Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds

Moritz Buck,Stefan Bertilsson,Leyden Fernandez,Jakob Zopfi,Gaëtan Martin,Sari Peura,Sarahi L Garcia,Jatta Saarenheimo,Gustavo A Martinez-Rodriguez

doi:10.1038/s41597-021-00910-1

Abstract

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

Highlights

Background & SummaryStratified lakes are a typical feature of the northern landscapes and are significant sources of greenhouse gas (GHG) emissions[1]
These lakes largely reside in regions critically impacted by climate change[2] and the future contribution of these lakes to climate change via GHG emissions is dependent on the microorganisms inhabiting their waters[3,4]
Organisms residing in the anoxic compartment of these waters are of particular interest, as many of the more potent GHGs are produced under such conditions[1]

Summary

Background & Summary

Stratified lakes are a typical feature of the northern landscapes and are significant sources of greenhouse gas (GHG) emissions[1]. Our goal was to collect a comprehensive dataset that would allow broad analyses of the functioning of the microbial communities in oxygen stratified lakes with emphasis on lakes representing high carbon concentration but with variable environmental conditions with regards to nutrient concentrations, trophic state and other lake features. Based on this data, it is possible to describe the taxonomic identities and genome-encoded functional traits of the predominant microbes across boreal and subarctic lakes and ponds. This dataset can, be used for the exploration of population genomes, to study individual community members, and for deeper genome characterization of poorly known members of the resident communities, including their metabolic potentials

Methods

DNA quality control and library preparation for sequencing

Reads mapped to assemblies and binning of assemblies

Findings

Code availability