Department of Ecogenetics and Systems Biology - Division of Archaea Biology and Ecogenomics


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Urich

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Dipl.-Biol. Dr. Tim Urich

Room: 1.118
1090 Wien, Althanstraße 14 (UZA I)
T: +43-1-4277-76513
F: +43-1-4277-76513
tim.urich(at)univie.ac.at


RESEARCH INTERESTS

Microbiologist with background in environmental microbiology, physiology, biochemistry and structural biology. Research interest is focused on the interplay between the structure and function of biological systems at various scales, ranging from key-metabolic enzymes to complex natural microbial communities and global biogeochemical cycles.

RESEARCH AREAS

1) The structure and function of soil microbial communities

  • Ammonia oxidizing archaea: physiology and role in soil microbial communities
  • “eco-systems biology” and foodwebs
  • Inter-domain trophic interactions during plant litter degradation ( MICDIF)
  • The influence of heavy metals on the structure and function of soil microbial communities ( Neiker)


2) Arctic Microbes and Greenhouse Gases

  • Key functions and microorganisms in carbon cycling of arctic peatlands ( Molecular Environments)
  • The role of microorganisms in carbon cycling of arctic cryoturbated permafrost soils ( CryoCarb)
  • Diversity, abundance and activity of ammonia-oxidizing archaea in high-arctic soils.


3) Microbes in Macrobes


4) Chemolithoautotrophic microorganisms in volcanic environments

  • The structure and function of the microbiota at the northernmost hydrothermal vents on Earth ( CGB)
  • The microbiota in arctic thermal springs of Iceland and Svalbard
  • Sulfur oxidizers in marine and terrestrial volcanic environments ( CGB)


Collaborations

Prof. Mette Svenning (University of Tromso, Norway)
Dr. Ida Steen (University of Bergen, Norway)
Prof. Vigdis Torsvik (University of Bergen, Norway)
Prof. Lise Ovreas (University of Bergen, Norway)
Prof. Andreas Richter (University of Vienna, Austria)
Dr. Jiri Barta and Prof. Hana Santruckova (University of Southern Bohemia, Czech Republic)
Prof. Daniel Huson (University of Tübingen, Germany)
Prof. Peter Frenzel (MPI for Terrestrial Microbiology, Marburg, Germany)
Dr. Carlos Garbisu and Dr. Lur Epelde (NEIKER, Bilbao, Spain)
Prof. George Kowalchuk (NIOO, Netherlands)
Morton Poulsen (University of Arhus, Denmark)
Prof. Michael Schloter (Helmholtz Center Munich, Germany)
Dr. Jack Gilbert and Prof. Janet Jannson ( Earth Microbiome Project)


Member of National and international research networks
InflammoBiota
CryoCarb
MicDIF
MeCoMeCon
TerraGenome

CURRICULUM VITAE



PROFESSIONAL AND UNIVERSITY EDUCATION

2008-present University assistant at the Department of Ecogenomics and System Biology, Archaea Biology & Ecogenomics Division, University of Vienna, Austria

2005-2008 Post-doc in the group of Prof. Dr. Christa Schleper, University of Vienna, Austria (until 12/2007 at University of Bergen, Norway)

2001-2005 PhD student at Darmstadt University of Technology, Darmstadt, Germany. Thesis evaluated with summa cum laude (best 10 percent).
Supervisors: Dr. Arnulf Kletzin and Prof. Dr. Felicitas Pfeifer

2001 Diploma in Biology at Darmstadt University of Technology, Darmstadt, Germany. Supervisors: Dr. Arnulf Kletzin and Prof. Dr. Felicitas Pfeifer

1993-2001 Study of Biology, Darmstadt University of Technology, Darmstadt, Germany


PUBLICATIONS

Peer-reviewed
41.
Gentsch N, Mikutta R, Shibistova O, Wild B, Schnecker J, Richter A, Urich T, Šantrucková H, Barta J, Lashchinskiy N, Müller C, Fuß R, Guggenberger G (2015) Properties and bioavailability of particulate and mineral-associated organic matter in Arctic permafrost soils, Lower Kolyma Region, Russia. European Journal of Soil Science, Early View. doi: 10.1111/ejss.12269.

40. Tveit A,
Urich T, Frenzel P, Svenning MM (2015) Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proceedings of the National Academy of Sciences of the United States of America, Early Edition. doi/10.1073/pnas.1420797112.

39. Geisen S, Tveit A, Clark I, Richter A, Svenning MM, Bonkowski M,
Urich T (2015) Metatranscriptomic census of active protists in soils. ISME Journal. 27 March 2015 [e-pub]; doi: 10.1038/ismej.2015.30.

