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

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List of publicationswith the Division's affiliation:

Zhang MM, Alves RJE, Zhang DD, Han LL, He JZ, Li-Mei Zhang LM. (2017) Time-dependent shifts in populations and activity of bacterial and archaeal ammonia oxidizers in response to liming in acidic soils. Soil Biology and Biochemistry 112: 77-89.

Kerou M, Offre P, Valledor L, Abby S, Melcher M, Nagler M, Weckwerth W, Schleper C (2016) Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proceedings of the National Academy of Sciences of the United States of America (49): E7937-E7946. Doi: 10.1073/pnas.1601212113.

Jung M-Y, Kim J-G, Damste JS, Rijpstra WIC, Madsen EL, Kim S-J, Hong H, Si O-J, Kerou M, Schleper C, Rhee S-K (2016) A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. Environmental Microbiology Reports 8(6): 983-992. doi: 10.1111/1758-2229.12477.

Becker KW, Elling FJ, Yoshinaga MY,
Söllinger A, Urich T, Hinrichts KU (2016) Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens. Applied and Environmental Microbiology 82(15): 4505-16. doi: 10.1128/AEM.00772-16.

Abby S, Cury J, Guglielmini J, Neron B, Touchon M, Rocha EPC (2016) Identification of protein secretion systems in bacterial genomes. Scientific reports 6: 23080. doi: 10.1038/srep23080.

Zebec Z, Zink IA, Kerou M, Schleper C (2016) Efficient CRISPR-Mediated Post-Transcriptional Gene Silencing in a Hyperthermophilic Archaeon Using Multiplexed crRNA Expression. G3-Genes Genomes Genetics 6(10): 3161-3168. doi: 10.1534/g3.116.032482.

Taubner RS
, Rittmann SK (2016) Method for Indirect Quantification of CH4 via H2O Production Using Hydrogenotrophic Methanogens. Frontiers in Microbiology 7: 532. doi: 10.3389/fmicb.2016.00532.

Wild B, Gentsch N, Capek P, Diakova K,
Alves RJE, Barta J, Gittel A, Hugelius G, Knoltsch A, Kuhry P, Lashchinskiy N, Mikutta R, Palmtag J, Schleper C, Schnecker J, Shibistova O, Takriti M, Torsvik V, Urich T, Watzka M, Santruckova H, Guggenberger G, Richter A (2016) Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils. Scientific Reports 6: 25607. doi:10.1038/srep25607.

Kozlowski JA, Stieglmeier M, Schleper C, Klotz MG, Stein LY (2016) Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME Journal 10(8): 1836-1845. doi: 10.1038/ismej.2016.2.

Nesme J, Achouak W, Agathos S, Bailey M, Baldrian P, Brunel D, Frostegĺrd Ĺ, Heulin T, Jansson J, Jurkevitch E, Kruus K, Kowalchuk G, Lagares A, Lappin-Scott H, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold D, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch L, Schloter M,
Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sřrensen J, Sřrensen S, Tebbe C, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu Y-G, Vogel T, Simonet P (2016) Back to the Future of Soil Metagenomics. Frontiers in Microbiology 7:73. doi: 10.3389/fmicb.2016.00073.

Abby S
, Cury J, Guglielmini J, Néron B, Touchon M, Rocha E (2016) Identification of protein secretion systems in bacterial genomes. Scientific Reports 6: 23080. doi: 10.1038/srep23080.

Söllinger A
, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T (2016) Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiology Ecology 92(1). doi: 10.1093/femsec/fiv149.

Bayer B, Vojvoda J, Offre P, Alves RJE, Elisabeth NH, Garcia JA, Volland JM, Srivastava A, Schleper C, Herndl GJ (2016) Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. The ISME Journal 10: 1051-1063. doi: 10.1038/ismej.2015.200.

Bulgheresi S (2016) Bacterial cell biology outside the streetlight. Environmental Microbiology 18(8): 2305-2318. doi: 10.1111/1462-2920.13406

Bulgheresi S (2016) All the microbiology nematodes can teach us. FEMS Microbiology Ecology 92(2): fiw007. Doi: 10.1093/femsec/fiw007.

