Towards engineering degradation of the explosive pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine in the rhizosphere

Nature-based approaches to reducing the environmental risk of organic contaminants resulting from military activities

As is the case with many other industrial activities, the organic contaminants at military-impacted sites may pose significant hazards to the environment and human health. Given the expected increase in defense investments globally, there is a need to make society aware of the risks of emissions of organic contaminants generated by military activities and to advance risk minimization approaches. The most recent advances in environmental analytical chemistry, persistence, bioavailability and risk assessment of organic contaminants indicate that efficient risk reductions through biological means are possible. This review debates the organic contaminants of interest associated with military activities, the methodology used to extract and analyze these contaminants, and the nature-based remediation technologies available to recover these sites. In addition, we revise the military environmental regulatory frameworks designed to sustain such actions. Military activities that potentially release organic contaminants on land could be classified as infrastructure and base operations, training exercises and armed conflicts; additionally, chemicals may include potentially toxic compounds, energetic compounds, chemical warfare agents and military chemical compounds. Fuel components, PFASs, TNT, RDX and dyphenylcyanoarsine are examples of organic contaminants of environmental concern. Particularly in the case of potentially toxic and energetic compounds, bioremediation and phytoremediation are considered eco-friendly and low-cost technologies that can be used to remediate these contaminated sites. In addition, this article identifies implementing the bioavailability of organic contaminants as a justifiable approach to facilitate the application of these nature-based approaches and to reduce remediation costs. More realistic risk assessment in combination with new and economically feasible remediation methods that reduce risk by reducing bioavailability (instead of lowering the total contaminant concentration) will serve as an incentive for the military and regulators to accept nature-based approaches.

A sketch of microbiological remediation of explosives-contaminated soil focused on state of art and the impact of technological advancement on hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation

When high-energy explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 2,4,6-trinitrotoluene (TNT) are discharged into the surrounding soil and water during production, testing, open dumping, military, or civil activities, they leave a toxic footprint. The US Environmental Protection Agency has labeled RDX as a potential human carcinogen that must be degraded from contaminated sites quickly. Bioremediation of RDX is an exciting prospect that has received much attention in recent years. However, a lack of understanding of RDX biodegradation and the limitations of current approaches have hampered the widespread use of biodegradation-based strategies for RDX remediation at contamination sites. Consequently, new bioremediation technologies are required to enhance performance. In this review, we explore the requirements for in-silico analysis for producing biological models of microbial remediation of RDX in soil. On the other hand, potential gene editing methods for getting the host with target gene sequences responsible for the breakdown of RDX are also reported. Microbial formulations and biosensors for detection and bioremediation are also briefly described. The biodegradation of RDX offers an alternative remediation method that is both cost-effective and ecologically acceptable. It has the potential to be used in conjunction with other cutting-edge technologies to further increase the efficiency of RDX degradation.

In-vessel composting of HMX and RDX contaminated sludge using microbes isolated from contaminated site

Current study was carried out with an objective to remediate highly contaminated sludge with HMX and RDX obtained from an explosive manufacturing facility in North India employing indigenous microbes, Arthrobacter subterraneus (isolate no. S2-TSB-17) and Bacillus sonorensis (isolate no. S8-TSB-4) which were isolated from the same contaminated site. In-vessel composting of the explosive contaminated sludge was performed in 12 different bioreactors using cow manure and garden waste as bulking agents. 78.5% degradation of HMX was observed in reactor no. 2 with Bacillus sonorensis having combination of 10% sludge, 70% cow manure and 20% garden waste on 80th day. Two secondary metabolites Bis(hydroxymethyl)nitramine and methylene dinitramine were identified while studying the degradation pathway. Similarly, degradation of 91.2% was observed for RDX in reactor no. 11 with consortia of Arthrobacter subterraneus and Bacillus sonorensis on 80th day. During the study, release of significant nitrate and nitrite ions were observed. It has already been established that RDX and HMX degradation leads to release of nitrite/nitrate ions. The highest nitrite (reactor no. 11) and nitrate (reactor no. 2) release observed were 24.02 ± 0.05 mg/kg and 30.65 ± 0.99 mg/kg on 50th and 70th day, respectively. Scanning electron microscopic studies confirmed the attachment and presence of microbes with solid surface and no deformation in structure was observed in the microbial cells due to contamination stress. Findings of the study concluded that in-vessel composting assisted with native bacterial species can be a potential technology for the treatment of explosive contaminated sludge at the contaminated sites.

