My research interests widely span several aspects of the biology of microorganisms. For this purpose we develop and apply metagenomic methodologies to study the physiology and interactions of microorganisms directly in their environment, without the need for cultivation.
Current research interests include:

• The role of gut microbiota in human and animal health and disease
• Microbes in permafrost soil and their role in global greenhouse gas emissions
• Metabolic and trophic interactions between soil microorganisms and their consequences for carbon and nitrogen cycling
• Methanogenic archaea: physiology and ecology of novel methanogens

Selected Projects

• Rumen Methanomassilicoccales as target for methane mitigation: eco-physiology and interactions assessed by integrated meta-omics. UniDocs Project funded by University of Vienna (2014-2017).
• Microbial genomes and community gene expression in high arctic terrestrial ecosystems. Norwegian Research Council NFR (2009-2014) PI Mette Svenning, Tromsø (Norway). Co-PI.

• Täumer J, Marhan S, Groß V, et. al. Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes. The ISME Journal; https://doi.org/10.1038/s41396-022-01229-4
   
• Söllinger A, Séneca J, Borg Dahl M, et al. Down-regulation of the bacterial protein biosynthesis machinery in response to weeks, years, and decades of soil warming. Sci Adv. 2022;8(12):eabm3230. PMID: 35333567
   
• Weil M, Hoff KJ, Meißner W, et al. Full genome sequence of a methanomassiliicoccales representative enriched from peat soil. Newton ILG, ed. Microbiol Resour Announc. 2021;10(48):e00443-21. PMID: 34854727
   
• Varsadiya M, Urich T, Hugelius G, Bárta J. Fungi in permafrost-affected soils of the canadian arctic: horizon- and site-specific keystone taxa revealed by co-occurrence network. Microorganisms. 2021;9(9):1943. PMID: 34611156
   
• Francis B, Urich T, Mikolasch A, Teeling H, Amann R. North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches. Environ Microbiome. 2021;16(1):15.PMID: 34404489
   
• Zühlke MK, Schlüter R, Mikolasch A, et al. Correction to: Biotransformation of bisphenol a analogues by the biphenyl-degrading bacterium Cupriavidus basilensis - a structure-biotransformation relationship. Appl Microbiol Biotechnol. 2021;105(14-15):6117. PMID: 34268582
   
• Petters S, Groß V, Söllinger A, et al. The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? ISME J. 2021;15(9):2665-2675.PMID: 33746204
   
• Bižić M, Klintzsch T, Ionescu D, et al. Aquatic and terrestrial cyanobacteria produce methane. Sci Adv. 2020;6(3):eaax5343. PMID: 31998836
   
• Sheffer MM, Uhl G, Prost S, Lueders T, Urich T, Bengtsson MM. Tissue- and population-level microbiome analysis of the wasp spider argiope bruennichi identified a novel dominant bacterial symbiont. Microorganisms. 2019;8(1). PMID: 31861544
   
• Čapek P, Manzoni S, Kaštovská E, Wild B, Diáková K, Bárta J, Schnecker J,Biasi C, Martikainen PJ, Alves RJE, Guggenberger G, Gentsch N, Hugelius G,Palmtag J, Mikutta R, Shibistova O, Urich T, Schleper C, Richter A, ŠantrůčkováH. A plant-microbe interaction framework explaining nutrient effects on primaryproduction. Nat Ecol Evol. 2018 Sep 10. doi: 10.1038/s41559-018-0662-8. [Epubahead of print] PubMed PMID:30201963.
   
• Söllinger A, Tveit AT, Poulsen M,Riedel K, et al. Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation. mSystems. 2018 Jul-Aug; 3(4): e00038-18.PMID:30116788.
   
• Gentsch N, Wild B, Mikutta R, Čapek P, Diáková K, Schrumpf M, Turner S, Minnich C, Schaarschmidt F, Shibistova O, Schnecker J, Urich T, Gittel A, Šantrůčková H, Bárta J, Lashchinskiy N, Fuß R, Richter A, Guggenberger G.Temperature response of permafrost soil carbon is attenuated by mineralprotection. Glob Chang Biol. 2018 Aug;24(8):3401-3415. doi: 10.1111/gcb.14316.Epub 2018 Jun 1. PubMed PMID:29774972.
   
• Alves RJE, Minh BQ,Urich T, Von haeseler A, Schleper C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun. 2018;9(1):1517, PMID:29666365.
   
• Giacomin P, Kraeuter A, Albornoz E, Jin S,Bengtsson MM, Gordon R, Woodruff T, Urich T, Sarnyai Z, Soares Magalhaes R. Chronic helminth infection in early life perturbs the gut-brain axis, alters behaviour and promotes neuropathology. J Infect Dis, in press. https://doi.org/10.1093/infdis/jiy092.
   
