Construction of PAH-degrading mixed microbial consortia by induced selection in soil

Enzymatic bioremediation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil: a study on the recombinant laccase TVL

Polycyclic aromatic hydrocarbons (PAHs) are pervasive and persistent pollutants in contaminated soil, posing a severe health and environmental threat. Enzymatic bioremediation presents a viable solution for the remediation of PAH-contaminated soil. In this study, a recombinant laccase with the encoding gene originating from Trametes villosa and recombinantly expressed in Aspergillus oryzae, designated as TVL, was discovered to possess strong PAH reduction capabilities. The specific enzyme activity of TVL was 73485 and 5102 LAMU/g enzyme protein at pH 5.0/7.0 and 37°C. Furthermore, it exhibited significant benzo[a]pyrene degradation, with 100% and 90.48% degradation at pH 5.0/7.0 after 24 h in the liquid phase. The degradation process of benzo[a]pyrene in soil was thoroughly investigated. Optimal conditions were identified as 15 mg/g NK-BSoil-3 and 1.35 mg/g HBT, resulting in a removal rate of 37.54% within 7 days when 0.01 U/g of TVL was applied. The potential mechanisms were investigated using molecular docking simulation. The binding energy between benzo[a]pyrene and TVL protein is notably robust, suggesting a higher propensity for enzyme binding. The TVL protein pocket contains nine amino acids that can interact most strongly with benzo[a]pyrene. Consequently, the recombinant laccase TVL holds considerable practical significance in bioremediation.

Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons

Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.

Importance of soil ecoenzyme stoichiometry for efficient polycyclic aromatic hydrocarbon biodegradation

Efficient remediation of soil contaminated by polycyclic aromatic hydrocarbons (PAHs) is challenging. To determine whether soil ecoenzyme stoichiometry influences PAH degradation under biostimulation and bioaugmentation, this study initially characterized soil ecoenzyme stoichiometry via a PAH degradation experiment and subsequently designed a validation experiment to answer this question. The results showed that inoculation of PAH degradation consortia ZY-PHE plus vanillate efficiently degraded phenanthrene with a K value of 0.471 (depending on first-order kinetics), followed by treatment with ZY-PHE and control. Ecoenzyme stoichiometry data revealed that the EEAC:N, vector length and angle increased before day five and decreased during the degradation process. In contrast, EEAN:P decreased and then increased. These results indicated that the rapid PAH degradation period induced more C limitation and organic P mineralization. Correlation analysis indicated that the degradation rate K was negatively correlated with vector length, EEAC:P, and EEAN:P, suggesting that C limitation and relatively less efficient P mineralization could inhibit biodegradation. Therefore, incorporating liable carbon and acid phosphatase or soluble P promoted PAH degradation in soils with ZY-PHE. This study provides novel insights into the relationship between soil ecoenzyme stoichiometry and PAH degradation. It is suggested that soil ecoenzyme stoichiometry be evaluated before designing bioremeiation stragtegies for PAH contanminated soils.

Risk assessment and biodegradation potential of PAHs originating from Map Ta Phut Industrial Estate, Rayong, Thailand

Petroleum hydrocarbon contamination is a serious concern across the globe. Here, the capability of native bacterial consortium enriched from sediment samples of Map Ta Phut Industrial Estate (MTPIE), Rayong, Thailand was described. The distribution of PAHs was assessed from the sediment samples collected from MTPIE by GC-FID and the toxic unit (TU) was calculated to assess the potential ecological risk to the surrounding biota. This study investigated the degradation potential and determined the PAH-degrading bacterial cultures by enriching collected sediments in PAHs mixtures (naphthalene, phenanthrene, and pyrene). The TPH degradation capacity of each bacterial consortium was validated in a soil microcosm using aged crude oil-contaminated soil. The MTPIE sediments were highly contaminated with PAHs (843.99-3904.39 ng g-1) and posed extremely high ecological risks to benthic biota (TU > 1). The consortium S5-P most significantly removed naphthalene (90.03%) and phenanthrene (88.14%) while the highest removal of pyrene was achieved by the S3-P consortium. Other consortia only partially degraded the PAHs. The dominant microbes in the consortia were determined using PCR-DGGE, it was found that the PAH degrading consortia were known PAH degraders such as Annwoodia, Bacillus, Brevibacillus, Lysinibacillus, Paracoccus, Rhodococcus, Sphingopyxis, Sulfurovum, and Sulfurimonas species and unknown PAH degraders such as Lithuaxuella species. The consortium S5-P showed the highest degradation capacity, removing 74.99% of TPHs in the soil microcosm. Furthermore, the inoculation of PAH-biodegrading bacterial consortia significantly promoted the catechol-2,3-dioxygenase (C23O) and dehydrogenase (DHA) activities which directly correlated with the degradation efficiency of petroleum hydrocarbons (p < 0.05).

