Publikationen Bernhard Fuchs

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  Barrero-Canosa J., Moraru C., Zeugner L., Fuchs B. M. and Amann R. (2017) Direct-geneFISH: A simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms. Env. Microbiol. 19, 70-82.
  Avci, B.; Hahnke, R. L.; Chafee, M.; Fischer, T.; Gruber-Vodicka, H.; Tegetmeyer, H. E.; Harder, J.; Fuchs, B. M.; Amann, R. I. & Teeling, H. (2017) Genomic and physiological analyses of 'Reinekea forsetii' reveal a versatile opportunistic lifestyle during spring algae blooms. Env. Microbiol., 2017, n/a-n/a



  Bennke C. M., Reintjes G., Schattenhofer M., Ellrott A., Wulf J., Zeder M. and Fuchs B. M. (2016) Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses. Appl. Environ. Microbiol. 82, 3289-3296.
  Bruder L. M., Dörkes M., Fuchs B. M., Ludwig W. and Liebl W. (2016) Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes. Syst. Appl. Microbiol. 39, 464-475.
  Dyksma S., Bischof K., Fuchs B. M., Hoffmann K., Meier D., Meyerdierks A., Pjevac P., Probandt D., Richter M., Stepanauskas R. and Mußmann M. (2016) Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J. 10, 1939-1953.
  Martinez-Perez C., Mohr W., Löscher C. R., Dekaezemacker J., Littmann S., Yilmaz P., Lehnen N., Fuchs B. M., Lavik G., Schmitz R. A., LaRoche J. and Kuypers M. M. M. (2016) The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. Nature Microbiology 1, 16163.
  Pizzetti I., Lupini G., Bernardi Aubry F., Acri F., Fuchs B. M. and Fazi S. (2016) Influence of the Po River runoff on the bacterioplankton community along trophic and salinity gradients in the Northern Adriatic Sea. Mar. Ecol. 37, 1386–1397.
  Schimak M. P., Kleiner M., Wetzel S., Liebeke M., Dubilier N. and Fuchs B. M. (2016) MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells. Appl. Environ. Microbiol. 82, 62-70.
  Teeling H., Fuchs B. M., Bennke C. M., Krüger K., Chafee M., Kappelmann L., Reintjes G., Waldmann J., Quast C., Glöckner F. O., Lucas J., Wichels A., Gerdts G., Wiltshire K. H. and Amann R. I. (2016) Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. eLife 5, e11888.



  Krupke A., Mohr W., LaRoche J., Fuchs B. M., Amann R. I. and Kuypers M. M. (2015) The effect of nutrients on carbon and nitrogen fixation by the UCYN-A - haptophyte symbiosis. ISME J. 9, 1635-1647.
  Pizzetti I., Schulz F., Tyml T., Fuchs B. M., Amann R., Horn M. and Fazi S. (2015) Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake. Env. Microbiol. 18, 2405–2417.
  Thiele S., Fuchs B. M., Amann R. and Iversen M. H. (2015) Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow. Appl. Environ. Microbiol. 81, 1463-1471.
  Yamaguchi T., Fuchs B. M., Amann R., Kawakami S., Kubota K., Hatamoto M. and Yamaguchi T. (2015) Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH). Syst. Appl. Microbiol. 38, 400-405.



  Krupke A., Lavik G., Halm H., Fuchs B. M., Amann R. I. and Kuypers M. M. M. (2014) Distribution of a consortium between unicellular algae and the N2 fixing cyanobacterium UCYN-A in the North Atlantic Ocean. Env. Microbiol. 16, 3153–3167.
  Bizic-Ionescu M., Zeder M., Ionescu D., Orlic S., Fuchs B. M., Grossart H.-P. and Amann R. (2014) Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization. Env. Microbiol. 17, 3500-3514.
  Hahnke R. L., Bennke C. M., Fuchs B. M., Mann A. J., Rhiel E., Teeling H., Amann R. and Harder J. (2014) Dilution cultivation of marine heterotrophic bacteria abundant after a spring phytoplankton bloom in the North Sea. Env. Microbiol. 17, 3515–3526.
  Thiele S., Wolf C., Schulz I. K., Assmy P., Metfies K. and Fuchs B. M. (2014) Stable Composition of the Nano- and Picoplankton Community during the Ocean Iron Fertilization Experiment LOHAFEX. PLoS ONE 9, e113244.



