Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures

Biodegradation of Naphthalene Using Biosurfactant Producing Fusarium proliferatum WC416 Isolated from Refinery Effluent

Naphthalene is one of the priority pollutants in the environment which can effectively managed through bioremediation approach. Here fungal remediation of PAHs may be cost-effective technology. In present research study, biodegradation of naphthalene at varying concentrations in laboratory scale was investigated using Fusarium proliferatum WC416 isolated from refinery effluent. Degradation of naphthalene was computed by high-performance liquid chromatography (HPLC) and gas chromatography -mass spectroscopy (GC-MS). The results show that Fusarium proliferatum WC416 has effectively degraded the naphthalene to salicylamide and salicylic acid. The highest degradation achieved was 83% for the concentration of 100 ppm followed 74% and 63% for the concentration of 250 ppm and 500 ppm respectively. The intermediates confirmed by GC-MS were salicylic acid (m/z identification 138) and salicylamide (m/z identification 137). During the study, fungal growth, COD, pH, and surface tension have been monitored, which show the continuous variation that indicates progressive biodegradation of naphthalene. The qualitative assessment of extracellular enzymes shows positive activity for lipase, manganese peroxidase, and laccase. The present study also assessed the biosurfactant production by fungus which was characterized as sophorolipid in nature. The study suggests that Fusarium proliferatum WC416 would be an efficient degrader of naphthalene for environmental clean-up.

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.

Harnessing fungal bio-electricity: a promising path to a cleaner environment

Integrating fungi into fuel cell systems presents a promising opportunity to address environmental pollution while simultaneously generating energy. This review explores the innovative concept of constructing wetlands as fuel cells for pollutant degradation, offering a practical and eco-friendly solution to pollution challenges. Fungi possess unique capabilities in producing power, fuel, and electricity through metabolic processes, drawing significant interest for applications in remediation and degradation. Limited data exist on fungi's ability to generate electricity during catalytic reactions involving various enzymes, especially while remediating pollutants. Certain species, such as Trametes versicolor, Ganoderma lucidum, Galactomyces reessii, Aspergillus spp., Kluyveromyce smarxianus, and Hansenula anomala, have been reported to generate electricity at 1200 mW/m3, 207 mW/m2, 1,163 mW/m3, 438 mW/m3, 850,000 mW/m3, and 2,900 mW/m3, respectively. Despite the eco-friendly potential compared to conventional methods, fungi's role remains largely unexplored. This review delves into fungi's exceptional potential as fuel cell catalysts, serving as anodic or cathodic agents to mitigate land, air, and water pollutants while simultaneously producing fuel and power. Applications cover a wide range of tasks, and the innovative concept of wetlands designed as fuel cells for pollutant degradation is discussed. Cost-effectiveness may vary depending on specific contexts and applications. Fungal fuel cells (FFCs) offer a versatile and innovative solution to global challenges, addressing the increasing demand for alternative bioenergy production amid population growth and expanding industrial activities. The mechanistic approach of fungal enzymes via microbial combinations and electrochemical fungal systems facilitates the oxidation of organic substrates, oxygen reduction, and ion exchange membrane orchestration of essential reactions. Fungal laccase plays a crucial role in pollutant removal and monitoring environmental contaminants. Fungal consortiums show remarkable potential in fine-tuning FFC performance, impacting both power generation and pollutant degradation. Beyond energy generation, fungal cells effectively remove pollutants. Overall, FFCs present a promising avenue to address energy needs and mitigate pollutants simultaneously.

Enrichment of polycyclic aromatic hydrocarbon metabolizing microorganisms on the oral mucosa of tobacco users

Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for a subset of skin microbes. In the human mouth, oral microbes have the potential to oxidize tobacco PAHs, thereby increasing these chemicals' ability to cause cancer of adjacent epithelium. We hypothesized that we could identify, in smokers, the oral mucosal microbes that can metabolize PAH. We isolated bacteria and fungi that survived long-term in minimal media with PAHs as the sole carbon source, under aerobic conditions, from the oral mucosa in 17 of 26 smokers and two of 14 nonsmokers. Of bacteria genera that survived harsh PAH exposure in vitro, most were found at trace levels, except for Staphylococcus, Actinomyces, and Kingella, which were more abundant. Two PAH-resistant strains of Candida albicans (C. albicans) were isolated from smokers. C. albicans was a prime candidate to contribute to carcinogenesis in tobacco users as it is found orally at high levels in tobacco users on the mucosa, and some Candida species can metabolize PAHs. However, when C. albicans isolates were tested for metabolism of two model PAH substrates, pyrene and phenanthrene, they were not capable, suggesting they cannot metabolize PAH under the conditions used. In conclusion, evidence for large scale microbial degradation of tobacco PAHs under aerobic conditions on the oral mucosa remains lacking, though nonabundant PAH metabolizers are certainly present.

Understanding the effective breakdown of PAH s in water through the use of g-C3N4-Ag-Cu-Ni nanocomposites

The research work aimed to explore the suitability of using a novel g- C3N4-Ag-Cu-Ni nanocomposite for the simultaneous degradation of pyrene in wastewater. The outcome revealed that the g- C3N4 phase was successfully fabricated on the g-C3N4-based compound, and the existence of the g- C3N4-based compound beneficially stabilized the Ag-Cu-Ni particles. The g- C3N4-Ag-Cu-Ni nanocomposite demonstrated excellent performance in pyrene degradation under various conditions. The degradation of pyrene increased with a rise in the dosage of g- C3N4-Ag-Cu-Ni. These findings indicate that the g- C3N4-Ag-Cu-Ni nanocomposite could be a promising material for water purification, especially for the simultaneous photocatalytic and antimicrobial treatment of contaminated water bodies. The study provides a helpful guide for future research in this field.

Degradation of crude oil-associated polycyclic aromatic hydrocarbons by marine-derived fungi

One of the major environmental concerns today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Crude oil is a complex mixture of hydrocarbons like alkanes, naphthene and polycyclic aromatic hydrocarbons (PAHs). PAHs are known to be highly toxic to humans and animals due to their carcinogenic and mutagenic effects. PAHs are environmentally recalcitrant due to their hydrophobicity which makes them difficult to degrade, thus making them persistent environmental contaminants. The mechanical and chemical methods in practice currently to remove hydrocarbon contaminants have limited effectiveness and are expensive. Bioremediation is a cost-effective technology for treating hydrocarbon-contaminated sites as it results in the complete mineralisation of the pollutant. This study demonstrates the degradation of crude oil and associated PAHs using ten fungal cultures isolated from the aquatic environment. The current study reported a 98.6% and 92.9% reduction in total PAHs in crude oil by Fusarium species, i.e. isolate NIOSN-T4 and NIOSN-T5, respectively. The fungal isolate, NIOSN-T4, identified as Fusarium equiseti, showed maximum PAH degradation efficiency of LMW PAHs 97.8%. NIOSN-M126, identified as Penicillium citrinum, exhibited a 100% removal of HMW PAHs. Microorganisms possess an untapped potential for various applications in biotechnology, and the current study demonstrated the potential of marine fungi for use in the bioremediation of xenobiotic hydrocarbons in the environment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03753-2.