Petersen JM, Kemper A, Gruber-Vodicka H, Cardini U, van der Geest M, Kleiner M,
Bulgheresi S, Mußmann M, Herbold C, Seah B, Antony CP, Liu D, Belitz A, Weber M (2016) Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation. Nature Microbiology 2: 16195. Doi: 10.1038/nmicrobiol.2016.195.

Noel SJ, Hřjberg O,
Urich T, Poulsen M (2016) Draft genome sequence of Candidatus Methanomethylophilus sp. 1R26, enriched from bovine rumen; a methanogenic archaeon belonging to the Methanomassiliicoccales order. Genome announcements 4(1): e01734-15. doi:10.1128/genomeA.01734-15.

Leisch N, Pende N, Weber PM, Gruber-Vodicka HR, Verheul J, Vischer NO, Abby S, Geier B, den Blaauwen T, Bulgheresi S (2016) Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra. Nature Microbiology 2: 16182. Doi: 10.1038/nmicrobiol.2016.182.

Bulgheresi S (2016) I, microbe. Nature Microbiology 1(8): 16117. Doi: 10.1038/nmicrobiol.2016.117.

Beulig F, Urich T, Nowak M, Gleixner G, Trumbore S, Gilfillan G, Fjelland K, Küsel K (2016) Altered carbon turnover processes and microbiomes in soils under longterm extremely high CO2 exposure. Nature Microbiology 1: 15025. doi: 10.1038/nmicrobiol.2015.25.

Taubner RS,
Schleper C, Firneis MG, Rittmann SK (2015) Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies. Life (Basel) 5(4):1652-86. doi: 10.3390/life5041652.

Rittmann SK (2015) A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems. Advances in Biochemical Engineering / Biotechnology 151:117-35. doi: 10.1007/978-3-319-21993-6_5. Review.

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 (2015) Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis. Frontiers in Microbiology 6:1408. doi: 10.3389/fmicb.2015.01408.

Hainzl E, Rauch I, Heider S, Berry D,
Schwab C, Lassnig C, Loy A, Urich T, Wagner M, Schleper C, Kenner L, Decker T, Strobl B, Müller M (2015) Intestinal epithelial cell tyrosine kinase 2 transduces interleukin-22 signals to protect from acute colitis. The Journal of Immunology 195(10): 5011–5024. doi: 10.4049/jimmunol.1402565.

Geisen S, Rosengarten J, Koller R, Mulder C,
Urich T, Bonkowski M (2015) Pack Hunting by a Common Soil Amoeba on Nematodes. Environmental Microbiology, Early View. June 16. doi: 10.1111/1462-2920.12949.

Yang K, Park CG, Cheong C,
Bulgheresi S, Zhang S, Zhang P, He Y, Jiang L, Huang H, Ding H, Wu Y, Wang S, Zhang L, Li A, Xia L, Bartra SS, Plano GV, Skurnik M, Klena JD, Chen T (2015) Host Langerin (CD207) is a receptor for Yersinia pestis phagocytosis and promotes dissemination. Immunology & Cell Biology 93(9): 815-24. doi:10.1038/icb.2015.46.

Rittmann SK, Seifert A, Herwig C (2015) Essential prerequisites for successful bioprocess development of biological CH4 production from CO2 and H2. Critical Reviews in Biotechnology 35(2):141-51. doi: 10.3109/07388551.2013.820685.

Montanaro J, Inic-Kanada A, Ladurner A, Stein E, Belij S, Bintner N, Schlacher S, Schuerer N, Mayr UB, Lubitz W, Leisch N, Barisani-Asenbauer T (2015) Escherichia coli Nissle 1917 bacterial ghosts retain crucial surface properties and express chlamydial antigen: an imaging study of a delivery system for the ocular surface. Drug design development and therapy 9: 3741-3754. doi: 10.2147/DDDT.S84370.

