Degradation of cyanide by Trichoderma mutants constructed by restriction enzyme mediated integration (REMI)

An Overview of Emerging Cyanide Bioremediation Methods

Cyanide compounds are hazardous compounds which are extremely toxic to living organisms, especially free cyanide in the form of hydrogen cyanide gas (HCN) and cyanide ion (CN−). These cyanide compounds are metabolic inhibitors since they can tightly bind to the metals of metalloenzymes. Anthropogenic sources contribute significantly to CN− contamination in the environment, more specifically to surface and underground waters. The treatment processes, such as chemical and physical treatment processes, have been implemented. However, these processes have drawbacks since they generate additional contaminants which further exacerbates the environmental pollution. The biological treatment techniques are mostly overlooked as an alternative to the conventional physical and chemical methods. However, the recent research has focused substantially on this method, with different reactor configurations that were proposed. However, minimal attention was given to the emerging technologies that sought to accelerate the treatment with a subsequent resource recovery from the process. Hence, this review focuses on the recent emerging tools that can be used to accelerate cyanide biodegradation. These tools include, amongst others, electro-bioremediation, anaerobic biodegradation and the use of microbial fuel cell technology. These processes were demonstrated to have the possibility of producing value-added products, such as biogas, co-factors of neurotransmitters and electricity from the treatment process.

Cyanide Biodegradation by Trichoderma harzianum and Cyanide Hydratase Network Analysis

Cyanide is a poisonous and dangerous chemical that binds to metals in metalloenzymes, especially cytochrome C oxidase and, thus, interferes with their functionalities. Different pathways and enzymes are involved during cyanide biodegradation, and cyanide hydratase is one of the enzymes that is involved in such a process. In this study, cyanide resistance and cyanide degradation were studied using 24 fungal strains in order to find the strain with the best capacity for cyanide bioremediation. To confirm the capacity of the tested strains, cyano-bioremediation and the presence of the gene that is responsible for the cyanide detoxification was assessed. From the tested organisms, Trichoderma harzianum (T. harzianum) had a significant capability to resist and degrade cyanide at a 15 mM concentration, where it achieved an efficiency of 75% in 7 days. The gene network analysis of enzymes that are involved in cyanide degradation revealed the involvement of cyanide hydratase, dipeptidase, carbon-nitrogen hydrolase-like protein, and ATP adenylyltransferase. This study revealed that T. harzianum was more efficient in degrading cyanide than the other tested fungal organisms, and molecular analysis confirmed the experimental observations.

Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification

Cyanide is a hazardous and detrimental chemical that causes the inactivation of the respiration system through the inactivation of cytochrome c oxidase. Because of the limitation in the number of cyanide-degrading enzymes, there is a great demand to design and introduce new enzymes with better functionality. This study developed an integrated method of protein-homology-modelling and ligand-docking protein-design approaches that reconstructs a better active site from cyanide hydratase (CHT) structure. Designing a mutant CHT (mCHT) can improve the CHT performance. A computational design procedure that focuses on mutation for constructing a new model of cyanide hydratase with better activity was used. In fact, this study predicted the three-dimensional (3D) structure of CHT for subsequent analysis. Inducing mutation on CHT of Trichoderma harzianum was performed and molecular docking was used to compare protein interaction with cyanide as a ligand in both CHT and mCHT. By combining multiple designed mutations, a significant improvement in docking for CHT was obtained. The results demonstrate computational capabilities for enhancing and accelerating enzyme activity. The result of sequence alignment and homology modeling show that catalytic triad (Cys-Glu-Lys) was conserved in CHT of Trichoderma harzianum. By inducing mutation in CHT structure, MolDock score enhanced from −18.1752 to −23.8575, thus the nucleophilic attack can occur rapidly by adding Cys in the catalytic cavity and the total charge of protein in pH 6.5 is increased from −6.0004 to −5.0004. Also, molecular dynamic simulation shows a stable protein-ligand complex model. These changes would help in the cyanide degradation process by mCHT.

