Genomic variation of microbial populations on a continuous 10,000-year sediment sequence from Lake Cadagno (Piora Valley, Switzerland)

Lake Cadagno is a meromictic Alpine lake located in the Piora Valley, Switzerland. In 2019, a 10,000-year (10 m)sediment sequence was collected and found to contain three main lithological units: glacial sediment deposited under oxic conditions; a Mn-rich and organic-matter-rich sediment layer deposited during the transition from an oxic late-glacial lake to the onset of anoxia, and dark, sulfidic sediments deposited during the period of euxinia to the present. This study investigates the relationships between the physical-chemical properties and microorganisms of the sediment sequenceusing genome-resolved and targeted metagenomics.   

Results show that 16S rRNA gene abundance peaks in upper 1-32 cm of the sediment core (10⁸ copies per gram of sediment) and decreases with depth. The abundance of a marker gene for sulfate reduction, dsrB, is positively correlated to 16S rRNA gene copy numbers, decreasing with depth from approximately 10⁸ copies per gram of sediment in the top 30 cm to 10⁴ gene copies per gram of sediment at 900 cm below the sediment depth.  These results suggest that sulfate-reducing microbial communities in surface sediments harvest the bioavailable oxidized sulfur inorganic species. In contrast, the presence of sulfate-reducing genes in sediments with sulfate concentrations below detection may indicate the engagement of microbial populations in sulfur cycling using alternative metabolic strategies (e.g. secondary fermentation).

 

Moreover, a clear differentiation between surface and deep sediment communities is observed. Sequencing of dsrB amplicons show a decrease in dsrB sequence richness with depth and sediment age. A clear transition from a surface section dominated (>80% relative abundance) by Deltaproteobacteria-related dsrB sequences from well-studied groups, to a deeper section below 40 cm dominated by a group of unclassified dsrB sequences most likely related to Firmicutes or Chloroflexi is also observed. The identity of these unclassified dsrB sequences will be determined by genome-resolved metagenomic sequencing (currently in progress). Furthermore, these analyses will give information on the presence of complete sulfate-reduction pathways and/or genes related to sulfur cycling in these microbial groups. By reconstructing the genomes of sulfate reducers and other microbial populations throughout the core, we will investigate whether there are genomic changes associated with the main geochemical trends. This work will enable us to assess the influence of a changing lake with the evolution of sediment-dwelling prokaryotic populations over thousands of years.