Research > Former Projects > Functional Metagenomics
Functional Metagenomics to Study Prokaryotes from Arctic/ Sub-Arctic Springs of Hydrothermal Origin
The majority, in fact >99 % of the microorganisms on this planet have not yet been cultured in the laboratory and therefore have remained mostly uncharacterized and also unexploited for biotechnological purposes. Recent advancements in genomic technologie s, so called metagenomics, now allow to study the genomic content of bacteria and archaea without the need of cultivation. We propose a metagenomic study on prokaryotes from high temperature environments (hyperthermophiles) of the arctic and subarctic. F or this purpose we will take samples from hot springs at Svalbard (sub-permafrost) and from terrestrial volcanic springs of Kamchatka and Iceland (in collaboration with Russian and Iclendic scientists). We will isolate high molecular weight DNA from these samples and will construct large-insert DNA libraries with techniques that we have developed (and patented) earlier. We will use these metagenomic libraries to screen for genome fragments of unknown species from archaea and bacteria using phylogenetic ma rker genes. Sequence analyses of those large genome fragments (of ca. 40 kb) will allow to uncover genes that give hints to the physiological potential and to adaptive features of as yet unknown extremophiles, thereby linking this information to the phylo genetic affiliation of the respective organisms. The Icelandic partner will screen metagenomic libraries for enzymes potentially useful in biotechnological applications, because they are adapated to high and/or fluctuating temperatures. The interdiscipli nary project involves the collaboration from 3 microbiological groups at the University of Bergen with geologists as well as bioinformaticians of the FUGE platform (functional genomics) CBU (computational biology platform at Univ. of Bergen) and Icelandic and Russian specialists of hyperthermophiles.
Duration: 01.01.2006 - 30.01.2011
Funding: Research Council of Norway 172206
Participants: Christa Schleper, Tim Urich
Urich T, Lanzén A, Stokke R, Bayer C, Pedersen RB, Thorseth I, Schleper C, Steen IH, Řvreas L (2014) Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environmental Microbiology. 2013 Sep 20. doi: 10.1111/1462-2920.12283. [Epub ahead of print].
Jorgensen S, Thorseth I, Pedersen R, Baumberger T, Schleper C (2013) Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge. Frontiers in Microbiology 4: 299.
Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C (2013) Metagenomics of Kamchatkan hot spring filaments reveal two new major(hyper)thermophilic lineages related to Thaumarchaeota. Research in Microbiology 164: 425-438. doi:pii: S0923-2508(13)00027-2. 10.1016/j.resmic.2013.02.006.
Jřrgensen S, Hannisdal B, Lanzen A, Baumberger T, Flesland K, Fonseca R, Ovreas L, Steen IH, Torseth IH, Pedersen RB, Schleper C (2012) Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proceedings of the National Academy of Sciences of the United States of America. 109(42): E2846-E2855. doi: 10.1073/pnas.1207574109.
Reigstad LJ, Jorgensen SL, Lauritzen SE, Schleper C, Urich T (2011) Sulfur-oxidizing chemolithotrophic proteobacteria dominate the microbiota in high arctic thermal springs on svalbard. Astrobiology 11(7): 665-678.
Reigstad LJ, Bartossek R, Schleper C (2011) Preparation of high-molecular weight DNA and metagenomic libraries from soils and hot springs. Methods in Enzymology 496:319-344.
Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends in Microbiology 18(8): 331-340.
Bartossek R, Nicol GW, Lanzen A, Klenk HP, Schleper C (2010) Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiology 12(4): 1075-1088.
Reigstad LH, Jorgensen SL, Schleper C (2010) Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka. ISME Journal 4(3): 346-356.
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3(6): e2527.
Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C (2008) Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiology Ecology 64(2): 167-174.