Bennke C. M., Neu T. R., Fuchs B. M. and Amann R. (2013) Mapping glycoconjugate-mediated interactions of marine Bacteroidetes with diatoms. Syst. Appl. Microbiol. 36, 417–425.
Gomez-Pereira P. R., Hartmann M., Grob C., Tarran G. A., Martin A. P., Fuchs B. M., Scanlan D. J. and Zubkov M. V. (2013a) Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre. ISME J. 7, 603-614.
Gomez-Pereira P. R., Kennaway G.,Fuchs B. M., Tarran G. A. and Zubkov M. V. (2013b) Flow cytometric identification of Mamiellales clade II in the Southern Atlantic Ocean. FEMS Microbiol. Ecol. 83, 664-671.
Hahnke R. L., Probian C., Fuchs B. M. and Harder J. (2013) Variations in pelagic bacterial communities in the North Atlantic Ocean coincide with water bodies. Aquat. Microb. Ecol. 71, 131-140.
Kolinko S., Wanner G., Katzmann E., Kiemer F., Fuchs B. M. and Schüler D. (2013) Clone libraries and single cell genome amplification reveal extended diversity of uncultivated magnetotactic bacteria from marine and freshwater environments. Env. Microbiol. 15, 1290-1301.
Krupke A., Musat N., LaRoche J., Mohr W., Fuchs B. M., Amann R. I., Kuypers M. M.M.. and Foster R. A. (2013) In situ identification and N2 and C fixation rates of uncultivated cyanobacteria populations. Syst. Appl. Microbiol. 36, 259–271.
Spring S., Riedel T., Spröer C., Yan S., Harder J. and Fuchs B. M. (2013) Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol. 13, 118.


Arnosti C., Fuchs B. M., Amann R. and Passow U. 2012. Contrasting extracellular enzyme activities of particle-associated bacteria from distinct provinces of the North Atlantic Ocean. Front. Aquat. Microbiol. 3, 425, 1-8
Gómez-Pereira P.R., Schüler M, Fuchs B. M., Bennke C., Teeling H., Waldmann J., Richter M., Barbe V., Bataille E., Glöckner F.O., Amann R. 2012. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ. Microbiol.14(1): 52-66.
Hill P. G., Heywood J. L., Holland R. J., Purdie D. A., Fuchs B. M. & Zubkov M. V. 2012. Internal and external influences on near-surface microbial community structure in the vicinity of the Cape Verde Islands, Microb. Ecol. 63 : 139-148.
Oberbeckmann S., Fuchs B. M., Meiners M., Wichels A., Wiltshire K. H. and Gerdts G. 2012. Seasonal dynamics and modeling of a Vibrio community in coastal waters of the North Sea. Microb. Ecol. 63, 543-551
Pizzetti, I., Fazi S., Fuchs B. M., and Amann R. 2012. High abundance of novel environmental chlamydiae in a Tyrrhenian coastal lake (Lago di Paola, Italy). Environ. Microbiol. Rep. 4, 446-452
Teeling H., Fuchs B. M. ,Becher D.,Klockow C., Gardebrecht A., Bennke C.M., Kassabgy M., S. Huang, A.J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F.D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K.H. Wiltshire, F.O. Glöckner, T. Schweder, and R. Amann. 2012. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608-611
Abstract- Full text - PDF
Thiele S., Fuchs B. M., Ramaiah N. and Amann R. 2012. Microbial community response during the iron fertilization experiment LOHAFEX. Appl. Environ. Microbiol. 78, 8803-8812


Moraru C., G. Moraru, B. M. Fuchs, andR. Amann. 2011. Concepts and software for a rational design of polynucleotide probes. Environ. Microbiol. Rep. 3:69–78.
Pizzetti I., A. Gobet, B. M. Fuchs, R. Amann,and S. Fazi. 2011. Abundance and diversity of Planctomycetes in a Tyrrhenian coastal system of central Italy. Aquat. Microb. Ecol. 65:129-139.
Pizzetti I., B. M. Fuchs, G. Gerdts, A. Wichels, K.H. Wiltshire, and R. Amann. 2011. Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea. Appl. Environ. Microbiol. 77:5009-5017.
Schattenhofer M., Wulf J., Kostadinov I., Glöckner F. O., Zubkov, M. V. and Fuchs B. M. (2011). Phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the North Atlantic Ocean. Syst. Appl. Microbiol. 34 : 470-475.
Thiele S., B. M. Fuchs, and R.I. Amann.2011. Identification of microorganisms using the ribosomal RNA approach and fluorescence in situ hybridization. In: Treatise on Water Science, vol. 3, pp. 171–189. Peter Wilderer (ed.) Oxford: Academic Press.
Weber M., Teeling H., Huang S., Waldmann J., Kassabgy M., Fuchs B. M., Klindworth A., Klockow C., Wichels A., Gerdts G., Amann R. and Glöckner F. O. (2011). Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics, ISME J. 5 : 918-928.