The bioremediation of the typical persistent organic pollutants (POPs) by microalgae-bacteria consortia: A systematic review

With industrialisation and the rapidly growing agricultural demand, many organic compounds have been leaked into the environment, causing serious damage to the biosphere. Persistent organic pollutants (POPs) are a type of toxic chemicals that are resistant to degradation through normal chemical, biological or photolytic approaches. With their stable chemical structures, POPs can be accumulated in the environment, and transported through wind and water, causing global environmental issues. Many researches have been conducted to remediate POPs contamination using various kinds of biological methods, and significant results have been seen. Microalgae-bacteria consortium is a newly developed concept for biological technology in contamination treatment, with the synergetic effects between microalgae and bacteria, their potential for pollutants degradation can be further released. In this review, two types of POPs (polychlorinated biphenyls and polycyclic aromatic hydrocarbons) are selected as the targeted pollutants to give a systematic analysis of the biodegradation through microalgae and bacteria, including the species selection, the identification of dominant enzymes, as well as the real application performance of the consortia. In the end, some outlooks and suggestions are given to further guide the development of applying microalgae-bacteria consortia in remediating POPs contamination. In general, the coculturing of microalgae and bacteria is a novel and efficient way to fulfil the advanced treatment of POPs in soil or liquid phase, and both monooxygenase and dioxygenase belonging to oxygenase play a vital role in the biodegradation of PCBs and PAHs. This review provides a general guide in the future investigation of biological treatment of POPs.

Using Fungi in Artificial Microbial Consortia to Solve Bioremediation Problems

There is currently growing interest in the creation of artificial microbial consortia, especially in the field of developing and applying various bioremediation processes. Heavy metals, dyes, synthetic polymers (microplastics), pesticides, polycyclic aromatic hydrocarbons and pharmaceutical agents are among the pollutants that have been mainly targeted by bioremediation based on various consortia containing fungi (mycelial types and yeasts). Such consortia can be designed both for the treatment of soil and water. This review is aimed at analyzing the recent achievements in the research of the artificial microbial consortia that are useful for environmental and bioremediation technologies, where various fungal cells are applied. The main tendencies in the formation of certain microbial combinations, and preferences in their forms for usage (suspended or immobilized), are evaluated using current publications, and the place of genetically modified cells in artificial consortia with fungi is assessed. The effect of multicomponence of the artificial consortia containing various fungal cells is estimated, as well as the influence of this factor on the functioning efficiency of the consortia and the pollutant removal efficacy. The conclusions of the review can be useful for the development of new mixed microbial biocatalysts and eco-compatible remediation processes that implement fungal cells.

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Development of a highly tolerant bacterial consortium for asphaltene biodegradation in soils

Asphaltenes are the most polar and heavy fraction of petroleum, and their complex structure and toxicity make them resistant to biodegradation. The ability to tolerate high asphaltene concentrations is crucial to reducing the toxicity-related inhibition of microbial growth and improving their capacity for adaptation, survival, and biodegradation in soils highly contaminated with asphaltenes. This study developed a highly tolerant consortium for efficient asphaltene biodegradation in soils from 22 bacterial isolates obtained from heavy-crude oil-contaminated soils. Isolates corresponded to the Rhodococcus, Bacillus, Stutzerimonas, Cellulosimicrobium, Pseudomonas, and Paenibacillus genera, among others, and used pure asphaltenes and heavy crude oil as the only carbon sources. Surface plate assays were used to evaluate the tolerance of individual isolates to asphaltenes, and the results showed variations in the extension and inhibition rates with maximum tolerance levels at 60,000 mg asphaltenes l-1. Inhibition assays were used to select non-antagonistic bacterial isolates among those showing the highest tolerance levels to asphaltenes. A consortium made up of the five most tolerant and non-antagonistic bacterial isolates was able to degrade up to 83 wt.% out of 10,000 mg asphaltenes kg-1 in the soil after 52 days. Due to its biological compatibility, high asphaltene tolerance, and ability to utilise it as a source of energy, the degrading consortium developed in this work has shown a high potential for soil bioremediation and is a promising candidate for the treatment of aged soil areas contaminated with heavy and extra-heavy crude oil. This would be the first research to assess and consider extreme bacterial tolerance and microbial antagonism between individual degrading microbes, leading to the development of an improved consortium capable of efficiently degrading high amounts of asphaltenes in soil.

Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review

A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.

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

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

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

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

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

Bioremediation of heavy oily sludge: a microcosms study

Oily sludge is a residue from the petroleum industry composed of a mixture of sand, water, metals, and high content of hydrocarbons (HCs). The heavy oily sludge used in this study originated from Colombian crude oil with high density and low American Petroleum Institute (API) gravity. The residual waste from heavy oil processing was subject to thermal and centrifugal extraction, resulting in heavy oily sludge with very high density and viscosity. Biodegradation of the total petroleum hydrocarbons (TPH) was tested in microcosms using several bioremediation approaches, including: biostimulation with bulking agents and nutrients, the surfactant Tween 80, and bioaugmentation. Select HC degrading bacteria were isolated based on their ability to grow and produce clear zones on different HCs. Degradation of TPH in the microcosms was monitored gravimetrically and with gas chromatography (GC). The TPH removal in all treatments ranged between 2 and 67%, regardless of the addition of microbial consortiums, amendments, or surfactants within the tested parameters. The results of this study demonstrated that bioremediation of heavy oily sludge presents greater challenges to achieve regulatory requirements. Additional physicochemical treatments analysis to remediate this recalcitrant material may be required to achieve a desirable degradation rate.

Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology

Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Construction of bifunctional bacterial community for co-contamination remediation: Pyrene biodegradation and cadmium biomineralization

Polycyclic aromatic hydrocarbons and heavy metals are typical pollutants in the non-ferrous metal smelting industry. The combination of biodegradation and biomineralization has great development potential for co-contamination removal as an environmentally friendly method. Pyrene (Pyr) and cadmium (Cd) were regarded as model pollutants of co-contamination in this study. A bifunctional bacterial community named Ycp was screened from a non-ferrous smelting slag field soil. The 16S rRNA gene high throughput sequencing analysis showed that Enterobacter was the dominant genus (99.1%). Ycp had adaptability under a wide range of environmental conditions (pH 3-9, salinity 0-10 g L^-1 NaCl, Pyr concentration 0-50 mg L^-1, Cd concentration 0-100 mg L^-1), and the removal rate of Pyr and Cd reached 41.8%-76.9%, 82.8%-98.8%, respectively. It was found that compound carbon sources had promoting effect on the removal of Pyr and Cd, with the maximum removal rate of 88.3% and 98.0%. According to the degradation products of Pyr by LC-MS analysis and the mineralized products of Cd²⁺ by XRD and SEM-EDS analysis, the mechanism of Ycp for co-contamination remediation was: Ycp biodegraded Pyr through salicylic acid and phthalic acid metabolic pathways, and biomineralized Cd²⁺ into CdCO₃ through microbially induced carbonate precipitation. This study provided a basis for microbial remediation of co-contamination.

Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing

Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a “top-down” synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L−1 CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only “functional bacteria” with degradation capacity but also “auxiliary bacteria” without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of “auxiliary bacteria” should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.

Phytoremediation of soil contaminated with weathered petroleum hydrocarbons by applying mineral fertilization, an anionic surfactant, or hydrocarbonoclastic bacteria

This study evaluated the effect of the application of mineral fertilization (F), the anionic surfactant Triton X-100 (TX100), or the inoculation with a hydrocarbooclastic bacterial consortium (BCons) on the growth of Clitoria ternatea during the phytoremediation of a Gleysol contaminated with weathered petroleum hydrocarbons (39,000 mg kg^-1 WPH) collected from La Venta, Tabasco (Mexico). The experiment consisted of a completely randomized design with seven treatments and four replications each under greenhouse conditions. The application of F (biostimulation) increased plant growth and biomass production; in contrast, TX100 only favored root biomass (11%) but significantly favored WPH degradation. Bioaugmentation with BCons did not show significant effects on plant growth. Nevertheless, the combination of biostimulation with bioaugmentation (BCons + F, BCons + TX100, and BCons + F+TX100) enhanced plant growth, hydrocarbonoclastic bacteria population, and WPH degradation when compared to treatments with the single application of bioaugmentation (BCons) or biostimulation (F).