• Bengtsson MM, Wagner K, Schwab C, Urich T, Battin TJ. Light availabilityimpacts structure and function of phototrophic stream biofilms across domains andtrophic levels. Mol Ecol. 2018 Jul;27(14):2913-2925. doi: 10.1111/mec.14696. Epub2018 Jun 4. PubMed PMID:29679511; PubMed Central PMCID: PMC6055792.

• Giacomin P, Kraeuter A, Albornoz E, Jin S, Bengtsson MM, Gordon R, Woodruff T, Urich T, Sarnyai Z, Soares Magalhaes R. Chronic helminth infection in early life perturbs the gut-brain axis, alters behaviour and promotes neuropathology. J Infect Dis, in press. https://doi.org/10.1093/infdis/jiy092.
   
• Santruckova H, Kotas P, Bárta J, Urich T, Čapek P, Palmtag J, Alves R, Biasi C, Diáková K, Gentsch N, Gittel A, Guggenberger G, Hugelius G, Kuhry P, Lashchinsky N, Martikainen P, Mikutta R, Schleper C, Schnecker J, Shibistova O, Wild B, Richter A. Significance of dark CO2 fixation in arctic soils. Soil Biology and Biochemistry, Volume 119, April 2018, Pages 11-21.
   
• Wild B, Alves R, Bárta J, Čapek P, Gentsch N, Gittel A, Guggenberger G, Hugelius G, Knoltsch A, Kuhry P, Lashchinskiy N, Mikutta R, Palmtag J, Prommer J, Šantrůčková H, Schnecker J, Shibistova O, Takriti M, Urich T, Richter A. Amino acid production exceeds plant nitrogen demand in Siberian tundra. Environmental Research Letters, 13 (2018) 034002.
   
• Dao T,G Guggenberger, N Gentsch, R Mikutta, L Sauheitl, O Shibistova, B Wild, J Schnecker, J Bárta, P Capek, A Gittel, N Lashchinskiy, T Urich, H Šantrůčková, A Richter. Fate of carbohydrates and lignin in north-east Siberian permafrost soils. Soil Biology and Biochemistry 116, 311-322.
   
• Thompson L, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 2017, pages 457–463.
   
• Choma M, Bárta J, Šantrůčková H, Urich T. Low abundance of Archaeorhizomycetes among fungi in soil metatranscriptomes. Sci Rep.2016 Dec 23;6:38455. PMID: 28009005.
   
• Kramer S, Dibbern D, Moll J, Huenninghaus M, Koller R, Krueger D, Marhan S, Urich T, Wubet T, Bonkowski M, Buscot F, Lueders T, Kandeler E. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil. Front Microbiol.2016 Sep 26;7:1524. PMID: 27725815.
   
• Capek P, Diakova K, Dickopp J, Barta J, Wild B, Schnecker J, Alves R, Aiglsdorfer S, Gerg Guggenberger G, Gentsch N, Hugelius G, Lashchinsky N, Gittel A, Schleper C, Mikutta R, Palmtag J, Shibistova O, Urich T, Richter A, Santruckova H. The effect of warming on the vulnerability of subducted organic carbon in arctic soils. Soil Biology and Biochemistry. Advanced online publication 4th August 2015.

• Becker KW, Elling FJ, Yoshinaga MY, Söllinger A, Urich T, Hinrichs KU. Unusual butane- and pentanetriol-based tetraether lipids in Methanomassiliicoccus luminyensis, a representative of the seventh order of methanogens. Appl Environ Microbiol.2016 May 13. PMID: 27208108.
   
• Wild B, Gentsch N, Čapek P, Diáková K, Alves RJ,, Bárta J, Gittel A,, Hugelius G, Knoltsch A,, Kuhry P, Lashchinskiy N, Mikutta R,, Palmtag J, Schleper C,, Schnecker J,,, Shibistova O,, Takriti M,,, Torsvik VL, Urich T,,, Watzka M, Šantrůčková H, Guggenberger G,, Richter A,. Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils. Sci Rep.2016 May 9;6:25607. PMID: 27157964.
   
• Noel SJ, Højberg O, Urich T, Poulsen M. Draft Genome Sequence of “Candidatus Methanomethylophilus” sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order. Genome Announc.2016 Feb 18;4(1). PMID: 26893425.
   
• Berry D, Kuzyk O, Rauch I, Heider S, Schwab C, Hainzl E, Decker T, Müller M, Strobl B, Schleper C, Urich T, Wagner M, Kenner L, Loy A. Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis. Front Microbiol.2015 Dec 15;6:1408. PMID: 26697002.
   
• Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol.2016 Jan;92(1). PMID: 26613748.
   
