B M Fuchs
Affiliation: Max Planck Institute for Marine Microbiology
- Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniquesRudolf Amann
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
Nat Rev Microbiol 6:339-48. 2008....
- The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probesSebastian 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...
- Graphical representation of ribosomal RNA probe accessibility data using ARB software packageYadhu 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...
- Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probesB 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...
- In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probesB 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...
- Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniquesB 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...
- Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesisBernhard 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...
- Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probesB 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...
- The identification of microorganisms by fluorescence in situ hybridisationR 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...
- Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North SeaIlaria Pizzetti
Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
Appl Environ Microbiol 77:5009-17. 2011..Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates...
- In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domainsJoão Inácio
Centro de Recursos Microbiológicos, Biotechnology Unit, Faculty of Sciences and Technology, New University of Lisbon, 2829 516 Caparica, Portugal
Appl Environ Microbiol 69:2899-905. 2003..This work contributes to a more rational design of species-specific probes for yeast identification and monitoring...
- Microbial control of phosphate in the nutrient-depleted North Atlantic subtropical gyreMikhail V Zubkov
National Oceanography Centre, Southampton SO143ZH, UK
Environ Microbiol 9:2079-89. 2007..3%) played minor roles in direct phosphate uptake. We have demonstrated that phosphate uptake in the oligotrophic gyre is rapid and dominated by two bacterial groups rather than by algae...
- Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling systemDagmar Woebken
Max Planck Institute for Marine Microbiology, Molecular Ecology, Celsiusstr 1, 28359 Bremen, Germany
Appl Environ Microbiol 73:4648-57. 2007....
- Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone librariesAndreas Schramm
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195-2700, USA
Environ Microbiol 4:713-20. 2002..In summary, Clone-FISH is a simple and fast technique, compatible with a wide variety of cloning vectors and hosts, that should have general utility for probe validation and screening of clone libraries...
- Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidationMarcel 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...
- High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic watersMikhail 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...
- In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probesSebastian 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...
- Flow sorting of marine bacterioplankton after fluorescence in situ hybridizationRaju 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...
- SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARBElmar Pruesse
Microbial Genomics Group, Max Planck Institute for Marine Microbiology
Nucleic Acids Res 35:7188-96. 2007..The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs...
- 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...