Enhancement of microbial 2,4,6-trinitrotoluene transformation with increased toxicity by exogenous nutrient amendment

Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior

Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60^T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60^T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH₄ ⁺ -N, and NO₃ ^- -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH₄ )₂ SO₄ and KNO₃ as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.

Synthesizing the impact of sea-dumped munition and related chemicals on humans and the environment

Marine environments are globally impacted by vast quantities of munition disposed following both World Wars. Dumped munitions contain conventional explosives, chemicals warfare agents as well as a variety of metals. Field monitoring studies around marine dumpsites report the presence of munition constituents in water and sediment samples. The growing interest and developments in the ocean as a new economic frontier underline the need to remediate existing dumpsites. Here, we provide a comprehensive assessment of the magnitude and potential risks associated with marine munition dumpsites. An overview of the global distribution of dumpsites identifying the most impacted areas is provided, followed by the currently available data on the detection of munition constituents in environmental samples and evidence of their toxic potential to human and environmental health. Finally, existing data gaps are identified and future research needs promoting better understanding of the impact of the dumped material on the marine environment suggested.

Transformation of 2, 4, 6-trinitrotoluene by Stenotrophomonas strain SG1 under aerobic and anaerobic conditions

TNT, or 2,4,6-trinitrotoluene, is a common explosive that can contaminate soil and groundwater in production sites, military training areas, and disposal locations. The compound is highly toxic; therefore, there is an urgent need to rehabilitate the impacted environments. Harnessing the microbial ability to biodegrade TNT into environmentally harmless compound(s) is one approach to remediating contaminated sites. In our study, we report on the genomic and metabolic ability of Stenotrophomonas strain SG1 to degrade TNT under aerobic and anaerobic conditions. The bacterial strain SG1 was first isolated as a contaminant from a culture of Diaphorobacter sp. strain DS2 over minimal media supplemented with TNT. The draft genome assembly of strain SG1 is ∼4.7 Mb and is distributed among 358 contigs. The homology search against the custom database of enzymes responsible for TNT biodegradation revealed the presence of three N-ethylmaleimide reductases (NemA) with a defined KEGG ortholog and KEGG pathway of TNT degradation. The presence of respiratory nitrate reductases has also been mapped, which supports denitrification under anaerobic conditions. Experimentally, the TNT transformation rate accelerated when carbon sources, such as sodium acetate, sodium citrate, sodium succinate, sucrose, and glucose (final concentration of 5 mM), were added. Citrate promoted the highest growth and TNT transformation ratio (88.35%) in 120 h. With the addition of 5 mM ammonium chloride, TNT completely disappeared in the citrate and sucrose-containing treatments in 120 h. However, higher biomass was obtained in the sucrose and glucose-containing treatments in 120 h. During incubation, the formation of amino dinitrotoluene isomers, dinitrotoluene isomers, trinitrobenzene, azoxy isomers, diaryl hydroxylamines, and corresponding secondary amines was confirmed by GC/MS and UPLC/MS. 2-Amino-4-nitrotoluene, 4-amino-2-nitrotoluene, and 2-amino-6-nitrotoluene were also identified in the culture supernatant by GC/MS. Under anaerobic conditions, TNT completely disappeared in the citrate and citrate plus nitrate treatments. Since the strain shows the ability to remove TNT, this research should be useful in basic research and practical applications for removing TNT from wastewater.

The elucidation of the biodegradation of nitrobenzene and p-nitrophenol of nitroreductase from Antarctic psychrophile Psychrobacter sp. ANT206 under low temperature

