Little is known on microbial activities in the sediments of large lowland rivers despite of their potentially high influence on biogeochemical budgets. Based on field measurements in a variety of sedimentary habitats typical for a large lowland river (Elbe, Germany), we present results on the abundance and production of sedimentary bacteria, the potential activity of a set of extracellular enzymes, and potential nitrification and denitrification rates. A diving bell was used to access the sediments in the central river channel, enabling us to sample down to 1 m sediment depth. Depth gradients of all measures of microbial activity were controlled by sediment structure, hydraulic conditions, as well as by the supply with organic carbon and nitrogen. Microbial heterotrophic activity was tightly coupled with the availability of carbon and nitrogen, whereas chemolithotrophic activity (nitrification rate) was related to the available surface area of particles. In the central bed of the river, bacterial production and extracellular enzyme activity remained high down to the deepest sediment layers investigated. Due to the large inner surface area and their connectivity with the surface water, the shifting sediments in the central channel of the river were microbially highly active There, vertically integrated bacterial production amounted to 0.95 g C m À3 h À1 , which was 2.9 to 5.5 times higher than in the nearshore habitats. We conclude that carbon and nitrogen cycling in the river is controlled by the live sediments of the central river channel, which thus represent a ''liver function'' in the river's metabolism.

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Previous observations of the co-occurrence of high mortality among benthic crustaceans and blooms of benthic microalgae in diesel fuel-contaminated saltmarsh sediments suggest that microalgal blooms are a response to reduced grazing pressure by crustaceans. Nevertheless, this and alternative hypotheses for microalgal blooms in contaminated sediments have not been explicitly examined.Here, we used microcosms of saltmarsh sediment to examine influences of diesel fuel on benthic microalgae as they relate to (i) direct effects associated with reduced grazing and (ii) indirect effects associated with enhanced nitrogen availability. In both diesel fuel-contaminated sediment and in sediment where grazing was experimentally reduced (by microwaving the sediment fraction >125 µm), microalgal biomass more than doubled after 5 days; while biomass in control microcosms did not change. NH 4 + efflux in diesel fuel-contaminated sediment was significantly higher than in uncontaminated sediment after 14 days. Microalgae in uncontaminated sediments were not nitrogen limited (NH 4 + additions did not stimulate growth). In diesel fuel-contaminated sediments, however, microalgae were nitrogen limited, and all ambient NH 4 + was consumed. We conclude that, in diesel fuel-contaminated sediments, grazer mortality leads to increased growth of microalgae and ultimately to nitrogen limitation; longerterm microalgal growth is supported by the enhanced flux of NH 4 + that occurs in contaminated sediments. The enhanced NH 4 + flux is likely a consequence of an altered microbial community and could have long-term biogeochemical consequences for the ecological health of contaminated coastal communities.

The microbial communities of three different habitat types and from two sediment depths in the River Elbe were investigated by fluorescence in situ hybridization at various levels of complexity. Differences in the microbial community composition of free-flowing river water, water within the hyporheic interstitial and sediment-associated bacteria were quantitatively analyzed using domain- and group-specific oligonucleotide probes. Qualitative data on the presence/absence of specific bacterial taxa were gathered using genus- and species-specific probes. The complete data set was statistically processed by univariate statistical approaches, and two-dimensional ordinations of nonmetric multidimensional scaling. The analysis showed: (1) that the resolution of microbial community structures at microenvironments, habitats and locations can be regulated by targeted application of oligonucleotides on phylogenetic levels ranging from domains to species, and (2) that an extensive qualitative presence/absence analysis of multiparallel hybridization assays enables a fine-scale apportionment of spatial differences in microbial community structures that is robust against apparent limitations of fluorescence in situ hybridization such as false positive hybridization signals or inaccessibility of in situ oligonucleotide probes. A general model for the correlation of the phylogenetic depth of focus and the relative spatial resolution of microbial communities by fluorescence in situ hybridization is presented.