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Peer-reviewed publications



Kitzinger K, Marchant HK, Bristow LA, Herbold CW, Padilla CC, Kidane AT, Littmann S, Daims H, Pjevac P, Stewart FJ, Wagner M, Kuypers MMM. (20XX) Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean. Manuscript submitted to Nature Communications

Weber PM, Moessel F*, Paredes GF*, Viehboeck T, Fischer N, Bulgheresi S. (2019) Symbionts maintain their chromosome orientation toward their host through a bidimensional segregation mode. Current Biology, in revision. *These authors contributed equally.

Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken DRichter A, Wanek W. (20XX) Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. Soil Biology and Biochemistry OA: CC BY-NC-ND



Baltar F, Bayer B, Bednarsek N, Deppeler S, Escribano R, Gonzalez CE, Hansman RL, Mishra RK, Moran MA, Repeta DJ, Robinson C, Sintes E, Tamburini C, Valentin LE, Herndl GJ (2019). Towards integrating evolution, metabolism and climate change studies of marine ecosystems. Trends in Ecology & Evolution. doi: 10.1016/j.tree.2019.07.003

Bayer B, Hansman R, Bittner M, Ortega-Noriega BE, Niggemann J, Dittmar T, Herndl GJ. (2019) Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ Microbioldoi:10.1111/1462-2920.14755

Bayer B, Pelikan C, Bittner M, Reinthaler T, Könneke M, Herndl GJ, Offre P. (2019) Proteomic response of three marine ammonia-oxidizing archaea towards hydrogen peroxide and their metabolic interactions with a heterotrophic alphaproteobacterium. mSystems 4(4): e00181-19. doi.org/10.1128/mSystems.00181-19. Gold OA.

Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M, Herndl GJ (2019). Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. Int J System Evol Microbiol 7:1892-1902. doi: 10.1099/ijsem.0.003360

Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C. (2019) Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability. Front Microbiol. 168. doi.org/10.3389/fmicb.2019.00168. Gold OA

Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MM, Bristow LA. (2019) Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nature Microbiology 4(2): 234-243. doi.org/10.1038/s41564-018-0316-2 PMID: 30531977. Green OA

Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R. (2019) An automated Raman-based platform for the sorting of live cells by functional properties. Nature Microbiology. 4: 1035–1048. doi.org/10.1038/s41564-019-0394-9. No OA

Lukumbuzya M, Schmid M, Pjevac P, Daims H. (2019) A multicolor fluorescence in situ hybridization approach using an extended set of fluorophores to visualize microorganisms. Frontiers Microbiol. 10: 1383. doi.org/10.3389/fmicb.2019.01383. Gold OA

Muck S, De Corte D, Clifford E, Bayer B, Herndl GJ, Sintes E (2019). Niche differentiation of aerobic and anaerobic ammonia oxidizers in a high latitude deep oxygen minimum zone. Front Microbiol 10:2141. doi: 10.3389/fmicb.2019.02141

Noll L, Zhang S, Zheng Q, Hu Y, Wanek W (2019) Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content. Soil Biology and Biochemistry 2019, 133: 37-49. doi.org/10.1016/j.soilbio.2019.02.016. OA: CC BY

Noll L, Zhang S, Wanek W (2019) Novel high-throughput approach to determine key processes of soil organic nitrogen cycling: Gross protein depolymerization and microbial amino acid uptake. Soil Biology and Biochemistry 2019, 130: 73-81. doi.org/10.1016/j.soilbio.2018.12.005. OA: CC BY-NC-ND

Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. (2019) Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Frontiers in Microbiology 10. doi.org/10.3389/fmicb.2019.00909. Gold OA

Preiner J, Wienkoop S, Weckwerth W, Oburger E. (2019) Molecular Mechanisms of Tungsten Toxicity Differ for Glycine max Depending on Nitrogen Regime. Frontiers in Plant Science 10: 1–23. doi.org/10.3389/fpls.2019.00367. Gold OA

Schneider S, Harant D, Bachmann G, Nägele T, Lang I, Wienkoop S. (2019) Subcellular Phenotyping: Using Proteomics to Quantitatively Link Subcellular Leaf Protein and Organelle Distribution Analyses of Pisum sativum Cultivars. Front. Plant Sci. 10: 638. doi.org/10.3389/fpls.2019.00638. Gold OA

Schneider S, Schintlmeister A, Becana M, Wagner M, Woebken D, Wienkoop S. (2019) Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis. Plant, Cell Environ. 42(4): 1180-1189. doi.org/10.1111/pce.13481

Schneider S, Turetschek R, Wedeking R, Wimmer MA, Wienkoop S. (2019) A Protein-Linger Strategy Keeps the Plant On-Hold After Rehydration of Drought-Stressed Beta vulgaris. Front. Plant Sci. 10: 381. doi.org/10.3389/fpls.2019.00381

Steiner PA, Sintes E, Simó R, De Corte D, Marić Pfannkuchen D, Ivančić I, Najdek M, Herndl GJ. (2019) Seasonal dynamics of marine snow-associated and free-living demethylating bacterial communities in the coastal northern Adriatic Sea. EMIRdoi.org/10.1111/1758-2229.12783

Steiner PA, De Corte D, Geijo J, Mena C, Yokokawa T, Rattei THerndl GJ. (2019) Highly variable mRNA half-life time within marine prokaryotic taxa and functional genes. Submitted to EMIhttps://doi.org/10.1111/1462-2920.14737