Psychrobacter is one important typical strain in the Antarctic environment. In our previous study, Psychrobacter sp. ANT206 from Antarctica with novel cold-adapted nitroreductase (PsNTR) could biodegrade nitrobenzene and p-nitrophenol in low temperature environment. In this study, the in-frame deletion mutant of psntr (Δpsntr-ANT206) that displayed well genetic stability and kanamycin resistance stability was constructed using allelic replacement method. Additionally, Δpsntr-ANT206 was more sensitive to nitrobenzene and p-nitrophenol in the comparison of heat and hyperosmolarity, suggesting that psntr gene participated in the regulation of the tolerance against nitro-aromatic compounds (NACs). Further analysis was conducted by integrated gas chromatography-mass spectrometry (GC-MS), and several metabolites were identified. Among them, ethylbenzene, L-Alanine, citric acid, aniline, 4-aminophenol and other metabolites were different between the wild-type strain and Δpsntr-ANT206 under nitrobenzene and p-nitrophenol stress at different time periods under low temperature, respectively. These data could increase the knowledge of the construction of deletion mutant strains and biodegradation mechanism of NACs of typical strains Psychrobacter from Antarctica, which would also provide the basis of the molecular technique on the regulation of bioremediation of the contaminants under low temperature in the future.

Exploring current tendencies in techniques and materials for immobilization of laccases - A review

Nanotechnology has transformed the science behind many biotechnological sectors, and applied bio-catalysis is not the exception. In 2017, the enzyme industry was valued at more than 7 billion USD and projected to 10.5 billion by 2024. The laccase enzyme is an oxidoreductase capable of oxidizing phenolic and non-phenolic compounds that have been considered an essential tool in the fields currently known as white biotechnology and green chemistry. Laccase is one of the most robust biocatalysts due to its wide applications in different environmental processes such as detecting and treating chemical pollutants and dyes and pharmaceutical removal. However, these biocatalytic processes are usually limited by the lack of stability of the enzyme, the half-life time, and the application feasibility at an industrial scale. Physical or chemical approaches have performed different laccase's immobilization methods to improve its catalytic properties and reuse. Emerging technologies have been proven to reduce the manufacturing process cost and increase application feasibility while looking for ecological and economical materials that can be used as support. Therefore, this review discusses the trends of enzyme immobilization recently studied, analyzing biomaterials and agro-industrial waste used for that intention, their advantages, and disadvantages. Finally, the work also highlights the performance obtained with these materials and current challenges and potential alternatives.

Biotransformation of 2,4,6-Trinitrotoluene by Pseudomonas sp. TNT3 isolated from Deception Island, Antarctica

2,4,6-Trinitrotoluene (TNT) is a nitroaromatic explosive, highly toxic and mutagenic for organisms. In this study, we report for the first time the screening and isolation of TNT-degrading bacteria from Antarctic environmental samples with potential use as bioremediation agents. Ten TNT-degrading bacterial strains were isolated from Deception Island. Among them, Pseudomonas sp. TNT3 was selected as the best candidate since it showed the highest tolerance, growth, and TNT biotransformation capabilities. Our results showed that TNT biotransformation involves the reduction of the nitro groups. Additionally, Pseudomonas sp. TNT3 was capable of transforming 100 mg/L TNT within 48 h at 28 °C, showing higher biotransformation capability than Pseudomonas putida KT2440, a known TNT-degrading bacterium. Functional annotation of Pseudomonas sp. TNT3 genome revealed a versatile set of molecular functions involved in xenobiotic degradation pathways. Two putative xenobiotic reductases (XenA_TNT3 and XenB_TNT3) were identified by means of homology searches and phylogenetic relationships. These enzymes were also characterized at molecular level using homology modelling and molecular dynamics simulations. Both enzymes share different levels of sequence similarity with other previously described TNT-degrading enzymes and with their closest potential homologues in databases.

