Chaperone-mediated thermotolerance in hyperthermophilic composting: Molecular-Level protein remodeling of microbial communities

Hyperthermophilic composting (HC) represents a promising approach for converting organic solid waste into valuable resources by leveraging extreme temperatures to enhance microbial degradation and detoxification processes. In this high-temperature environment, microbial communities undergo dynamic succession, where thermophilic bacteria dominate and drive efficient organic matter transformation through adapted metabolic pathways and stress responses. These adaptations include the stabilization of cellular structures and enzymes, often mediated by heat shock proteins (HSPs) that prevent protein misfolding under thermal stress. However, the integrated mechanisms linking community-level functional shifts to molecular-level protein remodeling in thermophiles during HC remain poorly understood. Here we show a coordinated interaction of functional succession and molecular adaptations within thermophilic bacteria in HC, which collectively achieve heat resistance. This interaction encompasses enhanced metabolic and genetic modules, accounting for 97% of the variance observed in thermophile abundance. Metagenomic analyses revealed upregulation of translation, transcription, amino acid metabolism, and cell wall biosynthesis, coupled with suppression of mobilome functions to maintain genomic stability, as confirmed by partial least squares path modeling and Boruta analyses. Molecular dynamics simulations of key enzymes from the thermophile Truepera further demonstrated intrinsic structural rigidity, reduced hydrophobic exposure, and hierarchical chaperone activity involving DNAJ, DNAK, and GroEL for protein repair. These findings enhance our comprehension of microbial thermotolerance and establish a foundation for optimizing composting efficiency and advancing heat-resistant microbial applications in biotechnology and waste management. Additionally, they offer insights into the evolution of thermophiles, protein engineering, and stress adaptation across various biological and industrial systems, thereby promoting the integration of environmental engineering and systems biology.