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The aim of this study was to compare structural differences in thenirS-type denitrifying microbial communities along the environmental gradientsobserved in the water column and coastal sediments of the Baltic Sea. Tolink community structure and environmental gradients, denitrifiercommunities were analyzed by terminal restriction fragment lengthpolymorphism (T-RFLP) based on nirS as a functional marker gene fordenitrification. nirS-type denitrifier community composition was further evaluatedby phylogenetic analysis of nirS sequences from clone libraries. T-RFLP analysisindicated some overlap but also major differences between communities fromthe water column and the sediment. Shifts in community composition along thebiogeochemical gradients were observed only in the water column whiledenitrifier communities were rather uniform within the upper 30 mm of thesediment. Specific terminal restriction fragments (T-RFs) indicative of thesulfidic zone suggest the presence of nitrate-reducing and sulfide-oxidizingmicroorganisms that were previously shown to be important at thesuboxic-sulfidic interface in the water column of the Baltic Sea.Phylogenetic analysis of nirS genes from the Baltic Sea and of sequences frommarine habitats all over the world indicated distinct denitrifiercommunities that grouped mostly according to their habitats. We suggest thatthese subgroups of denitrifiers had developed after selection throughseveral factors, i.e. their habitats (water column or sediment), impact byprevalent environmental conditions and isolation by large geographicdistances between habitats

&lt;I&gt;nirS&lt;/I&gt;-containing denitrifier communities in the water column and sediment of the Baltic Sea

<I>nirS</I>-containing denitrifier communities in the water column and sediment of the Baltic Sea