Bioaugmentation of Native Fungi, an Efficient Strategy for the Bioremediation of an Aged Industrially Polluted Soil With Heavy Hydrocarbons

Synergistic effects of surfactant biostimulation and indigenous fungal bioaugmentation for enhanced bioremediation of PAH-contaminated soils

Surfactant biostimulation and autochthonous fungal bioaugmentation have emerged as promising strategies for the bioremediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the mechanisms driving their combined effects remain poorly understood. This study investigates the degradation mechanisms associated with bioaugmentation using the indigenous fungus Aspergillus fumigatus LJD-29 and surfactant Tween 80. By employing stable-isotope probing and high-throughput sequencing, we comprehensively assessed these processes. In our study, the results demonstrate that both Aspergillus fumigatus LJD-29 and Tween 80 significantly enhanced the degradation efficiency of phenanthrene and modified the microbial community composition, particularly among active degraders. Extracellular enzymes were identified as key players in the phenanthrene transformation process. Tween 80 improved the bioavailability of phenanthrene, stimulating the growth of native PAH degraders, with Pseudonocardia emerging as a prominent genus. Although the combined surfactant-fungal treatment did not substantially increase terminal degradation efficiency due to limitations in phenanthrene bioavailability, it accelerated the degradation rate. Additionally, Tween 80 helped restore the microbial community structure disrupted by fungal bioaugmentation. These findings provide valuable insights into the mechanisms of surfactant biostimulation and indigenous fungal bioaugmentation, highlighting the potential of this integrated bioremediation strategy for managing PAH-contaminated soils.

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

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

Exploring Novel Fungal-Bacterial Consortia for Enhanced Petroleum Hydrocarbon Degradation

Bioremediation, involving the strategic use of microorganisms, has proven to be a cost-effective alternative for restoring areas impacted by persistent contaminants such as polycyclic aromatic hydrocarbons (PAHs). In this context, the aim of this study was to explore hydrocarbon-degrading microbial consortia by prospecting native species from soils contaminated with blends of diesel and biodiesel (20% biodiesel/80% diesel). After enrichment in a minimal medium containing diesel oil as the sole carbon source and based on 16S rRNA, Calmodulin and β-tubulin gene sequencing, seven fungi and 12 bacteria were identified. The drop collapse test indicated that all fungal and four bacterial strains were capable of producing biosurfactants with a surface tension reduction of ≥20%. Quantitative analysis of extracellular laccase production revealed superior enzyme activity among the bacterial strains, particularly for Stenotrophomonas maltophilia P05R11. Following antagonistic testing, four compatible consortia were formulated. The degradation analysis of PAHs and TPH (C5-C40) present in diesel oil revealed a significantly higher degradation capacity for the consortia compared to isolated strains. The best results were observed for a mixed bacterial-fungal consortium, composed of Trichoderma koningiopsis P05R2, Serratia marcescens P10R19 and Burkholderia cepacia P05R9, with a degradation spectrum of ≥91% for all eleven PAHs analyzed, removing 93.61% of total PAHs, and 93.52% of TPH (C5-C40). Furthermore, this study presents the first report of T. koningiopsis as a candidate for bioremediation of petroleum hydrocarbons.

The expansion of fungal organisms in environmental biotechnology

Fungal organisms hold vital roles in ecosystem processes. Despite their intricate entanglement with most life on earth and their powerful metabolic capacities, they remain under-represented in environmental biotechnology. The interest in applying fungal biotechnologies to different environments is growing, as light is shed on their versatile potential. A diversity of fungi can be harnessed to promote crop yield, remediate pollutants from terrestrial and aquatic environments, and mitigate climate change impacts. Current technological advancements, such as the increase in high-accuracy 'omics pipelines, provide improvement. However, it is emphasized that there are many knowledge gaps regarding applying fungal biotechnology at scale where other organisms are inherently present. Hence, there is a dire need to increase funding that enables in-depth studies on fungal processes, such as degradation capacities, metabolite production, and cross-kingdom interactions, that promote climate-smart biotechnologies.

Fungal Extracellular Enzymes from Aspergillus spp. as Promising Candidates for Extra-Heavy Oil Degradation and Enhanced Oil Recovery

Heavy crude oil (HCO) and extra-heavy crude oil (EHCO) with high viscosity and density pose enormous challenges to the exploitation of oil reserves. While bacteria are increasingly used in biocatalytic upgrading of HCO and EHCO, less attention has been paid to the potential of fungi. The aim of this study was to ascertain the role of fungal extracellular enzymes from Aspergillus spp. In the biodegradation of EHCO and their application potential for enhanced oil recovery. A. terreus HJ2 and A. nidulans HJ4 with the ability to biodegrade HCO were previously isolated from bitumen enrichment cultures. Both strains grew well on EHCO agar plates supplemented with a small amount of soluble starch (0.2%) and yeast extract (0.3%). Extracellular enzymes from each strain separately, as well as mixtures of the enzymes, exhibited EHCO degradation activity, leading to redistribution of hydrocarbons with substantial formation of biogases and organic acids in a 7-day period. Enzymatic degradation resulted in decreased contents of resins and asphaltenes, accompanied by increased contents of saturates and aromatics. Gas chromatography-mass spectrometry revealed distinct redistribution patterns of n-alkane in the biotreated oil. Enzymatic degradation additionally caused considerable reduction in oil viscosity (by 12.7%) and heavy metal concentrations (Ni, by 44.1%; Fe, by 54.0%; V, by 31.6%). The results provide empirical evidence for the application potential of fungal extracellular enzymes from Aspergillus spp. in EHCO recovery and biocatalytic upgrading of EHCO.

