Biodegradation of RDX and MNX with Rhodococcus sp. strain DN22: new insights into the degradation pathway

Multi-Omics Strategies to Investigate the Biodegradation of Hexahydro-1,3,5-trinitro-1,3,5-triazine in Rhodococcus sp. Strain DN22

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is an energetic and persistent explosive with long-lasting properties. Rhodococcus sp. strain DN22 has been discovered to be a microbe capable of degrading RDX. Herein, the complete genome of Rhodococcus sp. strain DN22 was sequenced and analyzed. The entire sequences of genes that encoded the two proteins participating in RDX degradation in Rhodococcus sp. strain DN22 were obtained, and were validated through proteomic data. In addition, few studies have investigated the physiological changes and metabolic pathways occurring within Rhodococcus sp. cells when treated with RDX, particularly through mass spectrometry-based omics. Hence, proteomic and metabolomic analyses were carried out on Rhodococcus sp. strain DN22 with the existence or lack of RDX in the medium. A total of 3186 proteins were identified between the two groups, with 115 proteins being significantly differentially expressed proteins. There were 1056 metabolites identified in total, among which 130 metabolites were significantly different. Through the combined analysis of differential proteomics and metabolomics, KEGG pathways including two-component system, ABC transporters, alanine, aspartate and glutamate metabolism, arginine biosynthesis, purine metabolism, nitrogen metabolism, and phosphotransferase system (PTS), were observed to be significantly enriched. These findings provided ponderable perspectives on the physiological alterations and metabolic pathways in Rhodococcus sp. strain DN22, responding to the existence or lack of RDX. This study is anticipated to expand the knowledge of Rhodococcus sp. strain DN22, as well as advancing understanding of microbial degradation.

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.

Exploring the Utility of Compound-Specific Isotope Analysis for Assessing Ferrous Iron-Mediated Reduction of RDX in the Subsurface

Subsurface contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) at ordnance production and testing sites is a problem because of the persistence, mobility, and toxicity of RDX and the formation of toxic products under anoxic conditions. While the utility of compound-specific isotope analysis for inferring natural attenuation pathways from stable isotope ratios has been demonstrated, the stable isotope fractionation for RDX reduction by iron-bearing minerals remains unknown. Here, we evaluated N and C isotope fractionation of RDX during reduction by Fe(II) associated with Fe minerals and natural sediments and applied N isotope ratios to the assessment of mineral-catalyzed RDX reduction in a contaminant plume and in sediment columns treated by in situ chemical reduction. Laboratory studies revealed that RDX was reduced to nitroso compounds without denitration and the concomitant ring cleavage. Fe(II)/iron oxide mineral-catalyzed reactions exhibited N isotope enrichment factors, ε_N, between -6.3±0.3‰ and -8.2±0.2‰, corresponding to an apparent ¹⁵N kinetic isotope effect of 1.04-1.05. The observed variations of the δ¹⁵N of ∼15‰ in RDX from groundwater samples suggested an extent of reductive transformation of 85% at an ammunition plant. Conversely, we observed masking of N isotope fractionation after RDX reduction in laboratory flow-through systems, which was presumably due to limited accessibility to reactive Fe(II).

RDX degradation by chemical oxidation using calcium peroxide in bench scale sludge systems

The ability of calcium peroxide (CaO₂) to degrade hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated soil slurries using CaO₂-based modified Fenton oxidation was investigated. Results showed that increasing the CaO₂ dose increased degradation rates of RDX and pH. RDX concentrations decreased to below detection after 18 h with 2 M and 2.5 M CaO₂, after 30 h with 1.5 M CaO₂, after 54 h with 1 M CaO₂, but 0.1 M CaO₂ achieved no significant RDX removal. Increasing the soil organic matter content decreased the rate and extent of RDX degradation. RDX degradation products 4-nitro-2,4-diazabutanal (NDAB) and methylenedinitramine (MEDINA) were quantified, and the greater accumulation of NDAB than MEDINA suggests denitration of RDX was the most likely initial degradation step. Isotopic ratios for nitrogen and oxygen associated with RDX oxidation are also consistent with either nitrification of NH₄⁺ from soil or precipitation. Existing technologies merely only extract energetics from soils for treatment ex situ, whereas the approach introduced herein destroys RDX in situ with a one-step application.

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.