Microbial Consortium HJ-SH with Very High Degradation Efficiency of Phenanthrene

Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as Pseudomonas sp., Stenotrophomonas sp., Delftia sp., Pseudomonas sp., Brevundimonas sp., Curtobacterium sp., and Microbacterium sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.

Fungal co-culture improves the biodegradation of hydrophobic VOCs gas mixtures in conventional biofilters and biotrickling filters

The present study systematically evaluated the potential of Candida subhashii, Fusarium solani and their consortium for the abatement of n-hexane, trichloroethylene (TCE), toluene and α-pinene in biofilters (BFs) and biotrickling filters (BTFs). Three 3.2 L BFs packed with polyurethane foam and operated at a gas residence time of 77 s with an air mixture of hydrophobic volatile organic compounds (VOCs) were inoculated with C. subhashii, F. solani and a combination of thereof. The systems were also operated under a BTF configuration with a liquid recirculating rate of 2.5 L h^-1. Steady state elimination capacities (ECs) of total VOCs of 17.4 ± 0.7 g m^-3 h^-1 for C. subhashii, 21.2 ± 0.8 g m^-3 h^-1 for F. solani and 24.4 ± 1.4 g m^-3 h^-1 for their consortium were recorded in BFs, which increased up to 27.2 ± 1.6 g m^-3 h^-1, 29.2 ± 1.9 g m^-3 h^-1, 37.7 ± 3.3 g m^-3 h^-1 in BTFs. BTFs supported a superior biodegradation performance compared to BF, regardless of the VOCs. Moreover, a more effective VOC biodegradation was observed when C. subhashii and F. solani were grown as a consortium. The microbial analysis conducted revealed that the fungi initially introduced in each BF represented the dominant species by the end of the experiment, with C. subhashii gradually overcoming F. solani in the system inoculated with the fungal consortium.

Improving mass transfer rates in microbial cell immobilization system for environmental applications: Synergistic interaction of cells on crude oil biodegradation

Among the various techniques used to clean up polluted environments, bioremediation is the most cost-effective and eco-friendly option. The diversity of microbial communities in a consortium can significantly affect the biodegradability of hazardous organic pollutants, particularly for in situ bioremediation processes. This is largely attributed to interactions between members of a consortium. In this study, the effect of internal diffusion limitations in substrate model biodegradation was firstly examined by immobilized bacterial cells at different particle sizes produced by the electrospray technique. According to the obtained results, for particles with large size, the effectiveness factors (η) were about 0.58-0.67, and the resistance to diffusive on the biodegradation rate was significant, while with decreasing the particle size, η increases and approaches about 1. After selection of suitable bead size, heavy crude oil biodegradation was investigated using a consortium consisting of three oil-degrading bacterial strains at different treatment systems. The removal rate in the suspended co-culture system stands at minimum value of 38% with all three strains which is an indicator of negative interactions among consortium members. Independent immobilization of microorganisms minimizes the competition and antagonistic interactions between strains and leads to more crude oil removal, so that, the biodegradation rate reached 60%.

Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils

A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.

Biodegradation performance and diversity of enriched bacterial consortia capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are key organic pollutants in the environment that pose threats to the ecosystem and human health. The degradation of high molecular weight (HMW) PAHs by enriched bacterial consortia has been previously studied, while the involved metabolisms and microbial communities are still unclear and warrant further investigations. In this study, five bacterial consortia capable of utilizing different PAHs (naphthalene, anthracene, and pyrene) as the sole carbon and energy sources were enriched from PAH-contaminated soil samples. Among the five consortia, consortium TC exhibited the highest pyrene degradation efficiency (91%) after 19 d of incubation. The degradation efficiency was further enhanced up to 99% by supplementing yeast extract. Besides, consortium TC showed tolerances to high concentrations of pyrene (up to 1000 mg/L) and different heavy metal stresses (including Zn²⁺, Cd²⁺, and Pb²⁺). The dominant genus in consortium TC, GS, and PL showing relatively higher degradation efficiency for anthracene and pyrene was Pseudomonas, whereas consortium PG and GD were predominated by genus Achromobacter and class Enterobacteriaceae, respectively. Consortium TC, as a highly efficient HMW PAH-degrading consortium, could be applied for synergistic biodegradation of HMW PAHs and in situ bioremediation of the sites contaminated with both PAHs and heavy metals.

The Influence of Crops on the Content of Polycyclic Aromatic Hydrocarbons in Soil Fertilized with Manure and Mineral Fertilizers

Polycyclic aromatic hydrocarbons (PAHs) are mainly accumulated in soil. Plants secrete enzymes that transform or biodegrade PAHs in soil. Some plant species are more effective in stimulating the biodegradation of these pollutants than other species. This study was undertaken to evaluate the influence of crop rotation on PAH concentrations in soil. Four crops were grown in rotation: sugar beets, spring barley, maize, and spring wheat. Soil samples for the study were obtained from a long-term field experiment established in 1986 in Bałcyny, Poland. The concentrations of PAHs were analyzed in soil samples gathered over a period of 12 years (1998-2009). An attempt was made to evaluate the effect of crop rotation (sugar beets, spring barley, maize, and spring wheat) on PAH concentrations in soil. The content of PAHs in soil samples was measured by gas chromatography with flame ionization detection. Data were processed statistically by repeated measures ANOVA. The concentrations of ∑16 PAHs were lowest in soil after sugar beet cultivation, and highest in soil after maize cultivation. It can be concluded that maize was the plant with the greatest adverse effect on the content of heavy PAH in the soil, a completely different effect can be attributed to spring wheat, which has always been shown to reduce the content of heavy PAH in the soil. Weather conditions affected PAHs levels in soil, and PAH content was highest in soil samples collected in a year with the driest growing season. This arrangement suggests a greater influence of weather conditions than of the cultivated plant.

Fungal-bacterial network in PAH-contaminated coastal marine sediment

Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.

Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes

Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.

