Quantifying the contribution of the rare biosphere and functional potential to the compacted clay baseliner of sanitary landfill.

Compacted clay liners (CCLs) are crucial for limiting leachate migration in landfills; however, their long-term stability may be compromised. This study at the Pulau Burung Sanitary Landfill (PBSL), Penang, Malaysia, quantified microbial community dynamics in CCLs, focused on rare and low-abundance taxa and their functional potential. Seasonal communities were profiled via 16 S rRNA gene sequencing and PICRUSt2 functional predictions. Environmental parameters and geotechnical properties remained stable, with only minor changes in microbial community structure and no significant differences in α- and β-diversity (p> 0.05). Abundant taxa contributed ~ 52% to β-diversity variation, while low-abundance and rare taxa contributed ~ 5.1% and ~ 42.9%, respectively. Dominant phyla included Pseudomonadota (37.1%), Actinomycetota (16.2%), Bacteroidota (12.7%), and Bacillota (8.6%). Rare and low-abundance groups, such as Desulfobacterota and Nanoarchaeota, exhibited heightened sensitivity to environmental stress. Partitioning of β-diversity indicated that abundant taxa explained ~ 65% of community heterogeneity, low-abundance taxa ~ 20%, and rare taxa ~ 15%. Functional inference implicated rare sulfate-reducing, iron-reducing, and EPS-producing taxa in the CCL. Prominent genera included Marinobacter, Acidiphilium, Pseudomonas, and Halomonas, with rare taxa cumulatively contributing ~ 17.5%. Statistical analyses (ANOVA with Benjamini–Hochberg correction) revealed significant differences in functional group abundances (p < 0.05), and permutation tests confirmed that rare taxa disproportionately influence predicted functions (p < 0.05). These results indicated that rare and low-abundance microbial taxa may influence the compacted clay liner performance. Their functional roles, despite limited abundance, warrant consideration in engineered barrier assessments due to their ecological and structural impact.