Biodegradation of benzo[a]pyrene in soil by Mucor sp. SF06 and Bacillus sp. SB02 co-immobilized on vermiculite

Benefits of Immobilized Bacteria in Bioremediation of Sites Contaminated with Toxic Organic Compounds

Although bioremediation is considered the most environmentally friendly and sustainable technique for remediating contaminated soil and water, it is most effective when combined with physicochemical methods, which allow for the preliminary removal of large quantities of pollutants. This allows microorganisms to efficiently eliminate the remaining contaminants. In addition to requiring the necessary genes and degradation pathways for specific substrates, as well as tolerance to adverse environmental conditions, microorganisms may perform below expectations. One typical reason for this is the high toxicity of xenobiotics present in large concentrations, stemming from the vulnerability of bacteria introduced to a contaminated site. This is especially true for planktonic bacteria, whereas bacteria within biofilms or microcolonies have significant advantages over their planktonic counterparts. A physical matrix is essential for the formation, maintenance, and survival of bacterial biofilms. By providing such a matrix for bacterial immobilization, the formation of biofilms can be facilitated and accelerated. Therefore, bioremediation combined with bacterial immobilization offers a comprehensive solution for environmental cleanup by harnessing the specialized metabolic activities of microorganisms while ensuring their retention and efficacy at target sites. In many cases, such bioremediation can also eliminate the need for physicochemical methods that are otherwise required to initially reduce contaminant concentrations. Then, it will be possible to use microorganisms for the remediation of higher concentrations of xenobiotics, significantly reducing costs while maintaining a rapid rate of remediation processes. This review explores the benefits of bacterial immobilization, highlighting materials and processes for developing an optimal immobilization matrix. It focuses on the following four key areas: (i) the types of organic pollutants impacting environmental and human health, (ii) the bacterial strains used in bioremediation processes, (iii) the types and benefits of immobilization, and (iv) the immobilization of bacterial cells on various carriers for targeted pollutant degradation.

Enhanced remediation of chlorpyrifos-contaminated soil by immobilized strain Bacillus H27

Chlorpyrifos is a pesticide widely used in agricultural production with a relatively long residual half-life in soil. Addressing the problem of residual chlorpyrifos is of universal concern. In this study, rice hull biochar was used as an immobilized carrier to prepare the immobilized strain H27 for the remediation of chlorpyrifos-contamination soil. Soil microorganisms after remediation were investigated by ecotoxicological methods. The immobilized strain H27 had the highest removal rate of chlorpyrifos when 10% bacterial solution was added to the liquid medium containing 0.075-0.109 mm diameter biochar cultured for 22 hr. This study on the removal of chlorpyrifos by immobilized strain H27 showed that the initial concentration of chlorpyrifos in solution was 25 mg/L, and the removal rate reached 97.4% after 7 days of culture. In the soil, the removal rate of the immobilized bacteria group increased throughout the experiment, which was significantly higher than that of the free bacteria and biochar treatment groups. The Biolog-ECO test, T-RFLP and RT-RCR were used to study the effects of the soil microbial community and nitrogen cycling functional genes during chlorpyrifos degradation. It was found that ICP group had the highest diversity index among the four treatment groups. The microflora of segment containing 114 bp was the dominant bacterial community, and the dominant microflora of the immobilized bacteria group was more evenly distributed. The influence of each treatment group on ammonia-oxidizing bacteria (AOB) was greater than on ammonia-oxidizing archaea (AOA). This study offers a sound scientific basis for the practical application of immobilized bacteria to reduce residual soil pesticides.

Remediation potential of an immobilized microbial consortium with corn straw as a carrier in polycyclic aromatic hydrocarbons contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are widespread in soils and threaten human health seriously. The immobilized microorganisms (IM) technique is an effective and environmentally sound approach for remediating PAH-contaminated soil. However, the knowledge of the remedial efficiency and the way IM operates using natural organic materials as carriers in complex soil environments is limited. In this study, we loaded a functional microbial consortium on corn straw to analyze the effect of IM on PAH concentration and explore the potential remediation mechanisms of IM in PAH-contaminated soil. The findings revealed that the removal rate of total PAHs in the soil was 88.25% with the application of IM after 20 days, which was 39.25% higher than the control treatment, suggesting that IM could more easily degrade PAHs in soil. The findings from high-throughput sequencing and quantitative PCR revealed that the addition of IM altered the bacterial community structure and key components of the bacterial network, enhanced cooperative relationships among bacteria, and increased the abundance of bacteria and functional gene copies such as nidA and nahAc in the soil, ultimately facilitating the degradation of PAHs in the soil. This study enhances our understanding of the potential applications of IM for the treatment of PAH-contaminated soil.

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.

