A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition

In the present study, an anaerobic microbial consortium for the degradation of hexahydro-1,3,5- trinitro-1,3,5-triazine (RDX) was selectively enriched with the co-addition of RDX and starch under nitrogen-deficient conditions. Microbial growth and anaerobic RDX biodegradation were effectively enhanced by the co-addition of RDX and starch, which resulted in increased RDX biotransformation to nitroso derivatives at a greater specific degradation rate than those for previously reported anaerobic RDX-degrading bacteria (isolates). The accumulation of the most toxic RDX degradation intermediate (MNX [hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine]) was significantly reduced by starch addition, suggesting improved RDX detoxification by the co-addition of RDX and starch. The subsequent MiSeq sequencing that targeted the bacterial 16S rRNA gene revealed that the Sporolactobacillus, Clostridium, and Paenibacillus populations were involved in the enhanced anaerobic RDX degradation. These results suggest that these three bacterial populations are important for anaerobic RDX degradation and detoxification. The findings from this work imply that the Sporolactobacillus, Clostridium, and Paenibacillus dominant microbial consortium may be valuable for the development of bioremediation resources for RDX-contaminated environments.

Manipulating redox conditions to enhance in situ bioremediation of RDX in groundwater at a contaminated site

Surficial application of waste glycerol (WG) for enhanced bioremediation was tested in situ at an old military range site to address hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) contaminated groundwater. This treatment was effective in inducing strong reducing conditions (range: -4 to -205 mV) and increasing the concentrations of organic carbon (from 10 to 729 mg/L) and fatty acids (from 0 to 940 mg/L) concomitantly with a decrease in RDX concentrations (range: 17 to 143 μg/L) to below detection limits (0.1 μg/L) in 2 of the 3 monitoring wells (MWs) evaluated. None of these changes were observed in the control MW. RDX disappeared without the detection of any common anaerobic nitroso degradation intermediates, with the exception of one MW where the concentration of organics did not significantly increase (range: 10 to 20 mg/L), suggesting the conditions were not favourable for biodegradation. Ecotoxicological analysis suggested that the use of WG may have some dose-related deleterious effects on different soil and aquatic receptors. Analysis of the microbial community composition, using 16S rRNA gene amplicon sequences, which provided insight into whether the process design had selected for and stimulated the optimal microbial populations, indicated co-existence of numerous Operational Taxonomic Units (OTUs) belonging to groups known to be capable of RDX degradation under anaerobic conditions, with a positive link between Geobacter spp. enrichment and the presence of RDX nitroso metabolites. Overall, the results from this field test show that this treatment process can provide an effective long-term, semi-passive remediation option for RDX contaminated groundwater.

Evaluation of Biostimulation and Bioaugmentation To Stimulate Hexahydro-1,3,5-trinitro-1,3,5,-triazine Degradation in an Aerobic Groundwater Aquifer

Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a toxic and mobile groundwater contaminant common to military sites. This study compared in situ RDX degradation rates following bioaugmentation with Gordonia sp. strain KTR9 (henceforth KTR9) to rates under biostimulation conditions in an RDX-contaminated aquifer in Umatilla, OR. Bioaugmentation was achieved by injecting site groundwater (6000 L) amended with KTR9 cells (10(8) cells mL(-1)) and low carbon substrate concentrations (<1 mM fructose) into site wells. Biostimulation (no added cells) was performed by injecting groundwater amended with low (<1 mM fructose) or high (>15 mM fructose) carbon substrate concentrations in an effort to stimulate aerobic or anaerobic microbial activity, respectively. Single-well push-pull tests were conducted to measure RDX degradation rates for each treatment. Average rate coefficients were 1.2 day(-1) for bioaugmentation and 0.7 day(-1) for high carbon biostimulation; rate coefficients for low carbon biostimulation were not significantly different from zero (p values ≥0.060). Our results suggest that bioaugmentation with KTR9 is a feasible strategy for in situ biodegradation of RDX and, at this site, is capable of achieving RDX concentration reductions comparable to those obtained by high carbon biostimulation while requiring ~97% less fructose. Bioaugmentation has potential to minimize substrate quantities and associated costs, as well as secondary groundwater quality impacts associated with anaerobic biostimulation processes (e.g., hydrogen sulfide, methane production) during full-scale RDX remediation.

