Michael Wagner

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. doi Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging
    Michael Wagner
    University of Vienna, Department of Microbial Ecology, Vienna 1090, Austria
    Annu Rev Microbiol 63:411-29. 2009
  2. pmc Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats
    Elena V Lebedeva
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 8:e80835. 2013
  3. doi New trends in fluorescence in situ hybridization for identification and functional analyses of microbes
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Curr Opin Biotechnol 23:96-102. 2012
  4. pmc New insights into metabolic properties of marine bacteria encoding proteorhodopsins
    Gazalah Sabehi
    Department of Biology, Technion Israel Institute of Technology, Haifa, Israel
    PLoS Biol 3:e273. 2005
  5. ncbi Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
    Curr Opin Biotechnol 17:83-91. 2006
  6. ncbi Unravelling microbial communities with DNA-microarrays: challenges and future directions
    Michael Wagner
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090, Wien, Austria
    Microb Ecol 53:498-506. 2007
  7. ncbi The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Austria
    Curr Opin Biotechnol 17:241-9. 2006
  8. ncbi Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes
    Michael Wagner
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Curr Opin Microbiol 6:302-9. 2003
  9. pmc Diversity of bacterial endosymbionts of environmental acanthamoeba isolates
    Stephan Schmitz-Esser
    Department of Microbial Ecology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    Appl Environ Microbiol 74:5822-31. 2008
  10. pmc A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
    Sebastian Lücker
    Department of Microbial Ecology, Ecology Centre, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 107:13479-84. 2010

Detail Information

Publications100

  1. doi Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging
    Michael Wagner
    University of Vienna, Department of Microbial Ecology, Vienna 1090, Austria
    Annu Rev Microbiol 63:411-29. 2009
    ..This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago...
  2. pmc Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats
    Elena V Lebedeva
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 8:e80835. 2013
    ..N. uzonensis", which potentially include genetic determinants of ecological niche differentiation. ..
  3. doi New trends in fluorescence in situ hybridization for identification and functional analyses of microbes
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Curr Opin Biotechnol 23:96-102. 2012
    ....
  4. pmc New insights into metabolic properties of marine bacteria encoding proteorhodopsins
    Gazalah Sabehi
    Department of Biology, Technion Israel Institute of Technology, Haifa, Israel
    PLoS Biol 3:e273. 2005
    ..Thus, these novel phototrophs are an unexpectedly large and metabolically diverse component of the marine microbial surface water...
  5. ncbi Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
    Curr Opin Biotechnol 17:83-91. 2006
    ..Isotope arrays have also been developed that exploit the parallel detection offered by DNA microarrays to measure incorporation of labelled substrate into the rRNA of many community members in a single experiment...
  6. ncbi Unravelling microbial communities with DNA-microarrays: challenges and future directions
    Michael Wagner
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090, Wien, Austria
    Microb Ecol 53:498-506. 2007
    ..Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities...
  7. ncbi The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Austria
    Curr Opin Biotechnol 17:241-9. 2006
    ..Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance...
  8. ncbi Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes
    Michael Wagner
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Curr Opin Microbiol 6:302-9. 2003
    ....
  9. pmc Diversity of bacterial endosymbionts of environmental acanthamoeba isolates
    Stephan Schmitz-Esser
    Department of Microbial Ecology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    Appl Environ Microbiol 74:5822-31. 2008
    ..This study provides evidence for the existence of only a small number of phylogenetically well-separated groups of obligate intracellular endosymbionts of acanthamoebae with global distribution...
  10. pmc A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
    Sebastian Lücker
    Department of Microbial Ecology, Ecology Centre, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 107:13479-84. 2010
    ....
  11. doi Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    Anja Spang
    University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Microbiol 18:331-40. 2010
    ....
  12. doi Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila
    Barbara S Sixt
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Proteomics 11:1868-92. 2011
    ..amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation...
  13. pmc Microorganisms with novel dissimilatory (bi)sulfite reductase genes are widespread and part of the core microbiota in low-sulfate peatlands
    Doris Steger
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Appl Environ Microbiol 77:1231-42. 2011
    ....
  14. doi High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont 'Candidatus Thiobios zoothamnicoli'
    Christian Rinke
    Department of Marine Biology, University of Vienna, Vienna, Austria
    FEMS Microbiol Ecol 67:229-41. 2009
    ..niveum with Cand. Thiobios zoothamnicoli is very specific as well as temporally and spatially stable...