Bioaugmentation as a green technology for hydrocarbon pollution remediation. Problems and prospects

Environmental pollution mitigation measure involving bioremediation technology is a sustainable intervention for a greener ecosystem biorecovery, especially the obnoxious hydrocarbons, xenobiotics, and other environmental pollutants induced by anthropogenic stressors. Several successful case studies have provided evidence to this paradigm including the putative adoption that the technology is eco-friendly, cost-effective, and shows a high tendency for total contaminants mineralization into innocuous bye-products. The present review reports advances in bioremediation, types, and strategies conventionally adopted in contaminant clean-up. It identified that natural attenuation and biostimulation are faced with notable limitations including the poor remedial outcome under the natural attenuation system and the residual contamination occasion following a biostimulation operation. It remarks that the use of genetically engineered microorganisms shows a potentially promising insight as a prudent remedial approach but is currently challenged by few ethical restrictions and the rural unavailability of the technology. It underscores that bioaugmentation, particularly the use of high cell density assemblages referred to as microbial consortia possess promising remedial prospects thus offers a more sustainable environmental security. The authors, therefore, recommend bioaugmentation for large scale contaminated sites in regions where environmental degradation is commonplace.

Negative correlations between cultivable and active-yet-uncultivable pyrene degraders explain the postponed bioaugmentation

Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs), but suffers from unsatisfactory performance in engineering practices, which is hypothetically explained by the complicated interactions between indigenous microbes and introduced degraders. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium (Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira) by magnetic-nanoparticle mediated isolation (MMI) from soils. Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, whilst increased by 30.17% by the active pyrene degrading consortium. Pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP) were enriched in MMI isolates and positively correlated with pyrene degradation efficiency. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas both phthalate and salicylate pathways were observed in the active pyrene degrading consortium. The results indicated that the uncultivable pyrene degraders were suitable for bioaugmentation, rather than cultivable Sphingomonas sp. YT1005. The negative correlations between Sphingomonas sp. YT1005 and the active-yet-uncultivable pyrene degraders were the underlying mechanisms of bioaugmentation postpone in engineering practices.

Biological Detoxification of Mycotoxins: Current Status and Future Advances

Mycotoxins are highly toxic metabolites produced by fungi that pose a huge threat to human and animal health. Contamination of food and feed with mycotoxins is a worldwide issue, which leads to huge financial losses, annually. Decades of research have developed various approaches to degrade mycotoxins, among which the biological methods have been proved to have great potential and advantages. This review provides an overview on the important advances in the biological removal of mycotoxins over the last decade. Here, we provided further insight into the chemical structures and the toxicity of the main mycotoxins. The innovative strategies including mycotoxin degradation by novel probiotics are summarized in an in-depth discussion on potentialities and limitations. We prospected the promising future for the development of multifunctional approaches using recombinant enzymes and microbial consortia for the simultaneous removal of multiple mycotoxins.

Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil

The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.

Success of microbial genes based transgenic crops: Bt and beyond Bt

Transgenic technology could hold the key to help farmers to fulfill the ever increasing fast-paced global demand for food. Microbes have always wondered us by their potentials and thriving abilities in the extreme conditions. The use of microorganisms as a gene source in transgenic development is a promising option for crop improvement. The aforesaid approach has already for improving the characteristics of food, industrial, horticulture, and floriculture crops. Many transgenic crops containing microbial genes have been accepted by the farmers and consumers worldwide over the last few decades. The acceptance has brought remarkable changes in the status of society by providing food safety, economic, and health benefits. Among transgenic plants harboring microbial genes, Bacillus thuringiensis (Bt) based transgenic were more focused and documented owing to its significant performance in controlling insects. However, other microbial gene-based transgenic plants have also reserved their places in the farmer's field globally. Therefore, in this review, we have thrown some light on successful transgenic plants harboring microbial genes other than Bt, having application in agriculture. Also, we presented the role of microbial genetic element and product thereof in the inception of biotechnology and discussed the potential of microbial genes in crop improvement.