Alonso, C.; Gómez-Pereira, P. R.; Ramette, A.; Ortega, L.; Fuchs, B. M. and Amann, R. (2010). Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata–South Atlantic Ocean, Aquat. Microb. Ecol. 61 : 57-72.
Amann, R. and Fuchs, B. M. (2008). Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques, Nature Rev. Microbiol. 6 : 339-348.
Amaral-Zettler, L.; Peplies, J.; Ramette, A.; Fuchs, B.; Ludwig, W. and Glöckner, F. O. (2008). Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany, Syst.Appl. Microbiol. 31 : 258-268.
Fuchs, B. M., S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glöckner, and R. Amann. 2007. Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc. Natl. Acad. Sci. 104:2891-2896
Fuchs B. M., Pernthaler J. and Amann R. (2007a) Single cell identification by fluorescence in situ hybridization. In: Reddy C., Beveridge T., Breznak J., Marzluf G., Schmidt T. and Snyder L. (Ed.), Methods for General and Molecular Microbiology, ASM Press.
Gomez-Pereira, P. R.; Fuchs, B. M.; Alonso, C.; Oliver, M. J.; van Beusekom, J. E. E. and Amann, R. (2010). Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean, ISME J. 4 : 472-487
Heywood, J. L., M. V. Zubkov, G. A. Tarran, B. M. Fuchs, and P. M. Holligan. (2006) Prokaryoplankton standing stocks in oligotrophic gyre and equatorial provinces of the Atlantic Ocean: Evaluation of inter-annual variability. Deep Sea Res.II 53:1530-1547
Julies, E.; Fuchs, B.; Arnosti, C. and Brüchert, V. (2010). Organic carbon degradation in anoxic organic-rich shelf sediments: Biogeochemical rates and microbial abundance, Geomicrobiol. J. 27 : 303-314.
Lavik, G.; Stührmann, T.; Brüchert, V.; Van der Plas, A.; Mohrholz, V.; Lam, P.; Mußmann, M.; Fuchs, B. M.; Amann, R.; Lass, U. and Kuypers, M. M. M. (2009). Detoxification of sulphidic African shelf waters by blooming chemolithotrophs, Nature 457 : 581-584.
Lösekann T., Knittel K., Nadalig T., Fuchs B., Niemann H., Boetius A. and Amann R. (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl. Environ. Microbiol. 73, 3348-3362.
Mary, I., J. L. Heywood, B. M. Fuchs, R. Amann, G. A. Tarran, P. H. Burkill, and M. V. Zubkov. (2006) SAR11 dominance among metabolically active low nucleic acid bacterioplankton in surface waters along an Atlantic meridional transect. Aquat. Microb. Ecol. 45:107-113
Moraru, C.; Lam, P.; Fuchs, B. M.; Kuypers, M. M. M. and Amann, R. (2010). GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms, Env. Microbiol. 12 : 3057-3073.
Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J. and Glöckner F. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196.
Simonato, F.; Gómez-Pereira, P. R.; Fuchs, B. M. and Amann, R. (2010). Bacterioplankton diversity and community composition in the southern lagoon of venice, Syst. Appl. Microbiol. 33 : 128-138.
Schattenhofer, M.; Fuchs, B. M.; Amann, R.; Zubkov, M. V.; Tarran, G. A. and Pernthaler, J. (2009). Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean, Env. Microbiol. 11 : 2078-2093.
Spring, S.; Lünsdorf, H.; Fuchs, B. M. and Tindall, B. J. (2009). The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov., PLoS ONE 4 : e4866and
Woebken D., Fuchs B. M., Kuypers M. M. M. and Amann R. (2007) Potential interactions of particle-associated Anammox Bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl. Environ. Microbiol. 73, 4648-4657.
Woebken, D.; Lam, P.; Kuypers, M. M.; Naqvi, S. W.; Kartal, B.; Strous, M.; Jetten, M. S.; Fuchs, B. M. and Amann, R. (2008). A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones, Env. Microbiol. 10 : 3106-3119.
Yan, S.; Fuchs, B. M.; Lenk, S.; Harder, J.; Wulf, J.; Jiao, N.-Z. and Amann, R. (2009). Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria, Syst. Appl. Microbiol. 32 : 124-139.
Zubkov M. V., Mary I., Woodward E. M. S., Warwick P. E., Fuchs B. M., Scanlan D. J. and Burkill P. H. (2007) Microbial control of phosphate in the nutrient-depleted North Atlantic subtropical gyre. Env. Microbiol. 9, 2079-2089.
Zubkov, M. V.; Tarran, G. A.; Mary, I. and Fuchs, B. M. (2008). Differential microbial uptake of dissolved amino acids and amino sugars in surface waters of the Atlantic Ocean, J. Plankton Res. 30 : 211-220.


