Evaluation of pyrene and tetracosane degradation by mixed-cultures of fungi and bacteria

Bioremediation of naphthenic acid by Bacillus subtilis: Degradation kinetics and pathway elucidation

Naphthenic acids, toxic and persistent carboxylic acids found in petroleum contaminated water, pose a significant environmental challenge, but bioremediation offers a promising and cost-effective solution for their treatment. The present study illustrates the ability of Bacillus subtilis to degrade commercial naphthenic acid (100 mg/L) in aerobic and microaerobic settings under optimized conditions (temperature 36 °C, pH 6.0, and salinity 0.5 %). The degradation was confirmed by 47.61 ± 3.609 % reduction in total organic carbon levels within 144 h, indicating the microbial potential to mineralize organic naphthenic acid in aqueous medium as a sole carbon source. Naphthenic acids, being structurally complex and comprising a diverse array of carboxylic acids, were further studied using two representative models, hexanoic acid (linear) and benzoic acid (aromatic). These representative acids were selected to investigate the degradation kinetics and to elucidate the underlying degradation mechanism. The growth kinetics of B. subtilis on hexanoic acid and benzoic acid followed the Monod growth model, with maximum specific growth rates (μmax) of 0.17344 ± 0.004 and 0.15088 ± 0.006 day-1 respectively. The biodegradation kinetics followed a non-linear first-order rate model, with rate constants (k) of 0.43 ± 0.084 h-1 for hexanoic acid and 0.12 ± 0.02 h-1 for benzoic acid. Corresponding half-lives (t1/2) were determined as 13.37 h for hexanoic acid and 29.52 h for benzoic acid, demonstrating a faster degradation rate for hexanoic acid compared to benzoic acid. GC-MS analysis elucidated the degradation pathway, catechol and muconic acid were identified as the key intermediates, which suggest a potential metabolic breakdown. Consequently, it demonstrates the potential of Bacillus subtilis for the effective removal of naphthenic acids from polluted wastewater.

One-pot bioconversion of fungal lipid to mycodiesel: a sustainable approach

The conversion of filamentous fungus-based feedstock into Biodiesel holds potential as a sustainable and eco-conscious method for producing alternative liquid fuels. This study examined the comparison of individual Fatty Acid Methyl Esters (FAME) of Aspergillus niger and Curvularia lunata with the consortium of both filamentous fungal cocktail Fatty acid methyl esters (cFAME), following a transesterification process that turned the fungal lipids into myco-based biodiesel productions. cFAME weighs 23.89 g and accumulates to 20.43 g of lipid yield, with 86% of cellular lipids; in contrast, A. niger weighs 12.65 g and pile up 9.5 g of lipid yield, with 75% of cellular lipid, also C. lunata exhibits 8.35 g of dry weight with 4.89 g of lipid concentration, with 59% of cellular lipids. A. niger was known to contain C16-C18 saturated and unsaturated fatty acids possess LAME (C18:2), OAFA (C18:1), and PAME (C16:0) were shown in high percentages accounted for 86.6% in A. niger. The results showed that PUFA was predominant over MUFA and SFA. C. lunata chiefly produces C16 and C18 fatty acids, which are considered favorable for combustion properties with oleic acid (C18:1), linoleic acid (C18:2), palmitic acid (C16:0), and stearic acid (C18:0), on the comparison. However, the FAME profile of C. lunata occupies only 39.07% of the biodiesel quality. Pentadecanoic acid, palmitic acid, palmitoleic acid, Oleic acid, Linolenic acid, Linoleic acis, and Hexanoic acid with the carbon range of C6:0 - C18:3 were observed in cFAME. Based on the biodiesel yield, cFAME scored 20.55%, whereas A. niger with 11.05 and C.lunata 2.45%, respectively. The presence of methyl esters containing various long-chain fatty acids indicates very effective biodiesel assets, as confirmed by GC-MS analysis, which evidenced ignition efficiency, among others. cFAMEs were impacted by high ignition efficiency with > 4 min. Consortium strategies seize attention in different dimensions and have been confirmed by their upregulation in their fatty acid profiles; in the future, the combination of high lipid holders among the fungal kingdom can be an alternative in myco-based biodiesel production.

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.

A comprehensive assessment of heavy metals, VOCs and petroleum hydrocarbon in different soil layers and groundwater at an abandoned Al/Cu industrial site

