Genome-resolved insights into microbial diversity and elemental cycling in Winogradsky columns

Abstract

Winogradsky columns are a classic model ecosystem for studying microbial biogeochemistry across steep gradients of oxygen and sulfide. They also remain widely used in microbiology education, introducing generations of students to microbial diversity. Yet, the genomic potential of their microbial communities remains uncharacterized. Here, we applied shotgun metagenomic sequencing to a Winogradsky column community at multiple depths, yielding 20 metagenome-assembled genomes (MAGs) representing diverse, largely uncultivated taxa. Genome-resolved analyses revealed metabolically diverse oxygenic and anoxygenic phototrophs that could potentially contribute to carbon and nitrogen fixation across all layers of the column. Most of these phototrophs also encoded one or more pathways for sulfur oxidation, which we speculated may support both energy conservation and/or sulfide detoxification by these populations. Complex carbon degradation capacity was also widespread across the MAGs, suggestive of the potential for the transformation of the column's amended organic matter (shredded coffee filters) into smaller depolymerization products and, through fermentation, organic acids. Together, these findings reveal how distinct microbial guilds might partition interconnected carbon, sulfur, and nitrogen transformations within redox-stratified systems.