R Amann

Summary

Affiliation: Max Planck Institute for Marine Microbiology
Country: Germany

Publications

  1. ncbi Utilization of tmRNA sequences for bacterial identification
    W Schönhuber
    Lehrstuhl für Mikrobielle Ökologie, Universitat Konstanz, Fach M654, Universitatsstrasse 10, D 78457 Konstanz, Germany
    BMC Microbiol 1:20. 2001
  2. ncbi Graphical representation of ribosomal RNA probe accessibility data using ARB software package
    Yadhu Kumar
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    BMC Bioinformatics 6:61. 2005
  3. ncbi The identification of microorganisms by fluorescence in situ hybridisation
    R Amann
    Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359, Bremen, Germany
    Curr Opin Biotechnol 12:231-6. 2001
  4. ncbi Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology
    R Amann
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    FEMS Microbiol Rev 24:555-65. 2000
  5. ncbi Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    Rudolf Amann
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
    Nat Rev Microbiol 6:339-48. 2008
  6. ncbi In situ methods for assessment of microorganisms and their activities
    R Amann
    Junior Group for Molecular Ecology, Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D 28359 Bremen, Germany
    Curr Opin Microbiol 1:352-8. 1998
  7. ncbi Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor
    A Schramm
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 64:3480-5. 1998
  8. ncbi Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea
    Tina Lösekann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, 28359 Bremen, Germany
    Appl Environ Microbiol 73:3348-62. 2007
  9. ncbi Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea
    Niculina Musat
    Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
    Syst Appl Microbiol 29:333-48. 2006
  10. ncbi Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes
    B M Fuchs
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 66:3603-7. 2000

Detail Information

Publications106 found, 100 shown here

  1. ncbi Utilization of tmRNA sequences for bacterial identification
    W Schönhuber
    Lehrstuhl für Mikrobielle Ökologie, Universitat Konstanz, Fach M654, Universitatsstrasse 10, D 78457 Konstanz, Germany
    BMC Microbiol 1:20. 2001
    ..To overcome these limitations, we examined the use of tmRNA for in situ identification. In E. coli, this stable 363 nucleotides long RNA is encoded by the ssrA gene, which is involved in the degradation of truncated proteins...
  2. ncbi Graphical representation of ribosomal RNA probe accessibility data using ARB software package
    Yadhu Kumar
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    BMC Bioinformatics 6:61. 2005
    ..Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments...
  3. ncbi The identification of microorganisms by fluorescence in situ hybridisation
    R Amann
    Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359, Bremen, Germany
    Curr Opin Biotechnol 12:231-6. 2001
    ..Over the past year there have been a number of methodological developments in this area and new applications of FISH in microbial ecology and biotechnology have been reported...
  4. ncbi Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology
    R Amann
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    FEMS Microbiol Rev 24:555-65. 2000
    ..In order to speed up the transformation of microbial ecology from a mostly descriptive to a hypothesis-driven, experimental science more intense use must be made of the taxonomic precision and quantitativeness of rRNA-targeted probes...
  5. ncbi Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    Rudolf Amann
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
    Nat Rev Microbiol 6:339-48. 2008
    ....
  6. ncbi In situ methods for assessment of microorganisms and their activities
    R Amann
    Junior Group for Molecular Ecology, Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D 28359 Bremen, Germany
    Curr Opin Microbiol 1:352-8. 1998
    ..The various new methods on their own bear high potential but it is the combination of studies on structure and function of microbial communities that will yield the most detailed insights in the way microorganisms operate in nature...
  7. ncbi Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor
    A Schramm
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 64:3480-5. 1998
    ..A second, smaller, morphologically and genetically different population of Nitrospira spp. was restricted to the outer nitrifying zones...
  8. ncbi Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea
    Tina Lösekann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, 28359 Bremen, Germany
    Appl Environ Microbiol 73:3348-62. 2007
    ..Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs...
  9. ncbi Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea
    Niculina Musat
    Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
    Syst Appl Microbiol 29:333-48. 2006
    ..2005)...