  15. pmc Lawsonia intracellularis contains a gene encoding a functional rickettsia-like ATP/ADP translocase for host exploitation
    Stephan Schmitz-Esser
    Universitat Wien, Department für Mikrobielle Okologie, Althanstr 14, A 1090 Vienna, Austria
    J Bacteriol 190:5746-52. 2008
    ..The occurrence of an ATP/ADP translocase in L. intracellularis is explained by a relatively recent horizontal gene transfer event with rickettsiae as donors...
  16. pmc Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
    Marc Mussmann
    Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:16771-6. 2011
    ..These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs...
  17. pmc The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria
    Stephan Schmitz-Esser
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    J Bacteriol 192:1045-57. 2010
    ....
  18. pmc Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility
    Kilian Stoecker
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 76:922-6. 2010
    ..Furthermore, Cy3-doubly labeled probes strongly increase in situ accessibility of rRNA target sites and thus provide more flexibility for probe design...
  19. pmc "Candidatus Thiobios zoothamnicoli," an ectosymbiotic bacterium covering the giant marine ciliate Zoothamnium niveum
    Christian Rinke
    Department of Marine Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Appl Environ Microbiol 72:2014-21. 2006
    ..The taxonomic status "Candidatus Thiobios zoothamnicoli" is proposed for the ectosymbiont of Z. niveum based on its ultrastructure, its 16S rRNA gene, the intergenic spacer region, and its partial 23S rRNA gene sequence...
  20. pmc amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
    Michael Pester
    Departments of Microbial Ecology, Computational Systems Biology Chemical Ecology and Ecosystem Research, University of Vienna, Althanstrasse 14, Vienna, Austria
    Environ Microbiol 14:525-39. 2012
    ....
  21. pmc 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales"
    Alexander Loy
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 71:1373-86. 2005
    ....
  22. pmc Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes
    Alexander Loy
    Department of Microbial Ecology, Universität Wein, Wein, Austria
    Environ Microbiol 11:289-99. 2009
    ....
  23. doi The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations
    Anja Spang
    Department of Genetics in Ecology, University of Vienna, Althanstr 14, 1090, Vienna, Austria
    Environ Microbiol 14:3122-45. 2012
    ..These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers...
  24. pmc Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi
    Georg Mlynek
    Department for Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A 1030 Vienna, Austria
    J Bacteriol 193:2408-17. 2011
    ..Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other nitrite oxidizers...
  25. ncbi 'Candidatus Protochlamydia amoebophila', an endosymbiont of Acanthamoeba spp
    Astrid Collingro
    Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
    Int J Syst Evol Microbiol 55:1863-6. 2005
    ..8%, respectively), observed in this analysis justify its classification in a new genus. Therefore, the name 'Candidatus Protochlamydia amoebophila' is proposed for the designation of the Acanthamoeba sp. symbiont UWE25 (=ATCC PRA-7)...
  26. ncbi Illuminating the evolutionary history of chlamydiae
    Matthias Horn
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Science 304:728-30. 2004
    ..Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells...
  27. pmc Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing
    David Berry
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 110:4720-5. 2013
    ..These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research...
  28. pmc probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007
    Alexander Loy
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, A 1090 Wien, Austria
    Nucleic Acids Res 35:D800-4. 2007
    ..probeBase is freely accessible at http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to probebase@microbial-ecology.net...
  29. pmc Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms
    Harald Ronald Gruber-Vodicka
    Department of Marine Biology, University of Vienna, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:12078-83. 2011
    ....
  30. pmc Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae)
    Elena R Toenshoff
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    ISME J 6:384-96. 2012
    ..adelgidicola' is an evolutionarily young bacteriocyte-associated symbiont, which has been acquired after diversification of adelgids from their aphid sister group...
  31. doi Chlamydia-like bacteria in respiratory samples of community-acquired pneumonia patients
    Susanne Haider
    Department of Microbial Ecology, University of Vienna, Althanstrasse, Vienna, Austria
    FEMS Microbiol Lett 281:198-202. 2008
    ..This study extends previous findings suggesting an association of Chlamydia-like bacteria with respiratory disease, but a causal link between these microorganisms and respiratory tract infections has yet to be established...
  32. ncbi Wastewater treatment: a model system for microbial ecology
    Holger Daims
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Biotechnol 24:483-9. 2006
    ..Here, we consider selected key findings to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology...
