Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation

Abstract

Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria , Acidobacteria , and Bacteroidetes , and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity’s role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.