Meta-transcriptomics to study the function and structure of complex microbial communities

We are interested in the characterisation of complex microbial communities with cultivation-independent molecular genomic approaches to disclose the ecological function of uncultured archaea and bacteria. Meta-genomic technologies have been used for many years for this purpose and as a logical next step we have recently established meta-transcriptomic approaches in our laboratory.
Meta-transcriptomics offers the opportunity to reach beyond the community’s genomic potential as assessed in DNA-based methods, towards its in situ activity. In addition, the analysis of the RNA pool of a community links its taxonomic structure and function, as it is naturally enriched not only in functionally but also taxonomically relevant molecules, i.e. mRNA and rRNA, respectively. In addition rRNA can be used for PCR-independent community profiling of all three domains of life.
We have established appropriate experimental and analytical procedures (the “double-RNA” approach) for in-depth characterization of microbial communities by studying mRNA and rRNA molecules simultaneously from the same sample.

We are especially interested in soil ecosystems as they cover almost all of the terrestrial area on Earth and have an indispensable ecological function in the global cycles of carbon, nitrogen and sulfur. Due to their physico-chemical complexity with many micro-niches, they teem with bio-diversity, both phylogenetically and functionally.

In addition, meta-transcriptomics is applied and further developed on different biological systems, such as sponges (host-symbiont) and hydrothermal vents.

Duration: 2012-2014

Funding Agency: University of Vienna

Participants: Christa Schleper, Tim Urich

Urich T, Lanzén A, Stokke R, Bayer C, Pedersen RB, Thorseth I, Schleper C, Steen IH, Øvreas 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].

Wilhelm L, Besember K, Fasching C, Urich T, Singer GA, Quince C, Battin TJ (2014) Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environmental Microbiology. 2014 FEB 18. doi: 10.1111/1462-2920.12392. [Epub ahead of print]

Prommer J, Wanek W, Hofhansl F, Trojan D, Offre P, Urich T, Schleper C, Sassmann S, Kitzler B, Soja G, Hood-Nowotny R (2014) Biochar Decelerates Soil Organic Nitrogen Cycling but Stimulates Soil Nitrification in a Temperate Arable Field Trial. PLOS One 9(1): e86388. doi: 10.1371/journal.pone.0086388.

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.

Vissers EW, Anselmetti FS, Bodelier PL, Muyzer G, Schleper C, Tourna M, Laanbroek HJ (2013) Temporal and Spatial Coexistence of Archaeal and Bacterial amoA Genes and Gene Transcripts in Lake Lucerne. Archaea - An International Microbiological Journal 2013: 289478; doi: 10.1155/2013/289478.

Vissers EW, Blaga CI, Bodelier PL, Muyzer G, Schleper C, Sinninghe Damsté JS, Tourna M, Laanbroek HJ (2013) Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake. FEMS Microbiology Ecology 83(2): 515-526. doi: 10.1111/1574-6941.12013.

Lanzèn A, Jørgensen SL, Huson DH, Garfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T (2012): CREST – Classification Resources for environmental Sequence Tags, PLOS One 7:e49334. doi:10.1371/journal.pone.0049334.

Tveit A, Schwacke R, Svenning MM, Urich T (2012) Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME Journal 7(2): 299-311. doi: 10.1038/ismej.2012.99.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH (2011) Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S21.

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.

Lanzén A, Jorgensen SL, Bengtsson MM, Jonassen I, Ovreas L, Urich T (2011) Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiology Ecology 77(3): 577-89.

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.

Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schläppy ML, Schleper C, Kuypers MM (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environmental Microbiology 11(9): 2228-2243.

Schauss K, Focks A, Leininger S, Kotzerke A, Heuer H, Thiele-Bruhn S, Sharma S, Wilke BM, Matthies M, Smalla K, Munch JC, Amelung W, Kaupenjohann M, Schloter M, Schleper C (2009) Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environmental Microbiology 11(2): 446-456.

Schleper C (2008) Microbial ecology: Metabolism of the deep. Nature 456(7223): 712-714.

Perevalova AA, Kolganova TV, Birkeland NK, Schleper C, Bonch-Osmolovskaya EA, Lebedinsky AV (2008) Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland. Applied and Environmental Microbiology 74(24): 7620-7628.

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.