  10. ncbi Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes
    B M Fuchs
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 66:3603-7. 2000
    ..We conclude that helpers can open inaccessible rRNA regions for FISH with oligonucleotide probes and will thereby further improve the applicability of this technique for in situ identification of microorganisms...
  11. ncbi The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions
    R Rossello-Mora
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Syst Appl Microbiol 22:237-48. 1999
    ..Their detection in high numbers in the field may indicate recent deposition events...
  12. ncbi On the occurrence of anoxic microniches, denitrification, and sulfate reduction in aerated activated sludge
    A Schramm
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 65:4189-96. 1999
    ....
  13. ncbi Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru margin
    Anna Blazejak
    Max Planck Institute of Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
    Appl Environ Microbiol 71:1553-61. 2005
    ..Such a phylogenetically diverse yet highly specific and stable association in which multiple bacterial phylotypes coexist within a single host has not been described previously for marine invertebrates...
  14. ncbi Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria
    F O Glöckner
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Appl Environ Microbiol 66:5053-65. 2000
    ....
  15. ncbi Microbial manganese and sulfate reduction in Black Sea shelf sediments
    B Thamdrup
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Appl Environ Microbiol 66:2888-97. 2000
    ....
  16. ncbi Microenvironments and distribution of nitrifying bacteria in a membrane-bound biofilm
    A Schramm
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Environ Microbiol 2:680-6. 2000
    ..can out-compete Nitrosospira and Nitrospira spp. at high substrate and oxygen concentrations. Additionally, they suggest microaerophilic behaviour of yet uncultured Nitrospira sp. as a factor of its environmental competitiveness...
  17. ncbi Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine Arctic sediments
    K Sahm
    Molecular Ecology Group, Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 65:3976-81. 1999
    ..Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments...
  18. ncbi Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria
    Shi Yan
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D 28359, Germany
    Syst Appl Microbiol 32:124-39. 2009
    ..An analysis of the frequencies of NOR5/OM60 16S rRNA genes in the Global Ocean Survey datasets provided further support for a marine cosmopolitan occurrence of NOR5/OM60, and a clear preference for coastal marine waters...
  19. ncbi Flow sorting of marine bacterioplankton after fluorescence in situ hybridization
    Raju Sekar
    , Celsiusstrasse 1, D-28359 Bremen, Germany
    Appl Environ Microbiol 70:6210-9. 2004
    ..This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats...
  20. ncbi Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system
    Dagmar Woebken
    Max Planck Institute for Marine Microbiology, Molecular Ecology, Celsiusstr 1, 28359 Bremen, Germany
    Appl Environ Microbiol 73:4648-57. 2007
    ....
  21. ncbi Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques
    B M Fuchs
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Environ Microbiol 2:191-201. 2000
    ..Furthermore, it was demonstrated that the combination of flow cytometric analysis and sorting combined with FISH and DGGE analysis presented a fairly rapid method of analysing the taxonomic composition of marine bacterioplankton...
  22. ncbi Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm
    A Gieseke
    Molecular Ecology Group, Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 67:1351-62. 2001
    ..Nitrite-oxidizing bacteria belonged exclusively to the genus Nitrospira and could be assigned to a 16S rRNA sequence cluster also found in other sequencing batch systems...
  23. ncbi Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments
    Katrin Knittel
    Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
    Int J Syst Evol Microbiol 55:781-6. 2005
    ..The names Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov. are proposed for SVAL-E(T) (=ATCC 700955(T)=DSM 13458(T)) and SVAL-D(T) (=ATCC 700954(T)=DSM 13453(T)), respectively...
  24. ncbi Distinct flavobacterial communities in contrasting water masses of the north Atlantic Ocean
    Paola R Gómez-Pereira
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    ISME J 4:472-87. 2010
    ..Our results suggest that different marine flavobacterial clades have distinct niches and different life strategies...
  25. ncbi Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton
    Jörg Peplies
    Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
    Syst Appl Microbiol 27:573-80. 2004
    ..For small clusters of high sequence similarity and single strains, up to 8 times more discriminating binding sites were provided by the 23S rRNA...