Collective absorption of 2,4,6-trinitrotoluene into lipid membranes and its effects on bilayer properties. A computational study

The widely used explosive, 2,4,6-trinitrotoluene (TNT), is a highly toxic chemical, which can cause hepatitis, cataracts, jaundice and so on, in humans. The interaction between TNT and biological membranes is crucial for understanding its toxic effects. Here, we mainly focused on molecular-level mechanisms for the collective adsorption of TNT into lipid membranes and the corresponding effects on bilayer properties by all-atom molecular dynamics simulations. We revealed that TNT can readily form an aggregate in the aqueous phase and quickly approach the surface of the membrane. At low concentrations of TNT (7 mol%), the aggregate is unstable and breaks up after several nanoseconds, and then the dispersed TNT molecules enter the membrane alone. At high concentrations (14 mol%), the aggregate is adsorbed as a whole and remains stable inside the membrane. After some of the TNT is absorbed by the membrane, the remaining TNT across the membrane would have greater permeability, i.e., the calculated permeability coefficient (P) is increased from 1.7 × 10^-2 to 18.3 cm s^-1. Correspondingly, a higher bioconcentration factor (BCF) was also observed. The increased level is more pronounced in the presence of TNT aggregates (i.e., high concentrations). This phenomenon is closely related to the strong interaction between TNT molecules. The results suggested that TNT molecules that have entered into the membrane can facilitate the membrane uptake, permeation and bioaccumulation of subsequent TNT molecules, exhibiting a synergistic effect. This work has a certain significance for understanding the toxicity of TNT.

Odd Loop Regions of XenA and XenB Enzymes Modulate Their Interaction with Nitro-explosives Compounds and Provide Structural Support for Their Regioselectivity

The nitro-explosive compounds 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, and 1,2,3-trinitroglycerol are persistent environmental contaminants. The presence of different functional groups in these molecules represents a great challenge to enzymatic catalysis. The chemical variety of these three substrates is such that they do not bind and interact with catalytic residues within an enzyme with the same affinity. In this context, two Xenobiotic Reductase enzymes produced by the bacteria Pseudomonas putida can catalyze the reduction of these compounds with different affinities and regioselectivity. The structural bases that support this substrate promiscuity and catalytic preferences are unknown. Therefore, through molecular dynamics simulations and free energy calculations, we explored the structural properties driving the specific interactions of these enzymes with their substrates and cofactor. Models of Xenobiotic Reductase A and B enzymes in complex with 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, or 1,2,3-trinitroglycerol were built, and the ligand enzyme interaction was simulated by molecular dynamics. The structural analysis of the molecular dynamics simulations shows that loops 3, 5, 7, 9, 11, and 13 of Xenobiotic Reductase B, and loops 4, 5, 7, 11, 13, and 15 Xenobiotic Reductase A, are in contact with the ligands during the first stages of the molecular recognition. These loops are the most flexible regions for both enzymes; however, Xenobiotic Reductase B presents a greater range of movement and a higher number of residues interacting with the ligands. Finally, the distance between the cofactor and the different reactive groups in the substrate reflects the regioselectivity of the enzymes, and the free energy calculations are consistent with the substrate specificity of both enzymes studied. The simulation shows a stable interaction between the aromatic ring of the substrates and Xenobiotic Reductase B. In contrast, a less stable interaction with the different nitro groups of the aromatic ligands was observed. In the case of 1,2,3-trinitroglycerol, Xenobiotic Reductase B interacts more closely with the nitro groups of carbon 1 or 3, while Xenobiotic Reductase A is more selective by nitro groups of carbon 2. The obtained results suggest that the flexibility of the loops in Xenobiotic Reductase B and the presence of polar and aromatic residues present in loops 5 and 7 are fundamental to determine the affinity of the enzyme with the different substrates, and they also contribute to the proper orientation of the ligands that directs the catalytic reaction.

Aerobic cometabolism of tetrabromobisphenol A by marine bacterial consortia

The coastal environments worldwide are subjected to increasing TBBPA contamination, but current knowledge on aerobic biodegradability of this compound by marine microbes is lacking. The aerobic removal of TBBPA using marine consortia under eight different cometabolic conditions was investigated here. Results showed that the composition and diversity of the TBBPA-degrading consortia had diverged after 120-day incubation. Pseudoalteromonas, Alteromonas, Glaciecola, Thalassomonas, and Limnobacter were the dominant genera in enrichment cultures. Furthermore, a combination of beef extract- and peptone-enriched marine consortia exhibited higher TBBPA removal efficiency (approximately 60%) than the other substrate amendments. Additionally, Alteromonas macleodii strain GCW was isolated from a culture of TBBPA-degrading consortium. This strain exhibited about 90% of degradation efficiency toward TBBPA (10 mg L^-1) after 10 days of incubation under aerobic cometabolic conditions. The intermediates in the degradation of TBBPA by A. macleodii strain GCW were analyzed and the degradation pathways were proposed, involving β-scission, debromination, and nitration routes.