Biocontrol potential of saline- or alkaline-tolerant Trichoderma asperellum mutants against three pathogenic fungi under saline or alkaline stress conditions

Salinity and alkalinity are major abiotic stresses that limit growth and development of poplar. We investigated biocontrol potential of saline- and alkaline-tolerant mutants of Trichoderma asperellum to mediate the effects of salinity or alkalinity stresses on Populus davidiana×P. alba var. pyramidalis (PdPap poplar) seedlings. A T-DNA insertion mutant library of T. asperellum was constructed using an Agrobacterium tumefaciens mediated transformation system; this process yielded sixty five positive transformants (T1-T65). The salinity tolerant mutant, T59, grew in Potato Dextrose Agar (PDA) containing up to 10% (1709.40mM) NaCl. Under NaCl-rich conditions, T59 was most effective in inhibiting Alternaria alternata (52.00%). The alkalinity tolerant mutants, T3 and T5, grew in PDA containing up to 0.4% (47.62mM) NaHCO₃. The ability of the T3 and T5 mutants to inhibit Fusarium oxysporum declined as NaHCO₃ concentrations increased. NaHCO₃ tolerance of the PdPap seedlings improved following treatment with the spores of the WT, T3, and T5 strains. The salinity tolerant mutant (T59) and two alkalinity tolerant mutants (T3 and T5) generated in this study can be applied to decrease the incidence of pathogenic fungi infection under saline or alkaline stress.

Perspectives of using fungi as bioresource for bioremediation of pesticides in the environment: a critical review

Pesticides are used for controlling the development of various pests in agricultural crops worldwide. Despite their agricultural benefits, pesticides are often considered a serious threat to the environment because of their persistent nature and the anomalies they create. Hence removal of such pesticides from the environment is a topic of interest for the researchers nowadays. During the recent years, use of biological resources to degrade or remove pesticides has emerged as a powerful tool for their in situ degradation and remediation. Fungi are among such bioresources that have been widely characterized and applied for biodegradation and bioremediation of pesticides. This review article presents the perspectives of using fungi for biodegradation and bioremediation of pesticides in liquid and soil media. This review clearly indicates that fungal isolates are an effective bioresource to degrade different pesticides including lindane, methamidophos, endosulfan, chlorpyrifos, atrazine, cypermethrin, dieldrin, methyl parathion, heptachlor, etc. However, rate of fungal degradation of pesticides depends on soil moisture content, nutrient availability, pH, temperature, oxygen level, etc. Fungal strains were found to harbor different processes including hydroxylation, demethylation, dechlorination, dioxygenation, esterification, dehydrochlorination, oxidation, etc during the biodegradation of different pesticides having varying functional groups. Moreover, the biodegradation of different pesticides was found to be mediated by involvement of different enzymes including laccase, hydrolase, peroxidase, esterase, dehydrogenase, manganese peroxidase, lignin peroxidase, etc. The recent advances in understanding the fungal biodegradation of pesticides focusing on the processes, pathways, genes/enzymes and factors affecting the biodegradation have also been presented in this review article.

Packed bed reactor for degradation of simulated cyanide-containing wastewater

The discharge of cyanide-containing effluents into the environment contaminates water bodies and soil. Effective methods of treatment which can detoxify cyanide are the need of the hour. The aim of the present study is to develop a bioreactor for complete degradation of cyanide using immobilized cells of Serratia marcescens RL2b. Alginate-entrapped cells of S. marcescens RL2b were used for complete degradation of cyanide in a packed bed reactor (PBR). Cells grown in minimal salt medium (pH 6.0) were harvested after 20 h and exhibited 0.4 U mg⁻¹ dcw activity and 99 % cyanide degradation in 10 h. These resting cells were entrapped using 3 % alginate beads and packed in a column reactor (20 × 1.7 cm). Simulated cyanide (12 mmol l⁻¹)-containing wastewater was loaded and fractions were collected after different time intervals at various flow rates. Complete degradation of 12 m mmol l⁻¹ (780 mg l⁻¹) cyanide in 10 h was observed at a flow rate of 1.5 ml h⁻¹. The degradation of cyanide in PBR showed direct dependence on retention time. The retention time of cyanide in the reactor was 9.27 h. The PBR can degrade 1.2 g of cyanide completely in 1 day.

Biodegradation of neonicotinoid insecticide, imidacloprid by restriction enzyme mediated integration (REMI) generated Trichoderma mutants

REMI (restriction enzyme-mediated integration) technique was employed to construct Trichoderma atroviride strain T23 mutants with degrading capability of neonicotinoid insecticide, imidacloprid. The plasmid pBluescript II KS-hph used for integration in REMI mutants was confirmed by PCR and Southern hybridization. Among 153 transformants, 57% of them have showed higher neonicotinoid insecticide, imidacloprid, degradation ability than the wild strain T23 (p<0.01). More specifically, seven single-copied T. atroviride T23 transformants have confirmed a 30% higher degradation rate than their parent isolate. Among all transformed mutants, a 95% imidacloprid degradation rate was identified as the highest. This study, thus, provided an effective approach for improving neonicotinoid insecticide-degrading capability using REMI transformed T. atroviride mutants.