SIP-metagenomics reveals key drivers of rhizospheric Benzo[a]pyrene bioremediation via bioaugmentation with indigenous soil microbes

Rhizoremediation and bioaugmentation have proven effective in promoting benzo[a]pyrene (BaP) degradation in contaminated soils. However, the mechanism underlying bioaugmented rhizospheric BaP degradation with native microbes is poorly understood. In this study, an indigenous BaP degrader (Stenotrophomonas BaP-1) isolated from petroleum-contaminated soil was introduced into ryegrass rhizosphere to investigate the relationship between indigenous degraders and rhizospheric BaP degradation. Stable isotope probing and 16S rRNA gene amplicon sequencing subsequently revealed 15 BaP degraders, 8 of which were directly associated with BaP degradation including Bradyrhizobium and Streptomyces. Bioaugmentation with strain BaP-1 significantly enhanced rhizospheric BaP degradation and shaped the microbial community structure. A correlation of BaP degraders, BaP degradation efficiency, and functional genes identified active degraders and genes encoding polycyclic aromatic hydrocarbon-ring hydroxylating dioxygenase (PAH-RHD) genes as the primary drivers of rhizospheric BaP degradation. Furthermore, strain BaP-1 was shown to not only engage in BaP metabolism but also to increase the abundance of other BaP degraders and PAH-RHD genes, resulting in enhanced rhizospheric BaP degradation. Metagenomic and correlation analyses indicated a significant positive relationship between glyoxylate and dicarboxylate metabolism and BaP degradation, suggesting a role for these pathways in rhizospheric BaP biodegradation. By identifying BaP degraders and characterizing their metabolic characteristics within intricate microbial communities, our study offers valuable insights into the mechanisms of bioaugmented rhizoremediation with indigenous bacteria for high-molecular-weight PAHs in petroleum-contaminated soils.

Enhancing biodegradation of aged hydrocarbon-contaminated soils through toluene addition: assessing effects on solid and slurry phase treatments

The main challenge in treating aged soils highly contaminated with total petroleum hydrocarbons (TPH) is to enhance their bioavailability for microbial degradation. Hydrocarbons in soils undergo chemical changes that make them more resistant to biodegradation. This study investigates toluene's efficacy in enhancing the biodegradation of aged hydrocarbon-contaminated soil containing 292,000 mg TPH kg-1 dry soil. Toluene's effect was compared between solid phase (SOP) and slurry phase (SLP) treatments using a microbial consortium isolated from Cyperus laxus rhizosphere. TPH biodegradation and microbial respiration were measured, the latter to estimate the respiratory quotient (RQ, the ratio between moles of carbon dioxide released and moles of oxygen absorbed during respiration). Toluene significantly accelerated TPH biodegradation in both treatments, achieving ~ 30% higher removal than in a non-solvent control, possibly through improved bioavailability of aromatic compounds and other low molecular weight compounds. According to the RQ analysis, toluene enhanced microbial respiratory processes and hydrocarbon catabolism with higher hydrocarbon mineralization (RQ =  ~ 0.5) in both SOP and SLP assays. Our results reveal toluene's potential to increase hydrocarbon availability and microbial degradation efficiency in aged contaminated soils; its use in various bioremediation techniques could be of broad applicability across diverse soil types and pollutants.

Three strategy rules of filamentous fungi in hydrocarbon remediation: an overview

Remediation of hydrocarbon contaminations requires much attention nowadays since it causes detrimental effects on land and even worse impacts on aquatic environments. Tools of bioremediation especially filamentous fungi permissible for cleaning up as much as conceivable, at least they turn into non-toxic residues with less consumed periods. Inorganic chemicals, CO2, H2O, and cell biomass are produced as a result of the breakdown and mineralization of petroleum hydrocarbon pollutants. This paper presents a detailed overview of three strategic rules of filamentous fungi in remediating the various aliphatic, and aromatic hydrocarbon compounds: utilizing carbons from hydrocarbons as sole energy, Co-metabolism manners (Enzymatic and Non-enzymatic theories), and Biosorption approaches. Upliftment in the degradation rate of complex hydrocarbon by the Filamentous Fungi in consortia scenario we can say, "Fungal Talk", which includes a variety of cellular mechanisms, including biosurfactant production, biomineralization, and precipitation, etc., This review not only displays its efficiency but showcases the field applications - cost-effective, reliable, eco-friendly, easy to culture as biomass, applicable in both land and any water bodies in operational environment cleanups. Nevertheless, the potentiality of fungi-human interaction has not been fully understood, henceforth further studies are highly endorsed with spore pathogenicity of the fungal species capable of high remediation rate, and the gene knockout study, if the specific peptides cause toxicity to any living matters via Genomics and Proteomics approaches, before application of any in situ or ex situ environments.

