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A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms.

Lukumbuzya M, Schmid M, Pjevac P, Daims H.

Front Microbiol. 2019 Jun 19;10:1383. doi: 10.3389/fmicb.2019.01383. eCollection 2019.


Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata.

Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold C, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H.

Nat Commun. 2019 Apr 23;10(1):1836. doi: 10.1038/s41467-019-09790-x.


Publisher Correction: An automated Raman-based platform for the sorting of live cells by functional properties.

Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R.

Nat Microbiol. 2019 May;4(5):902-903. doi: 10.1038/s41564-019-0446-1.


An automated Raman-based platform for the sorting of live cells by functional properties.

Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R.

Nat Microbiol. 2019 Jun;4(6):1035-1048. doi: 10.1038/s41564-019-0394-9. Epub 2019 Mar 18. Erratum in: Nat Microbiol. 2019 May;4(5):902-903.


The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge.

Sakoula D, Nowka B, Spieck E, Daims H, Lücker S.

Stand Genomic Sci. 2018 Nov 22;13:32. doi: 10.1186/s40793-018-0338-7. eCollection 2018.


Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.

Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H.

MBio. 2018 Jul 10;9(4). pii: e01186-18. doi: 10.1128/mBio.01186-18.



Daims H, Wagner M.

Trends Microbiol. 2018 May;26(5):462-463. doi: 10.1016/j.tim.2018.02.001. Epub 2018 Feb 28.


Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.

Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, Kirkegaard RH, de la Torre JR, Daims H, Wagner M.

Front Microbiol. 2018 Feb 14;9:193. doi: 10.3389/fmicb.2018.00193. eCollection 2018.


Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

Hausmann B, Pjevac P, Schreck K, Herbold CW, Daims H, Wagner M, Loy A.

Genome Announc. 2018 Jan 25;6(4). pii: e01524-17. doi: 10.1128/genomeA.01524-17.


Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus.

Füssel J, Lücker S, Yilmaz P, Nowka B, van Kessel MAHJ, Bourceau P, Hach PF, Littmann S, Berg J, Spieck E, Daims H, Kuypers MMM, Lam P.

Sci Adv. 2017 Nov 1;3(11):e1700807. doi: 10.1126/sciadv.1700807. eCollection 2017 Nov.


Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle.

Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M.

Nature. 2017 Sep 14;549(7671):269-272. doi: 10.1038/nature23679. Epub 2017 Aug 23.


AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment.

Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H.

Front Microbiol. 2017 Aug 4;8:1508. doi: 10.3389/fmicb.2017.01508. eCollection 2017.


Crenothrix are major methane consumers in stratified lakes.

Oswald K, Graf JS, Littmann S, Tienken D, Brand A, Wehrli B, Albertsen M, Daims H, Wagner M, Kuypers MM, Schubert CJ, Milucka J.

ISME J. 2017 Sep;11(9):2124-2140. doi: 10.1038/ismej.2017.77. Epub 2017 Jun 6.


Giant viruses with an expanded complement of translation system components.

Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T.

Science. 2017 Apr 7;356(6333):82-85. doi: 10.1126/science.aal4657.


Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification.

Hemp J, Lücker S, Schott J, Pace LA, Johnson JE, Schink B, Daims H, Fischer WW.

ISME J. 2016 Nov;10(11):2669-2678. doi: 10.1038/ismej.2016.56. Epub 2016 Apr 19.


A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria.

Daims H, Lücker S, Wagner M.

Trends Microbiol. 2016 Sep;24(9):699-712. doi: 10.1016/j.tim.2016.05.004. Epub 2016 Jun 6. Review.


Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH.

Hüpeden J, Wegen S, Off S, Lücker S, Bedarf Y, Daims H, Kühn C, Spieck E.

Appl Environ Microbiol. 2016 Jan 8;82(6):1838-45. doi: 10.1128/AEM.03163-15.


Complete nitrification by Nitrospira bacteria.

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M.

Nature. 2015 Dec 24;528(7583):504-9. doi: 10.1038/nature16461. Epub 2015 Nov 26.


Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.

Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H.

Proc Natl Acad Sci U S A. 2015 Sep 8;112(36):11371-6. doi: 10.1073/pnas.1506533112. Epub 2015 Aug 24.


Cyanate as an energy source for nitrifiers.

Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, von Bergen M, Lagkouvardos I, Karst SM, Galushko A, Koch H, Berry D, Daims H, Wagner M.

Nature. 2015 Aug 6;524(7563):105-8. doi: 10.1038/nature14856. Epub 2015 Jul 29.


Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages.

Nowka B, Off S, Daims H, Spieck E.

FEMS Microbiol Ecol. 2015 Mar;91(3). pii: fiu031. doi: 10.1093/femsec/fiu031. Epub 2014 Dec 20.


Dimeric chlorite dismutase from the nitrogen-fixing cyanobacterium Cyanothece sp. PCC7425.

Schaffner I, Hofbauer S, Krutzler M, Pirker KF, Bellei M, Stadlmayr G, Mlynek G, Djinovic-Carugo K, Battistuzzi G, Furtmüller PG, Daims H, Obinger C.

Mol Microbiol. 2015 Jun;96(5):1053-68. doi: 10.1111/mmi.12989. Epub 2015 Apr 6.


Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes.

Hofbauer S, Hagmüller A, Schaffner I, Mlynek G, Krutzler M, Stadlmayr G, Pirker KF, Obinger C, Daims H, Djinović-Carugo K, Furtmüller PG.

Arch Biochem Biophys. 2015 May 15;574:36-48. doi: 10.1016/ Epub 2015 Jan 17.


Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation.

Nowka B, Daims H, Spieck E.

Appl Environ Microbiol. 2015 Jan;81(2):745-53. doi: 10.1128/AEM.02734-14. Epub 2014 Nov 14.


Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants.

Lücker S, Schwarz J, Gruber-Dorninger C, Spieck E, Wagner M, Daims H.

ISME J. 2015 Mar;9(3):708-20. doi: 10.1038/ismej.2014.158. Epub 2014 Sep 2.


Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation.

Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lücker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H.

Science. 2014 Aug 29;345(6200):1052-4. doi: 10.1126/science.1256985.


Functionally relevant diversity of closely related Nitrospira in activated sludge.

Gruber-Dorninger C, Pester M, Kitzinger K, Savio DF, Loy A, Rattei T, Wagner M, Daims H.

ISME J. 2015 Mar;9(3):643-55. doi: 10.1038/ismej.2014.156. Epub 2014 Aug 22.


Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization.

Remus-Emsermann MN, Lücker S, Müller DB, Potthoff E, Daims H, Vorholt JA.

Environ Microbiol. 2014 Jul;16(7):2329-40. doi: 10.1111/1462-2920.12482. Epub 2014 May 12.


Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.

Sorokin DY, Vejmelkova D, Lücker S, Streshinskaya GM, Rijpstra WI, Sinninghe Damsté JS, Kleerbezem R, van Loosdrecht M, Muyzer G, Daims H.

Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):1859-65. doi: 10.1099/ijs.0.062232-0. Epub 2014 Feb 26.


Three-dimensional stratification of bacterial biofilm populations in a moving bed biofilm reactor for nitritation-anammox.

Almstrand R, Persson F, Daims H, Ekenberg M, Christensson M, Wilén BM, Sörensson F, Hermansson M.

Int J Mol Sci. 2014 Jan 29;15(2):2191-206. doi: 10.3390/ijms15022191.


Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity.

Hofbauer S, Gysel K, Bellei M, Hagmüller A, Schaffner I, Mlynek G, Kostan J, Pirker KF, Daims H, Furtmüller PG, Battistuzzi G, Djinović-Carugo K, Obinger C.

Biochemistry. 2014 Jan 14;53(1):77-89. doi: 10.1021/bi401042z. Epub 2014 Jan 3.


Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigor'eva NV, Galushko A, Schmid M, Palatinszky M, Le Paslier D, Daims H, Wagner M.

PLoS One. 2013 Nov 20;8(11):e80835. doi: 10.1371/journal.pone.0080835. eCollection 2013.


NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.

Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, Nowka B, Richter A, Spieck E, Lebedeva E, Loy A, Wagner M, Daims H.

Environ Microbiol. 2014 Oct;16(10):3055-71. doi: 10.1111/1462-2920.12300. Epub 2013 Nov 8.


New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms.

Almstrand R, Daims H, Persson F, Sörensson F, Hermansson M.

Appl Environ Microbiol. 2013 Oct;79(19):5978-87. doi: 10.1128/AEM.01727-13. Epub 2013 Jul 26.


Thermophilic biological nitrogen removal in industrial wastewater treatment.

Lopez-Vazquez CM, Kubare M, Saroj DP, Chikamba C, Schwarz J, Daims H, Brdjanovic D.

