Characterization of the microbial community of lotic organic aggregates (‘river snow’) in the Elbe River of Germany by cultivation and molecular methods

Abstract

Aerobic and anaerobic cultivation techniques, 16S rDNA-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates ('river snow') obtained from the river Elbe. In the course of the year the 'river snow' community changed. It was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and winter. In all 'river snow' samples, more than 70% of the bacteria counted with the general DNA stain DAPI also hybridized with the Bacteria-specific probe EUB338. In situ analysis of the bacterial 'river snow' community with a comprehensive suite of specific rRNA-targeted probes revealed population dynamics to be governed by seasonal factors. During all seasons, beta-Proteobacteria constituted the numerically most important bacterial group forming up to 54% of the total cell counts. In contrast to this, the relative abundance of other major bacterial lineages ranged from 2% for the order Planctomycetales to 36% for Cytophaga-Flavobacteria. Cultivation of 'river snow' under aerobic and anaerobic conditions with a variety of different media resulted in the isolation of 40 new bacterial strains. Phenotypic and phylogenetic analyses revealed these new strains to be mostly unknown organisms affiliated to different bacterial phyla. Application of newly developed specific oligonucleotide probes proved the cultivated bacteria, including clostridia and the numerically abundant beta-Proteobacteria, as relevant in situ members of the 'river snow' community.