Paenibacillus sp. Strain OL15 Immobilized in Agar as a Potential Bioremediator for Waste Lubricating Oil-Contaminated Soils and Insights into Soil Bacterial Communities Affected by Inoculations of the Strain and Environmental Factors

Waste lubricating oil is a widespread common soil pollutant. In this study, the waste lubricating oil degraders were isolated from the oil-contaminated soil. The bacterial strains OL6, OL15, and OL8, which tolerated a high concentration (10%) of waste lubricating oil, presented the degradation efficiency values (measured in culture broth) of 15.6 ± 0.6%, 15.5 ± 1%, and 14.8 ± 1%, respectively, and belonged to the genera Enterobacter, Paenibacillus, and Klebsiella, respectively. To maintain long survival, immobilization of a promising bioremediator, Paenibacillus sp. strain OL15, in agar exhibited the significantly highest number of surviving cells at the end of a 30-day incubation period, as compared to those in alginate and free cells. Remarkably, after being introduced into the soil contaminated with 10% waste lubricating oil, the strain OL15 immobilized in agar conferred the highest degradation percentage up to 45 ± 3%. Due to its merit as a promising soil pollutant degrader, we investigated the effect of an introduction of the strain OL15 on the alterations of a bacterial community in the oil-contaminated soil environments using 16S rRNA amplicon sequencing. The result revealed that the Proteobacteria, Acidobacteriota, Firmicutes, and Actinobacteriota were predominant phyla. The introduction of the strain affected the soil bacterial community structures by increasing total bacterial diversity and richness. The proportions of the genera Pseudomonas, Vibrio, Herbaspirillum, Pseudoalteromonas, Massilia, Duganella, Bacillus, Gordonia, and Sulfurospirillum were altered in response to the strain establishment. Soil pH, EC, OM, total N, P, Mg, Fe, and Zn were the major factors influencing the bacterial community compositions in the oil-contaminated soils.

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.

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.

Bamboo Tar as a Novel Fungicide: Its Chemical Components, Laboratory Evaluation, and Field Efficacy Against False Smut and Sheath Blight of Rice and Powdery Mildew and Fusarium Wilt of Cucumber

The application of agricultural and forest residues can benefit the environment and the economy; however, they also generate a large amount of byproducts. In this study, bamboo tar (BT), a waste product of bamboo charcoal production, was dissolved in natural ethanol and the surfactant alkyl glucoside to manufacture a 50% (wt/wt) BT emulsifiable concentrate (BTEC) biopesticide. BTEC was screened for fungicidal activity against pathogens. The greatest activity was seen against Ustilaginoidea virens with a half-maximal effective concentration (EC₅₀) value of 6 mg/liter. Four phytopathogenic fungi, Podosphaera xanthii, Rhizoctonia solani, Fusarium oxysporum, and Botrytis cinerea, showed EC₅₀ values of <60 mg/liter. Greenhouse tests in vivo showed 2,000 mg/liter BTEC had a 78.4% protective effect against U. virens, and replicated treatments had an 80.6% protective effect. In addition, replicated 2-year field trials were conducted in two geographic locations with four plant diseases: false smut (U. virens), rice sheath blight (Thanatephorus cucumeris [Frank] Donk), cucumber powdery mildew (P. xanthii), and cucumber Fusarium wilt (F. oxysporum). Results showed that 1,000 to 2,000 mg/liter BTEC significantly inhibited these diseases. Gas chromatography-mass spectrometry analysis showed that the total phenolic mass fractions of two BT samples were 45.39 and 48.26%. Eleven components were detected, and their percentage content was as follows (from high to low): 2,6-dimethoxyphenol > 2- or 4-ethylphenol > 2- or 4-methylphenol > phenol > 4-ethylguaiacol > dimethoxyphenol > 4-methylguaiacol > 4-propenyl-2,6-dimethoxyphenol > 2,4-dimethylphenol. Some of the phenolic compounds identified from the tar might be fungicidally active components. BT is a biochar waste, which has potential as a biofungicide and has promise in organic agriculture. The value of this tar may not be because of any fundamental physical differences from other synthetic fungicides but rather caused by reduced production expenses and more efficient use of waste products.

Mycoremediation of acetaminophen: Culture parameter optimization to improve efficacy

Untreated pharmaceutical pollution and their possibly toxic metabolites, resulting from overloaded wastewater treatment processes, end up in aquatic environments and are hazardous to the ecosystem homeostasis. Biological wastewater remediation could supplement traditional methods and overcome the release of these biologically active compounds in the environment. Mycoremediation is especially promising due to the unspecific nature of fungi to decompose compounds through exoenzymes and the uptake of compounds as nutrients. In the present study, we improved on the previous advances made using the fungus Mucor hiemalis to remediate one of the most commonly occurring pharmaceuticals, acetaminophen (APAP), at higher concentrations. The limitation of nitrogen, adjustment of pH, and comparison to, as well as co-cultivation with the white-rot fungus Phanerochaete chrysosporium, were tested. Nitrogen limitation did not significantly improve the APAP remediation efficiency of M. hiemalis. Maintaining the pH of the media improved the remediation restraint of 24 h previously observed. The APAP remediation efficiency of P. chrysosporium was far superior to that of M. hiemalis, and co-cultivation of the two resulted in a decreased remediation efficiency compared to P. chrysosporium in single.