Combining sequential extraction and 3D fluorescence to investigate the behavior of antibiotic and polycyclic aromatic hydrocarbons during solar drying of sewage sludge

Solar drying and liming are commonly used for sludge treatment, but little is known about their efficiency on antibiotics and Polycyclic Aromatic Hydrocarbons (PAHs) removal. This study aimed to investigate the removal of antibiotics and PAHs during solar drying of Limed Sludge (LS) and Non-Limed Sludge (NLS). Thus, organic matter fractionation and 3D fluorescence were used to assess the accessibility and the complexity of organic matter. 2 experiments have been conducted using LS and NLS for 45 days of drying in a pilot scale tunnel. Physicochemical results indicated significant decrease of water content (90%) for both sludge samples within 15 days of drying. For both treatments, the removal of total organic carbon and total nitrogen was low and similar for both treatments. Through this study, it has been confirmed that liming and drying contributed to a strong modification of the organic matter quality with an increase of its accessibility. On the other hand, drying alone increased the less accessible compartments, while the presence of lime affected the interconnexion between the organic matter pools. 3D fluorescence confirmed the obtained results and indicated that LS leads to obtaining more simple molecules in the most accessible compartments, while NLS leads to obtaining more complex molecules in the less accessible compartments. In addition, solar radiations and leaching may contribute to the significant removal (p < 0.01) of roxithromycin, benzo(a)anthracene, chrysene, benzo[k]fluoranthene, benzo[a]pyrene, and benzo(g, h, i) perylene in the presence of lime. Furthermore, the evolution of organic matter pools in terms of accessibility and complexity may drive the bioavailability of these pollutants, leading to their significant removal.

Mineralization of pyrene (polycyclic aromatic hydrocarbon) in clay soil supplemented with animal organic carbon source

Biostimulation of polycyclic aromatic hydrocarbons (PAHs) is a major concern in the environment due to their toxic nature and ubiquitous occurrence. The study aimed to determine the best animal supplement of organic carbon source (cow dung, goat dung, pig dung and poultry (fowl droppings) and indigenous microbes capable of mineralizing pyrene in clay soil. Clay soil sample was collected from the top surface soil (0 - 15 cm) in Ikpoba River and upper Lawani river bank, both in Benin City with the aid of stainless steel trowel and gloved hands and stored in a polyethylene bag. The isolation and identification process were evaluated by staining method, microscopic examination and biochemical tests. The degradation experiment was conducted in bioreactors and supplemented cow dung, pig dung, goat dung and fowl droppings were added in varying amounts of 25 g/l, 50 g/l, 75 g/l and 100 g/l. The potential effects of animal organic carbon as nutrient supplements to enhance mineralization of pyrene were investigated. The rates of mineralization of pyrene were studied for a remediation period of 35 days at room temperature of about 25 °C. Results obtained from microbial isolation showed that B. substilis and A. niger were the most populated in the soil and were therefore selected. The degradation experiment showed that mixed culture of B. substilis and A. niger using 50 g/l supplement with the dungs and droppings gave the highest percentage degradation with fowl droppings 98.3%, pig dung 98.1%, goat dung 97.8%, and cow dung 97.7%. The least degradation was observed in supplement with 100 g/l in a single culture of A. niger with fowl droppings yielded 64.5% degradation, pig dung 63.8%, goat dung 63.7% and cow dung 62.7%. The overall results of the study showed that 50 g/l of animal wastes supplement in the ratio of 1:4 with pyrene contaminated soils are most effective in degradation processes. Also the mixed culture of bacteria and fungi enhanced pyrene mineralization and degradation more than single culture.

Bacterial diversity and competitors for degradation of hazardous oil refining waste under selective pressures of temperature and oxygen

Oil refining waste (ORW) contains complex, hazardous, and refractory components, causing more severe long-term environmental pollution than petroleum. Here, ORW was used to simulate the accelerated domestication of bacteria from oily sludges and polymer-flooding wastewater, and the effects of key factors, oxygen and temperature, on the ORW degradation were evaluated. Bacterial communities acclimated respectively in 30/60 °C, aerobic/anaerobic conditions showed differentiated degradation rates of ORW, ranging from 5% to 34%. High-throughput amplicon sequencing and ORW component analysis revealed significant correlation between bacterial diversity/biomass and degradation efficiency/substrate preference. Under mesophilic and oxygen-rich condition, the high biomass and abundant biodiversity with diverse genes and pathways for petroleum hydrocarbons degradation, effectively promoted the rapid and multi-component degradation of ORW. While under harsh conditions, a few dominant genera still contributed to ORW degradation, although the biodiversity was severely restricted. The typical dominant facultative anaerobes Bacillus (up to 99.8% abundance anaerobically) and Geobacillus (up to 99.9% abundance aerobically and anaerobically) showed oxygen-independent sustainable degradation ability and broad-spectrum of temperature adaptability, making them promising and competitive bioremediation candidates for future application. Our findings provide important strategies for practical bioremediation of varied environments polluted by hazardous ORW.

Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria

Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.

Profiling of seasonal variation in and cancer risk assessment of benzo(a)pyrene and heavy metals in drinking water from Kirkuk city, Iraq

Water samples at 13 sites were analyzed to evaluate heavy metals (cobalt, lead, manganese, copper) and benzo(a)pyrene using 2 methods of analysis (high-performance liquid chromatography (HPLC) and enzyme-linked immunosorbent assay (ELISA) kits). The Lesser Zap River is the main tributary of the Tigris and is used as a main source of drinking water in Kirkuk city through the General Kirkuk project. Risk evaluation for benzo(a)pyrene and lead in water samples was accomplished by Monte Carlo simulation. The highest concentrations of B(a)P were recorded at sites S7 and S5, with levels of 0.192 and 0.122 µg L^-1 detected by HPLC and ELISA, respectively. The WHO guidelines for benzo[a]pyrene in drinking water recommend 0.7 µg L ^-1, and none of the samples surpassed this level; moreover, B(a)P levels exceeded EPA standards in 2014 (0.01 µg L^-1), particularly when the liquid-liquid extraction method with HPLC was used. Carcinogenic risks for human adults and children exist and are highest during the rainy season as compared with the carcinogenic risk during the dry season and risks for children exceed those of adults. This indicates that the 2^nd round of sampling (winter season) harbors more carcinogenic risk than the 1^st round of sampling (dry season).

An insight on microbial degradation of benzo[a]pyrene: current status and advances in research

Benzo[a]pyrene (BaP) is a high molecular weight polycyclic aromatic hydrocarbon produced as a result of incomplete combustion of organic substances. Over the years, the release of BaP in the atmosphere has increased rapidly, risking human lives. BaP can form bonds with DNA leading to the formation of DNA adducts thereby causing cancer. Therefore addressing the problem of its removal from the environment is quite pertinent though it calls for a very cumbersome and tedious process owing to its recalcitrant nature. To resolve such issues many efforts have been made to develop physical and chemical technologies of BaP degradation which have neither been cost-effective nor eco-friendly. Microbial degradation of BaP, on the other hand, has gained much attention due to added advantage of the high level of microbial diversity enabling great potential to degrade the substance without impairing environmental sustainability. Microorganisms produce enzymes like oxygenases, hydrolases and cytochrome P450 that enable BaP degradation. However, microbial degradation of BaP is restricted due to several factors related to its bio-availability and soil properties. Technologies like bio-augmentation and bio-stimulation have served to enhance the degradation rate of BaP. Besides, advanced technologies such as omics and nano-technology have opened new doors for a better future of microbial degradation of BaP and related compounds.

