Unlocking the power of lake multiproxy analyses by understanding subsurface biosphere processes

Lake sediments bear valuable information allowing multidisciplinary research to address paleoclimatic and paleoenvironmental reconstructions at regional to global scales. Sedimentological, geochemical, paleontological and biological tools are commonly used to tackle these questions, which are generally driven by a set of intricated parameters. Among them, the importance of biogeochemical cycling is largely acknowledged in the lake (paleo-) water columns and has been at the heart of most paleolimnological studies. The way these signals are transferred to lake sediments has largely been studied. However, microbial communities - the principal actors in the biogeochemical cycling framework - keep being active in the sediment, and continue to influence the preservation and retention of organic and inorganic matter while buried. Gathered within the “early diagenesis” black box, these processes, once qualified, can help better interpret the proxies they may influence, and even constitute new ones. Within this work, we provide examples showing that the integration of studies of the subsurface biosphere within geo- and paleo-limnology investigations can help unlock or secure the potential of multiproxy analysis for reconstructing the paleoenvironments, paleoclimates and paleo-ecology of lake basins. The use of now well-developed OMICS methods, through the analysis of environmental and/or ancient DNA and lipids in particular has been coupled to mineralogical, isotopic and magnetic information in the Dead Sea (Levant) to demonstrate the differential preservation of mineralogic and sedimentologic signals along the last two glacial-interglacial cycles (Thomas et al., 2015, 2016; Ebert et al., 2018). Similar signals have been unlocked in Lake Towuti (Indonesia) and in Laguna Potrok Aike (Argentina) (Vuillemin et al., 2015, 2017). In Lake Ohrid (North Macedonia/Albania), environmental DNA has provided limited inputs on that perspective (Thomas et al., 2020), but has shown that ancient/fossil DNA could provide valuable information regarding the lake primary productivity and the status of its watershed land-cover. Integrating OMICS methods to tackle the identity and activity of the ancient and modern subsurface biosphere of lakes therefore holds an immense potential not only for microbiology investigations, but also for paleoclimatic and paleoenvironmental reconstructions.

Ebert et al. (2018) Overwriting of sedimentary magnetism by bacterially mediated mineral alteration. Geology 46, 2–5.

Thomas et al. (2016) Microbial sedimentary imprint on the deep Dead Sea sediment. The Depositional Record 1–21.

Thomas et al. (2020) Weak influence of paleoenvironmental conditions on the subsurface biosphere of lake ohrid over the last 515 ka. Microorganisms 8, 1–20.

Thomas et al. (2015) Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea. Geobiology 13, 546–561.

Vuillemin et al. (2015) Recording of climate and diagenesis through fossil pigments and sedimentary DNA at Laguna Potrok Aike, Argentina. Biogeosciences Discussions 12, 18345–18388.

Vuillemin et al. (2017) Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti , Indonesia. Frontiers in Microbiology 8, 1–15.