Čapek P, Diakova K, Dickopp JE, Bárta J, Wild B, Schnecker J, Alves RJE, Aiglsdorfer S, Guggenberger G, Gentsch N, Hugelius G, Lashchinskiy N, Gittel A, Schleper C, Mikutta R, Palmtag J, Shibistova O, Urich T, Richter A, Šantrůčková H (2015) The effect of warming on the vulnerability of subducted organic carbon in arctic soils. Soil Biology & Biochemistry 90: 19-29. doi:10.1016/j.soilbio.2015.07.013.

Wild B, Schnecker J, Knoltsch A, Takriti M, Mooshammer M, Gentsch N, Mikutta R,
Alves RJE, Gittel A, Lashchinskiy N, Richter A (2015) Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in Western Siberia. Global Biogeochemical Cycles 29: 567–582. doi:10.1002/2015GB005084.

Spang A, Saw JH, Jřrgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R,
Schleper C, Guy L, Ettema TJ (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521(7551): 173-179. doi:10.1038/nature14447.

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 66(4): 722-734. doi: 10.1111/ejss.12269.

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 112(19): E2507-E2516. doi:10.1073/pnas.1420797112.

Taylor AE, Taylor K, Tennigkeit B, Palatinszky M, Stieglmeier M, Myrold DD, Schleper C, Wagner M, Bottomley PJ (2015) Inhibitory effects of c2 to c10 1-alkynes on ammonia oxidation in two nitrososphaera species. Applied and environmental microbiology 81(6): 1942-1948. doi: 10.1128/AEM.03688-14.

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 29:–4542. doi:10.5194/bgd-12-2697-2015.

Schnecker J, Wild B, Takriti M,
Alves RJE, Gentsch N, Gittel A, Hofer A, Klaus K, Knoltsch A, Lashchinskiy N, Mikutta R, Richter A (2015) Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia. Soil Biology and Biochemistry 83: 106-115. doi:10.1016/j.soilbio.2015.01.016.

Geisen S, Tveit A, Clark I, Richter A, Svenning MM, Bonkowski M,
Urich T (2015) Metatranscriptomic census of active protists in soils. The ISME Journal 9: 2178-2190.

Recuenco-Munoz L,
Offre P, Valledor L, Lyon D, Weckwerth W, Wienkoop S (2015) Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass Western approach. Journal of Proteomics 113: 143-153. doi: 10.1016/j.jprot.2014.09.026.

Rittmann S, Lee H, Lim J, Kim T, Kang S (2015) One-carbon substrate-based biohydrogen production: Microbes, mechanism, and productivity. Biotechnology Advances 33(1): 165-177. doi:10.1016/j.biotechadv.2014.11.004.

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:

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.

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.

Offre P, Kerou M, Spang A, Schleper C (2014) Variability of the transporter gene complement in ammonia-oxidizing archaea. Trends in Microbiology 22(12): 665-675. doi: 10.1016/j.tim.2014.07.007.

Pende N, Leisch N, Gruber-Vodicka H, Heindl N, Ott J, den Blaauwen T, Bulgheresi S (2014) Size-independent symmetric division in extraordinarily long cells. Nature Communications 5: 4803. doi:10.1038/ncomms5803.

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 (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.

Stieglmeier M, Klingl A, Alves RJE, Rittmann SK, Melcher M, Leisch N, Schleper C (2014) Nitrosophaera viennensis sp. nov., an aerobic and mesophilic ammonia-oxidizing archaeon from soil and member of the archaeal phylum Thaumarchaeota. International Journal of Systematic and Ecolutionary Microbiology 64(Pt 8): 2738-52. doi: 10.1099/ijs.0.063172-0.

Hanak AM, Nagler M, Weinmaier T, Sun X, Fragner L, Schwab C, Rattei T, Ulrich K, Ewald D, Engel M, Schloter M, Bittner R, Schleper C, Weckwerth W (2014) Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus. Genome Announcements. March/April 2014 2(2): e00276-14. doi: 10.1128/genomeA.00276-14.

