Biogeosciences www.biogeosciences.net 1726-4170 1726-4189 4 3 2007 10.5194/bg-4-255-2007 http://www.biogeosciences.net/4/255/2007/ http://www.biogeosciences.net/4/255/2007/bg-4-255-2007.html http://www.biogeosciences.net/4/255/2007/bg-4-255-2007.pdf 255 268 2007-05-10 nirS-containing denitrifier communities in the water column and sediment of the Baltic Sea S. Falk M. Hannig C. Gliesche R. Wardenga M. Köster K. Jürgens G. Braker braker@mpi-marburg.mpg.de Institut für Ökologie, Ernst-Moritz-Arndt-Universität, Schwedenhagen 6, 18565 Kloster, Hiddensee, Germany Baltic Sea Research Institute, Seestrasse 15, 18119 Warnemünde, Germany Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany Institute for Chemistry and Biochemistry, Ernst-Moritz-Arndt-University, Soldmannstraße 16, 17487 Greifswald, Germany The aim of this study was to compare structural differences in the nirS-type denitrifying microbial communities along the environmental gradients observed in the water column and coastal sediments of the Baltic Sea. To link community structure and environmental gradients, denitrifier communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) based on nirS as a functional marker gene for denitrification. nirS-type denitrifier community composition was further evaluated by phylogenetic analysis of nirS sequences from clone libraries. T-RFLP analysis indicated some overlap but also major differences between communities from the water column and the sediment. Shifts in community composition along the biogeochemical gradients were observed only in the water column while denitrifier communities were rather uniform within the upper 30 mm of the sediment. Specific terminal restriction fragments (T-RFs) indicative of the sulfidic zone suggest the presence of nitrate-reducing and sulfide-oxidizing microorganisms that were previously shown to be important at the suboxic-sulfidic interface in the water column of the Baltic Sea. Phylogenetic analysis of nirS genes from the Baltic Sea and of sequences from marine habitats all over the world indicated distinct denitrifier communities that grouped mostly according to their habitats. 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