Right on target: using plants and microbes to remediate explosives

Review of Explosive Contamination and Bioremediation: Insights from Microbial and Bio-Omic Approaches

Soil pollution by TNT(2,4,6-trinitrotoluene), RDX(hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane), and HMX(octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), resulting from the use of explosives, poses significant challenges, leading to adverse effects such as toxicity and alteration of microbial communities. Consequently, there is a growing need for effective bioremediation strategies to mitigate this damage. This review focuses on Microbial and Bio-omics perspectives within the realm of soil pollution caused by explosive compounds. A comprehensive analysis was conducted, reviewing 79 articles meeting bibliometric criteria from the Web of Science and Scopus databases from 2013 to 2023. Additionally, relevant patents were scrutinized to establish a comprehensive research database. The synthesis of these findings serves as a critical resource, enhancing our understanding of challenges such as toxicity, soil alterations, and microbial stress, as well as exploring bio-omics techniques like metagenomics, transcriptomics, and proteomics in the context of environmental remediation. The review underscores the importance of exploring various remediation approaches, including mycorrhiza remediation, phytoremediation, bioaugmentation, and biostimulation. Moreover, an examination of patented technologies reveals refined and efficient processes that integrate microorganisms and environmental engineering. Notably, China and the United States are pioneers in this field, based on previous successful bioremediation endeavors. This review underscores research's vital role in soil pollution via innovative, sustainable bioremediation for explosives.

Actinobacterial peroxidase-mediated biodeterioration of hazardous explosive, 2, 4, 6, trinitrophenol by in silico and in vitro approaches

Explosives are perilous and noxious to aquatic biota disrupting their endocrinal systems. Supplementarily, they exhibit carcinogenic, teratogenic and mutagenic effects on humans and animals. Henceforth, the current study has been targeted to biotransform the explosive, 2, 4, 6 trinitrophenol (TNP) by wetland peroxidase from Streptomyces coelicolor. A total peroxidase yield of 20,779 mg/l with 51.6 folds of purification was observed. In silico molecular docking cum in vitro appraisals were accomplished to assess binding energy and interacting binding site residues of peroxidase and TNP complex. TNP required a minimal binding energy of-6.91 kJ/mol and was subjected to biodeterioration (89.73%) by peroxidase in purified form, with 45 kDa and a similarity score of 34 by MASCOT protein analysis. Moreover, the peroxidase activity was confirmed with Zymogram analysis. Characterization of peroxidase revealed that optimum values of pH and temperature as 6 and 40 °C, respectively, with their corresponding stability varying from 3.5 to 7. Interestingly, the kinetic parameters such as Km and Vmax on 2,2'-azino-bis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and H2O2 were 19.27 µm and 0.41 µm/min; 21.4 µm and 0.1 µm/min, respectively. Among the diverse substrates, chemicals and trace elements, ABTS (40 mM), citric acid (5 mM) and Fe2+ (5 mM) displayed the highest peroxidase activity. Computational docking and in vitro results were corroborative and UV-Vis spectroscopy, HPLC, FTIR and GC-MS indicated the presence of simple metabolites of TNP such as nitrophenols and benzoquinone, showcasing the efficacy of S. coelicolor peroxidase to biotransform TNP. Henceforth, the current study offers a promising channel for biological treatment of explosive munitions, establishing a sustainable green earth.

Creation of Environmentally Friendly Super "Dinitrotoluene Scavenger" Plants

Pervasive environmental contamination due to the uncontrolled dispersal of 2,4-dinitrotoluene (2,4-DNT) represents a substantial global health risk, demanding urgent intervention for the removal of this detrimental compound from affected sites and the promotion of ecological restoration. Conventional methodologies, however, are energy-intensive, susceptible to secondary pollution, and may inadvertently increase carbon emissions. In this study, a 2,4-DNT degradation module is designed, assembled, and validated in rice plants. Consequently, the modified rice plants acquire the ability to counteract the phytotoxicity of 2,4-DNT. The most significant finding of this study is that these modified rice plants can completely degrade 2,4-DNT into innocuous substances and subsequently introduce them into the tricarboxylic acid cycle. Further, research reveals that the modified rice plants enable the rapid phytoremediation of 2,4-DNT-contaminated soil. This innovative, eco-friendly phytoremediation approach for dinitrotoluene-contaminated soil and water demonstrates significant potential across diverse regions, substantially contributing to carbon neutrality and sustainable development objectives by repurposing carbon and energy from organic contaminants.

