A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats

This study investigated the bacterial and fungal communities, along with their functional gene profiles, in two long-term heavy metal-contaminated sites in the United States: the Savannah River Site (SRS) and the Oak Ridge Reservation (ORR). Soil samples were categorized based on total mercury (THg), methyl mercury (MeHg), and bioavailable mercury (BioaHg) into high, medium, and low contamination levels. Using qPCR, amplicon sequencing, and shotgun metagenomics, we examined the long-term impacts of mercury contamination on microbial taxonomic composition and gene functions. Taxonomic analysis revealed the dominance of bacterial genera Bradyrhizobium , Geobacter , and Burkholderia , previously identified in our studies at the SRS and ORR sites. Among fungi, Fusarium , Pseudogymnoascus , and Aspergillus were the most abundant. Bacterial alpha diversity declined with increasing contamination, whereas fungal alpha diversity remained stable, with the highest diversity observed at the low-contamination site. Canonical correspondence analysis (CCA) linked Burkholderia and Pseudomonas with THg and MeHg, while Pedosphaera and Candidatus Solibacter were associated with BioaHg. Fungal phyla Ascomycota and Basidiomycota correlated with THg and MeHg, whereas Blastocladiomycota was associated with BioaHg. Functional analysis via shotgun metagenomics and PICRUSt2 identified an enrichment of stress response genes, membrane transporters, and metabolic pathways essential for microbial survival in contaminated environments. Genes encoding carbohydrate metabolism, amino acid processing, and protein metabolism were consistently dominant across contamination levels and sampling seasons. These findings highlight the adaptive strategies of soil microbiomes in mercury-contaminated environments, emphasizing their potential role in bioremediation and ecosystem restoration, thus paving the way for improved environmental management and remediation strategies of former nuclear legacy contaminated ecosystems.