Adsorption-Degradation of Polycyclic Aromatic Hydrocarbons in Soil by Immobilized Mixed Bacteria and Its Effect on Microbial Communities

The combined action of biosorption and biodegradation can achieve a remarkable reduction of organic pollutants. In this study, Pseudomonas sp. SDR4 and Mortierella alpina JDR7 were selected as the representative microorganisms to investigate adsorption and degradation of polycyclic aromatic hydrocarbons (PAHs) in soil using immobilization technology and the subsequent change of the microbial community structure. The results showed that the adsorption capacity of immobilized carriers was much higher than that of dead microorganisms and that the addition of dead microorganisms did not affect the adsorption characteristics of immobilized carriers. The chemical reaction was the major factor controlling the adsorption rate of PAHs in sterilized soil (CK), nonsterilized soil (CK-1), and soil amended with dead body immobilized JDR7 and SDR4 mixed bacteria (MB-D). The growth and metabolism of Pseudomonas sp. SDR4 and M. alpina JDR7 are the main reason for enhanced PAH degradation in the soil amended with living body immobilized JDR7, SDR4 mixed bacteria (MB).

The Preliminary Study on the Association Between PAHs and Air Pollutants and Microbiota Diversity

The purpose of this study was to investigate the association among polycyclic aromatic hydrocarbons (PAHs) exposure and air pollutants and the diversity of microbiota. Daily average concentrations of six common air pollutants were obtained from China National Environmental Monitoring Centre. The PAHs exposure levels were evaluated by external and internal exposure detection methods, including monitoring atmospheric PAHs and urinary hydroxyl-polycyclic aromatic hydrocarbon (OH-PAH) metabolite levels. We analyzed the diversity of environmental and commensal bacterial communities with 16S rRNA gene sequencing and performed functional enrichment with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Correlation analysis and logistic regression modeling were conducted to evaluate the relationship of PAHs levels with air pollutants and microbial diversity. Correlation analysis found that the concentrations of atmospheric PAHs were significantly positively correlated with those of PM₁₀, NO₂, and SO₂. There also was a positive correlation between the abundance of the genus Micrococcus (Actinobacteria) and high molecular weight PAHs, and Bacillus, such as genera and low molecular weight PAHs in the atmosphere. Logistic regression showed that the level of urinary 1-OHPyrene was associated with childhood asthma after sex and age adjustment. The level of urinary 1-OHPyrene was significantly positively correlated with that of PM_2.5 and PM₁₀. In addition, the level of 1-OHPyrene was positively correlated with oral Prevotella-7 abundance. Functional enrichment analysis demonstrated that PAHs exposure may disturb signaling pathways by the imbalance of commensal microbiota, such as purine metabolism, pyrimidine metabolites, lipid metabolism, and one carbon pool by folate, which may contribute to public health issues. Our results confirmed that atmospheric PAHs and urinary 1-OHPyrene were correlated with part of six common air pollutants and indicated that PAHs pollution may alter both environmental and commensal microbiota communities associated with health-related problems. The potential health and environmental impacts of PAHs should be further explored.

Microbial Interaction with Clay Minerals and Its Environmental and Biotechnological Implications

Clay minerals are very common in nature and highly reactive minerals which are typical products of the weathering of the most abundant silicate minerals on the planet. Over recent decades there has been growing appreciation that the prime involvement of clay minerals in the geochemical cycling of elements and pedosphere genesis should take into account the biogeochemical activity of microorganisms. Microbial intimate interaction with clay minerals, that has taken place on Earth’s surface in a geological time-scale, represents a complex co-evolving system which is challenging to comprehend because of fragmented information and requires coordinated efforts from both clay scientists and microbiologists. This review covers some important aspects of the interactions of clay minerals with microorganisms at the different levels of complexity, starting from organic molecules, individual and aggregated microbial cells, fungal and bacterial symbioses with photosynthetic organisms, pedosphere, up to environmental and biotechnological implications. The review attempts to systematize our current general understanding of the processes of biogeochemical transformation of clay minerals by microorganisms. This paper also highlights some microbiological and biotechnological perspectives of the practical application of clay minerals–microbes interactions not only in microbial bioremediation and biodegradation of pollutants but also in areas related to agronomy and human and animal health.

Bead-immobilized Pseudomonas stutzeri Y2 prolongs functions to degrade s-triazine herbicides in industrial wastewater and maize fields

Functional durability of bio-augmented microbes in contaminated fields remains a major challenge in bioremediation. In the present study, various immobilization materials and compositional combinations were designed and compared to enhance the functional durability of Pseudomonas stutzeri sp. Y2 for degradation of simazine, one of the most used herbicides, in industrial wastewater and maize fields. Among four combinations of materials tested, the optimal combination obtained from the orthogonal array trials was 14% polyvinyl alcohol (PVA), 1-3% sodium alginate (SA), 2% activated carbon (AC), and 1-2% Y2 cells (PSC-Y2), which yielded 1.7 fold faster degradation of simazine at 50 mg L^-1 than that by free Y2 cells in the industrial wastewater. The degradation half-lives (DT₅₀) of simazine (10 mg L^-1) by free Y2 cells and PSC-Y2 was 1.1 d and 5.3 d in laboratory soil, respectively. The DT₅₀ of simazine by PSC-Y2 at the recommended and double dosages of simazine (0.45 and 0.9 g ai·m^-2) was 17.2 d and 12.4 d in the maize fields, respectively, in comparison with 23 d and 17.4 d by free Y2 cells. In addition, the PSC-Y2 degraded 100% of atrazine and terbuthylazine, and 96% of propazine at an initial concentration of 50 mg L^-1 each in 4 days. This study provides an immobilization strategy to stabilize bacteria and prolong bacterial functions to treat s-triazine herbicides contaminated water and soil.