Bioremediation of petroleum refinery wastewater by fungal stains isolated from the fishing harbour of Bizerte (Mediterranean Sea)

The study was conducted in order to explore the potential of fungi isolated from surface and bottom seawater collected from the fishing harbour of Bizerte on the bioremediation of industrial effluent (IE) contaminated by petroleum hydrocarbon. Among the 128 fungal isolates, 11 were isolated from surface seawater and 7 from bottom seawater, representing 18 taxa in total. The gas chromatography mass spectrometry (GC-MS) was used for the determination of hydrocarbon compounds in IE. An initial screening of fungal growth using six concentrations ranged between 20 and 70% (v/v) IE has allowed the identification of the optimal concentration for fungal growth as well as selection of species able to tolerate high amounts of hydrocarbon. Colorimetric test employing 2,6-dichlorophenol indophenol and gravimetric method was applied for the assessment of fungal growth using 20% EI. By checking the phylogenetic affiliation of the high-performing stains as identified using ITSr DNA sequence, a dominance of Ascomycetes was detected. Indeed, Aspergillus terreus and Penicillium expansum may degrade 82.07 and 81.76% of residual total petroleum hydrocarbon (TPH), respectively. Both species were collected from surface seawater. While, Aspergillus niger, Colletotrichum sp and Fusarium annulatum displayed comparable degradation rates 40.43%, 41.3%, and 42.03%, respectively. The lowest rate of degradation 33.62% was detected in Emericellopsis phycophila. All those species were isolated from bottom seawater, excepting A. niger isolated from surface water. This work highlighted the importance of exploring the potential of fungi isolated from the natural environment on the bioremediation of industrial effluent. Our results promoted the investigation of the potential of the high-performing isolates A. terreus and P. expansum on the bioremediation of IE at pilot-scale and then in situ.

Comparative Bioremediation of Tetradecane, Cyclohexanone and Cyclohexane by Filamentous Fungi from Polluted Habitats in Kazakhstan

Studying the fates of oil components and their interactions with ecological systems is essential for developing comprehensive management strategies and enhancing restoration following oil spill incidents. The potential expansion of Kazakhstan's role in the global oil market necessitates the existence of land-specific studies that contribute to the field of bioremediation. In this study, a set of experiments was designed to assess the growth and biodegradation capacities of eight fungal strains sourced from Kazakhstan soil when exposed to the hydrocarbon substrates from which they were initially isolated. The strains were identified as Aspergillus sp. SBUG-M1743, Penicillium javanicum SBUG-M1744, SBUG-M1770, Trichoderma harzianum SBUG-M1750 and Fusarium oxysporum SBUG-1746, SBUG-M1748, SBUG-M1768 and SBUG-M1769 using the internal transcribed spacer (ITS) region. Furthermore, microscopic and macroscopic evaluations agreed with the sequence-based identification. Aspergillus sp. SBUG-M1743 and P. javanicum SBUG-M1744 displayed remarkable biodegradation capabilities in the presence of tetradecane with up to a 9-fold biomass increase in the static cultures. T. harzianum SBUG-M1750 exhibited poor growth, which was a consequence of its low efficiency of tetradecane degradation. Monocarboxylic acids were the main degradation products by SBUG-M1743, SBUG-M1744, SBUG-M1750, and SBUG-M1770 indicating the monoterminal degradation pathway through β-oxidation, while the additional detection of dicarboxylic acid in SBUG-M1768 and SBUG-M1769 cultures was indicative of the fungus' ability to undertake both monoterminal and diterminal degradation pathways. F. oxysporum SBUG-M1746 and SBUG-M1748 in the presence of cyclohexanone showed a doubling of the biomass with the ability to degrade the substrate almost completely in shake cultures. F. oxysporum SBUG-M1746 was also able to degrade cyclohexane completely and excreted all possible metabolites of the degradation pathway. Understanding the degradation potential of these fungal isolates to different hydrocarbon substrates will help in developing effective bioremediation strategies tailored to local conditions.

Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.

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

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

Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment

Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

New frontiers of soil fungal microbiome and its application for biotechnology in agriculture

The fungi-based technology provided encouraging scenarios in the transition from a conventionally based economic system to the potential security of sources closely associated with the agricultural sphere such as the agriculture. In recent years, the intensification of fungi-based processes has generated significant gains, additionally to the production of materials with significant benefits and strong environmental importance. Furthermore, the growing concern for human health, especially in the agriculture scenario, has fostered the investigation of organisms with high biological and beneficial potential for use in agricultural systems. Accordingly, this study offered a comprehensive review of the diversity of the soil fungal microbiome and its main applications in a biotechnological approach aimed at agriculture and food chain-related areas. Moreover, the spectrum of opportunities and the extensive optimization platform for obtaining fungi compounds and metabolites are discussed. Finally, future perspectives regarding the insurgency of innovations and challenges on the broad rise of visionary solutions applied to the biotechnology context are provided.

Oil-Contaminated Soil Remediation with Biodegradation by Autochthonous Microorganisms and Phytoremediation by Maize (Zea mays)

Biological methods are currently the most commonly used methods for removing hazardous substances from land. This research work focuses on the remediation of oil-contaminated land. The biodegradation of aliphatic hydrocarbons and PAHs as a result of inoculation with biopreparations B1 and B2 was investigated. Biopreparation B1 was developed on the basis of autochthonous bacteria, consisting of strains Dietzia sp. IN118, Gordonia sp. IN101, Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus globerulus IN113 and Raoultella sp. IN109, whereas biopreparation B2 was enriched with fungi, such as Aspergillus sydowii, Aspergillus versicolor, Candida sp., Cladosporium halotolerans, Penicillium chrysogenum. As a result of biodegradation tests conducted under ex situ conditions for soil inoculated with biopreparation B1, the concentrations of TPH and PAH were reduced by 31.85% and 27.41%, respectively. Soil inoculation with biopreparation B2 turned out to be more effective, as a result of which the concentration of TPH was reduced by 41.67% and PAH by 34.73%. Another issue was the phytoremediation of the pre-treated G6-3B2 soil with the use of Zea mays. The tests were carried out in three systems (system 1-soil G6-3B2 + Zea mays; system 2-soil G6-3B2 + biopreparation B2 + Zea mays; system 3-soil G6-3B2 + biopreparation B2 with γ-PGA + Zea mays) for 6 months. The highest degree of TPH and PAH reduction was obtained in system 3, amounting to 65.35% and 60.80%, respectively. The lowest phytoremediation efficiency was recorded in the non-inoculated system 1, where the concentration of TPH was reduced by 22.80% and PAH by 18.48%. Toxicological tests carried out using PhytotoxkitTM, OstracodtoxkitTM and Microtox® Solid Phase tests confirmed the effectiveness of remediation procedures and showed a correlation between the concentration of petroleum hydrocarbons in the soil and its toxicity. The results obtained during the research indicate the great potential of bioremediation practices with the use of microbial biopreparations and Zea mays in the treatment of soils contaminated with petroleum hydrocarbons.