Synthetically engineered microbial scavengers for enhanced bioremediation

Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.

Effect of biostimulation and bioaugmentation on hydrocarbon degradation and detoxification of diesel-contaminated soil: a microcosm study

Soil contamination with diesel oil is quite common during processes of transport and storage. Bioremediation is considered a safe, economical, and environmentally friendly approach for contaminated soil treatment. In this context, studies using hydrocarbon bioremediation have focused on total petroleum hydrocarbon (TPH) analysis to assess process effectiveness, while ecotoxicity has been neglected. Thus, this study aimed to select a microbial consortium capable of detoxifying diesel oil and apply this consortium to the bioremediation of soil contaminated with this environmental pollutant through different bioremediation approaches. Gas chromatography (GC-FID) was used to analyze diesel oil degradation, while ecotoxicological bioassays with the bioindicators Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis sativus were used to assess detoxification. After 90 days of bioremediation, we found that the biostimulation and biostimulation/bioaugmentation approaches showed higher rates of diesel oil degradation in relation to natural attenuation (41.9 and 26.7%, respectively). Phytotoxicity increased in the biostimulation and biostimulation/bioaugmentation treatments during the degradation process, whereas in the Microtox test, the toxicity was the same in these treatments as that in the natural attenuation treatment. In both the phytotoxicity and Microtox tests, bioaugmentation treatment showed lower toxicity. However, compared with natural attenuation, this approach did not show satisfactory hydrocarbon degradation. Based on the microcosm experiments results, we conclude that a broader analysis of the success of bioremediation requires the performance of toxicity bioassays.

PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres

Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Futuristic avenues of metabolic engineering techniques in bioremediation

Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.

Difference in the rhizosphere microbiome of Melia azedarach during removal of benzo(a)pyrene from cadmium co-contaminated soil

Benzo(a)pyrene (BaP) is a highly persistent biohazard polyaromatic hydrocarbon and often reported to be present in soils co-contaminated with heavy metals. The present study explains the rhizodegradation of BaP using bacterial consortium in the rhizosphere of Melia azedarach, along with a change in taxonomical and functional properties of the rhizosphere microbiome. The relative abundance of most dominant phylum Proteobacteria was 2% higher with BaP, while in the presence of both BaP and Cd, its abundance was 2.2% lower. Functional metagenome analysis also revealed the shifting of microbial community and functional gene abundance in the favor of xenobiotic compound degradation upon augmentation of bacterial consortium. Interestingly, upon the addition of BaP the range of functional abundance for genes of PAH degradation (0.165-0.19%), was found to be decreasing. However, augmentation of a bacterial consortium led to an increase in its abundance including genes for degradation of benzoate (0.55-0.64%), toluene (0.2-0.22%), naphthalene (0.25-0.295%) irrespective of the addition of BaP and Cd. Moreover, under greenhouse condition, the application of M. azedarach-bacterial consortium enhanced the degradation of BaP in the rhizosphere (88%) after 60 days, significantly higher than degradation in bulk soil (68.22%). The analysis also showed an increase in degradation of BaP by 15% with plant-native microbe association than in bulk soil. Therefore, the association of M. azedarach-bacterial consortium enhanced the degradation of BaP in soil along with the taxonomical and functional attributes of the rhizosphere microbiome.

The crucial role of bacterial laccases in the bioremediation of petroleum hydrocarbons

Laccases (EC 1.10.3.2) are a class of metallo-oxidases found in a variety of fungi, plants, and bacteria as well as in certain insects. They can oxidize a wide variety of organic compounds and can be widely applied in many fields, especially in the field of biodegradation and detoxification of environmental pollutants. The practical efficacy of laccases depends on their ability to capture the target substance as well as their catalytic activity, which is related to their catalytic center, substrate selectivity, and substrate tolerance. Over the past few decades, many laccases have been identified in plants and fungi. Concurrently, bacterial laccases have received increasing attention because of their high thermostability and high tolerance to organic compounds. The aim of this review is to summarize the role of bacterial laccases in the bioremediation of petroleum hydrocarbons and to outline the correlation between the molecular structure of the mononuclear T1 Cu center of bacterial laccases and their substrate preference.

Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons

Mycoremediation holds great potential in remedying toxic environments contaminated with polyaromatic organic pollutants. To harness the natural process for practical applications, understanding the genetic and molecular basis of the remediation process is prerequisite. Compared to known bacterial degradation pathways of aromatic pollutants, however, the fungal degradation system is less studied and understanding of the genetic basis for biochemical activity is still incomplete. In this review, we surveyed recent findings from genomic and transcriptomic approaches to mycoremediation of aromatic pollutants, in company with the genomic basis of polycyclic aromatic hydrocarbon (PAH) degradation by basidiomycete fungi, Dentipellis sp. KUC8613. Unique features in the fungal degradation of PAHs were outlined by multiple cellular processes: (i) the initial oxidation of recalcitrant contaminants by various oxidoreductases including mono- and dioxygenases, (ii) the following detoxification, and (iii) the mineralization of activated pollutants that are common metabolism in many fungi. Along with the genomic data, the transcriptomic analysis not only posits a full repertoire of inducible genes that are common or specific to metabolize different PAHs but also leads to the discovery of uncharacterized genes with potential functions for bioremediation processes. In addition, the metagenomic study accesses community level of mycoremediation process to seek for the potential species or a microbial consortium in the natural environments. The comprehensive understanding of fungal degradation in multiple levels will accelerate practical application of mycoremediation. Key points • Mycoremediation of polyaromatic pollutants exploits a potent fungal degrader. • Fungal genomics provides a full repository of potential genes and enzymes. • Mycoremediation is a concerted cellular process involved with many novel genes. • Multi-omics approach enables the genome-scale reconstruction of remedying pathways.

Assessing interactions, predicting function, and increasing degradation potential of a PAH-degrading bacterial consortium by effect of an inoculant strain

A natural phenanthrene-degrading consortium CON was inoculated with an exogenous strain Sphingobium sp. (ex Sp. paucimobilis) 20006FA yielding the consortium called I-CON, in order to study ecological interactions into the bacterial community. DGGE and proteomic profiles and analyses by HTS (High-Throughput Sequencing) technologies demonstrated inoculant establishment and changes on CON composition. Inoculation increased degradation efficiency in I-CON and prevented intermediate HNA accumulation. This could be explained not only by the inoculation, but also by enrichment in Achromobacter genus at expense of a decrease in Klebsiella genus. After inoculation, cooperation between Sphingobium and Achromobacter genera were improved, thereby, some competition could have been generated, and as a consequence, species in minor proportion (cheaters), as Inquilinus sp. and Luteibacter sp., were not detected. Sequences of Sphingobium (corresponding to the inoculated strain) did not vary. PICRUSt predicted a network with bacterial phylotypes connected with enzymes, showing functional redundancy in the phenanthrene pathway, with exception of the first enzymes biphenyl-2,3-diol 1,2-dioxygenase and protocatechuate 4,5-dioxygenase that were only encoded in Sphingobium sp. This is the first report where a natural consortium that has been characterized by HTS technologies is inoculated with an exogenous strain in order to study competitiveness and interactions.

Investigation and Assessment for an effective approach to the reclamation of Polycyclic Aromatic Hydrocarbon (PAHs) contaminated site: SIN Bagnoli, Italy

Native plant species were screened for their remediation potential for the removal of Polycyclic Aromatic Hydrocarbons (PAHs) contaminated soil of Bagnoli brownfield site (Southern Italy). Soils at this site contain all of the PAHs congeners at concentration levels well above the contamination threshold limits established by Italian environmental legislation for residential/recreational land use, which represent the remediation target. The concentration of 13 High Molecular Weight Polycyclic Aromatic Hydrocarbons in soil rhizosphere, plants roots and plants leaves was assessed in order to evaluate native plants suitability for a gentle remediation of the study area. Analysis of soil microorganisms are provides important knowledge about bioremediation approach. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria are the main phyla of bacteria observed in polluted soil. Functional metagenomics showed changes in dioxygenases, laccase, protocatechuate, and benzoate-degrading enzyme genes. Indolacetic acid production, siderophores release, exopolysaccharides production and ammonia production are the key for the selection of the rhizosphere bacterial population. Our data demonstrated that the natural plant-bacteria partnership is the best strategy for the remediation of a PAHs-contaminated soil.

Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

Enhanced microbial degradation of benzo[a]pyrene by chemical oxidation

Chemical oxidation and microbial degradation are promising treatments to remediate soils contaminated with persistent organic pollutants. Moderate pre-oxidation is able to enhance the subsequent bioremediation of organic pollutants in soil. In this study, the effects of pre-oxidation on the subsequent biodegradation of benzo[a]pyrene (BaP) were evaluated. The tested oxidants included potassium permanganate (PP) and iron-activated sodium persulfate (PS) at the concentration of 1-40 mmol L^-1. The results showed that 20 mmol L^-1 PS and 10 mmol L^-1 PP treatments had the highest degradation efficiency of BaP in soil, up to 98.7% and 84.2%, without inhibiting subsequent microbial degradation. 10-20 mmol L^-1 of the two oxidants significantly promoted viability of microbial community. Especially, PS facilitated the occurrence of more PAHs-degrading microorganisms. The expression of PAH-degradation gene in PS treatment was significantly higher than that in PP treatment (P < 0.05), leading to 12.0-18.4% higher degradation efficiencies of BaP. In general, proper oxidants of moderate dosages were able to promote microbial bioremediation of persistent organic pollutants in soil.

Bioremediation of triphenyl phosphate in river water microcosms: Proteome alteration of Brevibacillus brevis and cytotoxicity assessments

Triphenyl phosphate (TPHP), an organophosphate flame retardant, was detected in river water samples collected from an electronic waste recycling area in Guiyu, Southern China. The concentrations of TPHP ranged from not detected to 347.2 ng/L, with an average of 138.8 ng/L. The bioaugmentation potential of Brevibacillus brevis on TPHP biodegradation by aerobic microcosms contained in river water from Guiyu was assessed. The results showed that TPHP degradation efficiency was significantly improved to 97.9% by bioaugmentation with B. brevis after 96 h incubation. A total of 182 significantly changed proteins in B. brevis were identified and quantified by isobaric tags for relative and absolute quantification (iTRAQ) in response to TPHP stress. The differentially expressed proteins were mainly associated with energy metabolism, lipid metabolism, cell wall biosynthesis, amino acid transport, and metabolism. The identification that proteins of B. brevis respond to TPHP existence provides novel insights into biodegradation mechanisms of bacteria under environmental stress. Additionally, cytotoxicity assays indicated that the degrading intermediates of TPHP, namely diphenyl phosphate and phenyl phosphate, were less cytotoxic to human HepG2 cells compared with TPHP. Collectively, these findings suggest that aerobic bioaugmentation with degrading microorganisms is a potential strategy for in situ treatment of TPHP-contaminated sites.

Rubber gloves biodegradation by a consortium, mixed culture and pure culture isolated from soil samples

An increasing production of natural rubber (NR) products has led to major challenges in waste management. In this study, the degradation of rubber latex gloves in a mineral salt medium (MSM) using a bacterial consortium, a mixed culture of the selected bacteria and a pure culture were studied. The highest 18% weight loss of the rubber gloves were detected after incubated with the mixed culture. The increased viable cell counts over incubation time indicated that cells used rubber gloves as sole carbon source leading to the degradation of the polymer. The growth behavior of NR-degrading bacteria on the latex gloves surface was investigated using the scanning electron microscope (SEM). The occurrence of the aldehyde groups in the degradation products was observed by Fourier Transform Infrared Spectroscopy analysis. Rhodococcus pyridinivorans strain F5 gave the highest weight loss of rubber gloves among the isolated strain and posses latex clearing protein encoded by lcp gene. The mixed culture of the selected strains showed the potential in degrading rubber within 30 days and is considered to be used efficiently for rubber product degradation. This is the first report to demonstrate a strong ability to degrade rubber by Rhodococcus pyridinivorans.

Biotechnological Advances for Restoring Degraded Land for Sustainable Development

Global land resources are under severe threat due to pollution and unsustainable land use practices. Restoring degraded land is imperative for regaining ecosystem services, such as biodiversity maintenance and nutrient and water cycling, and to meet the food, feed, fuel, and fibre requirements of present and future generations. While bioremediation is acknowledged as a promising technology for restoring polluted and degraded lands, its field potential is limited for various reasons. However, recent biotechnological advancements, including producing efficient microbial consortia, applying enzymes with higher degrees of specificity, and designing plants with specific microbial partners, are opening new prospects in remediation technology. This review provides insights into such promising ways to harness biotechnology as ecofriendly methods for remediation and restoration.