Functional Sea Ice Ecology: Molecular Biodiversity, Metatranscriptomics and Metagenomics
Final Report Abstract
Software for rDNA analyses: Phyloassigner was successfully published and applied in several project contexts related to marine protists diversity and community analyses. A dinoflagellate-specific application was designed. The phylogenetic placement approach was transferred to an application on coding sequences of ice binding genes to characterize their importance and their phylogenetic affiliation. Software for functional analyses: EggNOGblast was developed to screen sequencing reads for possible functional coding gene segments in a phylogenomics reference data. We faced problems with the taxonomic resolution on the level of input data. Only recently, within the MMETSP project, several new non-model organism transcriptome data have been made available that effectively could be incorporated in the reference data, extending the taxonomic range. Experimental: The experimental part of the project, conducted in the framework of a diploma thesis, did not result in enough good RNA samples for significant rRNA sequencing. Rather we obtained valuable experience for future sampling and processing which recently allowed successful new sampling and high-throughput sequencing of sea ice samples. Frickenhaus, S., Valentin, K., Diekmann, G.: Molecular Ecology of Sea Ice Communities in a changing world – the Genomic Perspective. Hochschule Bremerhaven, March 29/30 2011, http://epic.awi.de/36885/
Publications
- (2013) http://epic.awi.de/34193. Protist distribution in the Western Fram Strait in summer 2010 based on 454-pyrosequencing of the 18S rDNA, Journal of Phycology, 49 (5), pp. 996-1010
Kilias, E. , Wolf, C. , Nöthig, E. M. , Peeken, I. and Metfies, K.
(See online at https://doi.org/10.1111/jpy.12109) - (2013) Regional variability in eukaryotic protist communities in the Amundsen Sea, Antarctic Science 25 6, 741-751
Wolf C, Frickenhaus S, Kilias ES, Peeken I, Metfies K
(See online at https://doi.org/10.1017/S0954102013000229) - High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences. ISME J. 7, July 2013, 1322-1332
Vergin KL, Beszteri B, Monier A, Thrash JC, Temperton B, Treusch AH, Kilpert F, Worden AZ, Giovannoni SJ
(See online at https://doi.org/10.1038/ismej.2013.32) - (2014): The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing , PLoS Biology, 12 (6), e1001889
Keeling, P. J., ..., Worden, A. Z.
(See online at https://doi.org/10.1371/journal.pbio.1001889) - In situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice. The ISME Journal volume 9, pages 2537–2540 (2015)
Uhlig C, Kilpert F, Frickenhaus S, Kegel JU, Krell A, Mock T, Valentin K, Beszteri B
(See online at https://doi.org/10.1038/ismej.2015.43)