  33. pmc Sponge-associated microorganisms: evolution, ecology, and biotechnological potential
    Michael W Taylor
    Department of Microbial Ecology, University of Vienna, Althanstr 14, A 1090 Vienna, Austria
    Microbiol Mol Biol Rev 71:295-347. 2007
    ..We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations...
  34. doi Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae
    Susanne Haider
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Mol Microbiol 77:687-700. 2010
    ..These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms...
  35. pmc An Acanthamoeba sp. containing two phylogenetically different bacterial endosymbionts
    Eva Heinz
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090 Vienna, Austria
    Environ Microbiol 9:1604-9. 2007
    ..Further analysis of this stable relationship should provide novel insights into the complex interactions of intracellular multiple-partner associations...
  36. ncbi Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp
    Astrid Collingro
    Division of Microbial Ecology, Institute for Ecology and Conservation Biology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    Microbiology 151:301-9. 2005
    ....
  37. pmc A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
    Roland Hatzenpichler
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 105:2134-9. 2008
    ..1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA...
  38. ncbi Functional marker genes for identification of sulfate-reducing prokaryotes
    Michael Wagner
    University of Vienna, Department of Microbial Ecology, Wien, Austria
    Methods Enzymol 397:469-89. 2005
    ..9-kb-large dsrAB polymerase chain reaction amplification products, which efficiently increases the chance of retrieving rare and novel dsrAB sequence types from environmental samples...
  39. pmc Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH
    Tatsuhiko Hoshino
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, A 1090 Wien, Austria
    Appl Environ Microbiol 74:5068-77. 2008
    ..These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells)...
  40. doi Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges
    Doris Steger
    Department of Microbial Ecology, University of Vienna, Althanstr 14, A 1090 Vienna, Austria
    Environ Microbiol 10:1087-94. 2008
    ....
  41. pmc Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp
    Jan Dolinsek
    Department of Microbial Ecology, Ecology Centre, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 79:2027-37. 2013
    ..In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage...
  42. pmc The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology
    Michael Pester
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Curr Opin Microbiol 14:300-6. 2011
    ....
  43. ncbi Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, 1090, Vienna, Austria
    Appl Microbiol Biotechnol 75:237-48. 2007
    ..This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions...
  44. doi A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland
    Michael Pester
    Department of Microbial Ecology, University of Vienna, Wien, Austria
    ISME J 4:1591-602. 2010
    ....
  45. ncbi Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization
    Sebastian Lücker
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    J Microbiol Methods 69:523-8. 2007
    ..Additionally, six new FISH probes were developed for major deltaproteobacterial taxa, including a probe trio targeting most Deltaproteobacteria and Gemmatimonadetes...
  46. pmc Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae
    Eva Heinz
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
    BMC Genomics 10:634. 2009
    ..k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila...
  47. pmc Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion
    Doris Steger
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
    PLoS ONE 6:e23727. 2011
    ..In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained...
  48. ncbi Nitrite concentration influences the population structure of Nitrospira-like bacteria
    Frank Maixner
    , , Althanstrasse 14, A 1090 Vienna, Austria
    Environ Microbiol 8:1487-95. 2006
    ..Consistent with the observed localization patterns, a higher nitrite concentration selected for sublineage I but suppressed sublineage II Nitrospira...
  49. pmc Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil
    Maria Tourna
    Department of Genetics in Ecology, University of Vienna, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:8420-5. 2011
    ..Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms...
  50. doi Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies
    Eva Heinz
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Austria
    Proteomics 10:4363-76. 2010
    ..They reveal both fundamental differences and convergent evolution between pathogenic and symbiotic chlamydiae...
  51. pmc Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages
    Alexander Loy
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 70:6998-7009. 2004
    ..These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats...
  52. ncbi Bacterial endosymbionts of free-living amoebae
    Matthias Horn
    Division of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstr 14, 1090 Vienna, Austria
    J Eukaryot Microbiol 51:509-14. 2004
    ..Furthermore, phylogenetic analysis suggested that these mechanisms have been evolved by the ancestor of these amoeba symbionts in interplay with ancient unicellular eukaryotes...
  53. pmc Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the Chlamydiae
    Eva Heinz
    University of Vienna, Department of Microbial Ecology, Althanstrasse 14, A 1090 Vienna, Austria
    J Bacteriol 192:5093-102. 2010
    ..amoebophila shows that this strategy for host cell interaction is conserved among the chlamydiae and is used by chlamydial symbionts and pathogens alike...