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.

Degradation of phenanthrene and fluoranthene in a slurry bioreactor using free and Ca-alginate-immobilized Sphingomonas pseudosanguinis and Pseudomonas stutzeri bacteria

Biodegradation studies of three- and four-ring polycyclic aromatic hydrocarbons (PAHs) (phenanthrene [PHE] and fluoranthene [FLU]) were conducted using free and Ca-alginate-immobilized Sphingomonas pseudosanguinis strain J1-q (S1) and Pseudomonas stutzeri strain (S2) in bench-scale sediment slurry reactors. In this study, the effects of sodium alginate (SA) dosage on the characteristics of immobilized bacterial beads were investigated. The results indicated a 3% alginate concentration was optimal for immobilizing bacteria for PHE and FLU degradation. Scanning electron microscopy (SEM) images of the immobilized beads showed the presence of honeycomb structures and abundant interstices in the beads, which provided adequate space for microorganism adhesion and proliferation. The biodegradation of PHE and FLU using both free and immobilized bacteria fit a first-order reaction model well. The degradation efficiencies of PHE and FLU using immobilized bacteria were higher than those of free bacteria in sediment slurry reactors. The removal percentages of PHE and FLU using immobilized indigenous bacteria strain S1 after 42 d were 63.16% and 56.94%, respectively, which were higher than the removal percentages of exogenous strain S2.

Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation

Chlorophenols are widespread and of environmental concern due to their toxic and carcinogenic properties. Development of less costly and less technically challenging remediation methods are needed; therefore, we developed a formulation based on micronized vermiculite that, when air-dried, resulted in a granular product containing the 4-chlorophenol (4-CP)-degrading Gram-positive bacterium Arthrobacter chlorophenolicus A6. This formulation and stabilization method yielded survival rates of about 60% that remained stable in storage for at least 3 months at 4 °C. The 4-CP degradation by the formulated and desiccated A. chlorophenolicus A6 cells was compared to that of freshly grown cells in controlled-environment soil microcosms. The stabilized cells degraded 4-CP equally efficient as freshly grown cells in two different set-ups using both hygienized and non-treated soils. The desiccated microbial product was successfully employed in an outdoor pot trial showing its effectiveness under more realistic environmental conditions. No significant phytoremediation effects on 4-CP degradation were observed in the outdoor pot experiment. The 4-CP degradation kinetics from both the microcosms and the outdoor pot trial were used to generate a predictive model of 4-CP biodegradation potentially useful for larger-scale operations, enabling better bioremediation set-ups and saving of resources. This study also opens up the possibility of formulating and stabilizing also other Arthrobacter strains possessing different desirable pollutant-degrading capabilities.

Study on the diffusion coefficients for ammonia nitrogen and nitrite and nitrate in PVA gels

In order to quantify the proliferation of polyvinyl alcohol (PVA) gels in a matrix and optimize the performance of mass transfer, activated carbon (AC) and CaCO₃ were selected as adding materials in this experiment. For the performance of mass transfer, the optimal conditions were analyzed using response surface method (RSM) considering the inter-correlated effects of the amount of AC and CaCO₃. For RSM, 13 trials resulted in a partial cubic polynomial equation, which best predicted the amount of residual debris after homogenization. The results of the study show that the effective diffusion coefficient test device can analysis the diffusion rate nitrogen, nitrite and nitrate within the PVA gels quantitatively; adding appropriate amounts of AC and CaCO₃ in the biological active filter can improve the performance of mass transfer effectively; the maximum effective diffusion coefficient of nitrogen and nitrite and nitrate in the packing were 1.3637 × 10^-9 and 1.0850 × 10^-9 and 1.0199 × 10^-9 m²/s, respectively, at optimal addition amount.

Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp

Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments.

Biodegradation of fluoranthene by a newly isolated strain of Bacillus stratosphericus from Mediterranean seawater of the Sfax fishing harbour, Tunisia

A physico-chemical characterization of seawater taken from the fishing harbour of Sfax, Tunisia, revealed a contamination by organic and inorganic micropollutants. An aerobic marine halotolerant Bacillus stratosphericus strain FLU5 was isolated after enrichment on fluoranthene, a persistent and toxic polycyclic aromatic hydrocarbon (PAH). GC-MS analyses showed that strain FLU5 was capable of degrading almost 45 % of fluoranthene (100 mg l(-1)), without yeast extract added, after 30 days of incubation at 30 g l(-1) NaCl and 37 °C. In addition, the isolate FLU5 showed a remarkable capacity to grow on a wide range of aliphatic, aromatic and complex hydrocarbons. This strain could also synthesize a biosurfactant which was capable of reducing the surface tension of the cell-free medium, during the growth on fluoranthene. The biodegradative abilities of PAHs are promising and can be used to perform the bioremediation strategies of seawaters and marine sediments contaminated by hydrocarbons.