Riboflavin-mediated RDX transformation in the presence of Shewanella putrefaciens CN32 and lepidocrocite

The potential of riboflavin for the reductive degradation of a cyclic nitramine, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), was investigated in the presence of lepidocrocite and/or Shewanella putrefaciens CN32. RDX reduction by CN32 alone or CN32 with lepidocrocite was insignificant, while 110 μM RDX was completely reduced by CN32 with riboflavin in 78 h. The transformation products identified included nitroso metabolites, formaldehyde, and ammonium, indicating the ring cleavage of RDX. UV and visible light analysis revealed that riboflavin was microbially reduced by CN32, and that the reduced riboflavin was linked to the complete degradation of RDX. In the presence of both CN32 and lepidocrocite (γ-FeOOH), 100 μM-riboflavin increased the rate and extent of Fe(II) production as well as RDX reduction. An abiotic study also showed that Fe(II)-riboflavin complex, and Fe(II) adsorbed on lepidocrocite, reduced RDX by 48% and 21%, respectively. The findings in this study suggest that riboflavin-mediated RDX degradation pathways in subsurface environments are diverse and complex. However, riboflavin, either from bacteria or exogenous sources, can significantly increase RDX degradation. This will provide a sustainable clean-up option for explosive-contaminated subsurface environments.

Electron shuttle-mediated biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine adsorbed to granular activated carbon

Granular activated carbon (GAC) effectively removes hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from groundwater but generates RDX-laden GAC that must be disposed of or regenerated. Batch reactors containing GAC to which RDX was preadsorbed were used in experiments to test the potential for adsorbed RDX reduction and daughter product formation using (i) chemically reduced anthrahydroquinone-2,6-disulfonate (AH2QDS), (ii) resting Geobacter metallireducens strain GS-15, and (iii) a combined system containing AQDS and GS-15. Approximately 97.0% of the adsorbed RDX was transformed in each of these experimental systems by 90 h. Chemically reduced AQDS (AH2QDS) transformed 99.2% of adsorbed RDX; formaldehyde was produced rapidly and was stoichiometric (3 mol HCHO per mol RDX). Geobacter metallireducens also reduced RDX with and without AQDS present. This is the first study to demonstrate biological transformation of RDX adsorbed to GAC. Formaldehyde increased and then decreased in biological systems, suggesting a previously unreported capacity for G. metallireducens to oxidize formaldehyde, which was confirmed with resting cell suspensions. These data suggest the masses of GAC waste currently produced by activated carbon at RDX remediation sites can be minimized, decreasing the carbon footprint of the treatment technology. Alternatively, this strategy may be used to develop a Bio-GAC system for ex situ RDX treatment.

Enhanced biotransformation of nitrobenzene by the synergies of Shewanella species and mediator-functionalized polyurethane foam

The performance and mechanism of anaerobic treatment of nitrobenzene using the combination of Shewanella species and anthraquinone-2-sulfonate-modified polyurethane foam (Shewanella/AQS-PUF) were investigated. The results showed that Shewanella/AQS-PUF significantly accelerated nitrobenzene bio-reduction (95.6%) and aniline formation (94.3%) with nitrobenzene removal rate up to 0.13 mM h(-1). Moreover, there were synergistic effects between Shewanella species and AQS-PUF on promoting nitrobenzene biotransformation with 5-fold increase in first-order rate constant compared to that without AQS-PUF. During this process, AQS-PUF could induce Shewanella species to secrete more flavins (0.335 μM) as redox mediator for nitrobenzene bio-reduction. Meanwhile, it was also found that the bound EPS of Shewanella species could act as biocatalyst for nitrobenzene reduction and the addition of flavins enhanced its catalytic activity. This indicated that the EPS of Shewanella species was not only involved in direct bio-reduction of nitrobenzene, but also interacted with secreted flavins to mediate nitrobenzene bio-reduction.

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.