Amann, R., B. M. Fuchs, and S. Behrens. 2001. The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotechnol. 12:231-236
Behrens S., Fuchs B. M., Mueller F., Amann R. (2003) 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? Appl. Environ. Microbiol. 69:4935-4941
Behrens, S., C. Ruhland, J. Inacio, H. Huber, A. Fonseca, I. Spencer-Martins, B. M. Fuchs, and R. Amann. 2003. In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes. Appl. Environ. Microbiol. 69:1748-1758.
Behrens S., Fuchs B. M., Amann R. (2004) The Effect of Nucleobase-Specific Fluorescence Quenching on In Situ Hybridization with rRNA-Targeted Oligonucleotide Probes. Syst. Appl. Microbiol. 27:565-572
Fuchs, B. M., G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann. 1998. Flow cytometric analysis of the in-situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:4973-4982.
Fuchs, B. M., F. O. Glöckner, J. Wulf, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607
Fuchs, B. M., M. V. Zubkov, K. Sahm, P. H. Burkill, and R. Amann. 2000. Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Env. Microbiol. 2:191-202
Fuchs, B. M., K. Syutsubo, W. Ludwig, and R. Amann. 2001. In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 67:961-96
Fuchs, B. M., D. Woebken, M. V. Zubkov, P. H. Burkill, and R. Amann. (2005) Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquat. Microb. Ecol. 39:145-157
Glöckner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton composition in lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726
Inacio, J., S. Behrens, B. M. Fuchs, A. Fonseca, I. Spencer-Martins, and R. Amann. (2003). In Situ Accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-Labeled Oligonucleotide Probes Comprising the D1 and D2 Domains. Appl. Environ. Microbiol. 69:2899-2905
Kirchman, D. L., L. Y. Yu, B. M. Fuchs, and R. Amann. 2001. Structure of bacterial communities in aquatic systems as revealed by filter PCR. Aquat. Microb. Ecol. 26:13-2
Kumar, Y., R. Westram, S. Behrens, B. Fuchs, F. Glöckner, R. Amann, H. Meier, W. Ludwig. (2005) Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics 6:61
Kuypers, M. M. M., G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. B. Jorgensen, M. S. M. Jetten. (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. 102:6478-6483
Schönhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273
Schramm, A., B. M. Fuchs, J. L. Nielsen, M. Tonolla, and D. A. Stahl. 2002. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Env. Microbiol. 4:713-720
Sekar R., Fuchs B. M., Amann R., Pernthaler J. (2004) Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70:6210-6219
Snaidr, J., B. Fuchs, G. Wallner, M. Wagner, K.-H. Schleifer, and R. Amann. 1999. Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge. Env. Microbiol. 1:125-135
Wallner, G., B. Fuchs, S. Spring, W. Beisker, and R. Amann. 1997. Flow sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63:4223-4231
Zubkov, M. V., B. M. Fuchs, H. Eilers, P. H. Burkill, and R. Amann. 1999. Determination of total protein content of bacterial cells using SYPRO staining and flow cytometry. Appl. Environ. Microbiol. 65:3251-3257
Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2001. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropoinate in an algal bloom in the North Sea. Env. Microbiol. 3:304-311
Zubkov, M. V., B. M. Fuchs, P. H. Burkill, and R. Amann. 2001. Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl. Environ. Microbiol. 67:5210-5218
Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2002. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep-Sea Res. II 49:3017-3038
Zubkov, M. V., B. M. Fuchs, G. A. Tarran, P. H. Burkill, and R. Amann. 2002. Mesoscale distribution of dominant bacterioplankton groups in the northern North Sea in early summer. Aquat. Microb. Ecol. 29:135-144.
Zubkov, M. V., B. M. Fuchs, G. A. Tarran, P. H. Burkill, and R. Amann. (2003). High Rate of Uptake of Organic Nitrogen Compounds by Prochlorococcus Cyanobacteria as a Key to Their Dominance in Oligotrophic Oceanic Waters. Appl. Environ. Microbiol. 69:1299-1304.
Zubkov M.V., Tarran G.A., Fuchs B. M. (2004) Depth related amino acid uptake by Prochlorococcus cyanobacteria in the Southern Atlantic tropical gyre. FEMS Microbiol. Ecol. 50:153-161
Zubkov, M. V., J. I. Allen, B. M. Fuchs. (2004) Coexistence of dominant groups in marine bacterioplankton community - a combination of experimental and modelling approaches. J.Mar. Biol. Ass. UK 84:519-529
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