Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva (Switzerland–France)

Abstract

Measurements of chemical composition and biological parameters of sediment cores are used as proxies for changes in past environmental conditions and more recently the human impact on ecosystem health. In this study, endospore-forming bacteria are proposed as a new biological proxy for such paleoecological reconstructions. A sediment core providing a record for the past 90 years (137Cs and magnetic susceptibility dating) was retrieved from the Rhone Delta of Lake Geneva. X-ray fluorescence was analyzed at a 0.2-cm resolution, while DNA extracts, elemental geochemistry and grain size were obtained at 4-cm intervals. The total number of bacteria and endospore- forming bacteria were quantified by qPCR using the 16S rRNA gene and the endosporulation-specific spo0A gene. Furthermore, a spo0A fragment was subjected to amplicon sequencing to define OTUs (operational taxonomic units) and the phylogenetic affiliation of the endospore formers. The results showed that despite the fact that the quantity of extracted DNA decreased with the age of the sediment, the abundance of endospore-forming bacteria remained constant. However, the diversity of this group of bacteria changed significantly, reflecting the eutrophication of the lake from 1960 to 1990. The shift in community composition was linked to the dominance of anaerobic clostridia-like endospore formers. This trend has reversed in the last 10 years of the record, suggesting a recovery after perturbation. This study shows that the abundance and diversity of endospore-forming bacteria can be used as proxies to reconstruct lake history. We hereby successfully introduce a new strategy for paleoecology that could also be applied to ocean sediments and long sediment cores

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

“…Further, if there was no growth in the sediment, lineages that are potentially better suited for long-term survival than others would appear, such as spore-forming Bacteria (Firmicutes). However, we (and others: [27, 34]) did not observe an enrichment of this lineage with depth. In addition, the use of replicate cores in combination with our conservative stripping (see the “Methods” section) should have removed most of the random effects.…”

“…The decrease in DNA with depth that has been reported for freshwater sediments (e.g., [34]) is likely to result of nucleic acid degradation of dead organisms, particularly eukaryotes, whose biomass also decreases with depth. As a result, the decomposition of buried organisms should be a function of the active community which is itself buried over time.…”

“…Vice versa, temporal patterns of sedimentation will also influence the active microbial community, for example by shifting the redox gradient. Historically changing lake conditions are recorded in lake sediments as DNA and as chemical parameters (e.g., [34]). An important question that remains is how decomposition processes within the sediment redox gradient are related to the burial of OM, eukaryotes, and prokaryotes [35, 36].…”

The role of mass-transport deposits and turbidites in shaping modern lacustrine deepwater channels

“…1 and 3) displayed typical hemipelagic sediments consisting of couplets of brownish organic-rich silty layers and sub-mm thick calcite-rich white laminae. Calcite layers probably originate from endogenic calcite precipitation linked to spring-summer algal blooms (Wunderlin et al, 2014). The couplets are punctuated by mm-to cm-thick dark-grey silty detrital layers (Fig.…”

“…Radiometric-dated cores in C1 and C2 (Wunderlin et al, 2014) lacked indicators of flushing events reaching the distal fans for the last 90 years suggesting a disconnection of the feeding river mouth (i.e. Eau Froide River) and its subaquatic counterpart C1 during the last century.…”