Development of a real‐time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno

Abstract

Lake Cadagno is a crenogenic meromictic lake situated in the southern range of the Swiss Alps characterized by a compact chemocline that has been the object of many ecological studies. The population dynamics of phototrophic sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S rRNA gene clone library analysis. To reconstruct paleo‐microbial community dynamics, we developed a quantitative real‐time PCR methodology for specific detection of 16S rRNA gene sequences of purple and green sulfur bacteria populations from sediment samples. We detected fossil 16S rDNA of nine populations of phototrophic sulfur bacteria down to 9‐m sediment depth, corresponding to about 9500 years of the lake’s biogeological history. These results provide the first evidence for the presence of 16S rDNA of anoxygenic phototrophic bacteria in Holocene sediments of an alpine meromictic lake and indicate that the water column stratification and the bacterial plume were already present in Lake Cadagno thousands of years ago. The finding of Chlorobium clathratiforme remains in all the samples analyzed shows that this population, identified in the water column only in 2001, was already a part of the lake’s biota in the past.

Reconstructing long‐term human impacts on plant communities: an ecological approach based on lake sediment DNA

“…This sed aDNA constitutes a potential source of information to assess past lake communities (Ravasi et al . ; Stoof‐Leichsenring et al . ; Domaizon et al .…”

“…The DNA of a variety of taxa, including plants and mammals, can be directly obtained from recent and past sediments (Chariton et al 2010;Hofreiter et al 2012;Pedersen et al 2013;Willerslev et al 2014) even in the absence of visible macrofossils. This sedaDNA constitutes a potential source of information to assess past lake communities (Ravasi et al 2012;Stoof-Leichsenring et al 2012;Domaizon et al 2013), but also species assemblages from the surrounding terrestrial ecosystems (Jørgensen et al 2012;Parducci et al 2013;Pedersen et al 2013). Recent developments of highthroughput sequencing now allow massive sequencing of the ancient DNA contained in sedimentary archives.…”

Polymerase Chain Reaction (PCR): Principle and Applications

“…The type of identification depends simply on the choice of markers. Similarly, for varietal identification purposes, one can commonly proceed according to protocols derived from the PCR [64][65][66].…”

Reconstruction of Past Dynamics of Methane-Oxidizing Bacteria in Lake Sediments Using a Quantitative PCR Method: Connecting Past Environmental Changes and Microbial Community

“…DNA degradation over time and interactions with living microbial communities could affect the reliability of MOB aDNA results. Indeed, Ravasi et al (2012) reported important DNA degradation in a sediment core covering the Holocene period, leading to drastic decrease in total DNA concentrations over depth in core. Moreover, several studies have reported that active methanotrophic communities can live up to 20 cm deep in sediments of subarctic and arctic lakes (He et al 2012) and deep temperate lakes (Rahalkar et al 2009;Billard et al 2015), leading to potential increase in DNA concentrations and MOB proportions for the topmost part of a sediment core.…”

“…1200 years) and limited biases due to living microbial communities. Excellent DNA preservation provided by morphological and chemical properties of studied lakes ( Figure S1; deep water anoxia, light, and temperature stratifications; Coolen et al 2006;Corinaldesi et al 2008;Domaizon et al 2013), and the use relative quantification method could prevent effects of changes in aDNA extraction efficiency and aDNA preservation (Ravasi et al 2012) as well as interactions with living microbial communities. Sediment composition can also affect the efficiency of qPCR amplification by co-extracting inhibiting substances (Young et al 2014), but extra purification steps were added to eliminate these potential inhibitors and purify DNA extracts.…”