Appl Microbiol Biotechnol. 2014 Jan;98(2):945-56. doi: 10.1007/s00253-013-4950-6. Epub 2013 May 9.


Colonization of freshwater biofilms by nitrifying bacteria from activated sludge.

Mußmann M, Ribot M, von Schiller D, Merbt SN, Augspurger C, Karwautz C, Winkel M, Battin TJ, Martí E, Daims H.

FEMS Microbiol Ecol. 2013 Jul;85(1):104-15. doi: 10.1111/1574-6941.12103. Epub 2013 Apr 2.


The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.

Lücker S, Nowka B, Rattei T, Spieck E, Daims H.

Front Microbiol. 2013 Feb 21;4:27. doi: 10.3389/fmicb.2013.00027. eCollection 2013.


Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp.

Dolinšek J, Lagkouvardos I, Wanek W, Wagner M, Daims H.

Appl Environ Microbiol. 2013 Mar;79(6):2027-37. doi: 10.1128/AEM.03408-12. Epub 2013 Jan 18.


Structure and community composition of sprout-like bacterial aggregates in a Dinaric Karst subterranean stream.

Kostanjšek R, Pašić L, Daims H, Sket B.

Microb Ecol. 2013 Jul;66(1):5-18. doi: 10.1007/s00248-012-0172-1. Epub 2013 Jan 13.


Depletion of unwanted nucleic acid templates by selective cleavage: LNAzymes, catalytically active oligonucleotides containing locked nucleic acids, open a new window for detecting rare microbial community members.

Dolinsek J, Dorninger C, Lagkouvardos I, Wagner M, Daims H.

Appl Environ Microbiol. 2013 Mar;79(5):1534-44. doi: 10.1128/AEM.03392-12. Epub 2012 Dec 21.


Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases with diverse subunit and oligomeric structures.

Hofbauer S, Bellei M, Sündermann A, Pirker KF, Hagmüller A, Mlynek G, Kostan J, Daims H, Furtmüller PG, Djinović-Carugo K, Oostenbrink C, Battistuzzi G, Obinger C.

Biochemistry. 2012 Nov 27;51(47):9501-12. doi: 10.1021/bi3013033. Epub 2012 Nov 14.


Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.

Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WI, Damsté JS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MC, Daims H.

ISME J. 2012 Dec;6(12):2245-56. doi: 10.1038/ismej.2012.70. Epub 2012 Jul 5.


Impact of subunit and oligomeric structure on the thermal and conformational stability of chlorite dismutases.

Hofbauer S, Gysel K, Mlynek G, Kostan J, Hagmüller A, Daims H, Furtmüller PG, Djinović-Carugo K, Obinger C.

Biochim Biophys Acta. 2012 Sep;1824(9):1031-8. doi: 10.1016/j.bbapap.2012.05.012. Epub 2012 Jun 6.


Co-localized or randomly distributed? Pair cross correlation of in vivo grown subgingival biofilm bacteria quantified by digital image analysis.

Schillinger C, Petrich A, Lux R, Riep B, Kikhney J, Friedmann A, Wolinsky LE, Göbel UB, Daims H, Moter A.

PLoS One. 2012;7(5):e37583. doi: 10.1371/journal.pone.0037583. Epub 2012 May 24.


Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers.

Mussmann M, Brito I, Pitcher A, Sinninghe Damsté JS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen PH, Müller A, Daims H, Wagner M, Head IM.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16771-6. doi: 10.1073/pnas.1106427108. Epub 2011 Sep 19.


Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi.

Mlynek G, Sjöblom B, Kostan J, Füreder S, Maixner F, Gysel K, Furtmüller PG, Obinger C, Wagner M, Daims H, Djinović-Carugo K.

J Bacteriol. 2011 May;193(10):2408-17. doi: 10.1128/JB.01262-10. Epub 2011 Mar 25.


Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring.

Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S, Maixner F, Lipski A, Daims H, Spieck E.

FEMS Microbiol Ecol. 2011 Feb;75(2):195-204. doi: 10.1111/j.1574-6941.2010.01006.x. Epub 2010 Dec 8.


Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time.

Hall EK, Singer GA, Pölzl M, Hämmerle I, Schwarz C, Daims H, Maixner F, Battin TJ.

ISME J. 2011 Feb;5(2):196-208. doi: 10.1038/ismej.2010.115. Epub 2010 Aug 12.


A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.

Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damsté JS, Spieck E, Le Paslier D, Daims H.

Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13479-84. doi: 10.1073/pnas.1003860107. Epub 2010 Jul 12.

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