Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation

Investigating the Potential of Fusarium solani and Phanerochaete chrysosporium in the Removal of 2,4,6-TNT

Past and  recent applications of 2,4,6-trinitrotoluene (TNT) in military and civilian industries have led to contamination of soil and marine ecosystems. Among various TNT remediation techniques, biological remediation is widely accepted for its sustainability, low cost, and scalable applications. This study was designed to isolate a fungus strain from a TNT-contaminated soil to investigate its tolerance to and potential for removal of TNT. Thus, a soil column with a history of periodic TNT amendment was used to isolate dominant strains of fungi Fusarium solani isolate, which is not commonly reported for TNT mineralization and was found predominant in the subsurface layer of the TNT-amended soil. F. solani was investigated for TNT concentration tolerance at 30, 70, and 100 mg/L on agar plates and for TNT removal in liquid cultures at the same given concentrations. F. solani activity was compared with that of a reference soil-born fungus that has been intensively studied for TNT removal (Phanerochaete chrysosporium) obtained from the American Type Culture Collection. On agar media, F. solani showed a larger colony diameter than P. chrysosporium at similar TNT concentrations, indicating its high potential to tolerate toxic levels of TNT as found in contaminated sites. In the liquid culture medium, F. solani was able to significantly produce higher biomass than P. chrysosporium in all TNT concentrations. The TNT removal percentage from the liquid culture at the highest TNT concentration of 100 mg/L reached about 85% with F. solani, while P. chrysosporium was no better than 25% at the end of an 84-h incubation period. Results indicate a significant potential of using F. solani in the bioremediation of polluted TNT soils that overcome the high concentration barrier in the field. However, further investigation is needed to identify enzymatic potential and the most effective applications and possible limitations of this method on a large scale.

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.

Isolation and characterization of nitroguanidine-degrading microorganisms

Nitroguanidine (NQ) is a component of newly developed insensitive munition (IM) formulations which are more resistant to impact, friction, heat, or sparks than conventional explosives. NQ is also used to synthesize various organic compounds and herbicides, and has both human and environmental health impacts. Despite the wide application and associated health concerns, limited information is known regarding NQ biodegradation, and only one NQ-degrading pure culture identified as Variovorax strain VC1 has been characterized. Here, we present results for three new NQ-degrading bacterial strains isolated from soil, sediment, and a lab-scale aerobic membrane bioreactor (MBR), respectively. Each of these strains -utilizes NQ as a nitrogen (N) source rather than as a source of carbon or energy. The MBR strain, identified as Pseudomonas extremaustralis strain NQ5, is capable of degrading NQ at a rate of approximately 150 μmole L-1 h-1 under aerobic conditions with glucose as a sole carbon source - and NQ as a sole N source. The addition of NH4+ to strain NQ5 during active growth with NQ as a sole N source slowed the growth rate for several hours, and the strain released NH4+, presumably from NQ. When NO3- was added as an alternate N source under similar conditions, the NO3- was not consumed, but NH4+ release into the culture medium was again observed. Strain NQ5 was also able to utilize guanylurea, guanidine, and ethyl allophanate as N sources, and - tolerate salt concentrations as high as 4 % (as NaCl). The other two stains, NQ4 and NQ7, both identified as Arthrobacter spp., grew significantly slower than strain NQ5 under similar culture conditions and tolerated only ∼1 % NaCl. In addition, neither strain NQ4 nor strain NQ7 was able to degrade guanlyurea or ethyl allophanate, but each degraded guanidine. These strains, particularly strain NQ5, may have practical applications for in-situ and ex-situ NQ bioremediation.

Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., two new species with the ability to degrade TNT isolated from soil samples at Deception Island, maritime Antarctica

Two motile, rod-shaped, Gram-stain-negative bacterial strains, TNT11T and TNT19T, were isolated from soil samples collected at Deception Island, Antarctica. According to the 16S rRNA gene sequence similarity, both strains belong to the genus Pseudomonas. Further genomic analyses based on ANI and dDDH suggested that these strains were new species. Growth of strain TNT11T is observed at 0-30 ℃ (optimum, 20 ℃), pH 4.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum, 1% NaCl), while for TNT19T is observed at 0-30 ℃ (optimum between 15 and 20 ℃), pH 5.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum between 0 and 1% NaCl). The fatty acid profile consists of the major compounds; C16:0 and C16:1 ω6 for TNT11T, and C16:0 and C12:0 for TNT19T. Based on the draft genome sequences, the DNA G + C content for TNT11T is 60.43 mol% and 58.60 mol% for TNT19T. Based on this polyphasic study, TNT11T and TNT19T represent two novel species of the genus Pseudomonas, for which the proposed names are Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., respectively. The type strains are Pseudomonas violetae TNT11T (= RGM 3443T = LMG 32959T) and Pseudomonas emilianonis TNT19T (= RGM 3442T = LMG 32960T). Strains TNT11T and TNT19T were deposited to CChRGM and BCCM/LMG with entry numbers RGM 3443/LMG 32959 and RGM 3442/LMG 32960, respectively.

Cold adapted Pseudomonas: ecology to biotechnology

The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.

Solid medium for the direct isolation of bacterial colonies growing with polycyclic aromatic hydrocarbons or 2,4,6-trinitrotoluene (TNT)

Isolation of hydrocarbon-degrading bacteria is a key step for the study of microbiological diversity, metabolic pathways, and bioremediation. However current strategies lack simplicity and versatility. We developed an easy method for the screening and isolation of bacterial colonies capable of degrading hydrocarbons, such as diesel or polycyclic aromatic hydrocarbons (PAHs), as well as the pollutant explosive, 2,4,6-trinitrotoluene (TNT). The method uses a two-layer solid medium, with a layer of M9 medium, and a second layer containing the carbon source deposited through the evaporation of ethanol. Using this medium we grew hydrocarbon-degrading strains, as well as TNT-degrading isolates. We were able to isolate PAHs-degrading bacterial colonies directly from diesel-polluted soils. As a proof of concept, we used this method to isolate a phenanthrene-degrading bacteria, identified as Acinetobacter sp. and determined its ability to biodegrade this hydrocarbon.

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.

The characteristics and metabolic potentials of the soil bacterial community of two typical military demolition ranges in China

The response mechanism of soil microbiota in military polluted sites can effectively indicate the biotoxicity of ammunition. In this study, two military demolition ranges polluted soils of grenades and bullet were collected. According to high-throughput sequencing, after grenade explosion, the dominant bacteria in Site 1 (S1) are Proteobacteria (97.29 %) and Actinobacteria (1.05 %). The dominant bacterium in Site 2 (S2) is Proteobacteria (32.95 %), followed by Actinobacteria (31.17 %). After the military exercise, the soil bacterial diversity index declined significantly, and the bacterial communities interacted more closely. The indigenous bacteria in S1 were influenced more compared to those in S2. According to the environmental factor analysis, the bacteria composition can easily be influenced by heavy metals and organic pollutants, including Cu, Pb, Cr and Trinitrotoluene (TNT). About 269 metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in bacterial communities, including nutrition metabolism (C, 4.09 %; N, 1.14 %; S, 0.82 %), external pollutant metabolism (2.52 %) and heavy metal detoxication (2.12 %), respectively. The explosion of ammunition changes the basic metabolism of indigenous bacteria, and heavy metal stress inhibits the TNT degradation ability of bacterial communities. The pollution degree and community structure influence the metal detoxication strategy at the contaminated sites together. Heavy metal ions in S1 are mainly discharged through membrane transporters, while heavy metal ions in S2 are mainly degraded through lipid metabolism and biosynthesis of secondary metabolites. The results obtained in this study can provide deep insight into the response mechanism of the soil bacterial community in military demolition ranges with composite pollutions of heavy metals and organic substances. CAPSULE: Heavy metal stress changed the composition, interaction and metabolism of indigenous communities in military demolition ranges, especially the TNT degradation process.