Steroid degradation in Comamonas testosteroni

Steroid degradation by Comamonas testosteroni and Nocardia restrictus have been intensively studied for the purpose of obtaining materials for steroid drug synthesis. C. testosteroni degrades side chains and converts single/double bonds of certain steroid compounds to produce androsta-1,4-diene 3,17-dione or the derivative. Following 9α-hydroxylation leads to aromatization of the A-ring accompanied by cleavage of the B-ring, and aromatized A-ring is hydroxylated at C-4 position, cleaved at Δ4 by meta-cleavage, and divided into 2-hydroxyhexa-2,4-dienoic acid (A-ring) and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (B,C,D-ring) by hydrolysis. Reactions and the genes involved in the cleavage and the following degradation of the A-ring are similar to those for bacterial biphenyl degradation, and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid degradation is suggested to be mainly β-oxidation. Genes involved in A-ring aromatization and degradation form a gene cluster, and the genes involved in β-oxidation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid also comprise a large cluster of more than 10 genes. The DNA region between these two main steroid degradation gene clusters contain 3α-hydroxysteroid dehydrogenase gene, Δ5,3-ketosteroid isomerase gene, genes for inversion of an α-oriented-hydroxyl group to a β-oriented-hydroxyl group at C-12 position of cholic acid, and genes possibly involved in the degradation of a side chain at C-17 position of cholic acid, indicating this DNA region of more than 100kb to be a steroid degradation gene hot spot of C. testosteroni. Article from a special issue on steroids and microorganisms.

Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation

Shewanella halifaxensis and Shewanella sediminis were among a few aquatic gamma-proteobacteria that were psychrophiles and the first anaerobic bacteria that degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although many mesophilic or psychrophilic strains of Shewanella and gamma-proteobacteria were sequenced for their genomes, the genomic evolution pathways for temperature adaptation were poorly understood. On the other hand, the genes responsible for anaerobic RDX mineralization pathways remain unknown. To determine the unique genomic properties of bacteria responsible for both cold-adaptation and RDX degradation, the genomes of S. halifaxensis and S. sediminis were sequenced and compared with 108 other gamma-proteobacteria including Shewanella that differ in temperature and Na+ requirements, as well as RDX degradation capability. Results showed that for coping with marine environments their genomes had extensively exchanged with deep sea bacterial genomes. Many genes for Na+-dependent nutrient transporters were recruited to use the high Na+ content as an energy source. For coping with low temperatures, these two strains as well as other psychrophilic strains of Shewanella and gamma-proteobacteria were found to decrease their genome G+C content and proteome alanine, proline and arginine content (p-value <0.01) to increase protein structural flexibility. Compared to poorer RDX-degrading strains, S. halifaxensis and S. sediminis have more number of genes for cytochromes and other enzymes related to RDX metabolic pathways. Experimentally, one cytochrome was found induced in S. halifaxensis by RDX when the chemical was the sole terminal electron acceptor. The isolated protein degraded RDX by mono-denitration and was identified as a multiheme 52 kDa cytochrome using a proteomic approach. The present analyses provided the first insight into divergent genomic evolution of bacterial strains for adaptation to the specific cold marine conditions and to the degradation of the pollutant RDX. The present study also provided the first evidence for the involvement of a specific c-type cytochrome in anaerobic RDX metabolism.

The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

In the bacterial periplasm, the reduction of nitrate to nitrite is catalysed by a periplasmic nitrate reductase (NAP) system, which is a species-dependent assembly of protein subunits encoded by the nap operon. The reduction of nitrate catalysed by NAP takes place in the 90 kDa NapA subunit, which contains a Mo-bis-molybdopterin guanine dinucleotide cofactor and one [4Fe-4S] iron-sulfur cluster. A review of the nap operons in the genomes of 19 strains of Shewanella shows that most genomes contain two nap operons. This is an unusual feature of this genus. The two NAP isoforms each comprise three isoform-specific subunits - NapA, a di-haem cytochrome NapB, and a maturation chaperone NapD - but have different membrane-intrinsic subunits, and have been named NAP-alpha (NapEDABC) and NAP-beta (NapDAGHB). Sixteen Shewanella genomes encode both NAP-alpha and NAP-beta. The genome of the vigorous denitrifier Shewanella denitrificans OS217 encodes only NAP-alpha and the genome of the respiratory nitrate ammonifier Shewanella oneidensis MR-1 encodes only NAP-beta. This raises the possibility that NAP-alpha and NAP-beta are associated with physiologically distinct processes in the environmentally adaptable genus Shewanella.