Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains

Allosteric-Regulation-Based DNA Circuits in Saccharomyces cerevisiae to Detect Organic Acids and Monitor Hydrocarbon Metabolism In Vitro

We show the engineering of prokaryotic-transcription-factor-based biosensing devices in Saccharomyces cerevisiae cells for an in vitro detection of common hydrocarbon intermediates/metabolites and potentially, for monitoring of the metabolism of carbon compounds. We employed the bacterial receptor proteins MarR (multiple antibiotic-resistant receptor) and PdhR (pyruvate dehydrogenase-complex regulator) to detect benzoate/salicylate and pyruvate, respectively. The yeast-enhanced green fluorescence protein (yEGFP) was adopted as an output signal. Indeed, the engineered yeast strains showed a strong and dynamic fluorescent output signal in the presence of the input chemicals ranging from 2 fM up to 5 mM. In addition, we describe how to make use of these strains to assess over time the metabolism of complex hydrocarbon compounds due to the hydrocarbon-degrading fungus Trichoderma harzianum (KY488463).

The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.

Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy

The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the development of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well understood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombinant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.

Enhanced mercury phytoremediation by Pseudomonodictys pantanalensis sp. nov. A73 and Westerdykella aquatica P71

Mercury is a non-essential and toxic metal that induces toxicity in most organisms, but endophytic fungi can develop survival strategies to tolerate and respond to metal contaminants and other environmental stressors. The present study demonstrated the potential of mercury-resistant endophytic fungi in phytoremediation. We examined the functional traits involved in plant growth promotion, phytotoxicity mitigation, and mercury phytoremediation in seven fungi strains. The endophytic isolates synthesized the phytohormone indole-3-acetic acid, secreted siderophores, and solubilized phosphate in vitro. Inoculation of maize (Zea mays) plants with endophytes increased plant growth attributes by up to 76.25%. The endophytic fungi stimulated mercury uptake from the substrate and promoted its accumulation in plant tissues (t test, p < 0.05), preferentially in the roots, which thereby mitigated the impacts of metal phytotoxicity. Westerdykella aquatica P71 and the newly identified species Pseudomonodictys pantanalensis nov. A73 were the isolates that presented the best phytoremediation potential. Assembling and annotation of P. pantanalensis A73 and W. aquatica P71 genomes resulted in genome sizes of 45.7 and 31.8 Mb that encoded 17,774 and 11,240 protein-coding genes, respectively. Some clusters of genes detected were involved in the synthesis of secondary metabolites such as dimethylcoprogen (NRPS) and melanin (T1PKS), which are metal chelators with antioxidant activity; mercury resistance (merA and merR1); oxidative stress (PRX1 and TRX1); and plant growth promotion (trpS and iscU). Therefore, both fungi species are potential tools for the bioremediation of mercury-contaminated soils due to their ability to reduce phytotoxicity and assist phytoremediation.

An inclusive outlook on the fate and persistence of pesticides in the environment and integrated eco-technologies for their degradation

Intensive and inefficient exploitation of pesticides through modernized agricultural practices has caused severe pesticide contamination problems to the environment and become a crucial problem over a few decades. Due to their highly toxic and persistent properties, they affect and get accumulated in non-target organisms, including microbes, algae, invertebrates, plants as well as humans, and cause severe issues. Considering pesticide problems as a significant issue, researchers have investigated several approaches to rectify the pesticide contamination problems. Several analyses have provided an extensive discussion on pesticide degradation but using specific technology for specific pesticides. However, in the middle of this time, cleaner techniques are essential for reducing pesticide contamination problems safely and environmentally friendly. As per the research findings, no single research finding provides concrete discussion on cleaner tactics for the remediation of contaminated sites. Therefore, in this review paper, we have critically discussed cleaner options for dealing with pesticide contamination problems as well as their advantages and disadvantages have also been reviewed. As evident from the literature, microbial remediation, phytoremediation, composting, and photocatalytic degradation methods are efficient and sustainable and can be used for treatment at a large scale in engineered systems and in situ. However, more study on the bio-integrated system is required which may be more effective than existing technologies.

Catalases in the pathogenesis of Sporothrix schenckii research

Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H₂O₂, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.