Potential of Endophytic Bacterium Paenibacillus sp. PHE-3 Isolated from Plantago asiatica L. for Reduction of PAH Contamination in Plant Tissues

Endophytes are ubiquitous in plants, and they may have a natural capacity to biodegrade polycyclic aromatic hydrocarbons (PAHs). In our study, a phenanthrene-degrading endophytic Paenibacillus sp. PHE-3 was isolated from P. asiatica L. grown in a PAH-contaminated site. The effects of environmental variables on phenanthrene biodegradation by strain PHE-3 were studied, and the ability of strain PHE-3 to use high molecular weight PAH (HMW-PAH) as a sole carbon source was also evaluated. Our results indicated that pH value of 4.0–8.0, temperature of 30 °C–42 °C, initial phenanthrene concentration less than 100 mg·L⁻¹, and some additional nutrients are favorable for the biodegradation of phenanthrene by strain PHE-3. The maximum biodegradation efficiency of phenanthrene was achieved at 99.9% after 84 h cultivation with additional glutamate. Moreover, the phenanthrene biodegradation by strain PHE-3 was positively correlated with the catechol 2,3-dioxygenase activity (ρ = 0.981, p < 0.05), suggesting that strain PHE-3 had the capability of degrading HMW-PAHs. In the presence of other 2-, 3-ringed PAHs, strain PHE-3 effectively degraded HMW-PAHs through co-metabolism. The results of this study are beneficial in that the re-colonization potential and PAH degradation performance of endophytic Paenibacillus sp. PHE-3 may be applied towards reducing PAH contamination in plants.

Aerobic and anaerobic microbial degradation of crude (4-methylcyclohexyl)methanol in river sediments

Cyclohexane and some of its derivatives have been a major concern because of their significant adverse human health effects and widespread occurrence in the environment. The 2014 West Virginia chemical spill has raised public attention to (4-methylcyclohexyl)methanol (4-MCHM), one cyclohexane derivative, which is widely used in coal processing but largely ignored. In particular, the environmental fate of its primary components, cis- and trans-4-MCHM, remains largely unexplored. This study aimed to investigate the degradation kinetics and mineralization of cis- and trans-4-MCHM by sediment microorganisms under aerobic and anaerobic conditions. We found the removal of cis- and trans-4-MCHM was mainly attributed to biodegradation with little contribution from sorption. A nearly complete aerobic degradation of 4-MCHM occurred within 14 days, whereas the anaerobic degradation was reluctant with residual percentages of 62.6% of cis-4-MCHM and 85.0% of trans-4-MCHM after 16-day incubation. The cis-4-MCHM was degraded faster than the trans under both aerobic and anaerobic conditions, indicating an isomer-specific degradation could occur during the 4-MCHM degradation. Nitrate addition enhanced 4-MCHM mineralization by about 50% under both aerobic and anaerobic conditions. Both cis- and trans-4-MCHM fit well with the first-order kinetic model with respective degradation rates of 0.46-0.52 and 0.19-0.31 day(-)(1) under aerobic condition. Respective degradation rates of 0.041-0.095 and 0.013-0.052 day(-)(1) occurred under anaerobic condition. One bacterial strain capable of effectively degrading 4-MCHM isomers was isolated from river sediments and identified as Bacillus pumilus at the species level based on 16S rRNA gene sequence and 97% identity. Our findings will provide critical information for improving the prediction of the environmental fate of 4-MCHM and other cyclohexane derivatives with similar structure as well as enhancing the development of feasible treatment technologies to mitigate these compounds.

Variations in the bioavailability of polycyclic aromatic hydrocarbons in industrial and agricultural soils after bioremediation

The aim of this study was to demonstrate the variations in bioavailability remaining in industrial and agricultural soils contaminated by polycyclic aromatic hydrocarbons (PAHs) after bioremediation. After inoculation of Mycobacterium sp. and Mucor sp., PAH biodegradation was tested on a manufactured gas plant (MGP) soil and an agricultural soil. PAH bioavailability was assessed before and after biodegradation using solid-phase extraction (Tenax-TA extraction) and solid-phase micro-extraction (SPME) to represent bioaccessibility and chemical activity of PAHs, respectively. Only 3- and 4-ring PAHs were noticeably biodegradable in the MGP soil. PAH biodegradation in the agricultural soil was different from that in the MGP soil. The rapidly desorbing fractions (F(rap)) extracted by Tenax-TA and the freely dissolved concentrations of 3- and 4-ring PAHs determined by SPME from the MGP soil decreased after 30 days biodegradation; those values of the 5- and 6-ring PAHs changed to a lesser degree. For the agricultural soil, the F(rap) values of the 3- and 4-ring PAHs also decreased after the biodegradation experiment. The Tenax-TA extraction and the SPME have the potential to assess variations in the bioavailability of PAHs and the degree of biodegradation in contaminated MGP soils. In addition, Tenax-TA extraction is more sensitive than SPME when used in the agricultural soil.

