DNA-Metabarcoding of Plankton in East Africa (DFG)
Lake-sediment cores provide natural archives of past environmental changes, traditionally analyzed with sedimentological, geochemical and paleontological methods. More recently, samples from sediment cores have also been subjected to molecular DNA analysis, targeting either the living community of soil microbes or remnants of organisms that inhabited the lake and/ or its surface sediment in the past. The project proposed here aims at evaluating the possibility for DNA metabarcoding in the Chew Bahir sediment cores, combining state-of-the-art techniques of environmental genomics and ancient DNA analysis. The principal research questions addressed by the project are: (1) How far back in time can DNA remnants in the Chew Bahir sediment cores be extracted and analyzed? (2) How congruent are the results of PCR-based vs. hybridization- capture-based metabarcoding? and (3) What are the long-term trends and shifts in the plankton communities in the Chew Bahir record? The results of this project will provide an important contribution to the understanding of interactions between the environment and the biosphere in the past, particularly in sediments, in which microscopically recognizable organic remains are scarce or absent. Furthermore, we expect important methodological advances in the study of sediments of tropical lakes, which will be in future projects of great importance.
Publications:
Stoof-Liechsenring, K., Epp, L.E., Trauth, M.H., Tiedemann, R. (2012) Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation. Molecular Ecology, 21, 1918–1930.
Epp, L., Stoof-Leichsenring, K.R., Trauth, M.H., Tiedemann, R (2011) Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High Performance Liquid Chromatography (PCR-DHPLC). Molecular Ecology, 11, 842-853.
Stoof-Liechsenring, K., Junginger, A., Olaka, L.A., Tiedemann, R., Trauth, M.H. (2011) Environmental variability in Lake Naivasha, Kenya, over the last two centuries. Journal of Paleolimnology, 45, 353-367.
Epp, L., Stoof, K.R., Trauth, M.H., Tiedemann, R (2010) Historical genetics on sediment core from Kenyan lake sediments: Intraspecific genotype turnover in a tropical rotifer is related to past environmental changes.Journal of Paleolimnology, 43, 939-954.