Multi-generation reproductive toxicity of RDX and the involved signal pathways in Caenorhabditis elegans

As one of the most frequently used explosives, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) can cause persistent pollution in the environment, leading to the potential ecological threat crossing the generations. In this study, we employed Caenorhabditis elegans to explore the toxic effects of RDX on the parental and offspring worms and the involved signaling pathways. Exposure up to 1000 ng/mL of RDX produced a significant increase in reactive oxygen species (ROS) production, germ cell apoptosis, and decrease in eggs laid. Various mutants were used to demonstrate the RDX-induced apoptosis signaling pathway, and the metabolism of RDX in the nematodes was found related to cytochrome P450 and GST through RNA sequencing. Exposure of parental worms to RDX produced significant reproductive toxicity in F1 and F2, but was recovered in F3 and F4. The transgenerational effects were associated with the decreased expression of met-2, spr-5, and set-2. Our findings revealed the signaling pathways related to the reproductive toxicity caused by RDX in C. elegans and their future generations, which provided the basis for further exploration of the ecological risks of energetic compounds in the environment.

Determination of Ethylene Glycol Dinitrate in Environmental and Forensic Water Samples Using Microextraction by Packed Sorbent Followed by Gas Chromatography

Ethylene glycol dinitrate (EGDN) is a liquid nitrate ester, a secondary explosive. In the past, it was used as an explosive ingredient in dynamite along with nitroglycerine. Due to its various applications, the reliable detection of EGDN in the environment is a key issue for both forensic and environmental applications. In these areas, sensitive and reliable methods for determining the concentration of nitro compounds are needed. Microextraction by packed sorbent (MEPS) is an innovative approach to green technology in the sample preparation field. Compared to conventional solid-phase extraction (SPE), MEPS uses a smaller sample volume and can be easily combined with various chromatographic techniques. An important benefit is the reduction of sorbent amount and up to 100-times repeatable use compared to disposable SPE columns, thus reducing the costs of analysis as well as waste production. Optimal extraction parameters for isolating EGDN from water, e.g., 30 µL of toluene as extraction agent, working in one cycle and in draw/discard mode, were selected. Method validation was performed, obtaining a limit of detection and a limit of quantification of 0.45 pg/μL and 1.34 pg/μL, respectively. Accuracy in terms of recovery rates was evaluated over a wide concentration range, obtaining values from 83.7 to 90.0%. The satisfactory linearity expressed by the coefficient of determination was 0.9914. A matrix factor of −9.3% indicates a weak matrix effect. The application to real environmental water samples and a forensic post-blast wash water sample was realized. EGDN detection in the post-blast samples provides valuable information for forensic technicians.

Inhibition effect of 2,4,6-trinitrotoluene (TNT) on RDX degradation by rhodococcus strains isolated from contaminated soil and water

2,4,6-trinitrotoluene (TNT) is a highly toxic explosive that contaminates soil and water and may interfere with the degradation of co-occurring compounds, such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). We proposed that TNT may influence RDX-degrading bacteria via either general toxicity or a specific effect on the |RDX degradation mechanisms. Thus, we examined the impact of TNT on RDX degradation by Rhodococcus strains YH1, T7, and YY1, which were isolated from an explosives-polluted environment. Although partly degraded, TNT did not support the growth of any of the strains when used as either sole carbon or sole nitrogen sources, or as carbon and nitrogen sources. The incubation of a mixture of TNT (25 mg/l) and RDX (20 mg/l) completely inhibited RDX degradation. The effect of TNT on the cytochrome P450, catalyzing RDX degradation, was tested in a resting cell experiment, proving that TNT inhibits XplA protein activity. A dose-response experiment showed that the IC50/trans values for YH1, T7, and YY1 were 7.272, 5.098, and 9.140 (mg/l of TNT), respectively, illustrating variable sensitivity to TNT among the strains. The expression of xplA was also strongly suppressed by TNT. Cells that were pre-grown with RDX (allowing xplA expression) and incubated with ammonium chloride, glucose, and TNT, completely transformed into their amino dinitrotoluene isomers and formed azoxy toluene isomers. The presence of oxygen-insensitive nitroreductase that enable reduction of the nitro group in the presence of O2 in the genomes of these strains suggests that they are responsible for TNT transformation in the cultures. The experimental results concluded that TNT has an adverse effect on RDX degradation by the examined strains. It inhibits RDX degradation due to the direct impact on cytochrome P450, xplA, or its expression. The tested strains can transform TNT independently of RDX. Thus, degradation of both compounds is possible if TNT concentrations are below their IC50 values.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives

Environmental contamination by hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), and Octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches (WMS) in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of OTU's related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy, or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.

