Analysis of the prokaryotic groups evading universal primers in deep sea sediments

Project title

Analysis of the prokaryotic groups evading universal primers in deep sea sediments

Project supervisor

Sven Le Moine Bauer

Steffen Jørgensen

Project description

The deep sea and its microbial communities is one of the least explored ecosystems on our planet. Despite the high pressure, darkness and scarce food supply, prokaryotes are highly abundant in deep sea environments where they play a critical role in various biogeochemical processes. Furthermore, these microbes are targeted to find new bioremediation means, microbial biotechnology for potential energy sources and metabolic engineering, but also antibiotic development. Therefore, it is important to gain more knowledge about the prokaryotes in deep sea sediments. For prokaryotic community investigation, 16S rRNA gene sequencing with universal primer sets such as the 515F/806R and the modified 519F/805R are widely applied. Both primer sets are essential for molecular research and estimation of microbial abundance and diversity. The modification of the 519F/805R primer set is better at targeting Archaea as shown in the finding of numerous new archaeal lineages while the 515F/806R primer set provides a wide range of prokaryotic targets but was found to be more bacteria specific and can therefore underestimate the archaeal diversity. In general, it is established that the selection of different primer combinations would lead to different outcomes. In the case of the aforementioned primer sets, some taxomonic groups are known to evade detection. For example, various unknown Chlamydiae clades have been found to have high relative abundance in some deep sea sediments using specific primers while not being detected with the universal primer sets. Chlamydiae is known as an obligate intracellular eukaryotic symbiont/pathogen, yet they were not able to identify any possible eukaryotic hosts in the anoxic deep sea sediment. A second example is the detection of previously undetected strains of the Nanoarchaeota phylum in deep sea sediments using the same approach. Therefore, we can question what else we are overlooking in deep sea sediment communities. My study aims at investigating these untargeted prokaryotic groups by using specifically designed primers and interpret their potential functional role in deep sea sediment communities.