From microbial heterogeneity to evolutionary insights: A strain-resolved metagenomic study of H2S-induced changes in anaerobic biofilms

Abstract

The hidden layers of genomic diversity in microbiota of biotechnological interest have been only partially explored and a deeper investigation that overcome species level resolution is needed. CO2-fixating microbiota are prone to such evaluation as case study. A lab-scale trickle-bed reactor was employed to successfully achieve simultaneous biomethanation and desulfurization on artificial biogas and sulfur-rich biogas, and oxygen supplementation was also implemented. Under microaerophilic conditions, hydrogen sulfide removal efficiency of 81% and methane content of 95% were achieved. Methanobacterium sp. DTU45 emerged as predominant, and its metabolic function was tied to community-wide dynamics in sulfur catabolism. Genomic evolution was investigated in Gammaproteobacteria sp. DTU53, identified as the main contributor to microaerophilic desulfurization. Positive selection of variants in the hydrogen sulfide oxidation pathway was discovered and amino acid variants were localized on the sulfide entrance channel for sulfide:quinone oxidoreductase. Upon oxygen supplementation strain selection was the primary mechanism driving microbial adaptation, rather than a shift in species dominance. Selective pressure determined the emergence of new strains for example on Gammaproteobacteria sp. DTU53, providing in depth evidence of functional redundancy within the microbiome.