Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake

Abstract

Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA ) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia , Proteobacteria , Cyanobacteria , Bacteroidetes ) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota , Aminicenantes and Caldiserica ) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.

Eutrophication as a driver of microbial community structure in lake sediments

“…In addition to being driven by changes in OM sources and respiration reactions, the observed changes in microbial community structure with depth could also be caused by selective survival. Accordingly, taxa that were already present at the time of sediment deposition but are better equipped to persist under the low energy conditions associated with burial than other taxa would become dominant with increasing sediment depth (Lever et al ., 2015b; Petro et al ., 2017; Starnawski et al ., 2017; Rissanen et al ., 2019). Strong decreases in microbial diversity, that are consistent with survival of a small number of low‐energy resilient taxa, have been documented for the top 30 cm of Lake Stechlin (Wurzbacher et al ., 2017).…”

Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary

“…While it is possible that MOX occurs below the SMTZ at site A due to bioturbation, it is unlikely. More likely, the presence of type II MOB deeper in the sediments is the combined result of burial due to intensive sedimentation and selective survival (Rissanen et al 2019). Indeed, Type II MOB have been shown to be able to survive for extended periods in a dormant state and recover CH 4 oxidation capability even after decades of anoxic conditions (Roslev and King 1994).…”

Vertical changes in bacterial community composition down to a depth of 20 m on the degraded Loess Plateau in China

“…Generally, subsoil exhibits a firmer, finer texture, with much lower organic matter content than topsoil. These characteristics lead to a decrease of microbial biomass and enzyme activity along the soil profile from the topsoil down to 1‐m depth (Eilers, Debenport, Anderson, & Fierer, ; Rissanen et al, ; Sanaullah et al, ; Zhang et al, ). Although the subsoil usually contains relatively low‐nutrient availability, it contributes to the growth of the subsoil microbial biomass (Baldrian et al, ; Blume et al, ; Fierer, Schimel, & Holden, ; Fritze, Pietikainen, & Pennanen, ).…”