Synthetic Saccharomyces cerevisiae tolerate and degrade highly pollutant complex hydrocarbon mixture

Fungal laccase (Lac) has become a very useful biocatalyst in different industries, bio-refineries and, most importantly, bioremediation. Many reports have also linked hydrocarbon tolerance and degradation by various microorganisms with Lac secretion. In this study, Trametes trogii Lac (Ttlcc1) was engineered into Saccharomyces cerevisiae strain CEN.PK2-1 C under the constitutive GPD promoter (pGPD) for multi-fold synthesis with efficient hydrocarbon tolerance and degradation. Protein expression in heterologous hosts is strictly strain-specific, it can also be influenced by the synthetic design and culture conditions. We compared synthetic designs with different shuttle vectors for the yeast strains and investigated the best culture conditions by varying the pH, temperature, carbon, nitrogen sources, and CuSO₄ amount. Two S. cerevisiae strains were built in this study: byMM935 and byMM938. They carry the transcription unit pGPD-Ttlcc1-CYC1t either inside the pRSII406 integrative plasmid (byMM935) or the pRSII426 multicopy plasmid (byMM938). The performance of these two synthetic strains were studied by comparing them to the wild-type strain (byMM584). Both byMM935 and byMM938 showed significant response to different carbon sources (glucose, galactose, lactose, maltose, and sucrose), nitrogen sources (NH₄Cl, NH₄NO₃, KNO₃, malt extract, peptone, and yeast extract), and solid state fermentation of different plant biomasses (bagasse, banana peels, corn cob, mandarin peels, and peanut shells). They performed best in optimized growth conditions with specific carbon and nitrogen sources, and a preferred pH in the range 3.5-4.5, temperature between 30 and 40 ⁰C, and 1 mM CuSO_4. In optimized yeast-growth medium, strain byMM935 showed the highest laccase activities of 1.621 ± 0.063 U/mL at 64 h, whereas byMM938 gave its highest activity (1.417 ± 0.055 U/mL) at 48 h. In this work, we established, by using Bushnell Hass synthetic medium, that the new Ttlcc1-yeast strains tolerated extreme pH and complex hydrocarbon mixture (CHM) toxicity. They degraded 60-90% of the key components in CHM within 48 h, including poly-cyclic aromatic hydrocarbons, alkyl indenes, alkyl tetralines, alkyl benzenes, alkyl biphenyls, and BTEX (Benzene, Toluene, Ethylbenzene, and Xylenes). This is the first report on the hydrocarbon degradation potential of a Ttlcc1-yeast. Compared to the native organism, such synthetic strains are better suited for meeting growing demands and have potentials for application in large-scale in situ bioremediation of hydrocarbon-polluted sites.

Phytoremediation technology and food security impacts of heavy metal contaminated soils: A review of literature

Heavy metal accumulation in soil and water is one of major problems caused by inorganic contaminants. Their presence in agricultural soils in high quantities have impacted the food security significantly and, by extension, the human health. Amongst various physico-chemical methods available for remediation of heavy-metals-polluted-sites, phytoremediation approaches have been found to be safe and environment friendly. This review gathered scattered information on heavy metal phytoremediation studies published in both review and research articles. It described the impact of heavy metals on food security and comprehensively discussed the application of different phytoremediation approaches for treatment of heavy metal-polluted soils, the basic principles underlining them, their strengths and weaknesses. Our findings indicated that, while hundreds of hyper-accumulator plants are being reported yearly, only few describe limitations inherent in them, such as low growth rate, low biomass production, and low metal tolerance. Hence, this review also gave a detailed overview of research gaps in phytotechnology and advocates consideration of the 'omics' studies; genomics, proteomics, metabolomics and likes in selecting and enhancing potential plants for phytoremediation. For a sustainable large-scale phytoremediation application, we established a multi-technology repair strategy via the combination of different methods like application of biological composts, plant-growth promoting microorganisms, and phytohormones for stimulation of the plant-growth during phytoremediation. We also gave comprehensive insights to proper disposal of plants used for phytoremediation, this subject is often not well considered/planned while deciding the application of plants for removal of heavy metals from polluted environments.