Impact of glycerin and lignosulfonate on biodegradation of high explosives in soil

Soil microcosms were constructed and monitored to evaluate the impact of substrate addition and transient aerobic and anaerobic conditions on TNT, RDX and HMX biodegradation in grenade range soils. While TNT was rapidly biodegraded under both aerobic and anaerobic conditions with and without organic substrate, substantial biodegradation of RDX, HMX, and RDX daughter products was not observed under aerobic conditions. However, RDX and HMX were significantly biodegraded under anaerobic conditions, without accumulation of TNT or RDX daughter products (2-ADNT, 4-ADNT, MNX, DNX, and TNX). In separate microcosms containing grenade range soil, glycerin and lignosulfonate addition enhanced oxygen consumption, increasing the consumption rate >200% compared to untreated soils. Mathematical model simulations indicate that oxygen consumption rates of 5 to 20g/m³/d can be achieved with reasonable amendment loading rates. These results indicate that glycerin and lignosulfonate can be potentially used to stimulate RDX and HMX biodegradation by increasing oxygen consumption rates in soil.

Uptake and fate of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in coastal marine biota determined using a stable isotopic tracer, (15)N - [RDX]

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is globally one of the most commonly used military explosives and environmental contaminant. (15)N labeled RDX was added into a mesocosm containing 9 different coastal marine species in a time series experiment to quantify the uptake of RDX and assess the RDX derived (15)N retention into biota tissue. The (15)N attributed to munitions compounds reached steady state concentrations ranging from 0.04 to 0.67 μg (15)N g dw(-1), the bulk (15)N tissue concentration for all species was 1-2 orders of magnitude higher suggesting a common mechanism or pathway of RDX biotransformation and retention of (15)N. A toxicokinetic model was created that described the (15)N uptake, elimination, and transformation rates. While modeled uptake rates were within previous published values, elimination rates were several orders of magnitude smaller than previous studies ranging from 0.05 to 0.7 days(-1). These small elimination rates were offset by high rates of retention of (15)N previously not measured. Bioconcentration factors and related aqueous:organism ratios of compounds and tracer calculated using different tracer and non-tracer methods yielded a broad range of values (0.35-101.6 mL g(-1)) that were largely method dependent. Despite the method-derived variability, all values were generally low and consistent with little bioaccumulation potential. The use of (15)N labeled RDX in this study indicates four possible explanations for the observed distribution of compounds and tracer; each with unique potential implications for possible toxicological impacts in the coastal marine environment.

Relating Carbon and Nitrogen Isotope Effects to Reaction Mechanisms during Aerobic or Anaerobic Degradation of RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine) by Pure Bacterial Cultures

Kinetic isotopic fractionation of carbon and nitrogen during RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation was investigated with pure bacterial cultures under aerobic and anaerobic conditions. Relatively large bulk enrichments in (15)N were observed during biodegradation of RDX via anaerobic ring cleavage (ε(15)N = -12.7‰ ± 0.8‰) and anaerobic nitro reduction (ε(15)N = -9.9‰ ± 0.7‰), in comparison to smaller effects during biodegradation via aerobic denitration (ε(15)N = -2.4‰ ± 0.2‰). (13)C enrichment was negligible during aerobic RDX biodegradation (ε(13)C = -0.8‰ ± 0.5‰) but larger during anaerobic degradation (ε(13)C = -4.0‰ ± 0.8‰), with modest variability among genera. Dual-isotope ε(13)C/ε(15)N analyses indicated that the three biodegradation pathways could be distinguished isotopically from each other and from abiotic degradation mechanisms. Compared to the initial RDX bulk δ(15)N value of +9‰, δ(15)N values of the NO2 (-) released from RDX ranged from -7‰ to +2‰ during aerobic biodegradation and from -42‰ to -24‰ during anaerobic biodegradation. Numerical reaction models indicated that N isotope effects of NO2 (-) production were much larger than, but systematically related to, the bulk RDX N isotope effects with different bacteria. Apparent intrinsic ε(15)N-NO2 (-) values were consistent with an initial denitration pathway in the aerobic experiments and more complex processes of NO2 (-) formation associated with anaerobic ring cleavage. These results indicate the potential for isotopic analysis of residual RDX for the differentiation of degradation pathways and indicate that further efforts to examine the isotopic composition of potential RDX degradation products (e.g., NOx) in the environment are warranted.

IMPORTANCE

This work provides the first systematic evaluation of the isotopic fractionation of carbon and nitrogen in the organic explosive RDX during degradation by different pathways. It also provides data on the isotopic effects observed in the nitrite produced during RDX biodegradation. Both of these results could lead to better understanding of the fate of RDX in the environment and help improve monitoring and remediation technologies.

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site

This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

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.