Recent advances in biological removal of nitroaromatics from wastewater

Various nitroaromatic compounds (NACs) released into the environment cause potential threats to humans and animals. Biological treatment is valued for cost-effectiveness, environmental friendliness, and availability when treating wastewater containing NACs. Considering the significance and wide use of NACs, this review focuses on recent advances in biological treatment systems for NACs removal from wastewater. Meanwhile, factors affecting biodegradation and methods to enhance removal efficiency of NACs are discussed. The selection of biological treatment system needs to consider NACs loading and cost, and its performance is affected by configuration and operation strategy. Generally, sequential anaerobic-aerobic biological treatment systems perform better in mineralizing NACs and removing co-pollutants. Future research on mechanism exploration of NACs biotransformation and performance optimization will facilitate the large-scale application of biological treatment systems.

Analysis of the biodegradation and phytotoxicity mechanism of TNT, RDX, HMX in alfalfa (Medicago sativa)

The aim of this study was to reveal the mechanism underlying the toxicity of TNT (trinitrotoluene), RDX (cyclotrimethylene trinitroamine), and HMX (cyclotetramethylene tetranitramine) explosives pollution in plants. Here, the effects of exposure to these three explosives were examined on chlorophyll fluorescence, antioxidant enzyme activity, and the metabolite spectrum in alfalfa (Medicago sativa) plants. The degradation rates for TNT, RDX, and HMX by alfalfa were 26.8%, 20.4%, and 18.4%, respectively, under hydroponic conditions. TNT caused damage to the microstructure of the plant roots and inhibited photosynthesis, whereas RDX and HMX induced only minor changes. Exposure to any of the three explosives caused disturbances in the oxidase system. Non-targeted metabolomics identified a total of 6185 metabolites. TNT exposure induced the appearance of 609 differentially expressed metabolites (189 upregulated, 420 downregulated), RDX exposure induced 197 differentially expressed metabolites (155 upregulated and 42 downregulated), and HMX induced 234 differentially expressed metabolites (132 upregulated and 102 downregulated). Of these differentially expressed metabolites, lipids and lipid-like molecules were the main metabolites induced by explosives poisoning. TNT mainly caused significant changes in the alanine, aspartate, and glutamate metabolism metabolic pathways, RDX mainly caused disorders in the arginine biosynthesis metabolic pathway, and HMX disrupted the oxidative phosphorylation metabolic pathway. Taken together, the results show that exposure to TNT, RDX, and HMX leads to imbalances in plant photosynthetic characteristics and antioxidant enzyme systems, changes the basic metabolism of plants, and has significant ecotoxicity effects.

Field trial demonstrating phytoremediation of the military explosive RDX by XplA/XplB-expressing switchgrass

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a major component of munitions, is used extensively on military training ranges. As a result, widespread RDX pollution in groundwater and aquifers in the United States is now well documented. RDX is toxic, but its removal from training ranges is logistically challenging, lacking cost-effective and sustainable solutions. Previously, we have shown that thale cress (Arabidopsis thaliana) engineered to express two genes, xplA and xplB, encoding RDX-degrading enzymes from the soil bacterium Rhodococcus rhodochrous 11Y can break down this xenobiotic in laboratory studies. Here, we report the results of a 3-year field trial of XplA/XplB-expressing switchgrass (Panicum virgatum) conducted on three locations in a military site. Our data suggest that XplA/XplB switchgrass has in situ efficacy, with potential utility for detoxifying RDX on live-fire training ranges, munitions dumps and minefields.

Combined Biotic-Abiotic 2,4-Dinitroanisole Degradation in the Presence of Hexahydro-1,3,5-trinitro-1,3,5-triazine

The Department of Defense has developed new explosive formulations in which traditionally used cyclic nitramines such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) have been updated with the insensitive munition (IM) 2,4-dinitroanisole (DNAN). Understanding combined degradation of both compounds at explosive-contaminated sites will allow remediation approaches that simultaneously target both contaminants. DNAN reduction in the presence of RDX was evaluated in abiotic experiments using substoichiometric, stoichiometric, and superstoichiometric concentrations of ferrous iron and anthrahydroquinone disulfonate within a pH range from 7.0 to 9.0. Biological degradation was investigated in resting cell suspensions of Geobacter metallireducens strain GS-15, a model Fe(III)-reducing Bacteria. Cells were amended into anoxic tubes buffered at pH 7.0, with initial 100 μM DNAN and 40-50 μM RDX. In both abiotic and biological experiments, the DNAN was reduced through the intermediate 2-methoxy-5-nitroaniline or 4-methoxy-3-nitroaniline to 2,4-diaminoanisole. In biological experiments, the RDX was reduced to form methylenedinitramine, formaldehyde (HCHO), and ammonium (NH₄⁺). Cells were able to reduce both DNAN and RDX most readily in the presence of extracellular electron shuttles and/or Fe(III). DNAN degradation (abiotic and biotic) was faster than degradation of RDX, suggesting that the reduction of IMs will not be inhibited by cyclic nitramines, but degradation dynamics did change in mixtures when compared to singular compounds.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Biotransformation of xenobiotics by hairy roots

