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Nitrification is a crucial process in sediment nitrogen cycling. We compared two (15)N tracer-based nitrification measurement techniques (isotope pairing technique (IPT) combined with (15)N nitrate pool dilution and (15)N ammonium oxidation) and three different (15)N analyses from bottom water nitrate (ammonia diffusion, denitrifier and SPINMAS) in a sediment mesocosm. The (15)N nitrate pool dilution technique combined with IPT can be used to quantify the in situ nitrification, but the minimum detection limit for the total nitrification is higher than that in the (15)N ammonium oxidation technique. The (15)N ammonium oxidation technique, however, is not applicable for sediments that have high ammonium content. If nitrate concentration and the amount of (15)N label in the sample are low, the (15)N nitrate analysis should be done with the denitrifier method. In higher (15)N concentrations, the less sensitive SPINMAS method can also be applied. The ammonia diffusion method is not suitable for bottom water (15)N nitrate analyses.

Estuaries worldwide act as "filters" of land-derived nitrogen (N) loads, yet differences in coastal environmental settings can affect the N filter function. We investigated microbial N retention (nitrification, ammonium assimilation) and N removal (denitrification, anammox) processes in the aphotic benthic system (bottom boundary layer (BBL) and sediment) of two Baltic Sea estuaries differing in riverine N loads, trophic state, geomorphology, and sediment type. In the BBL, rates of nitrification (5–227 nmol N L -1 d -1) and ammonium assimilation (9–704 nmol N L -1 d -1) were not enhanced in the eutrophied Vistula Estuary compared to the oligotrophic Öre Estuary. No anammox was detected in the sediment of either estuary, while denitrification rates were twice as high in the eutrophied (352±123 µ mol N m -2 d -1) as in the oligotrophic estuary. Particulate organic matter (POM) was mainly of phytoplankton origin in the benthic systems of both estuaries. It seemed to control heterotrophic denitrification and ammonium assimilation as well as autotrophic nitrification by functioning as a substrate source of N and organic carbon. Our data suggest that in stratified estuaries, POM is an essential link between riverine N loads and benthic N turnover and may furthermore function as a temporary N reservoir. During long particle residence times or alongshore transport pathways, increased time is available for the recycling of N until its eventual removal, allowing effective coastal filtering even at low process rates. Understanding the key controls and microbial N processes in the coastal N filter therefore requires to also consider the effects of geomorphological and hydrological features. [ABSTRACT FROM AUTHOR]

The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase ( amoA ) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes. [ABSTRACT FROM AUTHOR]

Nitrification is a crucial process in sediment nitrogen cycling. We compared two 15N tracer-based nitrification measurement techniques (isotope pairing technique (IPT) combined with 15N nitrate pool dilution and 15N ammonium oxidation) and three different 15N analyses from bottom water nitrate (ammonia diffusion, denitrifier and SPINMAS) in a sediment mesocosm. The 15N nitrate pool dilution technique combined with IPT can be used to quantify the in situ nitrification, but the minimum detection limit for the total nitrification is higher than that in the 15N ammonium oxidation technique. The 15N ammonium oxidation technique, however, is not applicable for sediments that have high ammonium content. If nitrate concentration and the amount of 15N label in the sample are low, the 15N nitrate analysis should be done with the denitrifier method. In higher 15N concentrations, the less sensitive SPINMAS method can also be applied. The ammonia diffusion method is not suitable for bottom water 15N nitrate analyses. [ABSTRACT FROM AUTHOR]

A cyanobacterial bloom in the Gulf of Finland, Baltic Sea, was sampled throughout the development and senescence of aggregates in August 1999. While conditions inside the aggregates were favourable for denitrification (rich in nitrogen and carbon, with anoxic microzones), essentially none was detected by a sensitive isotope pairing method. Polymerase chain reaction-based methods, targeting functional genes encoding the key enzymes of denitrification and nitrification processes (nirS, nirK, amoA), revealed that the non-aggregated filaments harboured amoA gene fragments with high similarity to Nitrosospira amoA sequences, as well as both types of nitrite reductase genes, nirS and nirK. Only the nirS-type nitrite reductase gene and no amoA was detected in aggregated filaments. Thus, despite optimal environmental conditions and genetic potential for denitrification, the blooms of filamentous nitrogen-fixing cyanobacteria must be seen solely as a source, and not as a sink of nitrogen in the Baltic Sea. [Copyright &y& Elsevier]

The redoxclines that form between the oxic and anoxic water layers in the central Baltic Sea are sites of intensive nitrogen cycling. To gain better understanding of nitrification, we measured the biogeochemical properties along with potential nitrification rates and analyzed the assemblages of ammonia-oxidizing bacteria and archaea using functional gene microarrays. To estimate nitrification in the entire water column, we constructed a regression model for the nitrification rates and applied it to the conditions prevailing in the area in 2008–2012. The highest ammonia oxidation rates were found in a thin layer at the top of the redoxcline and the rates quickly decreased below detection limit when oxygen was exhausted. This is probably because extensive suboxic layers, which are known to harbor pelagic nitrification, are formed only for short periods after inflows in the Baltic Sea. The nitrification rates were some of the highest measured in the water columns, but the thickness of the layer where conditions were favorable for nitrification, was very small and it remained fairly stable between years. However, the depth of the nitrification layer varied substantially between years, particularly in the eastern Gotland Basin (EGB) due to turbulence in the water column. The ammonia oxidizer communities clustered differently between the eastern and western Gotland Basin (WGB) and the composition of ammonia-oxidizing assemblages correlated with the environmental variables. The ammonia oxidizer community composition was more even in the EGB, which may be related to physical instability of the redoxcline that does not allow predominance of a single archetype, whereas in the WGB, where the position of the redoxcline is more constant, the ammonia-oxidizing community was less even. Overall the ammonia-oxidizing communities in the Baltic Sea redoxclines were very evenly distributed compared to other marine environments where microarrays have been applied previously. [ABSTRACT FROM AUTHOR]