Biotransformation of trinitrotoluene by Citrobacter sp. YC4 and evaluation of its cyto-toxicological effects

Trinitrotoluene (TNT) is an explosive chemical generally used for military, civil and industrial purposes. Therefore, TNT residue can be found in soil and ground water as an environmental pollutant. The environmental control of TNT pollution has become a critical issue because of its potential toxicity and carcinogenicity. The aim of this study is to evaluate the cyto-toxicological effects of TNT after bioremediation. Citrobacter sp. YC4 is able to utilize TNT as a sole nitrogen source. Citrobacter sp. YC4 cells grown in medium with TNT as the sole nitrogen source (TNT-N) were able to rapidly degrade TNT, in contrast to cells grown in Luria Bertani medium as determined by resting cell suspension. The concentration of TNT decreased from 100 to 0 ppm within 10 h in the solution containing TNT mixed with TNT-N-grown YC4. The cytotoxicity of TNT and its degradation products generated by TNT-N-grown YC4 were assessed by WST-1-based cell cytotoxicity assays. Our results showed that the cytotoxic potential of solutions containing TNT decreased almost to the level of the control after a 1-h incubation with TNT-N-grown YC4 cells. The rapid conversion of TNT into possibly less toxic products by Citrobacter sp. YC4 proposes a bioremediation prospection.

Copper promotes E. coli laccase-mediated TNT biotransformation and alters the toxicity of TNT metabolites toward Tigriopus japonicus

Although laccase is involved in the biotransformation of 2,4,6-trinitrotoluene (TNT), little is known regarding the effect of E. coli laccase on TNT biotransformation. In this study, E. coli K12 served as the parental strain to construct a laccase deletion strain and two laccase-overexpressing strains. These E. coli strains were used to investigate the effect of laccase together with copper ions on the efficiency of TNT biotransformation, the variety of TNT biotransformation products generated and the toxicity of the TNT metabolites. The results showed that the laccase level was not relevant to TNT biotransformation in the soluble fraction of the culture medium. Conversely, TNT metabolites varied in the insoluble fraction analyzed by thin-layer chromatography (TLC). The insoluble fraction from the laccase-null strain showed fewer and relatively fainter spots than those detected in the wild-type and laccase-overexpressing strains, indicating that laccase expression levels were interrelated determinants of the varieties and amounts of TNT metabolites produced. In addition, the aquatic invertebrate Tigriopus japonicus was used to assess the toxicity of the TNT metabolites. The toxicity of the TNT metabolite mixture increased when the intracellular laccase level in strains increased or when purified E. coli recombinant Laccase (rLaccase) was added to the culture medium. Thus, our results suggest that laccase activity must be considered when performing microbial TNT remediation.

Biotechnological Advances for Restoring Degraded Land for Sustainable Development

Global land resources are under severe threat due to pollution and unsustainable land use practices. Restoring degraded land is imperative for regaining ecosystem services, such as biodiversity maintenance and nutrient and water cycling, and to meet the food, feed, fuel, and fibre requirements of present and future generations. While bioremediation is acknowledged as a promising technology for restoring polluted and degraded lands, its field potential is limited for various reasons. However, recent biotechnological advancements, including producing efficient microbial consortia, applying enzymes with higher degrees of specificity, and designing plants with specific microbial partners, are opening new prospects in remediation technology. This review provides insights into such promising ways to harness biotechnology as ecofriendly methods for remediation and restoration.