Disruption of hex1 in Trichoderma atroviride leads to loss of Woronin body and decreased tolerance to dichlorvos

The tolerance of Trichoderma species to organophosphorus pesticides is necessary for their application in the bioremediation of pesticide-polluted environments. In some cases, such a requirement is also key to the synergistic use of these fungi with chemical pesticides, aiming to broaden the scope of control targets to include both plant pathogens and insect pests. However, the mechanism of Trichoderma tolerance of organophosphorus pesticides remains unclear. To address this, we have analyzed the function of the putative dichlorvos-tolerance gene hex1 by knocking it out. The hex1-deleted mutant showed loss of Woronin bodies and decreased tolerance to the organophosphate, dichlorvos. Moreover, HEX1 localizes at the septal plugs in mycelium which may be involved in controlling intracellular movement of dichlorvos. hex1 thus is involved the tolerance to dichlorvos and the formation of Woronin bodies in Trichoderma atroviride.

Isolation and Identification of Pathogenicity Mutant of Curvularia lunata via Restriction Enzyme-Mediated Integration

In this report, 156 hygromycin-resistant mutants were generated via restriction enzyme-mediated insertional (REMI) mutagenesis. All mutants were subjected to a bioassay on detached leaves. Five mutants (T4, T39, T71, T91, and T135) showed reduced symptom development, whereas one mutant (T120) did not exhibit any symptoms on the leaves compared with the wild type. The pathogenicity of these mutants was further assayed through the spray inoculation of whole seedlings. The results demonstrated that the pathogenicity of the T4, T39, T71, T91, and T135 mutants was reduced, whereas the T120 mutant lost its pathogenicity. Southern blot analysis revealed that the plasmids were inserted at different sites in the genome with different copy numbers. Flanking sequences approximately 550, 860, and 150 bp were obtained from T7, T91, and T120, respectively through plasmids rescue. Sequence analysis of the flanking sequences from T7 and T91 showed no homology to any known sequences in GenBank. The flanking sequence from the T120 mutant was highly homologous to MAPKK kinases, which regulates sexual/asexual development, melanization, pathogenicity from Cochliobolus heterostrophus. These results indicate that REMI and plasmids rescue have great potential for finding pathogenicity genes.

Screening and identification of insertion mutants from Bipolaris eleusines by mutagenesis based on restriction enzyme-mediated integration

Ophiobolin A is sesterterpenoid-type phytotoxin and may be an important candidate for development of new crop protection and pharmaceutical products. The restriction enzyme-mediated integration (REMI) method was used to introduce the plasmid pSH75 into the ophiobolin A-producing filamentous fungus Bipolaris eleusines. A total of 323 stable transformants were obtained, all of which were capable of growing on potato-dextrose agar medium containing 200 μg mL(-1) hygromycin B. The transformation frequency was about 4-5 transformants μg(-1) plasmid DNA. An ophibolin A-deficient transformant (B014) was assessed and the presence of the hph gene in this transformant was confirmed by PCR. The cell-free cultural filtrates of this transformant showed significantly less inhibition on mycelial growth of the fungal pathogen Rhizoctoni solani but little effect on barnyard grass as opposed to that of the wild-type B. eleusines. There was no detectable amount of ophiobolin A in B014 samples measured with HPLC. This research suggests REMI as a potential approach for improving the production of ophiobolin A by B. eleusines via genetic engineering to upregulate certain genes responsible for desired biosynthetic pathways.

Proteomic analysis ofTrichoderma atroviridemycelia stressed by organophosphate pesticide dichlorvos

The proteomic approach is a powerful tool to study microbial response to environmental stress. To evaluate the responses of Trichoderma spp. to the organophosphate pesticide dichlorvos, mycelia of Trichoderma atroviride T23 were exposed to dichlorvos at concentrations of 0, 100, 300, 500, and 1000 µg/mL, respectively. Changes in protein expression were investigated using two-dimensional sodium dodecyl sulfate – polyacrylamide gel electrophoresis. Sixteen protein spots were differentially expressed. They were identified by MALDI–TOF/TOF MS and were found to be linked to energy metabolism, transport, signal transduction, and stress tolerance. Among stress-related proteins, glutathione peroxidase-like protein (GPX), 1,4-benzoquinone reductase, and HEX1 were upregulated by and cyclophilin A induced by 1000 µg/mL dichlorvos when compared with the control. These proteins were considered to be associated with fungal adaptation to adverse conditions. The results will help us to understand molecular mechanisms through which Trichoderma responds to organophosphate pesticides.