Zhang S, Zheng Q, Noll L, Hu Y, Wanek W (2019) Environmental effects on soil microbial nitrogen use efficiency are controlled by allocation of organic nitrogen to microbial growth and regulate gross N mineralization. Soil Biology and Biochemistry 2019, 135: 304-315. doi.org/10.1016/j.soilbio.2019.05.019. OA: CC BY-NC-ND

Zheng Q, Hu Y, Zhang S, Noll L, Boeckle T, Richter A, Wanek W (2019) Growth explains microbial carbon use efficiency across soils differing in land use and geology. Soil Biology and Biochemistry 128: 45-55. doi.org/10.1016/j.soilbio.2018.10.006. OA: CC BY-NC-ND



Abby SS1, Melcher M1, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C. (2018) Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. Front. Microbio. 9(28). doi.org/10.3389/fmicb.2018.00028. Gold OA 1contributed equally

Ghatak A, Chaturvedi P, Weckwerth W (2018) Metabolomics in Plant Stress Physiology. In RK Varshney, MK Pandey & A Chitikineni (eds), Plant Genetics and Molecular Biology. Advances in Biochemical Engineering/ Biotechnology 164: 187-236, Springer, Cham. doi.org/10.1007/10_2017_55 (Book Chapter)

Hannemann L, Lucaciu CR, Lucaciu CRSharma S, Rattei TRattei T, Mayer KFX, Gierl A, Frey M (2018) A promiscuous beta-glucosidase is involved in benzoazinoid deglycosylation in Lamium galeobodolon. Phytochemistry 156: 224-233. doi.org/10.1016/j.phytochem.2018.10.012.

Haselmair-Gosch C, Miosic S, Nitarska D, Roth BL, Walliser B, Paltram R, Lucaciu RC, Eidenberger L, Rattei T, Olbricht K, Stich K, Halbwirth H. (2018) Great Cause-Small Effect: Undeclared Genetically Engineered Orange Petunias Harbor an Inefficient Dihydroflavonol 4-Reductase. Frontiers in Plant Science 9: 149. doi.org/10.3389/fpls.2018.00149

Hu Y, Zheng Q, Zhang S, Noll L, Wanek W (2018) Significant release and microbial utilization of amino sugars and D-amino acid enantiomers from microbial cell wall decomposition in soils. Soil Biology and Biochemistry 2018, 123: 115-125. doi.org/10.1016/j.soilbio.2018.04.024. OA: CC BY-NC-ND

Jegadeesan S, Chaturvedi P, Ghatak A, Pressman E, Meir S, Faigenboim A, Rutley N, Beery A, Harel A, Weckwerth W, Firon N (2018) Proteomics of heat-stress and ethylene-mediated thermotolerance mechanisms in tomato pollen grains. Frontiers in Plant Science 871: 1558. doi.org/10.3389/fpls.2018.01558.

Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold CW, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H. (2018) Characterization of the first “Candidatus Nitrotoga” isolate reveals metabolic versatility and separate evolution of widespread nitrite-oxidizing bacteria. mBio 9(4): 01186-18. doi.org/10.1128/mBio.01619-18 PMCID: PMC6123444. Gold OA

Lepuschitz S, Huhulescu S, Hyden P, Springer B, Rattei T, Allerberger F, Mach RL, Ruppitsch W. (2018) Characterization of a community-acquired-MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates. Sci Rep 1: 9467. doi.org/10.1038/s41598-018-27781-8

Pende N, Wang J1Weber PM1, Verheul J, Kuru E, Simon KMR, Leisch N, VanNieuwenhze MS, Brun YV, den Blaauwen T2Bulgheresi S2 (2018). Host-polarized cell growth in animal symbionts. Current Biology 28(7): 1039-1051. doi.org/10.1016/j.cub.2018.02.028. Hybrid OA 1contributed equally 2contributed equally



Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, De La Torre JR, Becker KW, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. (2017) Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 19(7): 2681-2700. doi.org/10.1111/1462-2920.13759. Hybrid OA

Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R (2017) Proteomics survey of Solanaceae family: Current status and challenges ahead. Journal of Proteomics 169: 41-57. doi.org/10.1016/j.jprot.2017.05.016

Ghatak A, Chaturvedi P, Weckwerth W (2017) Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. Frontiers in Plant Science 8: 00757. doi.org/10.3389/fpls.2017.00757

Ott E, Fuchs F, Moeller R, Hemmersbach R, Kawaguchi Y, Yamagishi A, Weckwerth W, Milojevic T. (2017) Molecular response of Deinococcus radiodurans to simulated microgravity explored by proteometabolomic approach. PLoS One 12(12): e0189381. doi.org/10.1371/journal.pone.0189381 

Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. (2017) Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLOS ONE 12, e0189381. doi.org/10.1371/journal.pone.0189381. Gold OA



Bayer B, Vojvoda J, Offre P, Alves RJE, Garcia JHL, Volland JM, Srivastava A, Schleper C, Herndl GJ. (2016) Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. ISME J 10(5): 1051–1063. doi.org/10.1038/ismej.2015.200 PMCID: PMC4839502. Hybrid OA

Chaturvedi P, Ghatak A, Weckwerth W (2016) Pollen proteomics: from stress physiology to developmental priming. Plant Reproduction 29(1-2): 119 doi.org/10.1007/s00497-016-0283-9



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