The biological remediation of complex petroleum waste streams suffers from severe performance bottlenecks in industrial and marine settings due to the simultaneous thermal, osmotic and mechanical stress. In these hypersaline and multi-extreme matrices, such as produced water, coastal oil spills, and refinery lagoons, conventional mesophiles succumb to rapid plasmolysis, catalytic deceleration, and metabolic uncoupling. Halophilic microorganisms offer indispensable advantages for remediating these hostile environments; their specialized adaptations including acidic proteomes that resist salting-out, compatible solute accumulation that maintains cellular turgor, and cell-bound biosurfactant secretion preserve biocatalytic integrity where conventional degraders fail. This review provides a detailed overview of recent advances in the structural biology of extremophilic enzymes, biosurfactant-mediated interfacial bioavailability changes and genome-scale regulatory networks regulating hydrocarbonoclastic psychrophiles and halophiles. This article integrates structural insights, e.g. localized molecular flexibility of cold-active oxygenases and surface acidity stabilizing salt-tolerant biocatalysts, with functional multi-omics workflows that trace carbon flux from dynamic stress-sensing mechanisms to complete hydrocarbon mineralization. In addition, this paper discusses particular eco-physiological challenges of oil spills in the open ocean, such as the spatial compartmentalization of deep-water plumes, the dynamics of marine oil snow formation, and the metabolic trade-offs imposed by synthetic chemical dispersants. Also, this review discusses how the integration of high-throughput multi-omics data with artificial intelligence pipelines and predictive machine learning algorithms can accelerate strain engineering and bioprocess optimization. Finally, it offers a strong data-driven systems biology approach to move next-generation extremophilic bioprocesses from exploratory laboratory concepts to scalable, field-reproducible industrial realities.
Microorganisms inhabiting cold environments have gained increasing attention in recent decades due to their unique adaptation mechanisms that enable survival under extreme conditions. Growing evidence indicates that some cold-adapted bacteria possess phenotypic and genomic traits linked to pathogenicity, raising concerns about their potential environmental and public health relevance. Here, we characterized three culturable bacteria isolated from human-impacted snow in the French Alps (Chamrousse) and coastal Greenland (Nuuk). Snow samples were cultured on R2A medium, and isolates were identified by Sanger sequencing as Peribacillus, Sphingomonas, and Subtercola. Temperature tolerance, haemolytic activity, and antibiotic susceptibility were assessed by culture-based assays, while whole-genome sequencing was used to screen for antibiotic resistance and virulence-associated genes using reference databases. Only the Peribacillus isolate tolerated 37 °C and showed α-haemolysis. Antibiotic susceptibility testing indicated full susceptibility in Peribacillus, while Sphingomonas and Subtercola showed reduced susceptibility to a limited number of antibiotics, mainly to cefotaxime, chloramphenicol, and colistin. Genomes encoded genes associated with efflux, target modification, motility/adhesion, and stress adaptation, indicating environmental resilience rather than clinical pathogenicity. Overall, these isolates displayed limited pathogenic phenotypes with genomic traits primarily supporting environmental adaptation and survival.
Rahnella species are environmentally versatile bacteria widely distributed in terrestrial and aquatic ecosystems; however, the genomic basis of formaldehyde detoxification and stress adaptation in cryoconite-associated Rahnella remains poorly understood. In this study, we performed phylogenomic, comparative genomic, pan-genomic, stress-response, and functional analyses of Rahnella sp. PAMC25617 isolated from polar cryoconite to investigate glutathione (GSH)-dependent formaldehyde detoxification and its evolutionary conservation. Genome-based phylogeny, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH) analyses demonstrated that PAMC25617 represents a distinct genomic lineage within the genus Rahnella. The draft genome comprised 5.33 Mb with a GC content of 52
Geothermal hot springs provide important windows into the links among deep hydrothermal circulation, water–rock interaction, and microbial ecology in extreme environments. This study investigated six hot-spring water samples from Reshuigou, Guide County, Qinghai Province, by integrating hydrochemical analysis, PHREEQC mineral saturation calculations, microbial community profiling, RDA, PCoA environmental fitting, and Spearman correlation analysis. The Reshuigou waters were characterized by medium to high temperature, weak alkalinity, reducing conditions, and moderate to relatively high mineralization. Their hydrochemical facies were consistently of the Na+K/Cl–SO₄ type, reflecting deep-circulation water–rock interaction, sulfate and chloride inputs, silicate dissolution, and ion exchange. The microbial communities were dominated by Proteobacteria, Aquificota, Deinococcota, Chloroflexi, and Bacteroidota, with Hydrogenobacter, Thermus, Herbaspirillum, and Delftia as important genera. Phylum- and genus-level RDA accounted for 71.9 and 77.4
Palaeococcus pacificus DY20341T, a hyperthermophilic archaeon from deep sea hydrothermal sediments, grows at temperature range from 50 to 90 ℃ (Topt = 80℃). To explore the molecular basis of its thermal adaptation, we identified six representative hyperthermostable proteins from its cytosolic fraction that remained soluble after a stringent in vitro heat treatment at 100 °C. MALDI-TOF mass spectrometry identified these as an inorganic pyrophosphatase (PPase), a 5’-methylthioadenosine phosphorylase (MTAP), and four putative transporter components (one TRAP and three ABC transporter solute-binding proteins). RT-qPCR analysis revealed that the transcription of all six corresponding genes was significantly upregulated when the growth temperature was elevated from 80 °C to 90 °C, suggesting a potential role in the cellular response to heat stress. Biochemical characterization of the recombinant PPase demonstrated remarkable thermostability and an optimal temperature of 90 °C. Kinetic analysis revealed high catalytic efficiency, with a maximal specific activity of 590 ± 30 U/mg and a strong substrate affinity ( K_m = 6.24 µM). Phylogenetic analysis of the identified thermostable MTAP (PAP_00250) revealed its evolutionary origin from hyperthermophilic archaea, distinguishing it clearly from a second MTAP homolog (PAP_07050) in the genome, which aligns with mesophilic bacteria. The structural stability of the identified ABC and TRAP transporter components hypothesizes that efficient nutrient scavenging remains critical at extreme temperatures. Together, these findings provide valuable insights into the stable molecular machinery and potential physiological strategies enabling P. pacificus to thrive in hydrothermal environments.
