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

Abstract

Abstract. 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. We suggest that these subgroups of denitrifiers had developed after selection through several factors, i.e. their habitats (water column or sediment), impact by prevalent environmental conditions and isolation by large geographic distances between habitats.

Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

“…This result is unexpected considering that nirSdenitrifiers have been frequently found in estuarine and marine habitats (Braker et al 2000;Liu et al 2003;Jayakumar et al 2004;Santoro et al 2006) and have been reported previously in the water column and sediments of the Baltic Sea (Brettar et al 2001;Hannig et al 2006;Falk et al 2007). Therefore, we consider the restricted number of nirS sequences obtained here to reflect the actual situation at the sampling time, but not as an indication of the absence of nirS-denitrifiers in the water column of the Baltic Sea.…”

“…Different studies analyzing denitrifying bacterial communities in the Baltic Sea, the world's largest brackish environment, suggest relatively low diversity of nirS-denitrifying bacteria and have failed to recover nirK sequences from the water column and sediments (Brettar et al 2001;Hannig et al 2006;Falk et al 2007). However, recently a study in the suboxic zone of the water column (Oakley et al 2007) showed higher variation in nirK compared to nirS.…”

“…Recent studies using the nitrite reductase genes as functional molecular markers have significantly contributed to our understanding of the diversity of denitrifying bacteria in a variety of habitats including soils (Avrahami et al 2002;Priemé et al 2002;Rösch et al 2002;Throbäck et al 2004;Wolsing and Priemé 2004;Sharma et al 2005;Throbäck et al 2007), groundwater (Yan et al 2003), estuarine sediments (Nogales et al 2002;Santoro et al 2006), marine sediments (Braker et al 2000;Liu et al 2003;Hannig et al 2006;Falk et al 2007) and seawater (Tuomainen et al 2003;Jayakumar et al 2004;Castro-González et al 2005;Hannig et al 2006;Falk et al 2007;Oakley et al 2007). Comparatively, there are only few studies on the distribution of denitrifying bacteria in lakes and brackish water habitats.…”

Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria

“…Bourbonnais et al (24) found low diversity and an abundance of nirS-containing bacteria in diffuse hydrothermal vent fluids that were reportedly dominated by Epsilonproteobacteria, despite finding other evidence for substantial denitrification (44,45). Similar discrepancies between rate measurements (54)(55)(56) and nirS gene studies (12,20,21) have been reported for the Baltic Sea, where Epsilonproteobacteria of the genus Sulfurimonas are prominent (57,58), yet nirS community analysis found no genes related to this group (21). In both of these locations, the dominant Epsilonproteobacteria were not recovered using standard primers for diversity assessment of nirS genes, suggesting a need for a multiple-primer approach to better understand the structural dynamics of denitrifying communities in environments that favor autotrophic denitrification.…”

“…This interest is evidenced by the numerous studies of denitrifier functional gene diversity that have been undertaken in a variety of aquatic environments, including estuarine sediments (3)(4)(5)(6)(7), freshwater systems (8)(9)(10)(11)(12), coastal marine waters and sediments (4,5,(13)(14)(15), oxygen minimum zones and anoxic basins (12,(16)(17)(18)(19)(20)(21)(22)(23), hydrothermal vents (24,25), and deep-sea sediments (26). The ability to denitrify exists across a wide breadth of bacteria and archaea (2) that may be favored under different environmental conditions.…”