Effects of Adding Laccase to Bacterial Consortia Degrading Heavy Oil

High-efficiency bioremediation technology for heavy oil pollution has been a popular research topic in recent years. Laccase is very promising for the remediation of heavy oil pollution because it can not only convert bio-refractory hydrocarbons into less toxic or completely harmless compounds, but also accelerate the biodegradation efficiency of heavy oil. However, there are few reports on the use of laccase to enhance the biodegradation of heavy oil. In this study, we investigated the effect of laccase on the bacterial consortia degradation of heavy oil. The degradation efficiencies of bacterial consortia and the laccase-bacterial consortia were 60.6 ± 0.1% and 68.2 ± 0.6%, respectively, and the corresponding heavy oil degradation rate constants were 0.112 day−1 and 0.198 day−1, respectively. The addition of laccase increased the heavy oil biodegradation efficiency (p < 0.05) and biodegradation rate of the bacterial consortia. Moreover, gas chromatography–mass spectrometry analysis showed that the biodegradation efficiencies of the laccase-bacterial consortia for saturated hydrocarbons and aromatic hydrocarbons were 82.5 ± 0.7% and 76.2 ± 0.9%, respectively, which were 16.0 ± 0.3% and 13.0 ± 1.8% higher than those of the bacterial consortia, respectively. In addition, the degradation rate constants of the laccase-bacterial consortia for saturated hydrocarbons and aromatic hydrocarbons were 0.267 day−1 and 0.226 day−1, respectively, which were 1.07 and 1.15 times higher than those of the bacterial consortia, respectively. The degradation of C15 to C35 n-alkanes and 2 to 5-ring polycyclic aromatic hydrocarbons by laccase-bacterial consortia was higher than individual bacterial consortia. It is further seen that the addition of laccase significantly improved the biodegradation of long-chain n-alkanes of C22–C35 (p < 0.05). Overall, this study shows that the combination of laccase and bacterial consortia is an effective remediation technology for heavy oil pollution. Adding laccase can significantly improve the heavy oil biodegradation efficiency and biodegradation rate of the bacterial consortia.

Remediation of soil cadmium pollution by biomineralization using microbial-induced precipitation: a review

In recent years, with industrial pollution and the application of agricultural fertilizers with high cadmium (Cd) content, soil Cd pollution has become increasingly serious. A large amount of Cd is discharged into the environment, greatly endangering the stability of the ecological environment and human health. The use of microorganisms to induce Cd precipitation and mineralization is an important bioremediation method. Itis highly efficient, has a low cost, enables environmental protection, and convenient to operate. This article summarizes the pollution status, pollution source, biological toxicity and existing forms of Cd, as well as the biomineralization mechanism of microbial induced Cd(II) precipitation, mainly including microbial-induced carbonate precipitation, microbial-induced phosphate precipitation and microbial-induced sulfide precipitation. Factors affecting the bioremediation of Cd, such as pH, coexisting ions, and temperature, are introduced. Finally, the key points and difficulties of future microbe-induced Cd(II) biomineralization research are highlighted, providing a scientific basis and theoretical guidance for the application of microbe-induced Cd(II) immobilization in soil.

A crucial review on polycyclic aromatic Hydrocarbons - Environmental occurrence and strategies for microbial degradation

Over the last century, contamination of polycyclic aromatic hydrocarbons (PAHs) has risen tremendously due to the intensified industrial activities like petrochemical, pharmaceutical, insecticides and fertilizers applications. PAHs are a group of organic pollutants with adverse effects on both humans and the environment. These PAHs are widely distributed in various ecosystems including air, soil, marine water and sediments. Degradation of PAHs generally occurs through processes like photolysis, adsorption, volatilization, chemical degradation and microbial degradation. Microbial degradation of PAHs is done by the utilization of diverse microorganisms like algae, bacteria, fungi which are readily compatible with biodegrading/bio transforming PAHs into H₂O, CO₂ under aerobic, or CH₄ under anaerobic environment. The rate of PAHs degradation using microbes is mainly governed by various cultivation conditions like temperature, pH, nutrients availability, microbial population, chemical nature of PAHs, oxygen and degree of acclimation. Several microbial species including Selenastrum capricornutum, Ralstonia basilensis, Acinetobacter haemolyticus, Pseudomonas migulae, Sphingomonas yanoikuyae and Chlorella sorokiniana are known to degrade PAHs via biosorption and enzyme-mediated degradation. Numerous bacterial mediated PAHs degradation methods are studied globally. Among them, PAHs degradation by bacterial species like Pseudomonas fluorescence, Pseudomonas aeruginosa, Rhodococcus spp., Paenibacillus spp., Mycobacterium spp., and Haemophilus spp., by various degradation modes like biosurfactant, bioaugmentation, biostimulation and biofilms mediated are also investigated. In contrarily, PAHs degradation by fungal species such as Pleurotus ostreatus, Polyporus sulphureus, Fusarium oxysporum occurs using the activity of its ligninolytic enzymes such as lignin peroxidase, laccase, and manganese peroxidase. The present review highlighted on the PAHs degradation activity by the algal, fungal, bacterial species and also focused on their mode of degradation.

The remediation potential for PAHs of Verbascum sinuatum L. combined with an enhanced rhizosphere landscape: A full-scale mesocosm experiment

A full-scale mesocosm study was conducted to depict how integrated biological systems interact to adapt to contaminant stress and improve remediation of polycyclic aromatic hydrocarbons (PAHs)contaminated soils. The combination of Verbascum sinuatum L. and microbial consortium (fungi and bacteria) was employed along with three differently contaminated soils. After 240 days the highest PAHs removal (up to 68 %) and 6-rings compounds decrease was found in soil with lower pollution and cation exchange capacity. V. sinuatum showed a significant adaptability over time in terms of redox biology. Soil enzyme activities and microscopic evidences proved a rising plant-microorganisms association and a successful mycorrhization, arising from the inoculation of our consortia. In addition, an enhanced richness of PAHs degrading genes was achieved. Microbial co-metabolism, helped by the establishment of complex relationships with hosting plant, demonstrated to be suitable for the degradation of high molecular weight PAHs and represents a biotechnology with great prospects.

