Genome-resolved metagenomics reveals metabolically versatile Actinobacteria with extensive biosynthetic capacity in Hawaiian steam vents

Abstract

Geothermally active lava caves and hydrothermal steam vents are chemically heterogeneous subsurface environments that harbor diverse microbial communities, yet the ecological and metabolic roles of Actinobacteria in these systems remain poorly characterized. Here, we reconstructed and analyzed 58 actinobacterial metagenome-assembled genomes (MAGs) representing five classes. Comparative genomic analyses revealed broad metabolic versatility, including pathways for amino acid biosynthesis and utilization, central carbon metabolism, fatty acid degradation, and potential chemolithotrophic processes involving carbon monoxide and sulfur compounds. The MAGs also encoded diverse carbohydrate-active enzymes and peptidases suggesting substantial capacity for complex organic carbon and protein utilization. Genome mining identified 219 biosynthetic gene clusters spanning terpenes, ribosomally synthesized and post-translationally modified peptides, nonribosomal peptide synthetases, polyketide synthases, and β-lactones, highlighting extensive secondary-metabolite biosynthetic potential. Antibiotic resistance-associated genes were also detected in several MAGs, with glycopeptide-resistance-associated van genes particularly prevalent among Thermoleophilia. Sequence similarity network analysis revealed that several van-associated proteins from Thermoleophilia and UBA4738 shared substantial sequence similarity with homologs from other environmental Actinobacteria, suggesting broad conservation of these protein families. Collectively, these findings reveal metabolically and functionally diverse Actinobacteria with the genomic potential to participate in carbon and nutrient cycling, microbial interactions, secondary metabolism, and antibiotic resistance in geothermally active ecosystems. Importance Actinobacteria are among the most extensively studied bacterial groups for their roles in terrestrial ecosystems and their capacity to produce bioactive compounds, yet their diversity and ecological functions in geothermal environments remain largely unexplored. Hydrothermal steam vents provide a unique setting in which steep chemical gradients may select for unusual combinations of metabolic, biosynthetic, and stress-response traits. Our genome-resolved analysis of Actinobacteria from Hawaiian geothermal habitats expands the known functional landscape of this phylum and reveals substantial diversity among lineages that are rarely represented in cultivated genome collections. The resulting genomes provide a framework for linking phylogenetic diversity with ecological function and for identifying candidate pathways underlying persistence in chemically dynamic environments. More broadly, this study demonstrates the value of genome-resolved approaches for uncovering the functional potential of microbial lineages that remain inaccessible to conventional cultivation and provides targets for future experimental investigation.