Pharmaceutical active compounds in sewage sludge: Degradation improvement and conversion into an organic amendment by bioaugmentation-composting processes

Around 143,000 chemicals find their fate in wastewater treatment plants in the European Union. Low efficiency on their removal at lab-based studies and even poorer performance at large scale experiments have been reported. Here, a coupled biological technology (bioaugmentation and composting) is proposed and proved for pharmaceutical active compounds degradation and toxicity reduction. The optimization was conducted through in situ inoculation of Penicillium oxalicum XD 3.1 and an enriched consortium (obtained from non-digested sewage sludge), into pilot scale piles of sewage sludge under real conditions. This bioaugmentation-composting system allowed a better performance of micropollutants degradation (21 % from the total pharmaceuticals detected at the beginning of the experiment) than a traditional composting process. Particularly, inoculation with P. oxalicum allowed the degradation of some recalcitrant compounds like carbamazepine, cotinine and methadone, and also produced better stabilization features in the mature compost (significant passivation of copper and zinc, higher macronutrients value, adequate physicochemical conditions for soil direct application and less toxic effect on germination) compared to the control and the enriched culture. These findings provide a feasible, alternative strategy to obtain a safer mature compost and a better removal of micropollutants performance at large scale.

Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.

New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.

Advanced bioremediation by an amalgamation of nanotechnology and modern artificial intelligence for efficient restoration of crude petroleum oil-contaminated sites: a prospective study

Crude petroleum oil spillage is becoming a global concern for environmental pollution and poses a severe threat to flora and fauna. Bioremediation is considered a clean, eco-friendly, and cost-effective process to achieve success among the several technologies adopted to mitigate fossil fuel pollution. However, due to the hydrophobic and recalcitrant nature of the oily components, they are not readily bioavailable to the biological components for the remediation process. In the last decade, nanoparticle-based restoration of oil-contaminated, owing to several attractive properties, has gained significant momentum. Thus, intertwining nano- and bioremediation can lead to a suitable technology termed 'nanobioremediation' expected to nullify bioremediation's drawbacks. Furthermore, artificial intelligence (AI), an advanced and sophisticated technique that utilizes digital brains or software to perform different tasks, may radically transfer the bioremediation process to develop an efficient, faster, robust, and more accurate method for rehabilitating oil-contaminated systems. The present review outlines the critical issues associated with the conventional bioremediation process. It analyses the significance of the nanobioremediation process in combination with AI to overcome such drawbacks of a traditional approach for efficiently remedying crude petroleum oil-contaminated sites.

Enhanced bioremediation performance of diesel-contaminated soil by immobilized composite fungi on rice husk biochar

In response to the low removal capacity and poor tolerance of fungi to diesel-contaminated soil, a novel immobilization system using biochar to enhance composite fungi was proposed. Rice husk biochar (RHB) and sodium alginate (SA) were used as immobilization matrices for composite fungi, and the adsorption system (CFI-RHB) and the encapsulation system (CFI-RHB/SA) were obtained. CFI-RHB/SA exhibited the highest diesel removal efficiency (64.10%) in high diesel-contaminated soil over a 60-day remediation period compared to the free composite fungi (42.70%) and CFI-RHB (49.13%). SEM demonstrated that the composite fungi were confirmed to be well attached to the matrix in both CFI-RHB and CFI-RHB/SA. FTIR analysis revealed the appearance of new vibration peaks in diesel-contaminated soil remediated by immobilized microorganisms, demonstrating changes in the molecular structure of diesel before and after degradation. Furthermore, CFI-RHB/SA maintains a stable removal efficiency (>60%) in higher concentrations of diesel-contaminated soil. High-throughput sequencing results indicated that Fusarium and Penicillium played a key role in the removal of diesel contaminants. Meanwhile, both dominant genera were negatively correlated with diesel concentration. The addition of exogenous fungi stimulated the enrichment of functional fungi. The insights gained from experiment and theory help to provide a new understanding of immobilization techniques of composite fungi and the evolution of fungal community structure.

