By proposing a putative association between specific genomic features and macroscopic polymer degradation, this study suggests that Terrabacter sp.
Abstract
The freshwater isolate Terrabacter sp. AAH1 exhibits highly efficient poly(3-hydroxybutyrate) (PHB) biodegradation, achieving 98.02 ± 0.08% weight loss within 12 days. Scanning electron microscopy and Fourier-transform infrared spectroscopy demonstrated that this rapid disintegration is driven by extensive surface erosion and the hydrolytic cleavage of ester bonds. Comparative genomic analysis across related taxa revealed that while putative PHB depolymerase genes are present in a subset of Terrabacter and allied genera, strain AAH1 is distinguished by its candidate degradation phenotype. The strain’s genomic architecture is predicted to integrate a secreted putative PHB depolymerase with a predict metabolic suite for the degradation of PHB via 3-HB oxidation, SCOT-mediated acetoacetate activation, and β-oxidation-like pathway converging on the TCA cycle. In silico structural modeling and molecular docking further supported a hypothetical compartmentalized degradation system, in which the Sec-type secreted putative depolymerase Te_EPD is proposed to initiate extracellular PHB hydrolysis, while Te_YbfF, Te_AES1, and Te_AES2 predicted to lack signal peptides are tentatively assigned putative intracellular roles. Among the four candidates, Te_EPD exhibited a predicted binding affinity of –4.9 kcal/mol for the PHB trimer via a conserved Ser–Asp–His (S–D–H) catalytic triad, and was uniquely classified within the extracellular short-chain-length PHA depolymerase type 1 (e_dPHAscl_type1) family based on domain annotation and sequence motif analysis. By proposing a putative association between specific genomic features and macroscopic polymer degradation, this study suggests that Terrabacter sp. AAH1 may represent a candidate biocatalyst warranting further investigation for potential applications in bioplastic waste management.
ABSTRACT Polyethylene terephthalate (PET) waste represents a major environmental challenge due to limited recycling solutions. Thermophilic bacteria from geothermal environments harbor diverse enzymatic machinery adapted to extreme conditions, offering promising biocatalysts for plastic degradation; however, biological resources from Peru and other South American countries remain scarce. We characterized four bacterial strains isolated from two geothermal sites in Cajamarca, Peru, screened for PET hydrolysis at 50°C. Whole‐genome sequencing using hybrid assembly achieved near‐complete circular genomes. GTDB‐Tk classification identified three species: Neobacillus thermocopriae (strain 19A), Bacillus licheniformis (strains 16P and BI2), and Brevibacillus agri (strain BI8). Quantitative assays revealed that strain 16P achieved the highest mass loss (0.598%), followed by strain BI8 (0.449%). ATR‐FTIR analysis of the incubated sheets showed a significant reduction of the ester carbonyl index in strains 16P, 19A, and BI8 relative to both non‐incubated PET and an abiotic control, whereas strain BI2 did not differ from the controls, indicating preferential modification of ester bonds at the sheet surface. Genome mining and structure‐based homology searches identified multiple candidate enzymes similar to validated PETases and carboxylesterases, including PETase46‐like homologs in strains BI8 and 16P and a terephthalate‐active carboxylesterase homolog in strain 16P. Molecular docking supported the conservation of catalytic geometry and substrate‐binding sites in these candidates. This work represents one of the first systematic genomic and structural characterizations of putative PET‐hydrolases in Peruvian geothermal bacteria, expanding knowledge of extremophile diversity and advancing thermostable enzymes for sustainable plastic waste management.
Marco A Rivera-Jacinto, Claudia Rodríguez-Ulloa, Sara R Briones-Ramírez et al.· MicrobiologyOpen· 0 citations
Findings reveal that the enhanced desilication by BM3 is associated with coordinated metabolic reprogramming and a more reactive EPS-mineral interface, providing an effective biological pretreatment for disrupting silicate matrices and improving scandium recovery from refractory tailings.
Mengqi Liu, Bo Li, Feiyan Tan et al.· Bioresource Technology· 0 citations
Findings indicate that A. guillouiae I-MWF can mediate partial PET depolymerisation without assimilating the resulting monomers, while preferentially growing on lipid-like substrates, suggesting adaptation to hydrocarbon-rich environments.
Naheed Akhtar, A. Najjari, Anna Magnone et al.· BMC Microbiology· 0 citations
Local enrichment of acidic residues on the PlGH3 surface could generate a negative electrostatic potential, which enables adaptation to high-salt and alkaline environments, thereby sustaining the enzyme's catalytic activity under such extreme conditions.
Kaijuan Wu, Ke Guo, Zheng Yu et al.· Applied Biochemistry and Bio...· 0 citations
Insights are provided into putative glycosyl hydrolase candidates for efficient lignocellulosic waste pre-treatment and significant predicted halophilic and thermostable properties are revealed, suggesting these putative enzymes may endure industrial conditions.
Zhen Wei Tan, Muhamad Naim Abd Malek, Kah Yaw Ee et al.· Journal of General and Appli...· 0 citations
Polyhydroxyalkanoates (PHAs) are biodegradable microbial polyesters that may reduce dependence on petroleum-derived plastics, but broader use remains constrained by production costs and tightly controlled cultivation. Thermophilic microorganisms have attracted increasing attention as promising PHA producers because they can be cultivated at elevated temperatures, reducing contamination risks and operational costs. In this study, a thermophilic Geobacillus sp. strain SL28 isolated from a Vietnamese hot spring was evaluated for its PHA-producing capability. Temperature, initial pH, carbon and nitrogen sources, C/N ratio, and cultivation time were examined. Intracellular inclusions were assessed by Sudan Black B and Nile Blue A staining and transmission electron microscopy, whereas the recovered polymer was characterized by FE-SEM, Fourier-transform infrared spectroscopy (FTIR), gas chromatography–mass spectrometry (GC–MS), 1H- and 13C-nuclear magnetic resonance (NMR) spectroscopy, capillary viscometry, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and tensile testing. Under the optimized cultivation conditions identified by one-factor experimentation (50 °C, pH 7.0, sucrose, peptone, C/N 25:1, and 72 h), SL28 reached a dry cell weight of 2.215 ± 0.16 g/L and a PHA concentration of 1.383 ± 0.04 g/L, equivalent to 62.57 ± 2.82% of DCW. Structural characterization confirmed that the recovered polymer was poly(3-hydroxybutyrate) (PHB). The purified PHB also exhibited favorable thermal stability, a relatively high molecular weight, and satisfactory mechanical properties. These results demonstrate the potential of thermophilic Geobacillus sp. SL28 as a promising candidate for PHB production.
D. Q. Nguyen, T. Do, N. Lai et al.· Processes· 0 citations