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. IMPACT STATEMENT Although Winogradsky columns have served as both an enrichment platform and teaching staple for over a century, the microorganisms associated with their characteristic redox stratification have not been characterized at the genomic level. Here, we reconstruct genomes from a column community, showing how largely uncultivated taxa divide carbon, sulfur, and nitrogen cycling across the column’s gradients of oxygen and sulfide. This work transforms a widely used—yet genomically opaque—system into a now genome-resolved model for studying microbial community metabolism, with value for both researchers investigating redox-stratified environments and educators introducing students to microbial diversity and metabolism. DATA SUMMARY Metagenome-assembled genomes and read libraries are available in the following KBase narrative: https://doi.org/10.25982/266974.4/3412610. Both individual and merged (i.e., the library used for the co-assembly) read libraries are deposited in the Sequence Read Archive: SRR40126710-14 and SRR40144435. MAGs with greater than 90% completion were also deposited with NCBI with the BioSample numbers: SAMN62641021-31 [REVIEW NOTE: NCBI IS STILL PROCESSING THESE SUBMISSIONS BUT THE MAGS ARE AVAILABLE THROUGH THE KBASE NARRATIVE DOI]. Note that we use GTDB taxonomy throughout the paper, which does not always align with NCBI taxonomy, though the strain names are consistent. All sequencing data deposited with NCBI are associated with the BioProject: PRJNA1511471