Petroleum-Degrading Fungal Isolates for the Treatment of Soil Microcosms

The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms in aerobic conditions. The bioaugmentation processes were carried out using selected hydrocarbonoclastic fungal strains in mono or co-cultures. Results demonstrated the petroleum-degrading potential of six fungal isolates, namely KBR1 and KBR8 (indigenous) and KBR1-1, KB4, KB2 and LB3 (exogenous). Based on the molecular and phylogenetic analysis, KBR1 and KB8 were identified as Aspergillus niger [MW699896] and tubingensis [MW699895], while KBR1-1, KB4, KB2 and LB3 were affiliated with the genera Syncephalastrum sp. [MZ817958], Paecilomyces formosus [MW699897], Fusarium chlamydosporum [MZ817957] and Coniochaeta sp. [MW699893], respectively. The highest rate of TPH degradation was recorded in soil microcosm treatments (SMT) after 60 days by inoculation with Paecilomyces formosus 97 ± 2.54%, followed by bioaugmentation with the native strain Aspergillus niger (92 ± 1.83%) and then by the fungal consortium (84 ± 2.21%). The statistical analysis of the results showed significant differences.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Use of wood and cork in biofilters for the simultaneous removal of nitrates and pesticides from groundwater

About 13% and 7% of monitored groundwater stations in Europe exceed the permitted levels of nitrates (50 mg NO₃^- L^-1) or pesticides (0.1 μg L^-1), respectively. Although slow sand filtration can remove nitrates via denitrification when oxygen is limited, it requires an organic carbon source. The present study evaluates the performance of the use of wood pellets and granulated cork as carbon sources in bench-scale biofilters operated under water-saturated and water-unsaturated conditions for more than 400 days. The biofilters were monitored for nitrate (200 mg L^-1) and pesticide (mecoprop, diuron, atrazine, and bromacil, each at a concentration of 5 μg L^-1) attenuation, as well as for the formation of nitrite and pesticide transformation products. Microbiological characterization of each biofilter was also performed. The water-saturated wood biofilter achieved the best nitrate removal (>99%), while the cork biofilters lost all denitrification power over time (from 38% to no removal). The unsaturated biofilter columns were not effective for removing nitrates (20-30% removal). As for pesticides, all the biofilters achieved high removal rates of mecoprop and diuron (>99% and >75%, respectively). Atrazine removal was better in the wood-pellet biofilters than the cork ones (68-96% vs. 31-38%). Bromacil was only removed in the water-unsaturated cork biofilter (67%). However, a bromacil transformation product was formed there. The water-saturated wood biofilter contained the highest number of denitrifying microorganisms, with Methyloversatilis as the characteristic genus. Microbial composition could explain the high removal of pesticides and nitrates achieved in the wood-pellet biofilter. Overall, the results indicate that wood-pellet biofilters operated under water-saturated conditions are a good solution for treating groundwater contaminated with nitrates and pesticides.

Enhanced Bioremediation of Aged Polycyclic Aromatic Hydrocarbons in Soil Using Immobilized Microbial Consortia Combined with Strengthening Remediation Strategies

Microbial biodegradation is considered as one of the most effective strategies for the remediation of soil contaminated with polycyclic aromatic hydrocarbons (PAHs). To improve the degradation efficiency of PAHs, PAH-degrading consortia combined with strengthening remediation strategies was used in this study. The PAH biodegrading performance of seven bacterial consortia constructed by different ratios of Mycobacterium gilvum MI, Mycobacterium sp. ZL7 and Rhodococcus rhodochrous Q3 was evaluated in an aqueous system containing phenanthrene, pyrene, benzo[a]pyrene and benzo[b]fluoranthene. Bacterial consortium H6 (Q3:ZL7:MI = 1:2:2) performed a high degrading efficiency of 59% in 8 days. The H6 was subsequently screened to explore its potential ability and performance to degrade aged PAHs in soils from a coking plant and the effects of strengthening strategies on the aged PAH degradation, including the addition of glucose or sodium dodecyl benzene sulfonate (SDBS) individually or as a mixture along immobilization of the inoculant on biochar. The highest degradation efficiencies, which were 15% and 60% for low-molecular-weight (LMW) PAHs and high-molecular-weight (HMW) PAHs, respectively, were observed in the treatment using immobilized microbial consortium H6 combined with the addition of glucose and SDBS after 24 days incubation. This study provides new insights and guidance for future remediation of aged PAH contaminated soils.

Potential Utilization of Bacterial Consortium of Symbionts Marine Sponges in Removing Polyaromatic Hydrocarbons and Heavy Metals, Review

Toxic materials in waste generally contain several components of the global trending pollutant category, especially PAHs and heavy metals. Bioremediation technology for waste management that utilizes microorganisms (bacteria) has not been fully capable of breaking down these toxic materials into simple and environmentally friendly chemical products. This review paper examines the potential application of a consortium of marine sponge symbionts with high performance and efficiency in removing PAHs and heavy metal contaminants. The method was carried out through a review of several related research articles by the author and published by other researchers. The results of the study conclude that the development of global trending pollutant (GTP) bioremediation technology could be carried out to increase the efficiency of remediation. Several types of marine sponge symbiont bacteria, hydrocarbonoclastic (R-1), metalloclastic (R-2), and metallo-hydro-carbonoclastic (R-3), have the potential to be applied to improve waste removal performance. A consortium of crystalline bacterial preparations is required to mobilize into GTP-exposed sites rapidly. Bacterial symbionts of marine sponges can be traced mainly to sea sponges, whose body surface is covered with mucus.