Soil indigenous microorganisms weaken the synergy of Massilia sp. WF1 and Phanerochaete chrysosporium in phenanthrene biodegradation

Biodegradation is a promising way to reduce phenanthrene (PHE) in environment. PHE biodegradation by bioaugmentation of axenic and mixed cultures of Massilia sp. WF1 (a highly efficient PHE-degrading bacteria) and Phanerochaete chrysosporium (P. chrysosporium, an extensively researched model fungus in organic pollutant bioremediation) was investigated in aqueous and autoclaved/un-autoclaved soil cultures. In the liquid cultures, the strain WF1 could use PHE (ca. 10 mg L^-1) as the sole carbon source, and the presence of d-fructose (500 mg L^-1) had no obvious effect on its PHE degradation; while the opposite was observed for P. chrysosporium. The bioaugmentation of strain WF1 and P. chrysosporium co-culture showed the highest PHE-degradation efficiency, especially in the aqueous and the autoclaved soil (PHE, ca. 50 mg kg^-1) cultures, indicating a synergistic interaction of the co-culture during PHE dissipation. It was further observed that the indigenous microorganisms (mainly the Gram-positive bacteria) played a dominant role during PHE biodegradation and showed an antagonistic action against the strain WF1-P. chrysosporium co-culture, which weakened the synergistic action of the co-culture in the un-autoclaved soil. Besides, the abundances of PAH-RHDα GP and nidA genes were negatively correlated with residual PHE in the soil. Our findings provide the scientific support for bioremediation of PAHs in environment.

Potential use of fungal-bacterial co-cultures for the removal of organic pollutants

Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.

Graphene environmental biodegradation: Wood degrading and saprotrophic fungi oxidize few-layer graphene

The environmental biodegradability profile of graphene related materials (GRMs) is important to know in order to predict whether these materials will accumulate in soil or will be transformed by primary decomposers. In this study, few-layer graphene (FLG) was exposed to living and devitalized axenic cultures of two white-rot basidiomycetes (Bjerkandera adusta and Phanerochaete chrysosporium) and one soil saprotrophic ascomycete (Morchella esculenta) with or without lignin, for a period of four months. Over this time, the increase of fungal biomass and presence of H₂O₂ and oxidizing enzymes [laccase/peroxidase and lignin peroxidase (LiP)] in growth media was assessed by gravimetric and spectrophotometric measurements, respectively. Raman spectroscopy and transmission electron microscopy (TEM) were used to compare the structure of FLG before and after incubation. All of the test fungi decreased pH in growth media and released H₂O₂ and laccase/peroxidase, but only basidiomycetes released LiP. Independent of growth media composition all fungi were found to be capable to oxidize FLG to a graphene oxide-like material, including M. esculenta, which released only laccase/peroxidase, i.e. the most common enzymes among primary decomposers. These findings suggest that FLG involuntarily released into terrestrial environments would likely be oxidized by soil microflora.

A comprehensive feasibility study of effectiveness and environmental impact of PAH bioremediation using an indigenous microbial degrader consortium and a novel strain Stenotrophomonas maltophilia CPHE1 isolated from an industrial polluted soil

Polycyclic Aromatic Hydrocarbons (PAHs) are major toxic and recalcitrant pollutants in the environment. This study assessed the capacity of an isolated soil microbial consortium (OMC) to biodegrade PAHs. OMC was able to reach 100% biodegradation of naphthalene, acenaphthylene, acenaphthene, fluorene and phenanthrene in solution, and up to 76% and 50% of anthracene and fluoranthene, respectively, from a mix of 16 PAHs. To measure phenanthrene (PHE) mineralization, OMC and eight strains isolated from OMC were used and identified by PCR amplification of the gene 16S ribosomal RNA. A novel Stenotrophomonas maltophilia CPHE1, not previously described as a PAH degrader, was able to mineralize almost 40% PHE and biodegrade 90.5% in solution, in comparison to OMC that reached 100% PHE degradation, but only 18.8% mineralization. Based on metabolites identified during PHE degradation and on the detection of two genes (PAH RHDα and nahAc) in OMC consortium, two possible via were described for its degradation, through salicylic and phthalic acid. PAH RHDα, which codified the first step on PHE biodegradation pathway, was also found in the DNA of S. maltophilia CPHE1. An ecotoxicology study showed that PHE bioremediation after inoculating S. maltophilia CPHE1 for 30 days decreased by half the solution toxicity.

Bioaugmentation strategy to enhance polycyclic aromatic hydrocarbons anaerobic biodegradation in contaminated soils

This paper proposes an innovative bioaugmentation approach for the remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soils, based on a novel habitat-based strategy. This approach was tested using two inocula (i-24 and i-96) previously enriched through an anaerobic digestion process on wheat straw. It relies on the application of allochthonous microorganisms characterized by specific functional roles obtained by mimicking a natural hydrolytic environment such as the rumen. The inocula efficiency was tested in presence of naphthalene alone, benzo[a]pyrene alone, and a mix of both of them. In single-contamination tests, i-24 inoculum showed the highest biodegradation rates (84.7% for naphthalene and 51.7% for benzo[a]pyrene). These values were almost 1.2 times higher than those obtained for both contaminants with i-96 inoculum and in the control test in presence of naphthalene alone, while they were 3 times higher compared to the control test in presence of benzo[a]pyrene alone. In mixed-contamination tests, i-96 inoculum showed final biodegradation efficiencies for naphthalene and benzo[a]pyrene between 1.1 and 1.5 higher than i-24 inoculum or autochthonous biomass. Total microbial abundances increased in the bioaugmented tests in line with the PAH degradation. The microbial community structure showed the highest diversity at the end of the experiment in almost all cases. Values of the Firmicutes active fraction up to 7 times lower were observed in the i-24 bioaugmented tests compared to i-96 and control tests. This study highlights a successful bioaugmentation strategy with biological components that can be reused in multiple processes supporting an integrated and environmentally sustainable bioremediation system.

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites

BACKGROUND

Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.

RESULTS

The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.

CONCLUSIONS

Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.

