community of soil

The dissipation of chlorpyrifos (CP) and its hydrolytic metabolite 3,5,6-trichloro-2-pyridinol (TCP) in the soil is crucial for safe agriculture. However, there is still lacking relevant information about its dissipation under different vegetation for remediation purposes. In the present study, evaluation of dissipation of CP and TCP in non-planted and planted soil with different cultivars of three types of aromatic grass viz Cymbopogon martinii (Roxb. Wats), Cymbopogon flexuosus, and Chrysopogon zizaniodes (L.) Nash was examined in light of soil enzyme kinetics, microbial communities, and root exudation. Results revealed that the dissipation of CP was well-fitted into a single first-order exponential model (SFO). A significant reduction in the half-life (DT₅₀) of CP was observed in planted soil (30-63 days) than in non-planted soil (95 days). The presence of TCP in all soil samples was observed. The three types of the inhibitory effect of CP i.e. linear mixed inhibition (increase in enzyme-substrate affinity (Km) and decrease in enzyme pool (Vmax), un-competitive inhibition (decrease in Km and Vmax), and simple competitive inhibition were observed on soil enzymes involved in mineralization of carbon, nitrogen, phosphorus, and sulfur. The improvement in the enzyme pool (Vmax) was observed in planted soil. Streptomyces, Clostridium, Kaistobacter, Planctomyces, and Bacillus were the dominant genera in CP stress soil. CP contamination in soil demonstrated a reduction of richness in microbial diversity and enhancement of functional gene family related to cellular process, metabolism, genetic, and environmental information processing. Among all the cultivars, C. flexuosus cultivars demonstrated a higher dissipation rate of CP along with more root exudation.

Anaerobic biodegradation of polycyclic aromatic hydrocarbons

Although many anaerobic microorganisms that can degrade PAHs have been harnessed, there is still a large gap between laboratory achievements and practical applications. Here, we review the recent advances in the biodegradation of PAHs under anoxic conditions and highlight the mechanistic insights into the metabolic pathways and functional genes. Achievements of practical application and enhancing strategies of anaerobic PAHs bioremediation in soil were summarized. Based on the concerned issues during research, perspectives of further development were proposed including time-consuming enrichment, byproducts with unknown toxicity, and activity inhibition with low temperatures. In addition, meta-omics, synthetic biology and engineering microbiome of developing microbial inoculum for anaerobic bioremediation applications are discussed. We anticipate that integrating the theoretical research on PAHs anaerobic biodegradation and its successful application will advance the development of anaerobic bioremediation.

Synergistic effects of rice husk biochar and aerobic composting for heavy oil-contaminated soil remediation and microbial community succession evaluation

Soil petroleum pollution is an urgent problem in modern society, which seriously threatens the ecological balance and environmental safety. Aerobic composting technology is considered economically acceptable and technologically feasible for the soil remediation. In this study, the combined experiment of aerobic composting with the addition of biochar materials was conducted for the remediation of heavy oil-contaminated soil, and treatments with 0, 5, 10 and 15 wt% biochar dosages were labeled as CK, C5, C10 and C15, respectively. Conventional parameters (temperature, pH, NH₄⁺-N and NO₃^--N) and enzyme activities (urease, cellulase, dehydrogenase and polyphenol oxidase) during the composting process were systematically investigated. Remediation performance and functional microbial community abundance were also characterized. According to experimental consequences, removal efficiencies of CK, C5, C10 and C15 were 48.0%, 68.1%, 72.0% and 73.9%, respectively. The comparison with abiotic treatments corroborated that biostimulation rather than adsorption effect was the main removal mechanism during the biochar-assisted composting process. Noteworthy, the biochar addition regulated the succession process of microbial community and increased the abundance of microorganisms related to petroleum degradation at the genus level. This work demonstrated that aerobic composting with biochar amendment would be a fascinating technology for petroleum-contaminated soil remediation.

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.

Current Trends in Bioaugmentation Tools for Bioremediation: A Critical Review of Advances and Knowledge Gaps

Bioaugmentation is widely used in soil bioremediation, wastewater treatment, and air biofiltration. The addition of microbial biomass to contaminated areas can considerably improve their biodegradation performance. Nevertheless, analyses of large data sets on the topic available in literature do not provide a comprehensive view of the mechanisms responsible for inoculum-assisted stimulation. On the one hand, there is no universal mechanism of bioaugmentation for a broad spectrum of environmental conditions, contaminants, and technology operation concepts. On the other hand, further analyses of bioaugmentation outcomes under laboratory conditions and in the field will strengthen the theoretical basis for a better prediction of bioremediation processes under certain conditions. This review focuses on the following aspects: (i) choosing the source of microorganisms and the isolation procedure; (ii) preparation of the inoculum, e.g., cultivation of single strains or consortia, adaptation; (iii) application of immobilised cells; (iv) application schemes for soil, water bodies, bioreactors, and hydroponics; and (v) microbial succession and biodiversity. Reviews of recent scientific papers dating mostly from 2022-2023, as well as our own long-term studies, are provided here.

Effects of co-modified biochar immobilized laccase on remediation and bacterial community of PAHs-contaminated soil

Considering the stability and economy of immobilized enzymes, this study prepared co-modified biochar immobilized laccase product named Fe₃O₄@NaBC@GA@LC via orthogonal experimental design and explored its possibility of remediating polycyclic aromatic hydrocarbons (PAHs) contaminated soil in steel plants. Compared with the free laccase treatment, the relative activity of Fe₃O₄@NaBC@GA@LC remained 60 % after 50 days of incubation at room temperature. The relative activity of Fe₃O₄@NaBC@GA@LC could still retain nearly 80 % after five reuses. In the process of simulating the PAHs-contaminated site treatment experiment in Hangzhou Iron and steel plant, immobilized laccase exhibited efficient adsorption and degradation performances and even the removal rate of 5-ring PAHs reached more than 90 % in 40 days, resulting in improving urease activity and dehydrogenase in the soil and promoted the growth of a PAH degrading bacteria (Massilia). Our results further explained the efficient degradation effects of Fe₃O₄@NaBC@GA@LC on PAHs, which make it a promising candidate for PAHs-contaminated soil remediation.