Fungal assisted bio-treatment of environmental pollutants with comprehensive emphasis on noxious heavy metals: Recent updates

In the present time of speedy developments and industrialization, heavy metals are being uncovered in aquatic environment and soil via refining, electroplating, processing, mining, metallurgical activities, dyeing and other several metallic and metal based industrial and synthetic activities. Heavy metals like lead (Pb), mercury (Hg), cadmium (Cd), arsenic (As), Zinc (Zn), Cobalt (Co), Iron (Fe), and many other are considered as seriously noxious and toxic for the aquatic environment, human, and other aquatic lives and have damaging influences. Such heavy metals, which are very tough to be degraded, can be managed by reducing their potential through various processes like removal, precipitation, oxidation-reduction, bio-sorption, recovery, bioaccumulation, bio-mineralization etc. Microbes are known as talented bio-agents for the heavy metals detoxification process and fungi are one of the cherished bio-sources that show noteworthy aptitude of heavy metal sorption and metal tolerance. Thus, the main objective of the authors was to come with a comprehensive review having methodological insights on the novel and recent results in the field of mycoremediation of heavy metals. This review significantly assesses the potential talent of fungi in heavy metal detoxification and thus, in environmental restoration. Many reported works, methodologies and mechanistic sights have been evaluated to explore the fungal-assisted heavy metal remediation. Herein, a compact and effectual discussion on the recent mycoremediation studies of organic pollutants like dyes, petroleum, pesticides, insecticides, herbicides, and pharmaceutical wastes have also been presented.

Potential of bioaugmentation of heavy metal contaminated soils in the Zambian Copperbelt using autochthonous filamentous fungi

There is great potential to remediate heavy metal contaminated environments through bioaugmentation with filamentous fungi. However, these fungi have been poorly investigated in most developing countries, such as Zambia. Therefore, the present study aimed at isolating indigenous filamentous fungi from heavy metal contaminated soil and to explore their potential for use in bioaugmentation. The conventional streak plate method was used to isolate fungi from heavy metal-contaminated soil. Filamentous fungal isolates were identified using morphological and molecular techniques. The radial growth diameter technique was used to evaluate heavy metal tolerance of the fungi. The most abundant and highly tolerant fungi, identified as Aspergillus transmontanensis, Cladosporium cladosporioides, and Geotrichum candidum species, were used to bioremediate heavy metal contaminated soil samples with uncontaminated soil sample being employed as a control. A maximum tolerance index (TI) between 0.7 and 11.0 was observed for A. transmontanensis, and G. candidum while C. cladosporioides displayed the TI between 0.2 and 1.2 in the presence of 1,000 ppm of Cu, Co, Fe, Mn, and Zn. The interspecific interaction was analyzed to determine the compatibility among isolates. Our results showed mutual intermingling between the three evaluated fungal species, which confirms their common influence in biomineralization of heavy metals in contaminated soils. Maximum bio-removal capacities after 90 days were 72% for Cu, 99.8% for Co, 60.6% for Fe, 82.2% for Mn, and 100% for both Pb and Zn. This study has demonstrated the potential of highly resistant autochthonous fungal isolates to remediate the heavy metal contamination problem.

Accelerated PAH Transformation in the Presence of Dye Industry Landfill Leachate Combined with Fungal Membrane Lipid Changes

The ascomycete fungus Nectriella pironii, previously isolated from soil continuously contaminated by dye industry waste, was used for the biodegradation of phenanthrene (PHE), benz[a]anthracene (B[a]A), and benz[a]pyrene (B[a]P). The degradation of polycyclic aromatic hydrocarbons (PAHs) by N. pironii was accelerated in the presence of landfill leachate (LL) collected from the area of fungus isolation. The rate of cometabolic elimination of PHE and B[a]P in the presence of LL was, respectively, 75% and 94% higher than in its absence. LC-MS/MS analysis revealed that PAHs were converted to less-toxic derivatives. The parallel lipidomic study showed changes in membrane lipids, including a significant increase in the content of phosphatidylcholine (PC) (almost double) and saturated phospholipid fatty acids (PLFAs) and a simultaneous reduction (twofold) in the content of phosphatidylethanolamine (PE) and unsaturated PLFAs, which may have promoted the fungus to PHE + LL adaptation. In the presence of PHE, an intense lipid peroxidation (fivefold) was observed, confirming the stabilization of the cell membrane and its extended integrity. Determining the course of elimination and adaptation to harmful pollutants is essential for the design of efficient bioremediation systems in the future.

Current and emerging trends in bioaugmentation of organic contaminated soils: A review

Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.

Green synthesis of biogenetic Te(0) nanoparticles by high tellurite tolerance fungus Mortierella sp. AB1 with antibacterial activity

Tellurite [Te(IV)] is a high-toxicity metalloid. In this study, a fungus with high Te(IV) resistance was isolated. Strain AB1 could efficiently reduce highly toxic Te(IV) to less toxic Te(0). The reduced products formed rod-shaped biogenetic Te(0) nanoparticles (Bio-TeNPs) intracellularly. Further TEM-element mapping, FTIR, and XPS analysis showed that the extracted Bio-TeNPs ranged from 100 to 500 nm and consisted of Te(0), proteins, lipids, aromatic compounds, and carbohydrates. Moreover, Bio-TeNPs exhibited excellent antibacterial ability against Shigella dysenteriae, Escherichia coli, Enterobacter sakazakii, and Salmonella typhimurium according to inhibition zone tests. Further growth and live/dead staining experiments showed that E. coli and S. typhimurium were significantly inhibited by Bio-TeNPs, and cells were broken or shriveled after treatment with Bio-TeNPs based on SEM observation. Additionally, the antioxidant and cytotoxicity tests showed that the Bio-TeNPs exhibited excellent antioxidant capacity with no cytotoxicity. All these results suggested that strain AB1 showed great potential in bioremediation and Bio-TeNPs were excellent antibacterial nanomaterials with no cytotoxicity.