38. Gentsch N, Mikutta R, Alves RJE, Barta J, Capek P, Gittel A, Hugelius G, Kuhry P, Lashchinskiy N, Palmtag J, Richter A, Šantrucková H, Schnecker J, Shibistova O,
Urich T, Wild B, Guggenberger G (2015) Storage and transformation of organic matter fractions in cryoturbated permafrost soils across the Siberian Arctic. Biogeosciences Discuss 12: 2697–2743. doi:10.5194/bgd-12-2697-2015.

37. Epelde L, Lanzén A, Blanco F,
Urich T, Garbisu C (2015) Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine. FEMS Microbiol Ecology 91(1): 1-11. doi: http://dx.doi.org/10.1093/femsec/fiu007.

36. Gittel A, Barta J, Lacmanova I, Schnecker J, Wild B, Capek P, Kaiser C, Torsvik V, Richter A, Schleper C,
Urich T (2014) Site- and horizon-specific pattern of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Frontiers in Microbiology - Terrestrial Microbiology 5: 541. doi: 10.3389/fmicb.2014.00541.

35. Tveit A,
Urich T, Svenning MM (2014) Metatranscriptomic analysis of Arctic peat soil microbiota. Applied and Environmental Microbiology 80(18): 5761. doi:10.1128/AEM.01030-14.

34. Rauch I, Hainzl E, Rosebrock F, Heider S, Scwab C, Berry D, Stoiber D, Wagner M, Schleper C, Loy A,
Urich T, Müller M, Strobl B, Kenner L, Decker T (2014) Type I interferons have opposing effects during the emergence and recovery phases of colitis. European Journal of Immunology 44(9): 2749-2760. doi: 10.1002/eji.201344401.

33. Schnecker J, Wild B, Hofhansl F, Alves R, Bárta J, Čapek P, Fuchslueger L, Gentsch N, Gittel A, Guggenberger G, Hofer A, Kienzl S, Knoltsch A, Lashchinskiy N, Mikutta R, Šantrůčková H, Shibistova O, Takriti M,
Urich T, Weltin G, Richter A (2014) Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils. PLoS One 9(4): e94076. doi: 10.1371/journal.pone.0094076.

32. Wild B, Schnecker J, Alves R, Barsukov P, Bárta J, Čapek P, Gentsch N, Gittel A, Guggenberger G, Lashchinskiy N, Mikutta R, Rusalimova O, Šantrůčková H, Shibistova O,
Urich T, Watzka M, Zrazhevskaya G, Richter A (2014) Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. Soil Biology & Biochemistry 75: 143-151. doi: 10.1016/j.soilbio.2014.04.014.

31. 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 16(9): 2699-2710. doi: 10.1111/1462-2920.12283.

30. Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, März J, Lashchinskiy N, Čapek P, Šantrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik V, Schleper C, Urich T (2014) Distinct microbial communities associated with buried soils in the Siberian tundra. ISME Journal 8: 841-853. doi: 10.1038/ismej.2013.219.

29. 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 16(8): 2514-2524. doi: 10.1111/1462-2920.12392.

28. 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 (2014) Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME Journal 8: 1101-1114. doi: 10.1038/ismej.2013.223.

27. Schwab C, Tveit A, Schleper C, Urich T (2014) Gene expression of lactobacilli in murine forestomach biofilms. Microbial Biotechnology 7(4): 347-359. doi: 10.1111/1751-7915.12126.

26. 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.

25. Wild B, Schnecker J, Bárta J, Capek P, Guggenberger G, Hofhansl F, Hugelius G, Kaiser C, Kuhry P, Lashchinsky N, Mikutta C, Mooshammer M, Palmtag J, Šantrucková H, Shibistova O,
Urich T, Zimov SA, Richter A (2013) From proteins to nitrate: Nitrogen dynamics in organic, cryoturbated and mineral horizons of tundra soil. Soil Biology and Biochemistry 67(100): 85-93. doi: 10.1016/j.soilbio.2013.08.004.

24. Shen T, Stieglmeier M, Dai J,
Urich T, Schleper C (2013) Responses of the terrestrial ammonia oxidizing archaeon Ca. Nitrososphaera viennensis and the ammonia oxidizing bacterium Nitrosospira multiformis to nitrification inhibitors. FEMS Microbiology Letters 344(2): 121-129. doi: 10.1111/1574-6968.12164.

23. Alves RJ, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C,
Urich T (2013) Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. ISME Journal 7(8): 1620-1631. doi: 10.1038/ismej.2013.35.

22. Poulsen M, Schwab C, Jensen B, Engberg R, Spang A, Canibe N, Hřjberg O, Milinovich G, Fragner L, Schleper C, Weckwerth W, Lund P, Schramm A,
Urich T (2013) Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. nature communications 4: 1428. doi: 10.1038/ncomms2432.

21. Tveit A, Schwacke R, Svenning MM, Urich T (2013) Organic carbon transformations in high-Arctic peat soils: Key functions and microorganisms. ISME Journal 7(2): 299-311. doi: 10.1038/ismej.2012.99.