  26. ncbi Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture
    J Pernthaler
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Appl Environ Microbiol 67:2145-55. 2001
    ..The community structure of pelagic microbial assemblages can therefore be influenced by the taxonomic composition of the predator community...
  27. ncbi Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the beta-subclass of Proteobacteria
    R Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Environ Microbiol 1:145-57. 1999
    ....
  28. ncbi Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors
    A Schramm
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 65:3690-6. 1999
    ..Therefore, it was possible for the first time to estimate the cell-specific activity of Nitrosospira spp. and hitherto-uncultured Nitrospira-like bacteria in situ...
  29. ncbi Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm
    N Dubilier
    Max Planck Institute of Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Nature 411:298-302. 2001
    ..Thus, these symbionts do not compete for resources but rather share a mutalistic relationship with each other in an endosymbiotic sulphur cycle, in addition to their symbiotic relationship with the oligochaete host...
  30. ncbi Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean
    Martha Schattenhofer
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Environ Microbiol 11:2078-93. 2009
    ..Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance...
  31. ncbi Bacterioplankton diversity and community composition in the Southern Lagoon of Venice
    Francesca Simonato
    Max Planck Institute for Marine Microbiology MPIMM, Celsiusstrasse 1, D 28359 Bremen, Germany
    Syst Appl Microbiol 33:128-38. 2010
    ..Interestingly, the alphaproteobacterial SAR11 clade and related clusters were also present in high abundances at the inlet and within the lagoon, which was indicative of inflow of water from the open sea...
  32. ncbi A marine microbial consortium apparently mediating anaerobic oxidation of methane
    A Boetius
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Nature 407:623-6. 2000
    ..These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane...
  33. ncbi In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes
    B M Fuchs
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 67:961-8. 2001
    ..coli, which may be extrapolated to other bacteria. Thereby, it may contribute to a better exploitation of the high potential of the 23S rRNA for identification of bacteria in the future...
  34. ncbi The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments
    R Rabus
    Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 6:887-902. 2004
    ..psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features...
  35. ncbi Single-stranded conformational polymorphism for separation of mixed rRNAS (rRNA-SSCP): a new method for profiling microbial communities
    Barbara J MacGregor
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany
    Syst Appl Microbiol 29:661-70. 2006
    ....
  36. ncbi Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations
    Emilio O Casamayor
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 68:1706-14. 2002
    ....
  37. ncbi In situ distribution and activity of nitrifying bacteria in freshwater sediment
    Dörte Altmann
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Environ Microbiol 5:798-803. 2003
    ..For the first time, Nitrospira-like bacteria could be quantified and correlated with in situ nitrite oxidation rates in a sediment. Estimated cell-specific nitrite oxidation rates were 1.2-2.7 fmol NO2- cell-1 h-1...
  38. ncbi Growth patterns of two marine isolates: adaptations to substrate patchiness?
    A Pernthaler
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 67:4077-83. 2001
    ..Different growth responses to substrate gradients could thus be another facet affecting the competition between marine bacteria and may help to explain community shifts observed during enrichments...
  39. ncbi Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds
    M Stoffels
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Appl Environ Microbiol 64:930-9. 1998
    ..Bacteria hybridizing with the probe Bcv13b represented the main Solvesso100-degrading population in the reactor...
  40. ncbi Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink
    Helge Niemann
    Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
    Nature 443:854-8. 2006
    ..This mechanism limits the capacity of the microbial methane filter at active marine mud volcanoes to <40% of the total flux...
  41. ncbi Detoxification of sulphidic African shelf waters by blooming chemolithotrophs
    Gaute Lavik
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Nature 457:581-4. 2009
    ..Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities...
  42. ncbi A conspicuous nickel protein in microbial mats that oxidize methane anaerobically
    Martin Krüger
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Nature 426:878-81. 2003
    ..Sequence analyses revealed similarities to methyl-coenzyme M reductase from methanogenic archaea. The abundance of the nickel protein (7% of extracted proteins) in the mat suggests an important role in AOM...