• Hainzl E, Stockinger S, Rauch I, Heider S, Berry D, Lassnig C, Schwab C, Rosebrock F, Milinovich G, Schlederer M, Wagner M, Schleper C, Loy A, Urich T, Kenner L, Han X, Decker T, Strobl B, Müller M. Intestinal Epithelial Cell Tyrosine Kinase 2 Transduces IL-22 Signals To Protect from Acute Colitis. J Immunol.2015 Nov 15;195(10):5011-24. PMID: 26432894.
   
• Geisen S,, Rosengarten J, Koller R,, Mulder C, Urich T,, Bonkowski M. Pack hunting by a common soil amoeba on nematodes. Environ Microbiol.2015 Nov;17(11):4538-46. PMID: 26079718.
   
• Tveit AT, Urich T, Frenzel P, Svenning MM. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proc Natl Acad Sci U S A.2015 May 12;112(19):E2507-16. PMID: 25918393.
   
• Geisen S,, Tveit AT, Clark IM, Richter A, Svenning MM, Bonkowski M, Urich T. Metatranscriptomic census of active protists in soils. ISME J.2015 Oct;9(10):2178-90. PMID: 25822483.
   
• Epelde L, Lanzén A, Blanco F, Urich T, Garbisu C. Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine. FEMS Microbiol Ecol.2015 Jan;91(1):1-11. PMID: 25764532.
   
• Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Capek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol.2014 Oct 16;5:541. PMID: 25360132.
   
• Wild B, Schnecker J, Alves RJ, Barsukov P, Bárta J, Capek P, Gentsch N, Gittel A, Guggenberger G, Lashchinskiy N, Mikutta R, Rusalimova O, Santrůčková H, Shibistova O, Urich T, Watzka M, Zrazhevskaya G, Richter A. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. Soil Biol Biochem.2014 Aug;75(100):143-151. PMID: 25089062.
   
• Tveit AT, Urich T, Svenning MM. Metatranscriptomic analysis of arctic peat soil microbiota. Appl Environ Microbiol.2014 Sep;80(18):5761-72. PMID: 25015892.
   
• Rauch I, Hainzl E, Rosebrock F, Heider S, Schwab C, Berry D, Stoiber D, Wagner M, Schleper C, Loy A, Urich T, Müller M, Strobl B, Kenner L, Decker T. Type I interferons have opposing effects during the emergence and recovery phases of colitis. Eur J Immunol.2014 Sep;44(9):2749-60. PMID: 24975266.
   
• Schnecker J, Wild B, Hofhansl F, Eloy Alves RJ, Bárta J, Capek P, Fuchslueger L, Gentsch N, Gittel A, Guggenberger G, Hofer A, Kienzl S, Knoltsch A, Lashchinskiy N, Mikutta R, Santrůčková H, Shibistova O, Takriti M, Urich T, Weltin G, Richter A. Effects of soil organic matter properties and microbial community composition on enzyme activities in cryoturbated arctic soils. PLoS One.2014 Apr 4;9(4):e94076. PMID: 24705618.
   
• Schwab C, Tveit AT, Schleper C, Urich T. Gene expression of lactobacilli in murine forestomach biofilms. Microb Biotechnol.2014 Jul;7(4):347-59. PMID: 24702817.
   
• Prommer J, Wanek W, Hofhansl F, Trojan D, Offre P, Urich T, Schleper C, Sassmann S, Kitzler B, Soja G, Hood-Nowotny RC. Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial. PLoS One.2014 Jan 30;9(1):e86388. PMID: 24497947.
   
• Wilhelm L, Besemer K, Fasching C, Urich T, Singer GA, Quince C, Battin TJ. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environ Microbiol.2014 Aug;16(8):2514-24. PMID: 24428193.
   
• Schwab C, Berry D, Rauch I, Rennisch I, Ramesmayer J, Hainzl E, Heider S, Decker T, Kenner L, Müller M, Strobl B, Wagner M, Schleper C, Loy A, Urich T. Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J.2014 May;8(5):1101-14. PMID: 24401855.
   
• Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Capek P, Santrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C, Urich T. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J.2014 Apr;8(4):841-53. PMID: 24335828.
   
• Wild B, Schnecker J, Bárta J, Capek P, Guggenberger G, Hofhansl F, Kaiser C, Lashchinsky N, Mikutta R, Mooshammer M, Santrůčková H, Shibistova O, Urich T, Zimov SA, Richter A. Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland. Soil Biol Biochem.2013 Dec;67(100):85-93. PMID: 24302785.
   
• Urich T, Lanzén A, Stokke R, Pedersen RB, Bayer C, Thorseth IH, Schleper C, Steen IH, Ovreas L. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ Microbiol.2014 Sep;16(9):2699-710. PMID: 24112684.
   