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

The concurrence of structurally complex petroleum-associated contaminants at relatively high concentrations, with diverse climatic conditions and textural soil characteristics, hinders conventional bioremediation processes. Recalcitrant compounds such as high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and heavy alkanes commonly remain after standard soil bioremediation at concentrations above regulatory limits. The present study assessed the potential of native fungal bioaugmentation as a strategy to promote the bioremediation of an aged industrially polluted soil enriched with heavy hydrocarbon fractions. Microcosms assays were performed by means of biostimulation and bioaugmentation, by inoculating a defined consortium of six potentially hydrocarbonoclastic fungi belonging to the genera Penicillium, Ulocladium, Aspergillus, and Fusarium, which were isolated previously from the polluted soil. The biodegradation performance of fungal bioaugmentation was compared with soil biostimulation (water and nutrient addition) and with untreated soil as a control. Fungal bioaugmentation resulted in a higher biodegradation of total petroleum hydrocarbons (TPH) and of HMW-PAHs than with biostimulation. TPH (C14-C35) decreased by a 39.90 ± 1.99% in bioaugmented microcosms vs. a 24.17 ± 1.31% in biostimulated microcosms. As for the effect of fungal bioaugmentation on HMW-PAHs, the 5-ringed benzo(a)fluoranthene and benzo(a)pyrene were reduced by a 36% and 46%, respectively, while the 6-ringed benzoperylene decreased by a 28%, after 120 days of treatment. Biostimulated microcosm exhibited a significantly lower reduction of 5- and 6-ringed PAHs (8% and 5% respectively). Higher TPH and HMW-PAHs biodegradation levels in bioaugmented microcosms were also associated to a significant decrease in acute ecotoxicity (EC50) by Vibrio fischeri bioluminiscence inhibition assays. Molecular profiling and counting of viable hydrocarbon-degrading bacteria from soil microcosms revealed that fungal bioaugmentation promoted the growth of autochthonous active hydrocarbon-degrading bacteria. The implementation of such an approach to enhance hydrocarbon biodegradation should be considered as a novel bioremediation strategy for the treatment of the most recalcitrant and highly genotoxic hydrocarbons in aged industrially polluted soils.

Revealing of Non-Cultivable Bacteria Associated with the Mycelium of Fungi in the Kerosene-Degrading Community Isolated from the Contaminated Jet Fuel

Fuel (especially kerosene) biodamage is a challenge for global industry. In aviation, where kerosene is a widely used type of fuel, its biodeterioration leads to significant damage. Six isolates of micromycetes from the TS-1 aviation kerosene samples were obtained. Their ability to grow on the fuel was studied, and the difference between biodegradation ability was shown. Micromycetes belonged to the Talaromyces, Penicillium, and Aspergillus genera. It was impossible to obtain bacterial isolates associated with their mycelium. However, 16S rRNA metabarcoding and microscopic observations revealed the presence of bacteria in the micromycete isolates. It seems to be that kerosene-degrading fungi were associated with uncultured bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were abundant in the fungal cultures isolated from the TS-1 jet fuel samples. Most genera among these phyla are known as hydrocarbon degraders. Only bacteria-containing micromycete isolates were able to grow on the kerosene. Most likely, kerosene degradation mechanisms are based on synergism of bacteria and fungi.

Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene

Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.

Co-enhanced activated sludge system by static magnetic field and two halotolerant yeasts for azo dye treatment

The effect of static magnetic field (SMF) on azo dye Acid Red B (ARB) decolorization by the co-culture of activated sludge (AS) and two halotolerant yeasts Candida tropicalis A1 and Pichia occidentalis A2 was investigated. Microbial community structure of the co-cultures before and after treatment with SMFs of different intensity was analyzed through high-throughput sequencing and quantitative real-time polymerase chain reaction. The results showed that ARB decolorization efficiency by the defined co-culture was 1.25-fold to 1.51-fold elevated by 24.6-305.0 mT SMF. The best ARB decolorization and chemical oxygen demand (COD) removal performances by the co-culture were both achieved with 95.0 mT SMF. By contrast, biomass multiplication and sedimentation property of AS systems were not significantly influenced by SMF. Higher activities of intracellular key enzymes were determined (with 95.0 mT SMF) as responsible for better decolorization and COD removal performances. Bacteria belonging to Prolixibacter, Corynebacterium, Pelagibacterium, Demequina, and Sphingobacterium which might be responsible for azo dye decolorization and aromatic compounds biodegradation were significantly enriched only in presence of SMF. Fungal genera Candida and Pichia were also significantly enriched by 41.4-305.0 mT SMF, which might be responsible for higher treatment efficiency. PRACTITIONER POINTS: Dye degradation was enhanced by combination of static magnetic field and yeasts. Improvement of enzyme activity was responsible for better treatment performance. Putative azo-degrading-related bacteria and fungi were selectively enriched. High relative abundance of Candida and Pichia ensured high decolorization effects. Potentially effective improvement of bioprocesses for treating hypersaline wastewater.

Beneficial biofilms for land rehabilitation and fertilization

The acquisition of a biofilm lifestyle is common in nature for microorganisms. It increases their biotic and abiotic stress tolerance and their capability to provide ecosystem services. Although diminutive communities, soil beneficial biofilms are essential for nutrient cycling, soil stabilization and direct or indirect promotion of plant development. Some biofilms represent valid biotechnological tools to deal with problems related to soil degradation, which threat food quality and the maintenance of ecosystem functions. Three genres of biofilms: rhizobacterial biofilms, fungal-bacterial biofilms and biocrusts are reviewed, and their beneficial effects on the environment outlined. Their induction by microbial inoculation represents a potential eco-friendly and sustainable approach to restore lost ecosystem functions and counteract the effects of soil erosion. Yet, some existing knowledge and methodological gaps, that will be discussed here, still hamper the optimization of this technology, and its application at its full potential.

Enhanced biotreatability of petroleum hydrocarbon-contaminated mining waste coupled with the attenuation of acid drainage production

A biostimulation study was conducted on mining waste residue with nutrient (nitrogen and phosphorus) and/or liming agent (ash or CaCO₃ ) amendment to assess petroleum hydrocarbon (PHC) biodegradation efficiency by indigenous microorganisms. Compounds accumulated and/or released by treated samples were also monitored to determine the potential for acid mine drainage production during biostimulation. The potential for natural attenuation (i.e., the biodegradation of PHC contamination) was initially low but increased significantly upon nutrient addition. The best results were obtained when nutrient addition was coupled with the addition of a liming agent, notably CaCO₃ , which contributed to maintaining near-neutral pH values. In fact, during treatment without a liming agent, pH decreased due to the oxidation of sulfide minerals, resulting in acid mine drainage production with increased metals released into sample leachates. Sulfur- and iron-oxidizing bacteria were detected primarily in samples not amended with liming agents, and the predominant organisms were affiliated with Acidithiobacillus spp. and Acidiphilium spp. Overall, the results of the present study demonstrated that amendment with a liming agent when treating PHC-contaminated mining waste residue contributes to maintaining a pH close to neutrality, mitigates sulfate release, and reduces the release of metals without negatively affecting the activity of PHC degraders.