Compound pollution at industrial sites impedes urban development, especially when there is a lack of understanding about the spatial variations of internal pollution in industrial areas producing light-weight materials. In this study, spatial distribution and ecological risks of potentially toxic elements (PTEs), volatile organic compounds (VOCs), and petroleum hydrocarbons (C10-40) in the soil and groundwater of an Al/Cu (aluminum/copper) industrial site have been analyzed comprehensively. Results revealed the progressive clustering of pollutants in different soil layers, which indicated varying levels of penetration and migration of pollutants from the surface downward. Furthermore, severity of pollution varied according to pollutant type, with Cu (5-10,228 mg kg-1) often exceeding the background levels significantly (>40). Cd (0.03-2.60 mg kg-1) and Hg (0.01-3.73 mg kg-1) were found at elevated concentrations in deeper soil layers, suggesting distinct variations of PTEs across different soil depths. Among the more hazardous VOCS, polychlorinated biphenyls (1.80-234 μg kg-1) were particularly prevalent in the deeper layers of soil. Petroleum hydrocarbons (C10-40) were widely detected (6-582 mg kg-1), showing significant migration potential from surface to deep soil. These findings suggest that prolonged industrial activities lead to deep-seated accumulation of pollutants, which also impacts the groundwater, contributing to long-term dispersion of contaminants. Furthermore, multivariate statistical analysis indicated certain positive correlations among the distribution of Cu, Pb and petroleum hydrocarbons, indicating possible coupling of these pollutants. Severe Cu pollution caused an ecological risk in the surface soil layer (covering >20 % area of high pollution site, contributing >40 % ecological risk). While the Hg and Cd posed significant risks in the deeper soil layers, showing higher risk coefficients and mobility. The study provides crucial insights into the transformation of urban areas with a history of industrial uses into community spaces and highlights the risks posed by the remaining pollutants.

Enhancing bacterial biodegradation of n-hexane by utilizing the adsorption capacity of non-degrading fungi

Biodegradation of hydrophobic volatile organic compounds (VOCs) such as n-hexane is limited by their poor accessibility. Constructing fungal-bacterial degradation alliances is an effective approach, but the role of those fungi without the capability to degrade VOCs may have been overlooked. In this study, a non-n-hexane-degrading fungus, Fusarium keratoplasticum FK, was utilized to enhance n-hexane degradation by the bacterium Mycobacterium neworleansense WCJ. It was shown that strain WCJ removed 64.84% of n-hexane (at a concentration of 648.20 mg L-1) over 3 d, and 84.04% after introducing strain FK. Microbial growth kinetic studies revealed that the growth of strain WCJ was also promoted. Through a stepwise adsorption-degradation experiment combined with qPCR technology, it was found that the strain WCJ could utilize the n-hexane pre-adsorbed by strain FK, with an increase in copy number from 108.2662 to 108.7731. Therefore, the non-degrading fungi can improved the accessibility of n-hexane by providing n-hexane adsorbed by the mycelium to the degrading bacteria. In addition, the adsorption tests and characterization of the fungal samples before and after Soxhlet extraction indicated that the adsorption of n-hexane on strain FK conformed to Lagergren's pseudo-second-order kinetics and Freundlich adsorption isotherms, and was correlated with the presence of lipids and nonpolar groups. This study emphasizes the potential role of non-degrading fungi in bioremediation and proposes a viable strategy to enhance the bacterial degradation of hydrophobic VOCs.

Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches

The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions.

Polycyclic aromatic hydrocarbon: underpinning the contribution of specialist microbial species to contaminant mitigation in the soil

The persistence of PAHs poses a significant challenge for conventional remediation approaches, necessitating the exploration of alternative, sustainable strategies for their mitigation. This review underscores the vital role of specialized microbial species (nitrogen-fixing, phosphate-solubilizing, and biosurfactant-producing bacteria) in tackling the environmental impact of polycyclic aromatic hydrocarbons (PAHs). These resistant compounds demand innovative remediation strategies. The study explores microbial metabolic capabilities for converting complex PAHs into less harmful byproducts, ensuring sustainable mitigation. Synthesizing literature from 2016 to 2023, it covers PAH characteristics, sources, and associated risks. Degradation mechanisms by bacteria and fungi, key species, and enzymatic processes are examined. Nitrogen-fixing and phosphate-solubilizing bacteria contributions in symbiotic relationships with plants are highlighted. Biosurfactant-producing bacteria enhance PAH solubility, expanding microbial accessibility for degradation. Cutting-edge trends in omics technologies, synthetic biology, genetic engineering, and nano-remediation offer promising avenues. Recommendations emphasize genetic regulation, field-scale studies, sustainability assessments, interdisciplinary collaboration, and knowledge dissemination. These insights pave the way for innovative, sustainable PAH-contaminated environment restoration.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Simultaneous bioreduction of tellurite and selenite by Yarrowia lipolytica, Trichosporon cutaneum, and their co-culture along with characterization of biosynthesized Te-Se nanoparticles

BACKGROUND

Natural and anthropogenic activities, such as weathering of rocks and industrial processes, result in the release of toxic oxyanions such as selenium (Se) and tellurium (Te) into the environment. Due to the high toxicity of these compounds, their removal from the environment is vital.

RESULTS

In this study, two yeast strains, Yarrowia lipolytica and Trichosporon cutaneum, were selected as the superior strains for the bioremediation of tellurium and selenium. The reduction analyses showed that exposure to selenite induced more detrimental effects on the strains compared to tellurite. In addition, co-reduction of pollutants displayed almost the same results in selenite reduction and more than ~ 20% higher tellurite reduction in 50 h, which shows that selenite triggered higher tellurite reduction in both strains. The selenite and tellurite kinetics of removal were consistent with the first-order model because of their inhibitory behavior. The result of several characterization experiments, such as FE-SEM (Field emission scanning electron microscopy), dynamic light scattering (DLS), Fourier-transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD), and dispersive X-ray (EDX) on Te-Se nanoparticles (NPs) revealed that the separated Te-Se NPs were needle-like, spherical, and amorphous, consisted of Te-Se NPs ranging from 25 to 171 nm in size, and their surface was covered with different biomolecules.

