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d -2-Hydroxyglutarate ( d -2-HG) is a metabolite involved in many physiological metabolic processes. When d -2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenase or d -2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 is identified as an allosteric transcriptional factor that negatively regulates d -2-HG dehydrogenase expression and responds to the presence of d -2-HG. Based on the allosteric effect of DhdR, a d -2-HG biosensor is developed by combining DhdR with amplified luminescent proximity homogeneous assay (AlphaScreen) technology. The biosensor is able to detect d -2-HG in serum, urine, and cell culture medium with high specificity and sensitivity. Additionally, this biosensor is used to identify the role of d -2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa , demonstrating its broad usages. d -2-hydroxyglutarate ( d -2-HG) is a metabolite that can be aberrantly accumulated and acts as a biomarker in many cancers. Here the authors report a d -2-HG biosensor based on the allosteric transcription factor DhdR which they use for detection in serum and urine.

This study present Achromobacter xylosoxidans RS1 as a facultative bacterium capable of simultaneous lignin modification and direct hydrogen production from untreated food waste—a dual metabolic capability that offers new opportunities for consolidated bioprocessing by Achromobacter species. A. xylosoxidans RS1 achieved 55.2% lignin decolorization over seven days in mineral salt medium, with HPLC detection of the aromatic intermediate ferulic acid (2.2 mg/L) confirming active oxidative lignin catabolism. Plate assays revealed robust hydrolytic enzyme activities, including proteases (20.5 mm), amylases (17.5 mm), xylanases (16.8 mm), and cellulases (8.2 mm). Whole-genome sequencing produced a 6.58 Mbp draft genome encoding 50 carbohydrate-active enzymes (CAZymes), including one AA10 lytic polysaccharide monooxygenase, five AA3 oxidases, one AA7 oxidase, and seven CE1 esterases. These enzymes support enhanced cellulolytic, xylanolytic, and lignin-modifying activities. Batch dark fermentation experiments demonstrated that A. xylosoxidans RS1 produced hydrogen yields ranging from 0.506 to 0.946 mol H₂ mol⁻¹ substrate across xylose, glucose, carboxymethyl cellulose, starch, and untreated food waste. Xylose supported the highest hydrogen production potential (225 mL, 0.735 mol H₂ mol⁻¹ substrate) with rapid production kinetics, indicating efficient pentose utilization. In contrast, untreated food waste yielded the maximum molar hydrogen output (165 mL, 0.946 mol H₂ mol⁻¹ substrate), attributable to its heterogeneous carbohydrate composition that enhanced enzymatic accessibility and substrate solubilization. These findings indicate that A. xylosoxidans RS1 harbors a functional repertoire of oxidative CAZymes and hydrogen-metabolism pathway, enabling it to valorize food waste into hydrogen. The draft genome provides a valuable resource for further studies on facultative bacteria in waste-to-energy applications.

Nanoplastics pose significant environmental problems due to their high mobility and increased toxicity. These particles can cause infertility and inflammation in aquatic organisms, disrupt microbial signaling and act as pollutants carrier. Despite extensive studies on their harmful impact on living organisms, the microbial degradation of nanoplastics is still under research. This study investigated the degradation of nanoplastics by isolating bacteria from the gut microbiome of Tenebrio molitor larvae fed various plastic diets. Five bacterial strains capable of degrading polystyrene were identified, with Achromobacter xylosoxidans M9 showing significant nanoplastic degradation abilities. Within 6 days, this strain reduced nanoplastic particle size by 92.3%, as confirmed by SEM and TEM analyses, and altered the chemical composition of the nanoplastics, indicating a potential for enhanced bioremediation strategies. The strain also caused a 7% weight loss in polystyrene film over 30 days, demonstrating its efficiency in degrading nanoplastics faster than polystyrene film. These findings might enhance plastic bioremediation strategies.

Arsenotrophic bacteria play an essential role in lowering arsenic contamination by converting toxic arsenite [As (III)] to less toxic and less bio-accumulative arsenate [As (V)]. The current study focused on the qualitative and electrocatalytic detection of the arsenite oxidation potential of an arsenite-oxidizing bacteria A. xylosoxidans BHW-15 (retrieved from As-contaminated tube well water), which could significantly contribute to arsenic detoxification, accumulation, and immobilization while also providing a scientific foundation for future electrochemical sensor development. The minimum inhibitory concentration (MIC) value for the bacteria was 15 mM As (III). Scanning Electron Microscopy (SEM) investigation validated its intracellular As uptake capacity and demonstrated a substantial association with the MIC value. During the stationary phase, the strain’s As (III) transformation efficiency was 0.0224 mM/h. Molecular analysis by real-time qPCR showed arsenite oxidase ( aio A) gene expression increased 1.6-fold in the presence of As (III) compared to the untreated cells. The immobilized whole-cell also showed As (III) conversion up to 18 days. To analyze the electrochemical oxidation in water, we developed a modified GCE/P-Arg/ErGO-AuNPs electrode, which successfully sensed and quantified conversion of As (III) into As (V) by accepting electrons; implying a functional As oxidase enzyme activity in the cells. To the best of our knowledge, this is the first report on the electrochemical observation of the As-transformation mechanism with Achromobacter sp . Furthermore, the current work highlighted that our isolate might be employed as a promising candidate for arsenic bioremediation, and information acquired from this study may be helpful to open a new window for the development of a cost-effective, eco-friendly biosensor for arsenic species detection in the future.

Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.

Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme–substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His226 had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.

Organophosphates (OPs) constitute a significant proportion of pesticides currently used worldwide in agriculture. Widespread and repeated application of these insecticides contaminates the soil and water, posing significant non-target toxicity risks to other organisms within the ecosystem. Acute pesticide exposure causes toxicity to insects, plants, animals, and humans, and thus emphasizes the need for sustainable management. Bacterial degradation of pesticides has been considered as a preferred strategy. In the present study, the phyllosphere of water hyacinth ( Eichhornia crassipes ) was explored for the chlorpyrifos degrading bacteria using Culture-independent and culture-dependent methods. Culture-independent study revealed 44,514 operational taxonomic units (OTUs) that were classified into 16 phyla and 330 genera, with dominating genera such as Acinetobacter, Paenibacillus, Pseudomonas, Sphingobacterium, and Achromobacter . Culture-dependent method yielded Achromobacter xylosoxidans and Stutzerimonas stutzeri as chlorpyrifos tolerant and degraders. These isolated strains exhibited enhanced growth as a consortium with chlorpyrifos as the only carbon source. The consortia effectively degrade 98% of chlorpyrifos within seven days, indicating its potential for pesticide degradation. Proteomics analysis revealed upregulation of key enzymes implicated in chlorpyrifos degradation, such as phosphodiesterase, metallo-beta-lactamases and oxidoreductase. The down-regulation of stress-response proteins suggests an adaptive tolerance to the pesticide. This study justifies the potential of consortia of isolated strains in the degradation of chlorpyrifos and may be developed into a promising and eco-friendly approach for remediating chlorpyrifos-contaminated environments.

Pure cultures have been found to degrade pharmaceutical compounds. However, these cultures are rarely characterized kinetically at environmentally relevant concentrations. This study investigated the kinetics of sulfamethoxazole (SMX) degradation by Achromobacter denitrificans strain PR1 at a wide range of concentrations, from ng/L to mg/L, to assess the feasibility of using it for bioaugmentation purposes. Complete removal of SMX occurred for all concentrations tested, i.e., 150 mg/L, 500 µg/L, 20 µg/L, and 600 ng/L. The reaction rate coefficients (k bio ) for the strain at the ng/L SMX range were: 63.4 ± 8.6, 570.1 ± 15.1 and 414.9 ± 124.2 L/g X SS ·day), for tests fed without a supplemental carbon source, with acetate, and with succinate, respectively. These results were significantly higher than the value reported for non-augmented activated sludge (0.41 L/(g  X SS ·day) with hundreds of ng/L of SMX. The simultaneous consumption of an additional carbon source and SMX suggested that the energetic efficiency of the cells, boosted by the presence of biogenic substrates, was important in increasing the SMX degradation rate. The accumulation of 3-amino-5-methylisoxazole was observed as the only metabolite, which was found to be non-toxic. SMX inhibited the Vibrio fischeri luminescence after 5 min of contact, with EC 50 values of about 53 mg/L. However, this study suggested that the strain PR1 still can degrade SMX up to 150 mg/L. The results of this work demonstrated that SMX degradation kinetics by A. denitrificans PR1 compares favorably with activated sludge and the strain is a potentially interesting organism for bioaugmentation for SMX removal from polluted waters.

In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6–96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer–Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.

Nine diazotrophic bacteria were isolated from surface-sterilized roots and culms of wheat variety Malviya-234, which is grown with very low or no inputs of nitrogen fertilizer. Out of the nine bacteria, four showed indole acetic acid (IAA) production, and five were positive for P solubilization. One isolate, WM234C-3, showed appreciable level of nitrogenase activity, IAA production, and P solubilization ability, and was further characterized with a view to exploiting its plant growth promoting activity. Based on 16S rDNA sequence analysis, this isolate was identified as Achromobacter xylosoxidans. Diazotrophic nature of this particular isolate was confirmed by Western blot analysis of dinitrogenase reductase and amplification of nifH. Analysis of the nifH sequence showed close homology with typical diazotrophic bacteria. Endophytic nature and cross-infection ability of WM234C-3 were tested by molecular tagging with gusA fused to a constitutive promoter followed by inoculation onto rice seedlings in axenic conditions. At 21 days after inoculation, the roots showed blue staining, the most intense color being at the emergence of lateral roots and root tips. Microscopic observation confirmed colonization of gus-tagged WM234C-3 in the intercellular spaces of cortical as well as vascular zones of roots. Inoculation of gus-tagged WM234C-3 to rice plants resulted in significant increase in root/shoot length, fresh weight, and chlorophyll a content. Plant growth promoting features coupled with cross-infection ability suggest that this endophytic bacterium may be exploited as agricultural agent for various crops after a thorough and critical pathogenicity test.