Chemical and microbiological in situ characterization of benthic communities in sediments with different contamination levels

Background. River sediments are natural habitats of complex bacterial and fungal communities and therefore play a decisive role in the mineralization process of organic matter in freshwater systems. By means of comparative temporal and spatial analyses of microbial communities, the in situ impact of anthropogenically generated pollutants on these biofilm associations can be assessed and discriminated from seasonal variations. Aim. The aim was the adaptation of hybridization with fluorescently labelled rRNA-targeted oligonucleotides (FISH) for the in situ characterization of the structural and functional diversity of native microbial communities in complex lotic sediments. The impact of qualitatively and quantitatively different water pollutants on the microbial diversity, metabolic potential, and relative abundance of characteristic bacterial groups was assessed by oligonucleotide probes on different phylogenetic levels. In particular, sulfate reducing bacteria (SRB) were investigated to evaluate their potential applicability as microbial biomonitors in sediments. Methods. Sediment samples from the German lowland rivers Elbe and Oder were investigated over 12 months with regard to physico-chemical parameters and the composition of the attached microbial communities. Mechanical treatment including ultrasonification and sagitation under aerobic conditions combined with the use of pyrophosphate ensured the equal dispersion of fixed microbial cells within the sediment samples. The optimized whole-sediment FISH-technique was combined with an improved cell extraction procedure and applied, due to the specific grain size fraction distribution, at the different sampling sites. Results and discussion. Up to 85.6% of the total bacterial cell counts as determined by DAPI (4′, 6-diamidino-2-phenylindole) staining could be successfully monitored by the eubacterial oligonucleotide probe set EUB338, EUB338-II and EUB338-III, simultaneously indicating a high proportion of Eubacteria and the high metabolic potential of the bacterial community. Desulfobacteriaceae could be detected by the specific probe SRB385Db in various relative percentages ranging from 2.4 to 16.0% of the total bacterial cell counts. The total number of bacteria and the metabolic potential of sediment related bacteria were barely affected by the different pollution pattern of the sampling sites. Conclusions. The pre-treatment step as conducted by cell extraction as well as the FISH hybridization procedure was successfully optimized to the specific conditions present within freshwater sediments. Beside seasonal variations, particularly occurring at hydrologically influenced sites, sampling sites with different pollution levels could be successfully distinguished by the relative abundance of Desulfobacteriaceae used as microbial indicator organisms. Outlook. The integration of ongoing insights into pollution induced changes of natural bacterial consortia should result in a system of ecotoxicological classes representing the different ecological status of riverine systems. Physiological directed methods like Community Level Physiological Profiling (CLPP) or Pollution Induced Community Tolerance (PICT), and structural techniques as FISH or microarrays should be used to investigate the influence of harmful substances on the biodiversity in natural microbial sediment communities.