A new approach for pyrene bioremediation using bacteria immobilized in layer-by-layer assembled microcapsules: dynamics of soil bacterial community

Pyrene-degrading bacteria immobilized in layer-by-layer assembled microcapsules were prepared and inoculated into pyrene-contaminated soil. The microcapsules enhanced the pyrene removal ability and improved the bacterial community construction.

In-Situ Remediation Approaches for the Management of Contaminated Sites: A Comprehensive Overview

Though several in-situ treatment methods exist to remediate polluted sites, selecting an appropriate site-specific remediation technology is challenging and is critical for successful clean up of polluted sites. Hence, a comprehensive overview of all the available remediation technologies to date is necessary to choose the right technology for an anticipated pollutant. This review has critically evaluated the (i) technological profile of existing in-situ remediation approaches for priority and emerging pollutants, (ii) recent innovative technologies for on-site pollutant remediation, and (iii) current challenges as well as future prospects for developing innovative approaches to enhance the efficacy of remediation at contaminated sites.

Adsorption-synergic biodegradation of diesel oil in synthetic seawater by acclimated strains immobilized on multifunctional materials

Using enrichment culture technique, three isolates marked as ODB-1, ODB-2 and ODB-3, were selected from oil contaminated seawater. 16S rDNA gene sequencing indicated that ODB-1 affiliated with Pseudomonas sp. while ODB-2 and ODB-3 affiliated with Brevundimonas sp. Subsequently, the bacterial cells were immobilized on the surface of expanded graphite (EG), expanded perlite (EP) and bamboo charcoal (BC). Among the three isolates, ODB-1 showed a strong binding to the bio-carriers through extracellular polysaccharides, while ODB-2 and ODB-3 made the adhesion to bio-carrier through direct physical adsorption. The immobilized bacteria exhibited good salinity tolerance compared with the planktonic bacteria. Their total diesel oil removal rates were more than 85% after 6 days' incubation. Adsorption-biodegradation process played an important role in the oil-pollution remediation. EG-bacteria system was treated as a promising remediation method, which achieved nearly 100% removal of diesel oil. Thereinto, over 83% removal of diesel oil owed to biodegradation.

Immobilization of Pseudomonas sp. DG17 onto sodium alginate-attapulgite-calcium carbonate

A strain of Pseudomonas sp. DG17, capable of degrading crude oil, was immobilized in sodium alginate-attapulgite-calcium carbonate for biodegradation of crude oil contaminated soil. In this work, proportion of independent variables, the laboratory immobilization parameters, the micromorphology and internal structure of the immobilized granule, as well as the crude oil biodegradation by sodium alginate-attapulgite-calcium carbonate immobilized cells and sodium alginate-attapulgite immobilized cells were studied to build the optimal immobilization carrier and granule-forming method. The results showed that the optimal concentrations of sodium alginate-attapulgite-calcium carbonate and calcium chloride were 2.5%-3.5%, 0.5%-1%, 3%-7% and 2%-4%, respectively. Meanwhile, the optimal bath temperature, embedding cell amount, reaction time and multiplication time were 50-60 °C, 2%, 18 h and 48 h, respectively. Moreover, biodegradation was enhanced by immobilized cells with a total petroleum hydrocarbon removal ranging from 33.56% ± 3.84% to 56.82% ± 3.26% after 20 days. The SEM results indicated that adding calcium carbonate was helpful to form internal honeycomb-like pores in the immobilized granules.

The Quality Control of Eutrophic Culture Sediment by Immobilized Cells and Conditions Manipulation

The sediment in intensive culture pond is overloaded by substantial unused nutrients and is conventionally discharged into adjacent coastal areas, which is detrimental to environment. This paper produced a preliminary quality control experiment to mitigate pollution of culture sediment by immobilized Bacillus sp. HSW cells on the composite carrier of sodium alginate and artificial zeolite. Glucose and calcium peroxide respectively were used to improve the sediment conditions of C/N ratio and oxygen level. The sediment quality was monitored periodically for 30 days. The results showed that biocontrol by immobilized Bacillus sp. HSW cells alone would be infeasible. However, the immobilized cells would better perform under controlled conditions. The significant decreases for total nitrogen (TN), total ammonia nitrogen (TAN), and organic nitrogen (ON) were observed at 71%, 91% and 64%, respectively. The phosphorus precipitated as phosphate raised approximately 120 mg/kg, and 60% of organic phosphorus was removed in 30 days. Moreover, the total bacteria abundance presented an obvious increase for over an order of magnitude, which was positive relationship (p < 0.01) to the removal rates of ON and OP. Therefore, the immobilized cells accompanied by environmental manipulation are promising for biocontrol of culture sediment.

Using biochar for remediation of soils contaminated with heavy metals and organic pollutants

Soil contamination with heavy metals and organic pollutants has increasingly become a serious global environmental issue in recent years. Considerable efforts have been made to remediate contaminated soils. Biochar has a large surface area, and high capacity to adsorb heavy metals and organic pollutants. Biochar can potentially be used to reduce the bioavailability and leachability of heavy metals and organic pollutants in soils through adsorption and other physicochemical reactions. Biochar is typically an alkaline material which can increase soil pH and contribute to stabilization of heavy metals. Application of biochar for remediation of contaminated soils may provide a new solution to the soil pollution problem. This paper provides an overview on the impact of biochar on the environmental fate and mobility of heavy metals and organic pollutants in contaminated soils and its implication for remediation of contaminated soils. Further research directions are identified to ensure a safe and sustainable use of biochar as a soil amendment for remediation of contaminated soils.