Microbial community structure and metabolome profiling characteristics of soil contaminated by TNT, RDX, and HMX

This experiment was conducted to evaluate the ecotoxicity of typical explosives and their mechanisms in the soil microenvironment. Here, TNT (trinitrotoluene), RDX (cyclotrimethylene trinitramine), and HMX (cyclotetramethylene tetranitramine) were used to simulate the soil pollution of single explosives and their combination. The changes in soil enzyme activity and microbial community structure and function were analyzed in soil, and the effects of explosives exposure on the soil metabolic spectrum were revealed by non-targeted metabonomics. TNT, RDX, and HMX exposure significantly inhibited soil microbial respiration and urease and dehydrogenase activities. Explosives treatment reduced the diversity and richness of the soil microbial community structure, and the microorganisms able to degrade explosives began to occupy the soil niche, with the Sphingomonadaceae, Actinobacteria, and Gammaproteobacteria showing significantly increased relative abundances. Non-targeted metabonomics analysis showed that the main soil differential metabolites under explosives stress were lipids and lipid-like molecules, organic acids and derivatives, with the phosphotransferase system (PTS) pathway the most enriched pathway. The metabolic pathways for carbohydrates, lipids, and amino acids in soil were specifically inhibited. Therefore, residues of TNT, RDX, and HMX in the soil could inhibit soil metabolic processes and change the structure of the soil microbial community.

Reductive Cytochrome P450 Reactions and Their Potential Role in Bioremediation

Cytochrome P450 enzymes, or P450s, are haem monooxygenases renowned for their ability to insert one atom from molecular oxygen into an exceptionally broad range of substrates while reducing the other atom to water. However, some substrates including many organohalide and nitro compounds present little or no opportunity for oxidation. Under hypoxic conditions P450s can perform reductive reactions, contributing electrons to drive reductive elimination reactions. P450s can catalyse dehalogenation and denitration of a range of environmentally persistent pollutants including halogenated hydrocarbons and nitroamine explosives. P450-mediated reductive dehalogenations were first discovered in the context of human pharmacology but have since been observed in a variety of organisms. Additionally, P450-mediated reductive denitration of synthetic explosives has been discovered in bacteria that inhabit contaminated soils. This review will examine the distribution of P450-mediated reductive dehalogenations and denitrations in nature and discuss synthetic biology approaches to developing P450-based reagents for bioremediation.

Bacilli-Mediated Degradation of Xenobiotic Compounds and Heavy Metals

Xenobiotic compounds are man-made compounds and widely used in dyes, drugs, pesticides, herbicides, insecticides, explosives, and other industrial chemicals. These compounds have been released into our soil and water due to anthropogenic activities and improper waste disposal practices and cause serious damage to aquatic and terrestrial ecosystems due to their toxic nature. The United States Environmental Protection Agency (USEPA) has listed several toxic substances as priority pollutants. Bacterial remediation is identified as an emerging technique to remove these substances from the environment. Many bacterial genera are actively involved in the degradation of toxic substances. Among the bacterial genera, the members of the genus Bacillus have a great potential to degrade or transform various toxic substances. Many Bacilli have been isolated and characterized by their ability to degrade or transform a wide range of compounds including both naturally occurring substances and xenobiotic compounds. This review describes the biodegradation potentials of Bacilli toward various toxic substances, including 4-chloro-2-nitrophenol, insecticides, pesticides, herbicides, explosives, drugs, polycyclic aromatic compounds, heavy metals, azo dyes, and aromatic acids. Besides, the advanced technologies used for bioremediation of environmental pollutants using Bacilli are also briefly described. This review will increase our understanding of Bacilli-mediated degradation of xenobiotic compounds and heavy metals.

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.