  43. ncbi Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica)
    Anja Heuchert
    Abt Marine Mikrobiologie, Universitat Bremen, Zentrum für Umweltforschung und Umwelttechnologie UFT, Bremen, Germany
    Syst Appl Microbiol 27:399-406. 2004
    ..8% renaturation to the respective strain. Based on the morphological, physiological and molecular properties of the new isolate, the name Psychrobacter nivimaris sp. nov. (type strain 88/2-7T) is proposed...
  44. ncbi Are readily culturable bacteria in coastal North Sea waters suppressed by selective grazing mortality?
    Christine Beardsley
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Appl Environ Microbiol 69:2624-30. 2003
    ....
  45. ncbi Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea
    Phyllis Lam
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 104:7104-9. 2007
    ....
  46. ncbi An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization
    Raju Sekar
    Max Planck Institute for Marine Microbiology, Celciusstrasse 1, D-28359 Bremen, Germany
    Appl Environ Microbiol 69:2928-35. 2003
    ..Our findings confirm that members of this lineage are among the numerically most important Bacteria of freshwater picoplankton...
  47. ncbi Identification of planctomycetes with order-, genus-, and strain-specific 16S rRNA-targeted probes
    D Gade
    Max Planck Institut für Marine Mikrobiologie, Celsiusstr 1, D 28359 Bremen, Germany
    Microb Ecol 47:243-51. 2004
    ..An unexpected result was the close phylogenetic relationship of the isolate from the sponge and the brackish water habitat Kiel Fjord as revealed by DNA/DNA hybridization...
  48. ncbi Nitrification in freshwater sediments as influenced by insect larvae: quantification by microsensors and fluorescence in situ hybridization
    D Altmann
    Max-Planck-Institute for Marine Microbiology, D-28359, Bremen, Germany
    Microb Ecol 48:145-53. 2004
    ..Partial digestion and redeposition of particle-associated bacteria by C. riparius larvae are believed to have caused this loss of metabolic activity...
  49. ncbi The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1T as revealed by whole genome comparisons
    Thierry Lombardot
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
    FEMS Microbiol Lett 242:137-45. 2005
    ..This strategy might provide a selective advantage for organisms living in habitats with frequently changing environmental conditions...
  50. ncbi Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes
    Dagmar Woebken
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    ISME J 1:419-35. 2007
    ..stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes...
  51. ncbi Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake
    Julia Arnds
    Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany
    Syst Appl Microbiol 33:139-48. 2010
    ..were omnipresent in low numbers (<1%). Verrucomicrobial abundance and community composition varied between the seasons, and between more and less humic basins, but were rather stable in oxic and seasonally anoxic waters...
  52. ncbi Molecular and morphological characterization of the association between bacterial endosymbionts and the marine nematode Astomonema sp. from the Bahamas
    Niculina Musat
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 9:1345-53. 2007
    ..symbionts use reduced sulfur compounds as an energy source to provide their hosts with nutrition...
  53. ncbi Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton
    Jörg Peplies
    Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 6:638-45. 2004
    ..1 x 10(8) cells. Our results demonstrate that major populations of marine bacterioplankton can be identified by microarray analysis in a fast and reliable way, even in relatively low volumes of sea water...
  54. ncbi Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea
    Annelie Pernthaler
    Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
    Appl Environ Microbiol 68:661-7. 2002
    ..g., coastal surface waters during spring and summer...
  55. ncbi Complete genome sequence of the marine planctomycete Pirellula sp. strain 1
    F O Glöckner
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 100:8298-303. 2003
    ..Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses...
  56. ncbi Insights into the genomes of archaea mediating the anaerobic oxidation of methane
    Anke Meyerdierks
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 7:1937-51. 2005
    ....
  57. ncbi High local and global diversity of Flavobacteria in marine plankton
    Cecilia Alonso
    Limnological Station Kilchberg, University of Zurich, Switzerland, and Max Planck Institute for Marine Microbiology, Bremen, Germany
    Environ Microbiol 9:1253-66. 2007
    ..Interestingly, only 15% of genera of Bacteroidetes from various aquatic environments appear to occur in more than one habitat type...
