Microbial community composition along a 50 000-year lacustrine sediment sequence

Abstract

For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth.

Microbial diversity of sediments from an inactive hydrothermal vent field, Southwest Indian Ridge

“…3a, c) could result from a decreasing flux rate of organic carbon along depth. After a certain depth, the species gradually adapts to the local environmental stress, commonly coupled with a relatively stable alpha diversity in sediments (Mahmoudi et al 2015;Vuillemin et al 2018). Although similar stable states of microbial communities were observed in our sediments, the fluctuation of alpha and beta diversity was somewhat larger than other samples (Figs.…”

Eutrophication as a driver of microbial community structure in lake sediments

“…Independent of trophic state, microbial communities in surface sediments are dominated by groups that are often abundant in lacustrine surface sediments, that is, α-, βand γ-Proteobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Acidobacteria and MGI Archaea (Kadnikov et al, 2012;Ruuskanen et al, 2018). Phyla that are common in anoxic (subsurface) sediments, that is, Chloroflexi, δ-Proteobacteria, Acetothermia, Aminicenantes, Bathyarchaeota, Lokiarchaeota and Altiarchaeales (Borrel et al, 2012;Vuillemin et al, 2018), increase in the top 5-10 cm and dominate below. Unlike a previous study (Wu et al, 2019), we observe no trends in community profiles in relation to water depth.…”

Microbial community composition and abundance after millennia of submarine permafrost warming

“…About 88 % of this carbon occurs in permafrost soils and deposits (Tarnocai et al, 2009). Permafrost harbours numerous ancient but viable cells (Bischoff et al, 2013;Gilichinsky et al, 2008;Graham et al, 2012;Koch et al, 2009;Mackelprang et al, 2011;Wagner et al, 2007) that can remain active at extremely low temperatures (Hultman et al, 2015;Rivkina et al, 2000). With increasing permafrost age, microbial communities show adaptations to the permafrost biophysical environment and specialize towards long-term survival strategies such as increased dormancy, DNA repair, or stress response (Johnson et al, 2007;Mackelprang et al, 2017).…”