Schnecker J, Wild B, Hofhansl F, Alves RJE, 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.

Wild B, Schnecker J, Alves RJE, 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.

Petersen S, Hřjberg O, Poulsen M,
Schwab C, Eriksen J (2014) Methanogenic community changes, and emissions of methane and other gases, during storage of acidified and untreated pig slurry. Journal of Applied Microbiology 117(1): 160-172. doi: 10.1111/jam.12498.

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.

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.

Stieglmeier M, Alves RJE, Schleper C
(2014) The Phylum Thaumarchaeota. In: The Prokaryotes - Other Major Lineages of Bacteria and The Archaea. Rosenberg, E., DeLong E.F., Lory, S., Stackebrandt, E., Thompson F. (Eds.) 4th ed. 2014 Springer-Verlag Berlin Heidelberg. doi: 10.1007/978-3-642-38954-2_338.

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.

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.

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.

Stieglmeier M, Mooshammer M, Kitzler B, Wanek W, Zechmeister-Boltenstern S, Richter A, Schleper C (2014) Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME Journal 8(5): 1135-1146. doi: 10.1038/ismej.2013.220.

Zebec Z, Manica A, Zhang J, White M, Schleper C (2014) CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus. Nucleic Acids Research 42(8):5280-5288. doi:10.1093/nar/gku161.

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.

Rittmann SKR, Holubar P (2014) Rapid extraction of total RNA from an anaerobic sludge biocoenosis. Folia Microbiologica: 127-132. doi: 10.1007/s12223-013-0274-2.


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.

Moissl-Eichinger C, Pukall R, Probst A, Stieglmeier M, Schwendner P, Mora M, Barczyk S, Bohmeier M, Rettberg P (2013) Lessons Learned from the microbial analysis of the Herschel spacecraft during assembly, integration and testing operations. Astrobiology 13(12): 1125-1139.

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

Manica A, Zebec Z, Steinkellner J, Schleper C (2013) Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus. Nucleic Acids Research 41(22): 10509-10517. doi: 10.1093/nar/gkt767.

Märtens B, Manoharadas S, Hasenöhrl D,
Manica A, Bläsi U (2013) Antisense regulation by transposon-derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Embo Reports 14(6): 527-533.

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.

Albers SV, Forterre P, Pranighvili D,
Schleper C (2013) The legacy of Carl Woese and Wolfram Zillig: from phylogeny to landmark discoveries. Nature Reviews Microbiology 11: 713-719.

Offre P, Spang A, Schleper C (2013) Archaea in Biogeochemical Cycles. Annual Review of Microbiology 67: 437-457.
Reproduced with permission from the Annual Review of Microbiology, Volume 67 (c) 2013 by Annual Reviews. Download.

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.

Manica A, Schleper C (2013) CRISPR-mediated defense mechanisms in the hyperthermophilic archaeal genus Sulfolobus. RNA Biology 10(5): 671-678. doi: 10.4161/rna.24154.

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.

Alves RJE, 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. .

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. .

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.

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.


Murfin K, Dillman A, Foster J,
Bulgheresi S, Slatko B, Sternberg P, Goodrich-Blair H (2012) Nematode-Bacterium Symbioses-Cooperation and Conflict Revealed in the "Omics" Age. Biological Bulletin 223(1): 85-102.

Lanzčn 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: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.

Leisch N
, Verheul J, Heindl NR, Gruber-Vodicka HR, Pende N, den Blaauwen T, Bulgheresi S (2012) Growth in width and FtsZ ring longitudinal positioning in a gammaproteobacterial symbiont. Current Biology 22(19): R831-832.

Spang A
, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M (2012) The genome of the ammonia-oxidizing Candidatus Nitrosopshaera gargensis: Insights into metabolic versatility and environmental adaptations. Environmental Microbiology 14(12): 3122-3145. DOI: 10.1111/j.1462-2920.2012.02893.x.

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.