20.
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 (2012) Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis. ISME Journal 6(11): 2091-2106. doi: 10.1038/ismej.2012.39.

19. Lanzén A, Jřrgensen SL, Huson DH, Garfer M, Grindhaug SH, Jonassen I, Řvreĺs L,
Urich T (2012): CREST – Classification Resources for environmental Sequence Tags. PLOS One 7(11): e49334. doi:10.1371/journal.pone.0049334.

18. Radax R, Rattei T, Lanzén A, Bayer C, Rapp HT,
Urich T, Schleper C (2012) Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community. Environmental Microbiology 14(5): 1308-24. doi: 10.1111/j.1462-2920.2012.02714.x.

17. 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): 665-78. doi: 10.1089/ast.2010.0551.

16. 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. doi: 10.1111/j.1574-6941.2011.01138.x.

15. Tourna M, Stiegelmayer M,
Urich T, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences U S A 108(20): 8420-5. doi: 10.1073/pnas.1013488108.

14. Veith A,
Urich T, Seyfarth K, Protze J, Frazăo C and Kletzin A (2011) Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of Acidianus ambivalens. Frontiers in Microbiology 2: 37. doi: 10.3389/fmicb.2011.00037

13. 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 Supplements 1: S21. doi:10.1186/1471-2105-12-S1-S21.

12.
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. doi: 10.1371/journal.pone.0002527.

11. 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): 167-74.

10. Prosinecki V, Botelho HM, Francese S, Mastrobuoni G, Moneti G, Urich T, Kletzin A, Gomes GM (2006) A proteomic approach towards the selection of proteins with enhanced intrinsic conformational stability. Journal of Proteome Research 5(10): 2720-6.

9. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC and Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-9.

8. Urich T, Gomes CM, Kletzin A and Frazăo C (2006) X-ray structure of a self-compartmentalising sulfur-cycle metalloenzyme. Science 311: 996-1000.

7. Albers SV, Jonuscheit M, Becker S, Urich T, Kletzin A, Tampé R, Driessen AJM and Schleper C (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus with an inducible gene expression system. Applied and Environmental Microbiology 72(1): 102-111.

6. Urich T, Kroke A, Bauer C, Seyfarth K, Reuff M and Kletzin A (2005) Identification of core active site residues of the sulfur oxygenase reductase from Acidianus ambivalens by site-directed mutagenesis. FEMS Microbiology Letters 248: 171-176.

5. Urich T, Coelho R, Kletzin A and Frazăo C (2005) The sulfur oxygenase reductase from Acidianus ambivalens is an icosatetramer as shown by crystallization and patterson analysis. Biochimica et Biophysica Acta 1747(2): 267-270.

4. Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM and Kletzin A (2004) Coupling of the pathway of sulfur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulfate:quinone oxidoreductase. Molecular Microbiology 53(4): 1147-60.

3. Urich T, Bandeiras TM, Leal SS, Rachel R, Albrecht T, Zimmermann P, Scholz C, Teixeira M, Gomes CM and Kletzin A (2004) The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Biochemical Journal 381: 137-46.

2. Kletzin A, Urich T, Müller F, Bandeiras TM and Gomes CM (2004) Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. Journal of Bioenergetics and Biomembranes 36: 77-91. Review.

1. Kletzin A, Lieke A, Urich T, Charlebois RL and Sensen CW (1999) Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics 152: 1307–1314.

Book chapters
1. Urich T and Schleper C (2011) The “double RNA” approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics. In: Handbook of Molecular Microbial Ecology, edited by F. de Bruin. ISBN-10: 0-470-92418-7.

Other publications


Urich T (2006) Elegante Katalyse im Nano-Kompartiment. Biospektrum 04.2006.

Urich T (2005) The sulfur oxygenase reductase from Acidianus ambivalens. Functional and structural characterisation of a sulfur-disproportionating enzyme. PhD-thesis, Department of Biology, Darmstadt University of Technology, Darmstadt, Germany.

Urich T (2001) A novel metabolic pathway in Archaea. Anaerobic sulfur disproport-ionation in Acidianus ambivalens and Sulfurisphaera sp. (German). Diplomarbeit (Master thesis equivalent), Department of Biology, Darmstadt University of Technology. Darmstadt, Germany.


FELLOWSHIPS AND AWARDS

EMBO long-term post-doctoral fellowship (2006-2008).

Marie Curie Host Fellowship for research visits at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal (2002-2004; 9-months grant; contract-No. HPMT-CT-2000-00045).

VAAM Promotionspreis from the German Microbiological Society "Vereinigung für Allgemeine und Angewandte Mikrobiologie" (VAAM): Award for the PhD thesis (2006).

Poster Award: 3rd price at the meeting "Archaea - the first generation", Hohenkammer, Germany (2005).

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