Chapter 4. Bacterial and archaeal DNA from lake sediments

Abstract

General microbial patterns of biogeography can be established based on sedimentary DNA (sedDNA) retrieved from diverse inland aquatic ecosystems, provided that certain variable environmental factors are taken into consideration in order to trace the admixture of prokaryotic sedDNA preserved in lacustrine sediments from source to sink. These include several watershed characteristics, such as climate and mineralogy in the catchment and degree of urbanization, which in turn determine the lake regime, productivity and geochemistry of the water body, redox conditions at the sediment-water interface, sedimentation rates and organic matter content over time.Records of environmental conditions through the preservation of prokaryotic sedDNA will partially be obscured by the presence of a subsurface biosphere that remains active during burial. Sediment colonization and selective growth of specific sub-populations of the resident microbiomes are inherent to the substrates available in lacustrine deposits. Microbial guilds reflective of respiration types and organic matter decomposition usually go hand-in-hand with the geochemical gradient that develops in the sedimentary column during early diagenetic processes, but may also prevail in specific stratigraphic intervals. Thus, the correct attribution of prokaryotic sedDNA sources to an environmental context is essential for resolving past and modern ecosystem functioning. Because the succession of microbial taxa pre-adapted to gradual depletion of electron donors and acceptors is relatively well known, sources of sedDNA inherent to resident microbial communities can be discriminated and provide evidence of diagenetic processes during burial. In contrast, ancient sources of sedDNA that persist in microbially active sediments are exposed to a constant turnover, leading to preferential preservation of dormant stages over free sedDNA.Bacteria and archaea are tremendously diverse, and therefore there is the need to rigorously assign their metabolic functions and assess their degree of activity along sediment archives. Beyond taxonomic surveys and geochemical profiling of the subsurface biosphere, novel procedures are being customized to sort, target, sequence and assemble sedDNA fragments of interest to unravel specific biogeochemical interactions in lacustrine ecosystems pertaining past and actual ecological changes at the local and global scale.