Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting

ABSTRACT Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa—such as Thermus thermophilus , Planifilum fulgidum , and Thermaerobacter spp.—were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management. IMPORTANCE Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies—such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.