Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes

Abstract

Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.