• Shen T, Stieglmeier M, Dai J, Urich T, Schleper C. Responses of the terrestrial ammonia-oxidizing archaeon Ca. Nitrososphaera viennensis and the ammonia-oxidizing bacterium Nitrosospira multiformis to nitrification inhibitors. FEMS Microbiol Lett.2013 Jul;344(2):121-9. PMID: 23617238.
   
• Alves RJ, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, Urich T. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. ISME J.2013 Aug;7(8):1620-31. PMID: 23466705.
   
• Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A, Canibe N, Højberg O, Milinovich G, Fragner L, Schleper C, Weckwerth W, Lund P, Schramm A, Urich T. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun.2013;4:1428. PMID: 23385573.
   
• Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T. CREST–classification resources for environmental sequence tags. PLoS One.2012;7(11):e49334. PMID: 23145153.
   
• Berry D, Schwab C, Milinovich G, Reichert J, Ben Mahfoudh K, Decker T, Engel M, Hai B, Hainzl E, Heider S, Kenner L, Müller M, Rauch I, Strobl B, Wagner M, Schleper C, Urich T, Loy A. Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis. ISME J.2012 Nov;6(11):2091-106. PMID: 22572638.
   
• Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T, Schleper C. Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol.2012 May;14(5):1308-24. PMID: 22364353.
   
• Reigstad LJ, Jorgensen SL, Lauritzen SE, Schleper C, Urich T. Sulfur-oxidizing chemolithotrophic proteobacteria dominate the microbiota in high arctic thermal springs on Svalbard. Astrobiology.2011 Sep;11(7):665-78. PMID: 21899440.
   
• Veith A, Urich T, Seyfarth K, Protze J, Frazão C, Kletzin A. Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens. Front Microbiol.2011 Mar 7;2:37. PMID: 21747782.
   
• Lanzén A, Jørgensen SL, Bengtsson MM, Jonassen I, Øvreås L, Urich T. Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol.2011 Sep;77(3):577-89. PMID: 21627670.
   
• Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A.2011 May 17;108(20):8420-5. PMID: 21525411.
   
• Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics.2011 Feb 15;12 Suppl 1:S21. PMID: 21342551.
   
• Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One.2008 Jun 25;3(6):e2527. PMID: 18575584.
   
• Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol.2008 May;64(2):167-74. PMID: 18355293.
   
• Prosinecki V, Botelho HM, Francese S, Mastrobuoni G, Moneti G, Urich T, Kletzin A, Gomes CM. A proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability. J Proteome Res.2006 Oct;5(10):2720-6. PMID: 17022643.
   
• Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature.2006 Aug 17;442(7104):806-9. PMID: 16915287.
   
• Urich T, Gomes CM, Kletzin A, Frazão C. X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science.2006 Feb 17;311(5763):996-1000. PMID: 16484493.
   
• Albers SV, Jonuscheit M, Dinkelaker S, Urich T, Kletzin A, Tampé R, Driessen AJ, Schleper C. Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microbiol.2006 Jan;72(1):102-11. PMID: 16391031.
   
• Urich T, Kroke A, Bauer C, Seyfarth K, Reuff M, Kletzin A. Identification of core active site residues of the sulfur oxygenase reductase from Acidianus ambivalens by site-directed mutagenesis. FEMS Microbiol Lett.2005 Jul 15;248(2):171-6. PMID: 15970399.
   
• Urich T, Coelho R, Kletzin A, Frazao C. The sulfur oxygenase reductase from Acidianus ambivalens is an icosatetramer as shown by crystallization and Patterson analysis. Biochim Biophys Acta.2005 Mar 14;1747(2):267-70. PMID: 15698962.
   
• Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol.2004 Aug;53(4):1147-60. PMID: 15306018.
   
• Kletzin A, Urich T, Müller F, Bandeiras TM, Gomes CM. Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. J Bioenerg Biomembr.2004 Feb;36(1):77-91. PMID: 15168612.
   
• Urich T, Bandeiras TM, Leal SS, Rachel R, Albrecht T, Zimmermann P, Scholz C, Teixeira M, Gomes CM, Kletzin A. The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Biochem J.2004 Jul 1;381(Pt 1):137-46. PMID: 15030315.
   
• Bosma GC, Kim J, Urich T, Fath DM, Cotticelli MG, Ruetsch NR, Radic MZ, Bosma MJ. DNA-dependent protein kinase activity is not required for immunoglobulin class switching. J Exp Med.2002 Dec 2;196(11):1483-95. PMID: 12461083.
   
• Kletzin A, Lieke A, Urich T, Charlebois RL, Sensen CW. Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics.1999 Aug;152(4):1307-14. PMID: 10430561.