  58. ncbi Picobenthic cyanobacterial populations revealed by 16S rRNA-targeted in situ hybridization
    Raeid M M Abed
    Max Planck Institute for Marine Microbiology, Celsiusstrasse1, D 28359 Bremen, Germany
    Environ Microbiol 4:375-82. 2002
    ..It is not known how widespread picobenthic cyanobacteria may be in other environments...
  59. ncbi Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis
    Bernhard M Fuchs
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 104:2891-6. 2007
    ..KT71 enables future experiments investigating the importance of this group of gammaproteobacterial AAnPs in coastal environments...
  60. ncbi Analysis of N-acetylglucosamine metabolism in the marine bacterium Pirellula sp. strain 1 by a proteomic approach
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Proteomics 2:649-55. 2002
    ..Thus the coding genes of three proteins expressed during growth of Pirellula sp. strain 1 on carbohydrates were identified and related by sequence similarity to carbohydrate metabolism...
  61. ncbi Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas
    Anna Blazejak
    Max Planck Institute of Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Appl Environ Microbiol 72:5527-36. 2006
    ....
  62. ncbi Insights into the genome of large sulfur bacteria revealed by analysis of single filaments
    Marc Mussmann
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    PLoS Biol 5:e230. 2007
    ..The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments...
  63. ncbi Evaluation of the use of multilocus sequence analysis (MLSA) to resolve taxonomic conflicts within the genus Marichromatium
    Wilbert Serrano
    Zentrum für Umweltforschung und nachhaltige Technologien, Fachbereich Biologie chemie, Abteilung Marine Mikrobiologie, Universitat Bremen, D 28359 Bremen, Germany
    Syst Appl Microbiol 33:116-21. 2010
    ..The reconstructed phylogenetic tree based on concatenation of six protein-coding genes was also highly congruent with the tree topology based on the 16S rRNA gene...
  64. ncbi Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group
    Anke Meyerdierks
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 12:422-39. 2010
    ..The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner...
  65. ncbi An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments
    Kousuke Ishii
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany
    FEMS Microbiol Ecol 50:203-13. 2004
    ..With the optimized CARD-FISH protocol, microbial populations could also be detected in deeper sediment horizons. Furthermore, the intensity of the CARD-FISH signals improved detection of rare organisms such as Archaea...
  66. ncbi Revising the nitrogen cycle in the Peruvian oxygen minimum zone
    Phyllis Lam
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 106:4752-7. 2009
    ....
  67. ncbi A new moderately thermophilic and high sulfide tolerant biotype of Marichromatium gracile, isolated from tidal sediments of the German Wadden Sea: Marichromatium gracile biotype thermosulfidiphilum
    Wilbert Serrano
    Zentrum für Umweltforschung und nachhaltige Technologien, Fachbereich Biologie chemie, Abteilung Marine Mikrobiologie, Universitat Bremen, D 28359 Bremen, Germany
    Syst Appl Microbiol 32:1-7. 2009
    ..Based upon high genomic similarity but different physiological properties of strain SW26 with respect to the type strain of M. gracile, a novel biotype, designated as M. gracile biotype thermosulfidiphilum is described...
  68. ncbi A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
    Niculina Musat
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 105:17861-6. 2008
    ....
  69. ncbi A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones
    Dagmar Woebken
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    Environ Microbiol 10:3106-19. 2008
    ....
  70. ncbi Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria
    Annelie Pernthaler
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrabetae 1, D 28359 Bremen, Germany
    Appl Environ Microbiol 70:5426-33. 2004
    ..Our protocol is transferable to many different types of samples with the need for only minor modifications of fixation and permeabilization procedures...
  71. ncbi Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer
    Marc Mussmann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
    J Bacteriol 187:7126-37. 2005
    ..The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway...