Identification of metabolites from benzo[a]pyrene oxidation by ligninolytic enzymes of Polyporus sp. S133

The biodegradation of benzo[a]pyrene (BaP) by using Polyporus sp. S133, a white-rot fungus isolated from oil-contaminated soil was investigated. Approximately 73% of the initial concentration of BaP was degraded within 30 d of incubation. The isolation and characterization of 3 metabolites by thin layer chromatography, column chromatography, and UV-vis spectrophotometry in combination with gas chromatography-mass spectrometry, indicated that Polyporus sp. S133 transformed BaP to BaP-1,6-quinone. This quinone was further degraded in 2 ways. First, BaP-1,6-quinone was decarboxylated and oxidized to form coumarin, which was then hydroxylated to hydroxycoumarin, and finally to hydroxyphenyl acetic acid by addition of an epoxide group. Second, Polyporus sp. S133 converted BaP-1,6-quinone into a major product, 1-hydroxy-2-naphthoic acid. During degradation, free extracellular laccase was detected with reduced activity of lignin peroxidase, manganese-dependent peroxidase and 2,3-dioxygenase, suggesting that laccase and 1,2-dioxygenase might play an important role in the transformation of PAHs compounds.

Biodegradation characteristics and bioaugmentation potential of a novel quinoline-degrading strain of Bacillus sp. isolated from petroleum-contaminated soil

Quinoline and its derivatives are widely considered to be environmental pollutants. In this study, the biodegradation characteristics and bioaugmentation potential for a novel strain were described. The strain, named Q2, which could utilize quinoline as the sole carbon, nitrogen and energy source, was isolated and identified as a Bacillus sp. The optimum temperature, initial pH and shaker rotary speed for quinoline degradation were 30°C, pH 8-10 and 100-200 rpm, respectively. During the biodegradation process, the quinoline-N was released as ammonium and the culture broth became yellow, pink and brown in turn, which indicated that several intermediates were generated. GC/MS analysis showed that 2(1H)-quinolinone and 8-hydroxycoumarin were produced. Furthermore, the bioaugmentation of Q2 into the sludge consortium, which was taken from refinery wastewater treatment plant, to degrade quinoline was investigated. The results showed that it could coexist with the other microbes and the remarkably enhanced quinoline biodegradation ability was achieved.

Degradation of pyrene by immobilized microorganisms in saline-alkaline soil

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) is very difficult in saline-alkaline soil due to the inhibition of microbial growth under saline-alkaline stress. The microorganisms that can most effectively degrade PAHs were screened by introducing microorganisms immobilized on farm byproducts and assessing the validity of the immobilizing technique for PAHs degradation in pyrene-contaminated saline-alkaline soil. Among the microorganisms examined, it was found that Mycobacterium sp. B2 is the best, and can degrade 82.2% and 83.2% of pyrene for free and immobilized cells after 30 days of incubation. The immobilization technique could increase the degradation of pyrene significantly, especially for fungi. The degradation of pyrene by the immobilized microorganisms Mucor sp. F2, fungal consortium MF and co-cultures of MB+MF was increased by 161.7% (P < 0.05), 60.1% (P < 0.05) and 59.6% (P < 0.05) after 30 days, respectively, when compared with free F2, MF and MB+MF. Scanning electron micrographs of the immobilized microstructure proved the positive effects of the immobilized microbial technique on pyrene remediation in saline-alkaline soil, as the interspace of the carrier material structure was relatively large, providing enough space for cell growth. Co-cultures of different bacterial and fungal species showed different abilities to degrade PAHs. The present study suggests that Mycobacterium sp. B2 can be employed for in situ bioremediation of PAHs in saline-alkaline soil, and immobilization of fungi on farm byproducts and nutrients as carriers will enhance fungus PAH-degradation ability in saline-alkaline soil.

Degradation pathway of pentachlorophenol by Mucor plumbeus involves phase II conjugation and oxidation-reduction reactions

Environmental pollution by pentachlorophenol (PCP) is a critical concern worldwide and fungal bioremediation constitutes an elegant and environment-friendly solution. Mucorales from the Zygomycota phylum are often observed to be competitive in field conditions and Mucor plumbeus, in particular, can efficiently deplete PCP from media. The pathway for PCP degradation used by this fungus has not been investigated. In this study, PCP-derived metabolites were identified by liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, including tetra- and tri-chlorohydroquinones and phase II-conjugated metabolites. Amongst the latter are the previously reported glucose, sulfate and ribose conjugates, and identified for the first time in fungi sulfate-glucose conjugates. A PCP transformation pathway for M. plumbeus is proposed, which excludes the involvement of cytochrome P-450 and extracellular ligninolytic enzymes.