Bioprospection of ligninolytic enzymes from marine origin filamentous fungi

Fungi are excellent producers of extracellular enzymes. Therefore, the present study aimed to investigate the screening of marine fungi, which are laccase and manganese peroxidase potential producers, in solid fermentation for future applications in bioremediation processes of contaminated sites. For this purpose, two-level factorial planning was adopted, using time (6 and 15 days) and the absence or presence of oil (0 and 1%) as factors. The semi-quantitative evaluation was carried out by calculating radial growth, enzyme activity and enzyme index by measuring phenol red or syringaldazine oxidation halo. The results showed that all the studied strains showed a positive result for manganese peroxidase production, with an enzymatic activity in solid medium less than 0.61, indicating a strongly positive activity. Through the enzyme index, the study also showed prominence for Penicillium sp. strains, with values > 2. The enzyme index increase in oil presence and the inexpressive use of the genera studied for ligninolytic enzymes production from crude oil demonstrated these data importance for fermentative processes optimization. Considering the ability of these strains to develop into recalcitrant compounds and the potential for manganese peroxidase production, they are indicated for exploitation in various bioremediation technologies, as well as other biotechnological applications.

Hydrocarbon biodegradation and transcriptome responses of cellulase, peroxidase, and laccase encoding genes inhabiting rhizospheric fungal isolates

By using the indigenous micro-organisms of the polluted environment to be treated, bioremediation can be a successful strategy. PCR and RT-PCR molecular techniques were applied to examine the evolution of fungal isolates through putative genes f ligninolytic enzymes like lignin peroxidase (LiP), laccase (LaC), manganese peroxidase (MnP), and cellulase (Cx) as a response to polluting of the environment by hydrocarbons. In this study, isolation of rhizospheric fungal isolates, molecular identification, crude oil tolerance, and enzyme excretions were demonstrated. From the date palm rhizosphere, 3 fungal isolates were isolated and characterized morphologically and molecularly by ITS ribosomal RNA (rRNA) sequencing. The isolates were identified as Aspergillus flavus AF15, Trichoderma harzianum TH07, and Fusarium solani FS12 through using the BLAST tool in NCBI. All fungal isolates showed high tolerance to crude oil and survived with various responses at the highest concentration (20%). Aspergillus flavus AF15 and Trichoderma harzianum TH07 demonstrated promising oil-degrading tolerance ability based on the dose inhibition response percentage (DIRP) of the fungal isolates. A. flavus had a powerful capacity to production Cx, LaC, LiP and MnP with a range from 83.7 to 96.3 mL. Molecularly, nine genes of the ligninolytic enzymes, cbh (cbhI.1, cbhI.1, cbhII) lcc, lig (1, 2, 4 and 6) and mnp were tested for presence and expression (by PCR and RT-PCR, respectively). PCR showed that all isolates contained all the nine genes examined, regardless of capacity to enzymes production profiles, so the presence responses of nine genes did not correlate with enzymes-production ability. Gene expression analysis shows a more diverse pattern for tested isolates for example, Aspergillus flavus AF15 had over-expression of lig and mnp genes, Fusarium solani FS12 have a weak signal with lcc gene while, Trichoderma harzianum TH07 showed moderate expression of mnp and lcc genes. The power of the transcription of the gene leads to increased enzyme secretion by fungal isolates. Fungi are important microorganisms in the clean-up of petroleum pollution. They have bioremediation highly potency that is related to their diverse production of these catalytic enzymes.

Genome-based engineering of ligninolytic enzymes in fungi

Background

Many fungi grow as saprobic organisms and obtain nutrients from a wide range of dead organic materials. Among saprobes, fungal species that grow on wood or in polluted environments have evolved prolific mechanisms for the production of degrading compounds, such as ligninolytic enzymes. These enzymes include arrays of intense redox-potential oxidoreductase, such as laccase, catalase, and peroxidases. The ability to produce ligninolytic enzymes makes a variety of fungal species suitable for application in many industries, including the production of biofuels and antibiotics, bioremediation, and biomedical application as biosensors. However, fungal ligninolytic enzymes are produced naturally in small quantities that may not meet the industrial or market demands. Over the last decade, combined synthetic biology and computational designs have yielded significant results in enhancing the synthesis of natural compounds in fungi.

Main body of the abstract

In this review, we gave insights into different protein engineering methods, including rational, semi-rational, and directed evolution approaches that have been employed to enhance the production of some important ligninolytic enzymes in fungi. We described the role of metabolic pathway engineering to optimize the synthesis of chemical compounds of interest in various fields. We highlighted synthetic biology novel techniques for biosynthetic gene cluster (BGC) activation in fungo and heterologous reconstruction of BGC in microbial cells. We also discussed in detail some recombinant ligninolytic enzymes that have been successfully enhanced and expressed in different heterologous hosts. Finally, we described recent advance in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) protein systems as the most promising biotechnology for large-scale production of ligninolytic enzymes.