  72. ncbi The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes
    Sebastian Behrens
    Max Planck Institute of Marine Microbiology, Bremen, Germany
    Syst Appl Microbiol 27:565-72. 2004
    ..Probes quenched upon hybridization to a guanine-rich region of purified RNA in solution were not quenched upon FISH. Among other factors the high protein concentration within cells may prevent quenching of probe fluorescence in situ...
  73. ncbi Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes
    Jörg Peplies
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Appl Environ Microbiol 69:1397-407. 2003
    ....
  74. ncbi Diversity and distribution of methanotrophic archaea at cold seeps
    Katrin Knittel
    Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany
    Appl Environ Microbiol 71:467-79. 2005
    ..These variations in the distribution, diversity, and morphology of methanotrophic consortia are discussed with respect to the presence of microbial ecotypes, niche formation, and biogeography...
  75. ncbi Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea
    Marc Mussmann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
    Environ Microbiol 7:405-18. 2005
    ..This group accounted for up to 6% of total cell numbers and even exceeded SRB numbers in upper sediment layers. These bacteria might substantially contribute to carbon mineralization via dissimilatory reduction of, e.g. Fe(III)...
  76. ncbi Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton
    Annelie Pernthaler
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Appl Environ Microbiol 68:5728-36. 2002
    ..The small size and low ribosome content of SAR86 cells are probably not indications of inactivity or dormancy...
  77. 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...
  78. ncbi Isolation of small-subunit rRNA for stable isotopic characterization
    Barbara J MacGregor
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Environ Microbiol 4:451-64. 2002
    ..SSU rRNA is therefore a promising biomarker for following the flow of carbon, and potentially nitrogen, in natural microbial populations. Some possible applications are discussed...
  79. ncbi Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages
    Falk Warnecke
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 6:242-53. 2004
    ..This points to the necessity to investigate genotypic variability, in situ abundances and activities of these Actinobacteria in freshwater plankton in greater detail by cultivation-independent techniques...
  80. ncbi In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm
    Armin Gieseke
    Microsensor Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 7:1392-404. 2005
    ..Net in situ carbon yields on N, expressed as e- equivalent ratios, varied between 0.005 and 0.018, and, thus, were in the lower range of data reported for pure cultures of nitrifiers...
  81. ncbi Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization
    Jakob Pernthaler
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Appl Environ Microbiol 69:2631-7. 2003
    ..Automated digital microscopy greatly facilitates the processing of numerous FISH-stained samples and might thus open new perspectives for bacterioplankton population ecology...
  82. ncbi Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation
    Marcel M M Kuypers
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Proc Natl Acad Sci U S A 102:6478-83. 2005
    ..We hypothesize that anammox could also be responsible for substantial nitrogen loss from other OMZ waters of the ocean...
  83. ncbi Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfobacterium autotrophicum using real-time RT-PCR
    Lev N Neretin
    Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 5:660-71. 2003
    ..The maximum DSR mRNA per-cell contents correlated with cell-specific sulphate reduction rates for all experiments. Environmental applications for the quantification of DSR mRNA are discussed...
  84. ncbi The species concept for prokaryotes
    R Rossello-Mora
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359, Bremen, Germany
    FEMS Microbiol Rev 25:39-67. 2001
    ..We suggest to refer it as a phylo-phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes...
  85. ncbi Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes
    B M Fuchs
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 64:4973-82. 1998
    ..Considering the high evolutionary conservation of 16S rRNA, the in situ accessibility map of E. coli should facilitate a more rational selection of probe target sites for other species as well...
  86. ncbi In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes
    Sebastian Behrens
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
    Appl Environ Microbiol 69:1748-58. 2003
    ..Finally, the 16S rRNA consensus model was compared to data on the in situ accessibility of the 18S rRNA of S. cerevisiae...
  87. ncbi Comparison of rRNA and polar-lipid-derived fatty acid biomarkers for assessment of 13C-substrate incorporation by microorganisms in marine sediments
    Barbara J MacGregor
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 72:5246-53. 2006
    ..We discuss possible ways to improve the probe-capture protocol and the sensitivity of the 13C analysis of the captured SSU rRNA...