CONCLUSIONS

Remarkably, this work shows, for the first time, the simultaneous bioreduction of tellurite and selenite and the production of Te-Se NPs using yeast strains, indicating their potential in this area, which may be applied to the nanotechnology industry and environmental remediation.

Molecular advances in mycoremediation of polycyclic aromatic hydrocarbons: Exploring fungal bacterial interactions

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous high global concern environmental pollutants and tend to bioaccumulate due to hydrophobic properties. These xenobiotics, having variable concentrations along different matrices, gradually undergo various physical, chemical, and biological transformation processes. Myco-remediation aids accelerated degradation by effectively transforming complex ring structures to oxidized/hydroxylated intermediates, which can further funnel to bacterial degradation pathways. Exploitation of such complementing fungal-bacterial enzymatic activity can overcome certain limitations of incomplete bioremediation process. Furthermore, high-throughput molecular methods can be employed to unveil community structure, taxon abundance, coexisting community interactions, and metabolic pathways under stressed conditions. The present review critically discusses the role of different fungal phyla in PAHs biotransformation and application of fungal-bacterial cocultures for enhanced mineralization. Moreover, recent advances in bioassays for PAH residue detection, monitoring, developing xenobiotics stress-tolerant strains, and application of fungal catabolic enzymes are highlighted. Application of next-generation sequencing methods to reveal complex ecological networks based on microbial community interactions and data analysis bias in performing such studies is further discussed in detail. Conclusively, the review underscores the application of mixed-culture approach by critically highlighting in situ fungal-bacterial community nexus and its role in complete mineralization of PAHs for the management of contaminated sites.

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.

Simultaneous bioremediation of phenol and tellurite by Lysinibacillus sp. EBL303 and characterization of biosynthesized Te nanoparticles

Aromatic compounds and metalloid oxyanions are abundant in the environment due to natural resources and industrial wastes. The high toxicity of phenol and tellurite poses a significant threat to all forms of life. A halotolerant bacterium was isolated and identified as Lysinibacillus sp. EBL303. The remediation analysis shows that 500 mg/L phenol and 0.5 mM tellurite can be remediated entirely in separate cultures within 74 and 56 h, respectively. In addition, co-remediation of pollutants resulted in the same phenol degradation and 27% less tellurite reduction within 98 h. Since phenol and tellurite exhibited inhibitory behavior, their removal kinetics fitted well with the first-order model. In the characterization of biosynthesized tellurium nanoparticles (TeNPs), transmission electron microscopy, dynamic light scattering, FE-SEM, and dispersive X-ray (EDX) showed that the separated intracellular TeNPs were spherical and consisted of only tellurium with 22-148 nm in size. Additionally, investigations using X-ray diffraction and Fourier-transform infrared spectroscopy revealed proteins and lipids covering the surface of these amorphous TeNPs. Remarkably, this study is the first report to demonstrate the simultaneous bioremediation of phenol and tellurite and the biosynthesis of TeNPs, indicating the potential of Lysinibacillus sp. EBL303 in this matter, which can be applied to environmental remediation and the nanotechnology industry.

Biodegradation of high molecular weight hydrocarbons under saline condition by halotolerant Bacillus subtilis and its mixed cultures with Pseudomonas species

Biodegradation of high-molecular-weight petroleum hydrocarbons in saline conditions appears to be complicated and requires further investigation. This study used heavy crude oil to enrich petroleum-degrading bacteria from oil-contaminated saline soils. Strain HG 01, with 100% sequence similarity to Bacillus subtilis, grew at a wide range of salinities and degraded 55.5 and 77.2% of 500 mg/l pyrene and 500 mg/l tetracosane, respectively, at 5% w/v NaCl. Additionally, a mixed-culture of HG 01 with Pseudomonas putida and Pseudomonas aeruginosa, named TMC, increased the yield of pyrene, and tetracosane degradation by about 20%. Replacing minimal medium with treated seawater (C/N/P adjusted to 100/10/1) enabled TMC to degrade more than 99% of pyrene and tetracosane, but TMC had lesser degradation in untreated seawater than in minimal medium. Also, the degradation kinetics of pyrene and tetracosane were fitted to a first-order model. Compared to B. subtilis, TMC increased pyrene and tetracosane's removal rate constant (K₁) from 0.063 and 0.110 per day to 0.123 and 0.246 per day. TMC also increased the maximum specific growth rate of B. subtilis, P. putida, and P. aeruginosa, respectively, 45% higher in pyrene, 24.5% in tetracosane, and 123.4% and 95.4% higher in pyrene and tetracosane.

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.