Sinninghe Damsté JS, Rijpstra WI, Hopmans EC, Jung MY, Kim JG, Rhee SK,
Stieglmeier M, Schleper C (2012) Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids of group I.1a and I.1b thaumarchaeota in soil. Applied and Environmental Microbiology 78(19): 6866-6874.

Dirks U, Gruber-Vodicka H,
Leisch N, Bulgheresi S, Egger, B, Ladurner P, Ott J (2012) Bacterial Symbiosis Maintenance in the Asexually Reproducing and Regenerating Flatworm Paracatenula galateia. PLoS ONE 7(4): e34709.

Bartossek R
, Spang A, Weidler G, Lanzen A, Schleper C (2012) Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group. Frontiers in Microbiology 3: 208. doi: 10.3389/fmicb.2012.00208.

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.

Radax R, Rattei T, Lanzen 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): 1308-1324. doi: 10.1111/j.1462-2920.2012.02714.x.

Radax R, Hoffmann F, Rapp HT, Leininger S, Schleper C (2012) Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges. Environmental Microbiology 14(4): 909-923. doi: 10.1111/j.1462-2920.2011.02661.x.


Gruber-Vodicka HR, Dirks U, Leisch N, Baranyi C, Stoecker K, Bulgheresi S, Heindl NR, Horn M, Lott C, Loy A, Wagner M, Ott, J (2011) Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms. Proceedings of the National Academy of Sciences of the United States of America 108(29):12078-12083.

Ajon M,
Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJM, Grogan DW, Albers SV, Schleper C (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Molecular Microbiology 82(4): 807-817.

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.

Reeve JN,
Schleper C (2011) Archaea: very diverse, often different but never bad?Current Opinion in Microbiology 14(3): 271-273.

Pester M,
Schleper C, Wagner M (2011) The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology 14(3): 300-306.

Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences of the United States of America 108(20): 8420-8425.

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. Front. Microbio. 2:37. doi: 10.3389/fmicb.2011.00037.

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.

Bulgheresi S (2011) Calling the roll on Laxus oneistus immune defense molecules. Symbiosis. 2011 Nov; 55(3):127-135.

Schmitz-Esser S, Penz T,
Spang A, Horn M (2011) A bacterial genome in transition – An exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus. BMC Bioinformatics 11(1) Article number 270.

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.

Svenning MM, Hestnes AG, Wartiainen I, Stein, LY, Klotz MG, Kalyuzhnaya MG,
Spang A, Bringel F, Vuilleumier S, Lajus A, Médigue C, Bruce DC, Cheng JF, Goodwin L, Ivanova N, Han J, Han CS, Hauser L, Held B, Land ML, Lapidus A, Lucas S, Nolan M, Pitluck S, Woyke T (2011) Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96. Journal of Bacteriology 193(22):6418-6419.

Manica A, Zebec Z, Teichmann D, Schleper C (2011) In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Molecular Microbiology 80(2): 481-491.

Krupovic M,
Spang A, Gribaldo S, Forterre P, Schleper C (2011) A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea. Biochemical Society Transactions 39(1): 82-88.

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.

Heindl NR, Gruber-Vodicka HR, Bayer C, Luecker S, Ott JA, Bulgheresi S (2011) First detection of thiotrophic symbiont phylotypes in the pelagic marine environment. FEMS Microbiology Ecology 77 (1): 223-227.

Bulgheresi S, Gruber-Vodicka HR, Heindl NR, Dirks U, Kostadinova M, Breiteneder H, Ott JA (2011) Sequence variability of the pattern recognition receptor Mermaid mediates specificity of marine nematode symbioses. ISME Journal 5(6): 986-998.


Bright M,
Bulgheresi S (2010) Microbial symbiont transmission. Nature Reviews Microbiology 8(3): 218-230.

Schleper C (2010) Ammonia oxidation: different niches for bacteria and archaea? ISME Journal 4(9): 1092-1094.

Rae RG,
Tourna M, Wilson MJ (2010) The slug parasitic nematode Phasmarhabditis hermaphrodita associates with complex and variable bacterial assemblages that do not affect its virulence. Journal of Invertebrate Pathology 104(3): 222-226.