  88. ncbi Simultaneous P and N removal in a sequencing batch biofilm reactor: insights from reactor- and microscale investigations
    A Giesek
    Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
    Water Res 36:501-9. 2002
    ..Therefore, simultaneous nitrification and phosphorus removal in a P removing SBBR appears to be only possible with a sufficiently long oxic period to ensure oxygen availability for nitrifiers...
  89. ncbi Application of tetranucleotide frequencies for the assignment of genomic fragments
    Hanno Teeling
    Department of Molecular Ecology, Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
    Environ Microbiol 6:938-47. 2004
    ....
  90. ncbi Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins
    Dörte Gade
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Proteomics 5:3654-71. 2005
    ..The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization...
  91. ncbi Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit?
    Sebastian Behrens
    Max Planck Institute of Marine Microbiology, Bremen Max Planck Institute of Molecular Genetics, Berlin, Germany
    Appl Environ Microbiol 69:4935-41. 2003
    ..The presence or absence of the strongly denaturing detergent sodium dodecyl sulfate had a much more pronounced effect than a change of fixative from paraformaldehyde to ethanol...
  92. ncbi Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice
    Robin Brinkmeyer
    Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
    Appl Environ Microbiol 69:6610-9. 2003
    ..A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes...
  93. ncbi Fate of heterotrophic microbes in pelagic habitats: focus on populations
    Jakob Pernthaler
    Limnological Station, Institute of Plant Biology, Seestrasse 187, CH 8802 Kilchberg, Switzerland
    Microbiol Mol Biol Rev 69:440-61. 2005
    ..An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed...
  94. ncbi High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters
    Mikhail V Zubkov
    Southampton Oceanography Centre, Southampton SO14 3ZH, United Kingdom
    Appl Environ Microbiol 69:1299-304. 2003
    ..This finding may provide a mechanism for Prochlorococcus' competitive dominance over both strictly autotrophic algae and other bacteria in oligotrophic regions sustained by nutrient remineralization via a microbial loop...
  95. ncbi A CARD-FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae
    Niina A Tujula
    Centre for Marine Biofouling and Bio-Innovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    J Microbiol Methods 65:604-7. 2006
    ....
  96. ncbi A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats
    Michael Kube
    Max Planck Institut fir Molekulare Genetik, Ihnestr. 73, D-14129 Berlin, Germany
    Syst Appl Microbiol 28:287-94. 2005
    ....
  97. ncbi Intraspecific comparative analysis of the species Salinibacter ruber
    Arantxa Peña
    Division de Microbiologia, Departamento de Fisiologia, Genética y Microbiología, Universidad de Alicante, Apto 99, 03080 Alicante, Spain
    Extremophiles 9:151-61. 2005
    ..Altogether the taxonomic study indicated that S. ruber remained highly homogeneous beyond any geographical barrier. However, genomic fingerprints indicated that populations from different isolation sites could still be discriminated...
  98. ncbi Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria
    Annelie Pernthaler
    Max-Planck-Institute for Marine Microbiology, D-28359 Bremen, Germany
    Appl Environ Microbiol 68:3094-101. 2002
    ..The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment...
  99. ncbi Symbiosis insights through metagenomic analysis of a microbial consortium
    Tanja Woyke
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 443:950-5. 2006
    ..We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits...
  100. ncbi Dual symbiosis in a Bathymodiolus sp. mussel from a methane seep on the Gabon continental margin (Southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills
    Sébastien Duperron
    IFREMER Départment Environnement Profond, Centre de Brest, Plouzane, Germany
    Appl Environ Microbiol 71:1694-700. 2005
    ....
  101. ncbi Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds
    Josefa Antón
    Departamento de Fisiologia, Genética y Microbiología, Universidad de Alicante, Spain
    Int J Syst Evol Microbiol 52:485-91. 2002
    ..Isolation of the organism now allows formal description of a novel genus and species, for which we propose the name Salinibacter ruber gen. nov., sp. nov. The type strain is strain M31T (= DSM 13855T = CECT 5946T)...