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

Abstract

The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.

Sequencing of the Whole Genome of a Bacterium of the Genus Achromobacter Reveals Its Potential for Xenobiotics Biodegradation

“…Genes for the benzene-to-succinyl-CoA metabolic pathway have been detected in the genome of Oceanimonas sp. GK1 [11], whereas they were not shown in the analyzed genomes of strains of the genus Pseudomonas [67]. Genes for benzoate and aminobenzoate degradation have been found in the genome of S. paucimobilis [68].…”

Review of Explosive Contamination and Bioremediation: Insights from Microbial and Bio-Omic Approaches

“…Bio-omics relies on transcriptomics to assess metabolic pathways and gene expression, which are critical for understanding adaptation, changes, and new dynamics in microbiomes in response to explosive pollution. Transcriptomics complements metagenomic profiling by offering a deeper understanding of the microbiota’s capacity for xenobiotic degradation, mineralization, and the reduction in toxicity caused by explosive pollution [ 47 ].…”

“…Transcriptomics is particularly valuable in assessing the response of microorganisms to highly toxic pollutants like RDX and HMX. It sheds light on the dysregulation of metabolic pathways and gene expression, revealing how microorganisms adapt to survive and proliferate under stressful conditions and face the challenges through time caused by these pollutants [ 47 ]. In the presence of HMX pollution, microorganisms may experience disruptions in important metabolic pathways like purine, amino sugar, and nucleotide sugar metabolism [ 50 ].…”

Cold adapted Pseudomonas: ecology to biotechnology

“…These properties allow Pseudomonas to inhabit most of the nutrient deficient locations. Pseudomonas tends to degrade a wide range of compatible solutes such as heterosides, aminoacids and sugars ( Craig et al, 2021 ) and organic compounds adopting various metabolic pathways such as Entner-Doudoroff pathway, β-ketoadipate pathway ( Cabrera et al, 2022 ) etc. The psychrophiles have been considered to possess the ability of tolerating far higher temperature ranges than the real ambient temperature from which they were isolated, when cultivated in-vivo ( Cavicchioli, 2016 ); for example, P. psychrophila MTCC12324 ( Abraham et al, 2020 ) and P. frederiksbergensis ( Cui et al, 2022 ) etc., were observed to grow between 4–37°C, Pseudomonas sp.…”