Improved phytoremediation of oilseed rape (Brassica napus) by Trichoderma mutant constructed by restriction enzyme-mediated integration (REMI) in cadmium polluted soil

In this study, oilseed rape (Brassica napus) was exploited in remediation of Cd-contaminated soil in combination of Trichodermakoningii. To improve its phytoextracting efficiency, restriction enzyme-mediated integration was used to construct Trichoderma mutants with higher Cd resistance. Of 200 mutants, 10 mutants were shown with higher Cd tolerance and enhanced ability of removing Cd from growth medium. In pot experiment, mutant P6 significantly alleviated the negative impacts of Cd on oilseed rape growth, and improved the Cd uptake ability of oilseed rape shoot in Cd contaminated soil (p<0.05). Based on the dry weight, the amounts of Cd in shoots of mutant P6 treated oilseed rape were increased by 23% and 38% per pot compared with wild type Trichoderma treatment; 53% and 107% against non-inoculated treatment, respectively, at 20 and 50mgCdkg(-1) soil. The results suggested the Trichoderma mutant-oilseed rape symbiosis system could be used in remediation of soil contaminated with heavy metal Cd.

Improved degradation of organophosphate dichlorvos by Trichoderma atroviride transformants generated by restriction enzyme-mediated integration (REMI)

A simple technique, REMI (restriction enzyme-mediated integration), was used to construct transformants of Trichoderma atroviride with improved capability of degrading organophosphate pesticide dichlorvos. Linearized DNA of plasmid pV2 bearing the hygromycin B phosphotransferase (hph) gene was inserted into chromosomes of wild strain T23 and transformation was confirmed by PCR and Southern blot analysis, respectively. Of 247 transformants, 76% showed improved dichlorvos degradation ability as compared to the parent strain T23 based on the least significant difference (LSD) test at p=0.01. Among them, 8 transformants exhibited 30% higher in degradation rate than the parent isolate. The highest dichlorvos degradation rate of the transformants was up to 96%. This study provided an effective approach for improving organophosphate pesticide-degrading capability of T. atroviride.

Efficient biodegradation of cyanide and ferrocyanide by Na-alginate beads immobilized with fungal cells of Trichoderma koningii

Cyanide or metal cyanide contaminations have become serious environmental and food-health problems. A fungal mutant of Trichoderma koningii, TkA8, constructed by restriction enzyme-mediated integration, has been verified to have a high cyanide degradation ability in our previous study. In this study, the mutant cells were entrapped in sodium-alginate (Na-alginate) immobilization beads to degrade cyanide and ferrocyanide in a liquid mineral medium. The results showed that the fungus in immobilization beads consisting of 3% Na-alginate and 3% CaCl2 could degrade cyanide more efficiently than a nonimmobilized fungal culture. For maximum degradation efficiency, the optimal ratio of Na-alginate and wet fungal biomass was 20:1 (m/m) and the initial pH was 6.5. In comparison, cell immobilization took at least 3 and 8 days earlier, respectively, to completely degrade cyanide and ferrocyanide. In addition, we showed that the immobilized beads could be easily recovered from the medium and reused for up to 5 batches without significant losses of fungal remediation abilities. The results of this study provide a promising alternative method for the large-scale remediation of soil or water systems from cyanide contamination.

Transformation of taxol-producing endophytic fungi by restriction enzyme-mediated integration (REMI)

The REMI method was used to introduce the plasmid pV2 harboring the hygromycin B phosphotransferase (hph) gene controlled by the Aspergillus nidulans trpC promoter and the trpC terminator into a taxol-producing endophytic fungus BT2. REMI transformation yielded stable transformants capable of continuing to grow on PDA medium containing 125 mug mL(-1) hygromycin B. The transformation efficiency was about 5-6 transformants mug(-1) plasmid DNA. The presence of hph gene in transformants was confirmed by PCR and Southern blot analyses. To the authors' knowledge, this is the first report on the transformation of taxol-producing endophytic fungi by the REMI technique. This study provides an effective approach for improving taxol production of endophytic fungi by the genetic engineering of taxol biosynthetic pathway genes in the future.