Interaction between indigenous hydrocarbon-degrading bacteria in reconstituted mixtures for remediation of weathered oil in soil

It has been demonstrated that biostimulation is necessary to investigate the interactions between indigenous bacteria and establish an approach for the bioremediation of soils contaminated with weathered oil. This was achieved by adjusting the carbon (C)/nitrogen (N)/phosphorus (P) ratio to 100/10/1 combined with the application of 0.8 mL/kg Tween-80. In addition, three indigenous bacteria isolated from the same soil were introduced solely or combined concomitantly with stimulation. Removal of n-alkanes and the ratios of n-heptadecane to pristane and n-octadecane to phytane were taken to indicate their biodegradation performance over a period of 16 weeks. One strain of Pseudomonas aeruginosa D7S1 improved the efficiency of the process of stimulation. However, another Pseudomonas aeruginosa, D5D1, inhibited the overall process when combined with other bacteria. One strain of Bacillus licheniformis D1D2 did not affect the process significantly. The Fourier transform infrared analysis of the residual hydrocarbons supported the conclusions pertaining to the biodegradation processes when probing the modifications in densities and stretching. The indigenous bacteria cannot mutually benefit from their metabolisms for bioremediation if augmented artificially. However, the strain Pseudomonas. aeruginosa D7S1 was able to perform better alone than in a consortium of indigenous bacteria.

Assessment of a novel microalgae-cork based technology for removing antibiotics, pesticides and nitrates from groundwater

Groundwater pollution has increased in recent years due to the intensification of agricultural and livestock activities. This results in a significant reduction in available freshwater resources. Here, we have studied the long term assessment of a green technology (1-4 L/day) based on a photobioreactor (PBR) containing immobilised microalgae-bacteria in polyurethane foam (PF) followed by a cork filter (CF) for removing nitrates, pesticides (atrazine and bromacil), and antibiotics (sulfamethoxazole and sulfacetamide) from groundwater. The prototype was moderately effective for removing nitrates (58%) at an HRT of 8 days, while its efficiency decreased at a HRT of 4 and 2 days (<20% removal). The combined use of PBR-CF enabled antibiotics and pesticides to be attenuated by up to 95% at an HRT of 8 days, but their attenuation decreased with shorter HRT, with pesticides being the compounds most affected (reducing from 97 to 98% at an HRT of 8 days to 23-45% at an HRT of 2 days). Pesticide transformation products were identified after the CF, supporting biodegradation as the main attenuation process. A gene-based metataxonomic assessment linked the attenuation of micropollutants to the presence of specific pesticide biodegradation species (e.g. genus Phenylobacterium, Sphingomonadaceae, and Caulobacteraceae). Therefore, the results highlighted the potential use of microalgae and cork to treat polluted groundwater.

Organic wastes bioremediation and its changing prospects

Increasing inappropriate anthropogenic activities and industrialization have resulted in severe environmental pollution worldwide. Their effective treatment is vital for general health concerns. Depending on the characteristics of pollutants, the severity of pollution may differ. For sustainable treatment of polluted environments, bioremediation is accepted as the most efficient, economical, and environmentally friendly method hence largely preferred. However, every bioremediation technique has its own unique advantages and limitations due to its defined applications criteria. In bioremediation, microorganisms play a decisive role in detoxification by degrading, mineralizing and accumulating various forms of harmful and biodegradable pollutants from the surroundings and transforming them into less lethal forms. Bioremediation is performed ex-situ or in-situ, based on location of polluted site as well as characteristics, type and strength of the pollutants. Furthermore, the most popular methodologies for bioremediation include bioaugmentation, biostimulation, bioattenuation among others which depend on the prevailing environmental factors into the microbial system. Implementing them appropriately and effectively under ex-situ or in-situ method is extremely important not only for obtaining efficient treatment but also for the best economic, environmental, and social impacts. Therefore, this review aims to analyze various bioremediation methods for organic pollutants remediation from soil/sediments and wastewater, their strength, limitation, and insights for the selection of appropriate bioremediation techniques based on nature, types, degree, and location of the pollution. The novelty aspect of the article is to give updates on several key supporting technologies which have recently emerged and exhibited great potential to enhance the present bioremediation efficiency such as nanobubble, engineered biochar, mixotrophic microalgae, nanotechnology etc. Moreover, amalgamation of these technologies with existing bioremediation facilities are significantly changing the scenario and scope of environmental remediation towards sustainable bioremediation.

Petroleum-contaminated soil: environmental occurrence and remediation strategies

Soil is an environmental matrix that carries life for all living things. With the rise of human activities and the acceleration of population, the soil has been exposed in part to pollution by the discharge of various xenobiotics and persistent pollutants into it. The disposal of toxic substances such as polycyclic aromatic hydrocarbons (PAHs) alters soil properties, affects microbial biodiversity, and damages objects. Considering the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and clean-up of PAH-polluted sites represents an important technological and environmental challenge for sustainable growth and development. Though several treatment methods to remediate PAH-polluted soils exist, interesting bacteria, fungi, and their enzymes receive considerable attention. The aim of the present review is to discuss PAHs' impact on soil properties. Also, this review illustrates physicochemical and biological remediation strategies for treating PAH-contaminated soil. The degradation pathways and contributing factors of microbial PAH-degradation are elucidated. This review also assesses the use of conventional microbial remediation compared to the application of genetically engineered microorganisms (GEM) that can provide a cost-effective and eco-friendly PAH-bioremediation strategy.