Bacteria-mediated PAH degradation in soil and sediment

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.

DDT degradation potential of cattle manure compost

The purpose of this study was to investigate the ability of cattle manure compost (CMC) to degrade 1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane (DDT). DDT was degraded during composting and 1,1-dichloro-2,2-bis (4-chlorophenyl) ethane (DDD) was detected as a metabolic product. Degradation of DDT at 60 degrees C was the most effective of all the stages of composting. Fourteen strains of fungi were isolated and identified from CMC, and most of them were closely related to Mucor circinelloides and Galactomyces geotrichum. These fungi demonstrated a high ability to degrade DDT both at 30 and 60 degrees C in potato dextrose broth (PDB) medium. DDD and 4,4-dichlorobenzophenone (DBP) were detected as metabolic products. Degradation of DDT-contaminated soil was also investigated. Composting materials in the mesophilic stage exhibited the highest ability to degrade DDT in un-sterilized (USL) contaminated soil during a 28d incubation period. The isolated fungi possessed the ability to degrade DDT in sterilized (SL) and un-sterilized (USL) soils. These results indicated that CMC contains fungi that can be potentially used for bioremediation in DDT-contaminated environments.

Biodegradation of 2-naphthol and its metabolites by coupling Aspergillus niger with Bacillus subtilis

To explore biodegradation of 2-naphthol and its metabolites accumulated in wastewater treatment, a series of bio-degradation experiments were conducted. Two main metabolites of 2-naphthol, 1,2-naphthalene-diol and 1,2-naphthoquinone, were identified by high-performance liquid chromatography with standards. Combining fungus Aspergillus niger with bacterium Bacillus subtilis in the treatment enhanced 2-naphthol degradation efficiency, lowered the accumulation of the two toxic metabolites. There were two main phases during the degradation process by the kinetic analysis: 2-naphthol was first partly degraded by the fungus, producing labile and easily accumulated metabolites, and then the metabolites were mainly degraded by the bacterium, attested by the degradation processes of 1,2-naphthalene-diol and 1,2-naphthoquinone as sole source of carbon and energy. Sodium succinate, as a co-metabolic substrate, was the most suitable compound for the continuous degradation. The optimum concentration of 2-naphthol was 50 mg/L. The overall 2-naphthol degradation rate was 92%, and the CODcr removal rate was 80% on day 10. These results indicated that high degradation rate of 2-naphthol should not be considered as the sole desirable criterion for the bioremediation of 2-naphthol-contaminated soils/wastewater.

Biodegradation of the low concentration of polycyclic aromatic hydrocarbons in soil by microbial consortium during incubation

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) (8.15 mg PAHs kg(-1) soil) in aged contaminated soil by isolated microbial consortium (five fungi and three bacteria) during the incubation of 64d is reported. The applied treatments were: (1) biodegradation by adding microbial consortium in sterile soils (BM); (2) biodegradation by adding microbial consortium in non-sterile soils (BMN); and (3) biodegradation by in situ "natural" microbes in non-sterile soils (BNN). The fungi in BM and BMN soils grew rapidly 0-4d during the incubation and then reached a relative equilibrium. In contrast the fungi in BNN soil remained at a constant level for the entire time. Comparison with the fungi, the bacteria in BNN soils grew rapidly during the incubation 0-2d and then reached a relative equilibrium, and those in BM and BMN soils grew slowly during the incubation of 64 d. After 64 d of incubation, the PAH biodegradations were 35%, 40.7% and 41.3% in BNN, BMN and BM, respectively. The significant release of sequestrated PAHs in aged contaminated soil was observed in this experiment, especially in the BM soil. Therefore, although bioaugmentation of introduced microbial consortium increased significantly the biodegradation of PAHs in aged contaminated soil with low PAH concentration, the creation of optimum of the environmental situation might be the best way to use bioremediation successfully in the field.

Synergistic degradation of 2-naphthol by Fusarium proliferatum and Bacillus subtilis in wastewater

2-Naphthol, which originates widely from various industrial activities, is toxic and thus harmful to human liver and kidney. A new compound biodegradation system was adopted to degrade 2-naphthol-contaminated wastewater. Enzymatic response to 2-naphthol biodegradation in the aqueous phase was also studied. As a co-metabolic substrate, salicylic acid could induce the two microorganisms to produce a large amount of degradation enzymes for 2-naphthol. The key enzymes were confirmed as polyphenol oxidase (PPO) and catechol 2,3-dioxygenase (C23O). The degradation extent of 2-naphthol, determined by high performance liquid chromatography (HPLC), was enhanced by nearly 15% on the 6th day after the addition of the co-metabolic substrate. The results obtained thus clearly indicated that the co-metabolic process was the most important factor affecting the degradation of the target contaminant. The optimal concentration of 2-naphthol was 150 mg L(-1), and the optimal pH value was 7.0. The degradation extent of 2-naphthol was further enhanced by nearly 10% after the addition of Tween 80, which increased the bioavailability of 2-naphthol. In a practical treatment of industrial wastewater from medical manufacture, the synergistic degradation system resulted in a high degradation efficiency of 2-naphthol although its lag time was a little long in the initial stage.