Short conclusion

Aggregation, expression, and regulation of ligninolytic enzymes in fungi require very complex procedures with many interfering factors. Synthetic and computational biology strategies, as explained in this review, are powerful tools that can be combined to solve these puzzles. These integrated strategies can lead to the production of enzymes with special abilities, such as wide substrate specifications, thermo-stability, tolerance to long time storage, and stability in different substrate conditions, such as pH and nutrients.

Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils

Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.

Hydrocarbon Degradation and Enzyme Activities of Aspergillus oryzae and Mucor irregularis Isolated from Nigerian Crude Oil-Polluted Sites

Many free-living saprobic fungi are nature recruited organisms for the degradation of wastes, ranging from lignocellulose biomass to organic/inorganic chemicals, aided by their production of enzymes. In this study, fungal strains were isolated from contaminated crude-oil fields in Nigeria. The dominant fungi were selected from each site and identified as Aspergillus oryzae and Mucor irregularis based on morphological and molecular characterization, with site percentage incidences of 56.67% and 66.70%, respectively. Selected strains response/tolerance to complex hydrocarbon (used engine oil) was studied by growing them on Bushnell Haas (BH) mineral agar supplemented with the hydrocarbon at different concentrations, i.e., 5%, 10%, 15%, and 20%, with a control having dextrose. Hydrocarbon degradation potentials of these fungi were confirmed in BH broth culture filtrates pre-supplemented with 1% engine oil after 15 days of incubation using GC/MS. In addition, the presence of putative enzymes, laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) was confirmed in culture filtrates using appropriate substrates. The analyzed fungi grew in hydrocarbon supplemented medium with no other carbon source and exhibited 39.40% and 45.85% dose inhibition response (DIR) respectively at 20% hydrocarbon concentration. An enzyme activity test revealed that these two fungi produced more Lac than MnP and LiP. It was also observed through the GC/MS analyses that while A. oryzae acted on all hydrocarbon components in the used engine oil, M. irregularis only degraded the long-chain hydrocarbons and BTEX. This study confirms that A. oryzae and M. irregularis have the potential to be exploited in the bio-treatment and removal of hydrocarbons from polluted soils.

Reconstruction of core microbes based on producing lignocellulolytic enzymes causing by bacterial inoculation during rice straw composting

The aim of this paper was to identify the core microbes of producing lignocellulolytic enzymes during rice straw composting with functional bacterial agents inoculation. The results indicated that inoculation functional bacterial agents accelerated the degradation of organic matter and coarse fiber content by 7.58%, 8.82%, which were due to the fact that key enzymes and core microbes were stimulated. In addition, inoculation have reconstructed core microbes of producing lignocellulase. Meanwhile, inoculation functional bacterial agents not only as core bacteria to produce cellulase, xylanase and manganese peroxidase (MnP), but also increased most core microbial abundance. Redundancy analysis indicated that CMCase, xylanase, total nitrogen and MnP as key factors to affect the degradation of organic fractions in the core bacterial communities, while in the core fungal communities, were mainly affected by environmental factors (except for MnP). This study provided a theoretical basis for the efficiently degradation during agricultural wastes composting.

A Fungal Ascorbate Oxidase with Unexpected Laccase Activity

Ascorbate oxidases are an enzyme group that has not been explored to a large extent. So far, mainly ascorbate oxidases from plants and only a few from fungi have been described. Although ascorbate oxidases belong to the well-studied enzyme family of multi-copper oxidases, their function is still unclear. In this study, Af_AO1, an enzyme from the fungus Aspergillus flavus, was characterized. Sequence analyses and copper content determination demonstrated Af_AO1 to belong to the multi-copper oxidase family. Biochemical characterization and 3D-modeling revealed a similarity to ascorbate oxidases, but also to laccases. Af_AO1 had a 10-fold higher affinity to ascorbic acid (K_M = 0.16 ± 0.03 mM) than to ABTS (K_M = 1.89 ± 0.12 mM). Furthermore, the best fitting 3D-model was based on the ascorbate oxidase from Cucurbita pepo var. melopepo. The laccase-like activity of Af_AO1 on ABTS (V_max = 11.56 ± 0.15 µM/min/mg) was, however, not negligible. On the other hand, other typical laccase substrates, such as syringaldezine and guaiacol, were not oxidized by Af_AO1. According to the biochemical and structural characterization, Af_AO1 was classified as ascorbate oxidase with unusual, laccase-like activity.

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.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.