Identification of microbial populations assimilating nitrogen from RDX in munitions contaminated military training range soils by high sensitivity stable isotope probing

The leaching of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) from particulates deposited in live-fire military training range soils contributes to significant pollution of groundwater. In situ microbial degradation has been proposed as a viable method for onsite containment of RDX. However, there is only a single report of RDX degradation in training range soils and the soil microbial communities involved in RDX degradation were not identified. Here we demonstrate aerobic RDX degradation in soils taken from a target area of an Eglin Air Force Base bombing range, C52N Cat's Eye, (Eglin, Florida U.S.A.). RDX-degradation activity was spatially heterogeneous (found in less than 30% of initial target area field samples) and dependent upon the addition of exogenous carbon sources to the soils. Therefore, biostimulation (with exogenous carbon sources) and bioaugmentation may be necessary to sustain timely and effective in situ microbial biodegradation of RDX. High sensitivity stable isotope probing analysis of extracted soils incubated with fully labeled (15)N-RDX revealed several organisms with (15)N-labeled DNA during RDX-degradation, including xplA-bearing organisms. Rhodococcus was the most prominent genus in the RDX-degrading soil slurries and was completely labeled with (15)N-nitrogen from the RDX. Rhodococcus and Williamsia species isolated from these soils were capable of using RDX as a sole nitrogen source and possessed the genes xplB and xplA associated with RDX-degradation, indicating these genes may be suitable genetic biomarkers for assessing RDX degradation potential in soils. Other highly labeled species were primarily Proteobacteria, including: Mesorhizobium sp., Variovorax sp., and Rhizobium sp.

Emerging chemicals and the evolution of biodegradation capacities and pathways in bacteria

The number of new chemicals produced is increasing daily by the thousands, and it is inevitable that many of these chemicals will reach the environment. Current research provides an understanding of how the evolution of promiscuous enzymes and the recruitment of enzymes available from the metagenome allows for the assembly of these pathways. Nevertheless, physicochemical constraints including bioavailability, bioaccessibility, and the structural variations of similar chemicals limit the evolution of biodegradation pathways. Similarly, physiological constraints related to kinetics and substrate utilization at low concentrations likewise limit chemical-enzyme interactions and consequently evolution. Considering these new data, the biodegradation decalogue still proves valid while at the same time the underlying mechanisms are better understood.

Insight on RDX degradation mechanism by Rhodococcus strains using 13C and 15N kinetic isotope effects

The explosive Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is known to be degraded aerobically by various isolates of the Rhodococcus species, with denitration being the key step, mediated by Cytochrome P450. Our study aimed at gaining insight into the RDX degradation mechanism by Rhodococcus species and comparing isotope effects associated with RDX degradation by distinct Rhodococcus strains. For these purposes, enrichment in (13)C and (15)N isotopes throughout RDX denitration was studied for three distinct Rhodococcus strains, isolated from soil and groundwater in an RDX-contaminated site. The observable (15)N enrichment throughout the reaction, together with minor (13)C enrichment, suggests that N-N bond cleavage is likely to be the key rate-limiting step in the reaction. The similarity in the kinetic (15)N isotope effect between the three tested strains suggests that either isotope-masking effects are negligible, or are of a similar extent for all tested strains. The lack of variability in the kinetic (15)N isotope effect allows the interpretation of environmental studies with greater confidence.

Biodegradation of RDX nitroso products MNX and TNX by cytochrome P450 XplA

Anaerobic transformation of the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by microorganisms involves sequential reduction of N-NO(2) to the corresponding N-NO groups resulting in the initial formation of MNX (hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine). MNX is further reduced to the dinitroso (DNX) and trinitroso (TNX) derivatives. In this paper, we describe the degradation of MNX and TNX by the unusual cytochrome P450 XplA that mediates metabolism of RDX in Rhodococcus rhodochrous strain 11Y. XplA is known to degrade RDX under aerobic and anaerobic conditions, and, in the present study, was found able to degrade MNX to give similar products distribution including NO(2)(-), NO(3)(-), N(2)O, and HCHO but with varying stoichiometric ratio, that is, 2.06, 0.33, 0.33, 1.18, and 1.52, 0.15, 1.04, 2.06, respectively. In addition, the ring cleavage product 4-nitro-2,4,-diazabutanal (NDAB) and a trace amount of another intermediate with a [M-H](-) at 102 Da, identified as ONNHCH(2)NHCHO (NO-NDAB), were detected mostly under aerobic conditions. Interestingly, degradation of TNX was observed only under anaerobic conditions in the presence of RDX and/or MNX. When we incubated RDX and its nitroso derivatives with XplA, we found that successive replacement of N-NO(2) by N-NO slowed the removal rate of the chemicals with degradation rates in the order RDX > MNX > DNX, suggesting that denitration was mainly responsible for initiating cyclic nitroamines degradation by XplA. This study revealed that XplA preferentially cleaved the N-NO(2) over the N-NO linkages, but could nevertheless degrade all three nitroso derivatives, demonstrating the potential for complete RDX removal in explosives-contaminated sites.