Recording of climate and diagenesis through sedimentary DNA and fossil pigments at Laguna Potrok Aike, Argentina

Abstract

Abstract. Aquatic sediments record past climatic conditions while providing a wide range of ecological niches for microorganisms. In theory, benthic microbial community composition should depend on environmental features and geochemical conditions of surrounding sediments, as well as ontogeny of the subsurface environment as sediment degraded. In principle, DNA in sediments should be composed of ancient and extant microbial elements persisting at different degrees of preservation, although to date few studies have quantified the relative influence of each factor in regulating final composition of total sedimentary DNA assemblage. Here geomicrobiological and phylogenetic analyses of a Patagonian maar lake were used to indicate that the different sedimentary microbial assemblages derive from specific lacustrine regimes during defined climatic periods. Two climatic intervals (Mid-Holocene, 5 ka BP; Last Glacial Maximum, 25 ka BP) whose sediments harbored active microbial populations were sampled for a comparative environmental study based on fossil pigments and 16S rRNA gene sequences. The genetic assemblage recovered from the Holocene record revealed a microbial community displaying metabolic complementarities that allowed prolonged degradation of organic matter to methane. The series of Archaea identified throughout the Holocene record indicated an age-related stratification of these populations brought on by environmental selection during early diagenesis. These characteristics were associated with sediments resulting from endorheic lake conditions and stable pelagic regime, high evaporative stress and concomitant high algal productivity. In contrast, sulphate-reducing bacteria and lithotrophic Archaea were predominant in sediments dated from the Last Glacial Maximum, in which pelagic clays alternated with fine volcanic material characteristic of a lake level highstand and freshwater conditions, but reduced water column productivity. Comparison of sedimentary DNA composition with that of fossil pigments suggested that post-depositional diagenesis resulted in a rapid change in the initial nucleic acid composition and overprint of phototrophic communities by heterotrophic assemblages with preserved pigment compositions. Long DNA sequences (1400–900 bp) appeared to derive from intact bacterial cells, whereas short fragments (290–150 bp) reflected extracellular DNA accumulation in ancient sediments. We conclude that sedimentary DNA obtained from lacustrine deposits provides essential genetic information to complement paleoenvironmental indicators and trace post-depositional diagenetic processes over tens of millennia. However, it remains difficult to estimate the time lag between original deposition of lacustrine sediments and establishment of the final composition of the sedimentary DNA assemblage.

Microbial community composition and abundance after millennia of submarine permafrost warming

“…Besides sub-seafloor sediments, Atribacteria were found to be abundant in lacustrine sediments in Argentina that were deposited under similar environmental conditions as C3, with permafrost and reduced vegetation in the catchment, an active hydrology reworking and dispersing the soils, and a very low organic carbon content. Also, climatic conditions in the sedimentation period of the lacustrine sediments were similar to that of Unit II in C3, covering the driest period of the record and overall positive temperatures (Vuillemin et al, 2018).…”

“…This suggestion is supported by similar findings in sea sediments as well as in lacustrine sediments. Microbial taxa of Arabian Sea sediments reflected past depositional conditions and exhibited paleoenvironmental selection (Orsi et al, 2017), while the microbial population in sediments of Laguna Potrok Aike in Argentina changed in response to both past environmental conditions and geochemical changes during burial (Vuillemin et al, 2018). The microbial commu-nities in core C3, which were most distinct from the other locations ( Fig.…”

“…Thereby, this study joins a number of other studies reporting on microbial groups that are referred to as "the paleome". Those studies found correlations between microbial diversity and past depositional conditions (Lyra et al, 2013;Orsi et al, 2017;Vuillemin et al, 2016). Marine communities were found in terrestrial settings or soil communities in (sub-)seafloor sediments (Ciobanu et al, 2012;Inagaki et al, 2015;Inagaki and Nealson, 2006).…”

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

“…However, the composition of buried eDNA results from a combination of sediment provenance, lacustrine conditions at the time of deposition and microbial growth and activity within sediments (Torti et al, 2015; Vuillemin et al, 2016a). This confounds the direct inference of paleoconditions from eDNA.…”

“…In ancient records, it is often best preserved within intact resting stages (Domaizon et al, 2017), such as pollens, planktonic cysts or endospores, which can then be used to trace past environmental changes (Coolen and Overmann, 1998, 2007; Parducci et al, 2005; Coolen et al, 2013) and complement other molecular indicators (Coolen et al, 2008, 2009; Boere et al, 2009; Vuillemin et al, 2014b, 2016a). However, persistent activity of microorganisms in sediments also alters this record due to selective preservation of previous assemblages (Boere et al, 2011a,b).…”