How synthetic biology can help bioremediation

The World Health Organization reported that "an estimated 12.6 million people died as a result of living or working in an unhealthy environment in 2012, nearly 1 in 4 of total global deaths". Air, water and soil pollution were the significant risk factors, and there is an urgent need for effective remediation strategies. But tackling this problem is not easy; there are many different types of pollutants, often widely dispersed, difficult to locate and identify, and in many cases cost-effective clean-up techniques are lacking. Biology offers enormous potential as a tool to develop microbial and plant-based solutions to remediate and restore our environment. Advances in synthetic biology are unlocking this potential enabling the design of tailor-made organisms for bioremediation. In this article, we showcase examples of xenobiotic clean-up to illustrate current achievements and discuss the limitations to advancing this promising technology to make real-world improvements in the remediation of global pollution.

Right on target: using plants and microbes to remediate explosives

While the immediate effect of explosives in armed conflicts is frequently in the public eye, until recently, the insidious, longer-term corollaries of these toxic compounds in the environment have gone largely unnoticed. Now, increased public awareness and concern are factors behind calls for more effective remediation solutions to these global pollutants. Scientists have been working on bioremediation projects in this area for several decades, characterizing genes, biochemical detoxification pathways, and field-applicable plant species. This review covers the progress made in understanding the fundamental biochemistry behind the detoxification of explosives, including new shock-insensitive explosive compounds; how field-relevant plant species have been characterized and genetically engineered; and the major roles that endophytic and rhizospheric microorganisms play in the detoxification of organic pollutants such as explosives.

Application of (13)C and (15)N stable isotope probing to characterize RDX degrading microbial communities under different electron-accepting conditions

This study identified microorganisms capable of using the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or its metabolites as carbon and/or nitrogen sources under different electron-accepting conditions using (13)C and (15)N stable isotope probing (SIP). Mesocosms were constructed using groundwater and aquifer solids from an RDX-contaminated aquifer. The mesocosms received succinate as a carbon source and one of four electron acceptors (nitrate, manganese(IV), iron(III), or sulfate) or no additional electron acceptor (to stimulate methanogenesis). When RDX degradation was observed, subsamples from each mesocosm were removed and amended with (13)C3- or ring-(15)N3-, nitro-(15)N3-, or fully-labeled (15)N6-RDX, followed by additional incubation and isolation of labeled nucleic acids. A total of fifteen 16S rRNA sequences, clustering in α- and γ-Proteobacteria, Clostridia, and Actinobacteria, were detected in the (13)C-DNA fractions. A total of twenty seven sequences were derived from different (15)N-DNA fractions, with the sequences clustered in α- and γ-Proteobacteria, and Clostridia. Interestingly, sequences identified as Desulfosporosinus sp. (in the Clostridia) were not only observed to incorporate the labeled (13)C or (15)N from labeled RDX, but also were detected under each of the different electron-accepting conditions. The data suggest that (13)C- and (15)N-SIP can be used to characterize microbial communities involved in RDX biodegradation, and that the dominant pathway of RDX biodegradation may differ under different electron-accepting conditions.

Improved RDX detoxification with starch addition using a novel nitrogen-fixing aerobic microbial consortium from soil contaminated with explosives

In this work, we developed and characterized a novel nitrogen-fixing aerobic microbial consortium for the complete detoxification of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Aerobic RDX biodegradation coupled with microbial growth and nitrogen fixation activity were effectively stimulated by the co-addition of starch and RDX under nitrogen limiting conditions. In the starch-stimulated nitrogen-fixing RDX degradative consortium, the RDX degradation activity was correlated with the xplA and nifH gene copy numbers, suggesting the involvement of nitrogen fixing populations in RDX biodegradation. Formate, nitrite, nitrate, and ammonia were detected as aerobic RDX degradation intermediates without the accumulation of any nitroso-derivatives or NDAB (4-nitro-2,4-diazabutanal), indicating nearly complete mineralization. Pyrosequencing targeting the bacterial 16S rRNA genes revealed that the Rhizobium, Rhizobacter and Terrimonas population increased as the RDX degradation activity increased, suggesting their involvement in the degradation process. These findings imply that the nitrogen-fixing aerobic RDX degrading consortium is a valuable microbial resource for improving the detoxification of RDX-contaminated soil or groundwater, especially when combined with rhizoremediation.