Abstract
Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as ε-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.
Highlights
Samples from the oxic epilimnion, the oxygen transition zone and the anoxic hypolimnion of three humic lakes were characterized by shotgun metagenomics and the representation of marker genes for key metabolic processes were compared
As relatively low amounts of DNA were retrieved from most samples, the DNA extracts were subjected to whole-genome amplification before sequencing. This procedure can potentially skew the distribution of genes or individual genomes compared to the original sample, but the practice of adding DNA to each reaction at concentrations ranging from 10 to 20 ng should minimize the possible representation-bias, which is an accelerating problem with low DNA quantities (
To conclude, stratified humic lakes present a unique lake environment where different metabolic pathways and organisms are separated and enriched in response to changing availability of nutrients and electron acceptors. While these lakes represent a source of greenhouse gases (GHG) emissions, they harbor high genetic potential for carbon and nitrogen assimilation in their deep anoxic layers
Summary
They are ice-covered during winter and stratified with regards to oxygen and temperature, except for reoccurring autumn- and less frequent spring-overturns (for lake characteristics, see Table 1)
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