  54. doi Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": identification of a catalytically important amino acid residue
    Julius Kostan
    Department for Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A 1030 Vienna, Austria
    J Struct Biol 172:331-42. 2010
    ..Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor...
  55. ncbi Crystal ball. The community level: physiology and interactions of prokaryotes in the wilderness
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Austria
    Environ Microbiol 7:483-5. 2005
  56. pmc Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis
    David Berry
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
    ISME J 6:2091-106. 2012
    ....
  57. pmc Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T
    Michael Pester
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
    J Bacteriol 194:6300-1. 2012
    ....
  58. pmc Barcoded primers used in multiplex amplicon pyrosequencing bias amplification
    David Berry
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Appl Environ Microbiol 77:7846-9. 2011
    ..We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries...
  59. ncbi daime, a novel image analysis program for microbial ecology and biofilm research
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Vienna, Austria
    Environ Microbiol 8:200-13. 2006
    ..This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms...
  60. pmc 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
    Jan Dolinsek
    Department of Microbial Ecology, Vienna Ecology Centre, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 79:1534-44. 2013
    ....
  61. pmc A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations
    Faris Behnam
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 78:5138-42. 2012
    ..Thus, this newly developed technique should be an attractive option for all researchers interested in applying conventional FISH methods for the study of microbial communities...
  62. pmc Sulfate-reducing microorganisms in wetlands - fameless actors in carbon cycling and climate change
    Michael Pester
    Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna Wien, Austria
    Front Microbiol 3:72. 2012
    ..The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change...
  63. pmc probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity
    Alexander Loy
    Department of Microbial Ecology, Universitat Wien, Althanstrasse 14, A 1090 Wien, Austria
    Environ Microbiol 10:2894-8. 2008
    ..Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers...
  64. doi In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs
    Holger Daims
    Department of Microbial Ecology, Ecology Center, University of Vienna, Vienna, Austria
    Methods Enzymol 496:185-215. 2011
    ....
  65. pmc ATP/ADP translocases: a common feature of obligate intracellular amoebal symbionts related to Chlamydiae and Rickettsiae
    Stephan Schmitz-Esser
    Abteilung Mikrobielle Okologie, Universitat Wien, A 1090 Vienna, Austria
    J Bacteriol 186:683-91. 2004
    ....
  66. pmc Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
    Maneesha P Ginige
    Advanced Wastewater Management Centre, The University of Queensland, St Lucia 4072, Queensland, Australia
    Appl Environ Microbiol 70:588-96. 2004
    ..We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges...
  67. ncbi A candidate NAD+ transporter in an intracellular bacterial symbiont related to Chlamydiae
    Ilka Haferkamp
    Pflanzenphysiologie, Universitat Kaiserslautern, D 67653 Kaiserslautern, Germany
    Nature 432:622-5. 2004
    ..This protein acts together with a newly discovered nucleotide transporter and an ATP/ADP translocase, and allows UWE25 to exploit its host cell by means of a sophisticated metabolic parasitism...
  68. ncbi Obligate bacterial endosymbionts of Acanthamoeba spp. related to the beta-Proteobacteria: proposal of 'Candidatus Procabacter acanthamoebae' gen. nov., sp. nov
    Matthias Horn
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Freising, Germany
    Int J Syst Evol Microbiol 52:599-605. 2002
    ....
  69. ncbi 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads
    Ulrike Purkhold
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    Int J Syst Evol Microbiol 53:1485-94. 2003
    ..In addition, 17 environmentally retrieved 16S rRNA gene sequences not assigned previously and all originating exclusively from marine or estuarine sites clearly belong to this lineage...
  70. ncbi Evolutionary history of the genus Listeria and its virulence genes
    Michael W Schmid
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, D 85350 Freising, Germany
    Syst Appl Microbiol 28:1-18. 2005
    ..innocua and L. welshimeri. This hypothesis is also supported by the location of the putative deletion breakpoints of the virulence gene cluster within L. innocua and L. welshimeri...
  71. pmc Amoebae as training grounds for intracellular bacterial pathogens
    Maelle Molmeret
    Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA
    Appl Environ Microbiol 71:20-8. 2005
  72. ncbi Modern scientific methods and their potential in wastewater science and technology
    Peter A Wilderer
    Institute of Water Quality Control and Waste Management, Technical University of Munich, Garching, Germany
    Water Res 36:370-93. 2002
    ..Both the paper and the questionnaire are aimed at encouraging scientists and engineers to enter into an intensive, mutually beneficial dialogue...