The exponential industrial growth we see today rides on the back of large scale production of chemicals, explosives and pharmaceutical products. However, the effluents getting released from their manufacturing units are greatly compromising the sustainability of our environment. With greater awareness of the imperative for environmental clean-up, a promising approach that is attracting increasing research interests is biodegradation of xenobiotics. In this approach, biotransformation has proven to be one of the most effective tools. While many different model frameworks have been used to study different aspects of biotransformation, hairy roots (HRs) have been found to be exceptionally valuable. HR cultures are preferred over other in-vitro model systems due to their biochemical stability and hormone-autotrophy. In addition, the multi-enzyme biosynthetic potential of HRs which is similar to the parent plant and their relatively low-cost cultural requirements further characterize their suitability for biotransformation. The recent progress observed in scale-up of HR cultures and understanding of functional genomics has opened up new dimensions providing valuable insights for industrial application. This review article summarizes the potential of HR cultures in the biotransformation of xenobiotics, their limitations in the application on a large scale and current strategies to alleviate them. Advancement in bioreactors engineering enabling large scale cultivation and modern gene technologies improving biotransformation efficiency promises to extend laboratory results to industrial applications.

Toxicity of Explosive Effluent by Alliumcepa and Germination Test

In this work the toxicity caused by explosive industries effluent (yellow water) at different levels of toxicity (genetic, cellular and organismal level) was evaluated by the Allium cepa test and the Sorghum sudanense germination. The results showed that the effluent paralyze the mitotic process, keeping the cells in the interphase, decreasing the mitotic index in A. cepa. Chromosomal abnormalities such as c-metaphases, adhesions, breaks, early ascending chromosomes and irregular nucleus were observed for this receptor species. The germination of S. sudanense was reduced, and the development of the radicles were affected, showing reduced tolerance index at the highest concentrations of the effluent. Thus, it is concluded that the effluent from the explosive industry is extremely toxic to the tested organisms, both in cellular and chromosomal level and also for seed germination.

Spatially-distinct redox conditions and degradation rates following field-scale bioaugmentation for RDX-contaminated groundwater remediation

In situ bioaugmentation for cleanup of an hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-contaminated groundwater plume was recently demonstrated. Results of a forced-gradient, field-scale cell transport test with Gordonia sp. KTR9 and Pseudomonas fluorescens strain I-C cells (henceforth "KTR9" and "Strain I-C") showed these strains were transported 13 m downgradient over 1 month. Abundances of xplA and xenB genes, respective indicators of KTR9 and Strain I-C, approached injection well cell densities at 6 m downgradient, whereas gene abundances (and conservative tracer) had begun to increase at 13 m downgradient at test conclusion. In situ push-pull tests were subsequently completed to measure RDX degradation rates in the bioaugmented wells under ambient gradient conditions. Time-series monitoring of RDX, RDX end-products, conservative tracer, xplA and xenB gene copy numbers and XplA and XenB protein abundance were used to assess the efficacy of bioaugmentation and to estimate the apparent first-order RDX degradation rates during each test. A collective evaluation of redox conditions, RDX end-products, varied RDX degradation kinetics, and biomarkers indicated that Strain I-C and KTR9 rapidly degraded RDX. Results showed bioaugmentation is a viable technology for accelerating RDX cleanup in the demonstration site aquifer and may be applicable to other sites. Full-scale implementation considerations are discussed.

Degradation of High Energy Materials Using Biological Reduction: A Rational Way to Reach Bioremediation

Explosives molecules have been widely used since World War II, leading to considerable contamination of soil and groundwater. Recently, bioremediation has emerged as an environmentally friendly approach to solve such contamination issues. However, the 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) explosive, which has very low solubility in water, does not provide satisfying results with this approach. In this study, we used a rational design strategy for improving the specificity of the nitroreductase from E. Cloacae (PDB ID 5J8G) toward HMX. We used the Coupled Moves algorithm from Rosetta to redesign the active site around HMX. Molecular Dynamics (MD) simulations and affinity calculations allowed us to study the newly designed protein. Five mutations were performed. The designed nitroreductase has a better fit with HMX. We observed more H-bonds, which productively stabilized the HMX molecule for the mutant than for the wild type enzyme. Thus, HMX’s nitro groups are close enough to the reductive cofactor to enable a hydride transfer. Also, the HMX affinity for the designed enzyme is better than for the wild type. These results are encouraging. However, the total reduction reaction implies numerous HMX derivatives, and each of them has to be tested to check how far the reaction can’ go.