Genome-resolved characterization of candidate thermotolerance traits and predicted protein conformational behavior in Calditerricola during hyperthermophilic composting of organic wastes.
An association-based multi-module framework of candidate traits linked to Calditerricola persistence during HC is defined, providing a genome-resolved basis for prioritizing testable thermotolerance targets in engineered high-temperature waste-treatment systems.
Abstract
Hyperthermophilic composting (HC) can generate temperatures above 80 °C without external heating, thereby accelerating organic-waste stabilization; however, how dominant heat-adapted microorganisms maintain cellular function under such extreme conditions remains unclear. Here, we integrated metagenomics, metagenome-assembled genome reconstruction, Calditerricola-resolved functional profiling, partial least squares path modeling, and molecular dynamics simulations to investigate candidate thermotolerance-related traits associated with Calditerricola enrichment during HC. The pile temperature reached 82.6 °C on day 2 and peaked at 86.6 °C on day 4, accompanied by progressive humification, with humic substances increasing from 40.45 to 51.28 mg/g and HA/FA reaching 3.45. Microbial communities differed significantly among composting phases (R2 = 0.975, P = 0.004), and Calditerricola increased from 0.02% in the initial phase to 6.1% in the thermophilic phase before declining to 0.7% in maturation. Community-level profiles showed comparatively modest variation in selected thermotolerance-related pathways, whereas the independently normalized Calditerricola profile displayed clearer phase-associated increases in functions linked to polyamine metabolism, membrane/envelope homeostasis, proteostasis, and DNA maintenance. Path modeling revealed consistent positive associations between Calditerricola enrichment and polyamine synthesis, membrane stability, and proteostasis. qPCR further revealed phase-associated increases in the community-level copy numbers of representative target genes, particularly polA and speE. During 100-ns simulations at 360 K, the predicted apo structures of PolA, AtpD, SpeE, and FabH retained their overall folds and comparatively stable catalytic-residue geometries. Together, these results define an association-based multi-module framework of candidate traits linked to Calditerricola persistence during HC, providing a genome-resolved basis for prioritizing testable thermotolerance targets in engineered high-temperature waste-treatment systems.
Polybutylene adipate terephthalate (PBAT) is a widely used biodegradable plastic, but its microbial degradation mechanisms and environmental responses remain poorly understood. In this study, two compost inocula (K and I) were used to establish PBAT enrichment cultures under mesophilic (35 °C, M) and thermophilic (58 °C, T) conditions, and the effects of temperature and inoculum source on bacterial community structure and PICRUSt2-derived predicted functional profiles were investigated. Surface analyses revealed cracking, erosion, and structural collapse of PBAT under all conditions, with more pronounced degradation in compost I-derived cultures. Microbial diversity decreased during enrichment, accompanied by dominance of specific genera. Under mesophilic conditions, Pseudoxanthomonas dominated (72.6%–91.0%) and showed strong positive correlations with predicted ester bond hydrolysis-related KOs (p < 0.05), suggesting a potential association with initial hydrolysis. Under thermophilic conditions, compost K cultures were dominated by Thermoflavifilum and Rhodothermus, which were mainly associated with predicted hydrolysis-related KOs, whereas compost I cultures were dominated by Thermoflavifilum and Thermopolyspora and showed stronger associations with predicted KOs related to adipate and terephthalic acid metabolism. Predicted aromatic intermediate metabolism-related KOs, including K04101, K01055, and K01607, were also higher in compost I-derived thermophilic cultures. Overall, temperature and inoculum composition jointly shaped bacterial community assembly and predicted PBAT degradation-related functional potential. Thermophilic conditions combined with compost I were associated with functionally differentiated bacterial communities and higher predicted potential for downstream PBAT-derived intermediate metabolism. These findings provide a microbial ecological basis for temperature- and inoculum-guided enrichment strategies to improve PBAT biodegradation and biodegradable plastic waste treatment.
Subin Hwang, Soo-Ye-On Lee, K. Cho· Journal of Polymers and the...· 0 citations
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
The behaviour of M.thermautotrophicus under suboptimal conditions is described and the need for further optimization to improve methane production yields is highlighted.
N. Hanišáková, Anna Štaud, Eva Kotrlová et al.· Bioresource Technology· 0 citations
Findings demonstrate that CtDnaJ.16 plays a strikingly haploid-specific role in thermotolerance, deepening the understanding of functional differentiation between allelic genes.
Lining Wang, Chaoxue Ma, Siyu Zhao et al.· Frontiers in Microbiology· 0 citations
The proteomic basis of thermal adaptation in P. plecoglossicida is revealed and molecular targets for engineering thermotolerant strains to optimize industrial 2-KGA fermentation are provided.
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Analysis revealed genes for metabolizing diverse carbohydrate sources, a complete ectoine synthesis cluster essential for halophily, and genes conferring tolerance to osmotic stress, low temperatures, and pH, underscoring its polyextremophilic capacity.
Ian Ariel Barbosa Nunes, Adan Rodrigues de Oliveira, Adonney Allan de Oliveira Veras et al.· Brazilian Journal of Microbi...· 0 citations