  73. pmc Discovery of the novel candidate phylum "Poribacteria" in marine sponges
    Lars Fieseler
    Zentrum für Infektionsforschung, Universitat Wurzburg, D 97070 Wuerzburg, Germany
    Appl Environ Microbiol 70:3724-32. 2004
    ..In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes...
  74. ncbi Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov
    Stefan Spring
    DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D 38124 Braunschweig, Germany
    Int J Syst Evol Microbiol 54:99-106. 2004
    ..This species has been wrongly classified, and it is proposed to reclassify it as Hylemonella gracilis gen. nov., comb. nov. The type strain is ATCC 19624T (=DSM 9158T)...
  75. ncbi Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis
    Markus Schmid
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, D 85350 Freising, Germany
    Water Res 37:2043-52. 2003
    ..This approach revealed shifts in floc volume, heterogeneity, and bacterial and chemical composition according to the settling quality of the flocs...
  76. ncbi Nitrifying and heterotrophic population dynamics in biofilm reactors: effects of hydraulic retention time and the presence of organic carbon
    Regina Nogueira
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, Freising, Germany
    Water Res 36:469-81. 2002
    ..Our results demonstrate that extension of the hydraulic retention time might be insufficient to improve combined nitrification and organic carbon removal in biofilm reactors...
  77. pmc The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function
    Justyna Adamczyk
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    Appl Environ Microbiol 69:6875-87. 2003
    ....
  78. ncbi Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov
    Stefan Spring
    DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D 38124 Braunschweig, Germany
    Int J Syst Evol Microbiol 55:621-9. 2005
    ..spinosa. This species has been misclassified, and it is proposed to transfer it to the new genus Malikia as Malikia spinosa gen. nov., comb. nov. The type strain is ATCC 14606(T) (=DSM 15801(T))...
  79. ncbi The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach
    Stefan Juretschko
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Freising, Germany
    Syst Appl Microbiol 25:84-99. 2002
    ..Taken together, this study provides the first encompassing, high-resolution insight into the in situ composition of the microbial community present in a full-scale, industrial wastewater treatment plant...
  80. pmc Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria
    Markus C Schmid
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Delft, The Netherlands
    Appl Environ Microbiol 71:1677-84. 2005
  81. ncbi Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah)
    Kasper Urup Kjeldsen
    Department of Microbiology, Institute of Biological Sciences, University of Aarhus, Aarhus C, Denmark
    FEMS Microbiol Ecol 60:287-98. 2007
    ....
  82. ncbi Microbial community composition and function in wastewater treatment plants
    Michael Wagner
    Microbial Ecology Group, Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Freising, Germany
    Antonie Van Leeuwenhoek 81:665-80. 2002
    ..Here we provide an overview of what is currently known about the identity and physiology of some of the microbial key players in activated sludge and biofilm systems...
  83. ncbi Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Marc Strous
    Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Nature 440:790-4. 2006
    ..Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility...
  84. doi Microbial diversity and the genetic nature of microbial species
    Mark Achtman
    Environmental Research Institute, University College Cork, Ireland
    Nat Rev Microbiol 6:431-40. 2008
    ..It summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level...
  85. ncbi Nucleic acid-based, cultivation-independent detection of Listeria spp and genotypes of L monocytogenes
    Michael Schmid
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, 85354 Freising, Germany
    FEMS Immunol Med Microbiol 35:215-25. 2003
    ..The amplification of non-specific PCR products from DNA of non-target strains was prevented by adding competitive primers. By applying this method, the rapid and reliable distinction of the three L. monocytogenes genotypes was possible...
  86. pmc Tapping the nucleotide pool of the host: novel nucleotide carrier proteins of Protochlamydia amoebophila
    Ilka Haferkamp
    Pflanzenphysiologie, Technische Universitat Kaiserslautern, Erwin Schrödinger Str, D 67653 Kaiserslautern, Germany
    Mol Microbiol 60:1534-45. 2006
    ..amoebophila in this and previous studies uncovered that these metabolically impaired bacteria are intimately connected with their host cell's metabolism in a surprisingly complex manner...
  87. pmc probeBase: an online resource for rRNA-targeted oligonucleotide probes
    Alexander Loy
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, D 85350 Freising, Germany
    Nucleic Acids Res 31:514-6. 2003
    ..Furthermore, the 'search target site' option provides guidance for the development of new FISH probes...
