Summary1. The impact of burrowing larvae of Ephoron virgo (Ephemeroptera, Polymitarcidae) on sediment microbiology has not been previously investigated because of difficulties in sampling the sediment of large rivers under in situ conditions. Therefore, we conducted experiments in the on‐ship Ecological Rhine Station of the University of Cologne (Germany), in which ambient conditions of the River Rhine can be closely mimicked.2. In two consecutive seasons, experimental flow channels were stocked with Ephoron larvae and continuously supplied with water taken directly from the River Rhine. Sediment from the immediate vicinity of Ephoron burrows (i.e. U‐shaped cavities reaching 10–80 mm deep into the sediment) and bulk sediment samples were analysed for (i) particulate organic matter content, (ii) microscale in situ distribution of O2, NO, and NH, and (iii) potential activities of exoenzymes.3. Sediment surrounding the Ephoron burrows had markedly higher organic matter contents and exoenzyme activities compared with the bulk sediment. Microsensor measurements demonstrated that local O2 and NO penetration into the sediment were greatly enhanced by larval ventilation behaviour. Volumetric O2 and NO turnover rates that were calculated from steady state concentration profiles measured directly in the burrow lining were considerably higher than at the sediment surface.4. In the sediment of the fast flowing River Rhine Ephoron burrows are preferential sites of organic matter accumulation and dissolved oxidant penetration. Our data suggest that the burrows are surrounded by a highly active microbial community that responds to the inputs from the water column with elevated O2 and NO turnover, and release of exoenzymes into the sediment pore water. Especially during periods of mass occurrence, the larvae of E. virgo may thus significantly contribute (i) to the ecological connection between the water column and the sediment and (ii) to biogeochemical processing of organic matter in the riverbed.

Two freshwater sediments (organic-poor and organic-rich) that contained their distinct natural microbial communities were incubated in experimental microcosms with either NH4+ or NO2− in the overlying water. Microsensor measurements revealed the thin oxic surface layer as a site of initially high rates of nitrification, i.e. O2, NH4+, and NO2− consumption, and NO3− production. Unexpectedly, during the subsequent 4-week incubation NH4+ consumption decreased in both sediment types and NO2− consumption decreased in the organic-rich sediment. In the organic-rich sediment O2 consumption and NO3− production paralleled these decreases, i.e. the reduced NH4+ and NO2− consumption rates were most probably due to reduced activity of nitrifiers. These microsensor data imply factors other than frequently suggested competition between nitrifiers and heterotrophs for NH4+, NO2− or O2 as causes for the loss of nitrification activity. We hypothesize that experimental manipulations (e.g. removal of macrofauna, redistribution of particulate organic matter, permanent nutrient enrichment) rendered the performance of the microbial community unstable. It is thus recommendable to restrict experiments in such commonly used model systems to the period of highest stability.

Nitrification was investigated in a model freshwater sediment by the combined use of microsensors and fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes. In situ nitrification activity was restricted mainly to the upper 2 mm of the sediment and coincided with the maximum abundance of nitrifying bacteria, i.e. 1.5 x 107 cells cm-3 for ammonia-oxidizing Beta-proteobacteria (AOB) and 8.6 x 107 cells cm-3 for Nitrospira-like nitrite-oxidizing bacteria (NOB). Cell numbers of AOB decreased more rapidly with depth than numbers of NOB. For the first time, Nitrospira-like bacteria could be quantified and correlated with in situ nitrite oxidation rates in a sediment. Estimated cell-specific nitrite oxidation rates were 1.2-2.7 fmol NO2- cell-1 h-1.