Carbonate and Oxalate Crystallization by Interaction of Calcite Marble with Bacillus subtilis and Bacillus subtilis–Aspergillus niger Association

Rock surfaces in natural systems are inhabited by multispecies communities of microorganisms. The biochemical activity of microorganisms and the patterns of microbial crystallization in these communities are mostly unexplored. Patterns of calcium carbonate and calcium oxalate crystallization induced by bacteria Bacillus subtilis and by B. subtilis together with Aspergillus niger on marble surface in vitro in liquid medium and in humidity chamber—were studied. Phase identification was supported by XRD, SEM, EDXS; metabolite composition was determined by GC–MS. It was found that the activity of B. subtilis–A. niger associations significantly differ from the activity of B. subtilis monocultures in the same trophic conditions. The phase composition and the morphology of the forming crystals are determined by the composition of the metabolites excreted by the microorganisms—particularly by the ratio of the concentrations of extracellular polymeric substances (EPS) and oxalic acid in the medium. The acidification activity of micromycetes may suppress the formation of bacterial EPS and prevent the formation of calcite. The present results can be used in the development of biotechnologies using microbial communities.

Bioremediation of intertidal zones polluted by heavy oil spilling using immobilized laccase-bacteria consortium

Heavy oil pollution in the intertidal zones has become a worldwide environmental problem. In this study, bioremediation on heavy oil pollutants in the intertidal zones using an immobilized laccase-bacteria consortium system was evaluated with the aid of intertidal experimental pools built in the coastal area. It is found that degradation efficiency of the immobilized laccase-bacteria consortium for heavy oil was 66.5% after 100 days remediation, with the reaction rate constant of 0.018 d^-1. Gas Chromatograph-Mass Spectrometer analysis shows that degradation efficiency of saturated hydrocarbons and aromatic hydrocarbons were 79.2% and 78.7%, which were 64.9% and 65.1% higher than control. It is further seen that degradation of long-chain n-alkanes of C26-C35 and polycyclic aromatic hydrocarbons with more than three rings were significant. Metagenomic analysis indicates that the immobilized laccase-bacterial consortium has not only increased the biodiversity of heavy oil degrading bacteria, but also accelerated the degradation of heavy oil.

Investigating the mycobiome of the Holcomb Creosote Superfund Site

Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.

Synergistic interaction of a consortium of the brown-rot fungus Fomitopsis pinicola and the bacterium Ralstonia pickettii for DDT biodegradation

1,1,1-Trichloro-2,2-bis (4-chlorophenyl) ethane (DDT) is a toxic and recalcitrant pesticide that has been greatly used to eradicate malaria mosquitos since the 1940s. However, the US Environmental Protection Agency banned and classified DDT as priority pollutants due to its negative impact on wildlife and human health. Considering its negative effects, it is necessary to develop effective methods of DDT degradation. A synergistic interaction of a consortium consisting of the brown-rot fungus Fomitopsis pinicola and the bacterium Ralstonia pickettii was adopted to degrade DDT. For the microbial consortia, F. pinicola was mixed with R. pickettii at 1, 3, 5, 7 and 10 ml (1 ml ≈ 1.44 × 1013 CFU) in a potato dextrose broth (PDB) medium to degrade DDT throughout the seven days incubation period. The degradation of DDT by only the fungus F. pinicola was roughly 42%, while by only R. pickettii was 31%. The addition of 3 ml of R. pickettii into F. pinicola culture presented appropriate optimization for efficient DDT degradation at roughly 61%. The DDT transformation pathway by co-inoculation of F. pinicola and R. pickettii showed that DDT was converted to 1,1-dichloro-2,2-bis(4-chlorophenyl) ethane (DDD), further transformed to 1,1-dichloro-2,2-bis(4-chlorophenyl) ethylene (DDE), and then ultimately transformed to 1-chloro-2,2-bis(4-chlorophenyl) ethylene (DDMU). These metabolites are less toxic than DDT. This research showed that R. picketti synergistically interacts with F. pinicola by enhancing DDT degradation.

Potential applications of microbial enhanced oil recovery to heavy oil

Heavy oil accounts for around one-third of total global oil and gas resources. The progressive depletion of conventional energy reserves has led to an increased emphasis on the efficient exploitation of heavy oil and bitumen reserves in order to meet energy demand. Therefore, it is imperative to develop new technologies for heavy oil upgrading and recovery. Biologically-based technology that involves using microorganisms or their metabolites to mobilize heavy oil trapped in reservoir rocks can make a significant contribution to the recovery of heavy oils. Here, the results of laboratory experiments and field trials applying microbial enhanced oil recovery (MEOR) technologies are summarized. This review provides an overview of the basic concepts, mechanisms, advantages, problems, and trends in MEOR, and demonstrates the credibility of MEOR methods for applications in enhanced heavy oil recovery and the petroleum refining processes. This technology is cost-effective and environmentally-friendly. The feasibility of MEOR technologies for heavier oil has not yet been fully realized due to the perceived process complexity and a lack of sufficient laboratory research and field test data. However, novel developments such as enzyme-enhanced oil recovery continues to improve MEOR methods.HighlightsHeavy oil represents the largest known potentially-recoverable petroleum energy resource.Novel biotechnological processes are needed to recover or upgrade heavy oil.Microbial technologies have great potential for heavy oil recovery.Microorganisms can produce metabolic byproducts to mobilize oil trapped in reservoirs.More technological research is needed to develop microbial enhanced oil recovery.

Effect of manure and mineral fertilisers on the content of light and heavy polycyclic aromatic hydrocarbons in soil

A study was conducted to explore the effects of fertilisation with farmyard manure (FYM) and mineral fertilisers on the content of PAHs in soil. The analyses were made on soil samples (collected in 1998–2009) from a long-term field experiment set up in 1986 in Bałcyny near Ostróda. The content of light and heavy polycyclic aromatic hydrocarbons was determined on a gas chromatograph coupled with an FID detector. The analytical data were processed statistically according to an analysis of variance with repeated measurements. The content of light and heavy polycyclic aromatic hydrocarbons was significantly higher in soil fertilised with FYM than in soil nourished only with mineral fertilisers. The effect of increasing doses of potassium on total light PAHs in soil depended on a fertilisation system – there was either a distinct decrease in soil fertilised with mineral substances alone or a slight increase in soil fertilised with manure. Regular soil liming significantly raised the ∑ of heavy PAHs in soil treated with manure but significantly decreased it in soil supplied only mineral fertilisers.