  88. ncbi Who eats what, where and when? Isotope-labelling experiments are coming of age
    Josh D Neufeld
    Department of Biological Sciences, University of Warwick, Coventry, UK
    ISME J 1:103-10. 2007
    ..We also highlight related isotope techniques that are in continued development and hold promise to transform the way we link phylogeny and function in complex microbial communities...
  89. ncbi A vista for microbial ecology and environmental biotechnology
    Bruce E Rittmann
    Center for Environmental Biotechnology, Arizona State University, USA
    Environ Sci Technol 40:1096-103. 2006
  90. pmc Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    Alexander Loy
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    Appl Environ Microbiol 68:5064-81. 2002
    ....
  91. pmc Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography
    Jeppe Lund Nielsen
    Department of Environmental Engineering, Aalborg University, DK 9000 Aalborg, Denmark
    Appl Environ Microbiol 68:4629-36. 2002
    ..Around 20% were identified as gamma Proteobacteria, and 10% were assigned to the delta subclass of Proteobacteria...
  92. pmc Detection and differentiation of chlamydiae by fluorescence in situ hybridization
    Sven Poppert
    Abteilung für Medizinische Mikrobiologie und Hygiene, Universitat Ulm, Ulm, Germany
    Appl Environ Microbiol 68:4081-9. 2002
    ..In contrast to previously established detection methods for chlamydiae, FISH was not susceptible to false-positive results and allows the detection of all recognized chlamydiae in one single step...
  93. pmc Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors
    Konrad Egli
    Swiss Federal Institute for Environmental Science and Technology EAWAG, CH 8600 Dubendorf, Switzerland
    Appl Environ Microbiol 69:3213-22. 2003
    ..2 day(-1) for the synthetic wastewater reactors). Despite similar reactor performance with respect to chemical parameters, the underlying community structures were different, which may have an influence on stability during perturbations...
  94. pmc Molecular evidence for a uniform microbial community in sponges from different oceans
    Ute Hentschel
    Institut für Molekulare Infektionsbiologie, Universitat Wurzburg, D 97070 Wurzburg, Germany
    Appl Environ Microbiol 68:4431-40. 2002
    ..A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms...
  95. pmc Filamentous "Epsilonproteobacteria" dominate microbial mats from sulfidic cave springs
    Annette Summers Engel
    Research Group for Microbial Geochemistry, Department of Geological Sciences, University of Texas at Austin, Austin, Texas 78712, USA
    Appl Environ Microbiol 69:5503-11. 2003
    ..This study further expands our perceptions of the diversity and geographic distribution of "Epsilonproteobacteria" in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems...
  96. ncbi Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm
    Armin Gieseke
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 5:355-69. 2003
    ..Results of functional and structural analyses are discussed with respect to specific niches of individual populations in this system...
  97. ncbi Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State
    Brett J Baker
    Dept of Biological Sciences, University of Wisconsin Milwaukee, 3209 N Maryland Ave Milwaukee, WI 53211, USA
    Environ Microbiol 5:267-77. 2003
    ..The dsr sequences recovered from the Washington State deep aquifer systems affiliated closely with the South African sequences, suggesting that Gram-positive sulphate-reducing bacteria are widely distributed in the deep subsurface...
  98. ncbi Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge
    Eva Spieck
    Universitat Hamburg, Biozentrum Klein Flottbek, Mikrobiologie, Ohnhorststr 18, D 22609 Hamburg, Germany
    Environ Microbiol 8:405-15. 2006
    ..The enriched strain is provisionally classified as 'Candidatus Nitrospira defluvii'...
  99. ncbi Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea
    Julie Leloup
    Max Planck Institute for Marine Microbiology, Department of Biogeochemistry, Celsiustr 1, 28395 Bremen, Germany
    Environ Microbiol 9:131-42. 2007
    ..Although these novel SRM were also abundant in sulfate-poor, methanogenic areas of the Black Sea sediment, their activities and possibly very versatile metabolic capabilities remain subject of further study...
  100. ncbi Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function
    Wei E Huang
    Biodiversity and Ecosystem Function Group, Molecular Microbial Ecology Section, Centre for Ecology and Hydrology Oxford, Mansfield Road, Oxford, OX1 3SR, UK
    Environ Microbiol 9:1878-89. 2007
    ....