Particulate organic matter controls benthic microbial N retention andN removal in contrasting estuaries of the Baltic Sea

Abstract. Estuaries worldwide are known to act as filters of land-derived N loads, yet their variable environmental settings can affect microbial nitrogen (N) retention and removal and thus the coastal filter function. We investigated microbial N-retention (nitrification, ammonium assimilation) and N-removal (denitrification, anammox) in the aphotic benthic systems (here defined as: bottom boundary layer [BBL] and sediment) of two Baltic Sea estuaries that differ in riverine N loads, trophic state, bottom topography, and sediment type. Contrary to our expectations, nitrification rates (5–227 nmol L −1  d −1 ) in the BBL neither differed between the eutrophied Vistula estuary and the oligotrophic Ore estuary, nor between seasons. Ammonium assimilation rates were slightly higher in the oligotrophic Ore estuary in spring but did not differ between estuaries in summer (9–704 nmol L −1  d −1 ). In the sediment, no anammox was found in either estuary and denitrification rates were higher in the eutrophied (349 ± 117 µmol N m −2  d −1 ) than in the oligotrophic estuary (138 ± 47 µmol N m −2  d −1 ). Irrespective of their differences, in both estuaries the quality of the mainly phytoplankton-derived particulate organic matter (POM) – evaluated by means of C : N and POC : Chl. a ratios – seemed to control N-cycling processes through the availability of particulate organic N and C as substrate sources. Our data suggest, that in stratified estuaries, phytoplankton-derived POM is an essential link between riverine N loads and benthic N cycling and may function as a temporary N reservoir via long particle residence time or coastal parallel transport. Even at low process rates, effective coastal filtering would thus be achieved by the increased time available for the recycling of N via microbial retention processes until its permanent removal via denitrification.