Schleper C, Nicol GW (2010) Ammonia-oxidising archaea-physiology, ecology and evolution. Advances in Microbial Physiology 57: 1-47.

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.

Bright M,
Bulgheresi S (2010) A complex journey: transmission of microbioal symbionts. Nature Reviews Microbiology 8(3): 218-230.

Tourna M, Freitag TE, Prosser JI (2010) Stable isotope probing analysis of interactions between ammonia oxidizers. Applied and Environmental Microbiology 76(8): 2468-2477.

Zhang LM,
Offre PR, He JZ, Verhamme DT, Nicol GW, Prosser JI (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Proceedings of the National Academy of Sciences of the United States of America 107(40): 17240-17245.

Milinovich GJ, Klieve AV, Pollitt CC, Trott DJ (2010) Microbial Events in the Hindgut During Carbohydrate-induced Equine Laminitis. Veterinary Clinics of North America - Equine Practice 26(1): 79-94.


Zaparty M, Esser D, Gertig S, Haferkamp P, Kouril T,
Manica A, Pham TK, Reimann J, Schreiber K, Sierocinski P, Teichmann D, van Wolferen M, von Jan M, Wieloch P, Albers SV, Driessen AJ, Klenk HP, Schleper C, Schomburg D, van der Oost J, Wright PC, Siebers B (2009) "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus. Extremophiles 14(1): 119-142.

Redder P, Peng X, Brügger K, Shah SA, Roesch F, Greve B, She Q,
Schleper C, Forterre P, Garrett RA, Prangishvili D (2009) Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environmental Microbiology 11(11): 2849-2862.

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.

Albers SV, Birkeland NK, Driessen AJ, Gertig S, Haferkamp P, Klenk HP, Kouril T,
Manica A, Pham TK, Ruoff P, Schleper C, Schomburg D, Sharkey KJ, Siebers B, Sierocinski P, Steuer R, van der Oost J, Westerhoff HV, Wieloch P, Wright PC, Zaparty M SulfoSYS (Sulfolobus Systems Biology) (2009) Towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochemical Society Transactions 37(Pt 1): 58-64.

Fröls S, White MF, Schleper C (2009) Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochemical Society Transactions 37(Pt 1): 36-41. Review.

Bayer C, Heindl RN, Rinke C, Lücker S, Ott JA, Bulgheresi S (2009) Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea. Environmental Microbiology reports 1(2): 136-144.

Mittal R,
Bulgheresi S, Emami C, Prasadarao NV (2009) Enterobacter sakazakii targets DC-SIGN to induce immunosuppressive responses in dendritic cells by modulating MAP kinases. The Journal of Immunology. 183(10): 6588-6599.


Zhang P, Skurnik M, Zhang S, Schwartz O, Kalyanasundaram R,
Bulgheresi S, He JJ, Klena JD, Hinnebusch B, Chen T (2008) Human dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin (CD209) is a receptor for Yersinia pestis that promotes phagocytosis by dendritic cells. Infection and Immunity 76(5): 2070-2079.

Nabatov AA, de Jong MAWP, de Witte L,
Bulgheresi S, Geijtenbeek THB (2008) C-type lectin Mermaid inhibits dendritic cell mediated Hiv-1 transmission to CD4+ T cell. Virology. 378(2): 323-328.

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

Tourna M, Freitag TE, Nicol GW, Prosser JI (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environmental Microbiology 10(5): 1357-1364.

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.

Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema, Driessen AJM, Schleper C, Albers SV (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Molecular Microbiololy 70(4): 938-52.

Nicol GW, Leininger S,
Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 10(11): 2966-2978.

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.


Fröls S, Gordon PM, Panlilio MA, Duggin ID, Bell SD, Sensen CW, Schleper C (2007) Response of the hyperthermophilic Archaeon Sulfolobus solfataricus to UV damage. Journal of Bacteriology 189: 8708-8718.

Fröls S, Gordon PM, Panlilio MA, Schleper C, Sensen CW (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365: 48-59.

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