Investigation of Global Trends of Pollutants in Marine Ecosystems around Barrang Caddi Island, Spermonde Archipelago Cluster: An Ecological Approach

High-quality marine ecosystems are free from global trending pollutants' (GTP) contaminants. Accuracy and caution are needed during the exploitation of marine resources during marine tourism to prevent future ecological hazards that cause chain effects on aquatic ecosystems and humans. This article identifies exposure to GTP: microplastic (MP); polycyclic aromatic hydrocarbons (PAH); pesticide residue (PR); heavy metal (HM); and medical waste (MW), in marine ecosystems in the marine tourism area (MTA) area and Barrang Caddi Island (BCI) waters. A combination of qualitative and quantitative analysis methods were used with analytical instruments and mathematical formulas. The search results show the average total abundance of MPs in seawater (5.47 units/m3) and fish samples (7.03 units/m3), as well as in the sediment and sponge samples (8.18 units/m3) and (8.32 units/m3). Based on an analysis of the polymer structure, it was identified that the dominant light group was MPs: polyethylene (PE); polypropylene (PP); polystyrene (PS); followed by polyamide-nylon (PA); and polycarbonate (PC). Several PAH pollutants were identified in the samples. In particular, naphthalene (NL) types were the most common pollutants in all of the samples, followed by pyrene (PN), and azulene (AZ). Pb+2 and Cu+2 pollutants around BCI were successfully calculated, showing average concentrations in seawater of 0.164 ± 0.0002 mg/L and 0.293 ± 0.0007 mg/L, respectively, while in fish, the concentrations were 1.811 ± 0.0002 µg/g and 4.372 ± 0.0003 µg/g, respectively. Based on these findings, the BCI area is not recommended as a marine tourism destination.

Surfactant-aided mycoremediation of soil contaminated with polycyclic aromatic hydrocarbons

Remediation of persistent polycyclic aromatic hydrocarbons (PAHs) contaminated soil has become a major challenge in recent years. Further, conventional application of bioaugmentation strategies for PAHs remediation require continuous supply of microbial specific nutrients, which makes these processes less feasible. Hence, the present study focused on PAHs remediation using surfactants along with wood assisted fungal system in a microcosm set up. In this study, in absence of surfactants, a saturation in PAHs degradation was noted in bioaugmentation with wood assisted fungal system (BAW) with 61 ± 1.25% degradation, followed by bioaugmentation with free fungi system (BAF) (54 ± 0.46%). However, with addition of 1500 mg/L of surface-active compounds (SAC), a maximum PAHs degradation in BAW (100%) and BAF (86 ± 1.30%) strategies were noted on 21st day. Irrespective of the strategies, presence of SAC and rhamnolipids enhanced PAHs degradation by increasing the enzymes production in Trametes hirsuta when compared to Triton x-100 and sodium dodecyl sulphate (SDS). Among the detected PAHs, 100% degradation within 17 days was noted for naphthalene and acenaphthene in SAC-supplemented BAW system. Further, ecotoxicity analysis established showed the LC50 of sediment soil at 26.5 ± 0.24%, which was reduced by an average of 71% after soil remediation. Hence, the current microcosm system proved that the application of SAC with BAW enhanced the PAHs remediation rate, which supports its application in real time soil remediation.

Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives

Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.

Efficiency of Penicillium canescens in Dissipating PAH in Industrial Aged Contaminated Soil Microcosms and Its Impact on Soil Organic Matter and Ecotoxicity

The filamentous fungus Penicillium canescens, isolated from oil-polluted soil, was evaluated for its ability to dissipate high-molecular-weight polycyclic aromatic hydrocarbons (PAH). The study was conducted in a microcosm containing 180 g of historical PAH-contaminated soil under non-sterile conditions with two incubation temperatures (14 °C and 18 °C) on a 12-h cycle. The experiment was conducted over 8 months, with four experimental conditions created by varying the volumes of the bulking agent and vegetable oil (olive oil) and the time of addition of these compounds. The PAH dissipation performance of the fungal augmentation treatment was compared with that achieved with a biostimulated soil (bulking agent and vegetable oil) and with the untreated soil as control. The greatest PAH dissipation was obtained with P. canescens bioaugmentation (35.71% ± 1.73), with 13 of the 16 US EPA PAH significantly dissipated, at rates above 18%, and particularly high-molecular-weight PAH, composed of more than three fused aromatic rings. Nematode toxicity tests indicated a significant decrease in the toxicity of soil bioaugmented by this fungus. Fulvic and humic contents were significantly increased by this treatment. All these results suggest that bioaugmentation with P. canescens can be used to restore soils with long-term PAH contamination.

Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO₂, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.

Innovative mycoremediation technique for treating unsterilized PCDD/F-contaminated field soil and the exploration of chlorinated metabolites

Mycoremediation of unsterilized PCDD/F-contaminated field soil was successfully demonstrated by solid-state fermentation coupled with Pleurotus pulmonarius utilizing a patented incubation approach. The experiments were carried out in four setups with two as controls. The contaminated soil was homogenously mixed with solid inocula, 1:0.5 dry w/w, resulting in an initial concentration of 4432 ± 623 ng WHO-TEQ kg^-1. After a 30-day incubation under controlled conditions, the overall removal (approx. 60%) was non-specific. The removal was attributed to degradation by extracellular ligninolytic enzymes and uptake into the fruiting tissue (~110 ng WHO-TEQ kg^-1 of mushroom). Furthermore, less recalcitrant chlorinated metabolites were found, implying ether bond cleavage and dechlorination happened during the mycoremediation. These metabolites resulted from the complex interaction between P. pulmonarius and the indigenous microbes from the unsterilized soil. This study provides a new step toward scaling up this mycoremediation technique to treat unsterilized PCDD/F-contaminated field soil.