Investigation into the microbial communities and associated crude oil-contamination along a Gulf War impacted groundwater system in Kuwait

During the First Gulf War (1991) a large number of oil wells were destroyed and oil fires subsequently extinguished with seawater. As a result Kuwait's sparse fresh groundwater resources were severely contaminated with crude oil. Since then limited research has focused on the microbial community ecology of the groundwater and their impact on the associated contamination. Here, the microbial community ecology (bacterial, archaeal and eukaryotic) and how it relates to the characteristics of the hydrocarbon contaminants were examined for the first time since the 1991 event. This study was conducted using 15 wells along the main groundwater flow direction and detected several potential hydrocarbon degrading microorganisms such as Hyphomicrobiaceae, Porphyromonadaceae and Eurotiomycetes. The beta diversity of the microbial communities correlated significantly with total petroleum hydrocarbon (TPH) concentrations and salinity. The TPH consisted mainly of polar compounds present as an unresolved complex mixture (UCM) of a highly recalcitrant nature. Based on the proportions of TPH to dissolved organic carbon (DOC), the results indicate that some minor biodegradation has occurred within highly contaminated aquifer zones. However, overall the results from this study suggest that the observed variations in TPH concentrations among the sampled wells are mainly induced by mixing/dilution with pristine groundwater rather than by biodegradation of the contaminants. The findings make an important contribution to better understand the fate of the groundwater pollution in Kuwait, with important implications for the design of future remediation efforts.

Enhanced phytoremediation of PAHs-contaminated soil from an industrial relocation site by Ochrobactrum sp

Nowadays, the remediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soil has received wide attention. In this work, Ochrobactrum sp. (PW) was isolated through selective enrichment from PAHs-contaminated soil in coking plant of Beijing, and the effects of PW on phytoremediation of that soil by alfalfa (Medicago sativa L.) and ryegrass (Lolium multiflorum Lam.) were investigated through pot experiments. Plant biomass, peroxidase (POD) activity, malondialdehyde (MDA) contents, soil enzyme activity (polyphenol oxidase and dehydrogenase activity), and residual concentration of PAHs in soils were determined to illustrate the ability of PW for enhancing the degradation of PAHs by plants. The results showed that the fresh weight of ryegrass and alfalfa inoculated with PW was significantly (p < 0.05) increased while the activity of POD and MDA contents were notably (p < 0.05) reduced than that without inoculation. Additionally, PW enhanced the activity of polyphenol oxidase and dehydrogenase in soil significantly (p < 0.05), and further enhanced the degradability of the system to PAHs. Different treatment methods could be ranked by the following order according to the degradability: SP (alfalfa + PW) > RP (ryegrass + PW) > PW (PW) > S (alfalfa) > R (ryegrass). The combined action of PW and alfalfa/ryegrass could accelerate the degradability of PAHs from soil contaminated by coking plants. PW could be used as potential bacteria to promote phytoremediation of the soil contaminated by PAHs.

Fire Phoenix facilitates phytoremediation of PAH-Cd co-contaminated soil through promotion of beneficial rhizosphere bacterial communities

Pot experiments were conducted in a growth chamber to evaluate the phytoremediation efficiency and rhizosphere regulation mechanism of Fire Phoenix (a mixture of Festuca L.) in polycyclic aromatic hydrocarbon-cadmium (PAH-Cd) co-contaminated soils. Plant biomass, removal rates of PAHs and Cd, soil enzyme activity, and soil bacterial community were determined. After 150 days of planting, the removal rates of the total 4 PAHs and Cd reached 64.57% and 40.93% in co-contaminated soils with low-PAH (104.79-144.87 mg·kg^-1), and 68.29% and 25.40% in co-contaminated soils with high-PAH (169.17-197.44 mg·kg^-1), respectively. The polyphenol oxidase (PPO) activity decreased in soils having Fire Phoenix, while the dehydrogenase (DHO) activity increased as the changes of DHO activity had a strong positive correlation with the removal rates of PAHs and Cd in the low-PAH soils (r = 0.862 (P < 0.006) and 0.913 (P < 0.002), respectively). Meanwhile, successional changes in the bacterial communities were detected using high-throughput 454 Gs-FLX pyrosequencing of the 16S rRNA, and these changes were especially apparent for the co-contaminated soils with the low PAH concentration. The Fire Phoenix could promote the growth of Mycobacterium, Dokdonella, Gordonia and Kaistobacter, which played important roles in PAHs degradation or Cd dissipation. These results indicated that Fire Phoenix could effectively motivate the soil enzyme and bacterial community and enhance the potential for phytoremediation of PAH-Cd co-contaminated soils.

Bioremediation of Unconventional Oil Contaminated Ecosystems under Natural and Assisted Conditions: A Review

It is a general understanding that unconventional oil is petroleum-extracted and processed into petroleum products using unconventional means. The recent growth in the United States shale oil production and the lack of refineries in Canada built for heavy crude processes have resulted in a significant increase in U.S imports of unconventional oil since 2018. This has increased the risk of incidents and catastrophic emergencies during the transportation of unconventional oils using transmission pipelines and train rails. A great deal of effort has been made to address the remediation of contaminated soil/sediment following the traditional oil spills. However, spill response and cleanup techniques (e.g., oil recuperation, soil-sediment-water treatments) showed slow and inefficient performance when it came to unconventional oil, bringing larger associated environmental impacts in need of investigation. To the best of our knowledge, there is no coherent review available on the biodegradability of unconventional oil, including Dilbit and Bakken oil. Hence, in view of the insufficient information and contrasting results obtained on the remediation of petroleum, this review is an attempt to fill the gap by presenting the collective understanding and critical analysis of the literature on bioremediation of products from the oil sand and shale (e.g., Dilbit and Bakken oil). This can help evaluate the different aspects of hydrocarbon biodegradation and identify the knowledge gaps in the literature.

Acinetobacter sp. as the key player in diesel oil degrading community exposed to PAHs and heavy metals

The aim of this study was to verify the hypothesis that a hydrocarbon degrading community isolated from a site heavily polluted with polycyclic aromatic hydrocarbons (PAHs) and heavy metals should exhibit a high activity and biodegradation efficiency, despite decreased biodiversity resulting from the presence of such contaminants. Microbial community isolated from soil collected at an abandoned creosote railway wood-sleepers impregnation plant using diesel oil was used during the studies. Four parallel systems spiked with diesel oil, diesel oil + PAHs, diesel oil + heavy metals and diesel oil + PAHs + heavy metals were analysed in terms of relative abundance and biodiversity of the microbial community (Illumina), biodegradation efficiency (GCMS) and cellular metabolic activity (flow cytometry). Principal Component Analysis and biodiversity parameters indicated that the mixture of PAHs and heavy metals was the dominant factor which resulted in the enrichment of the Gammaproteobacteria class. This was associated with higher degradation of additional PAHs in the presence of heavy metals and an increase of metabolically active sub-populations during flow cytometry analysis. The increased abundance of the Acinetobacter genus in systems with both PAHs and heavy metals implies that it may play a crucial role in soil populations exposed to mixed contaminations.