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, β‐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 β‐Proteobacteria, as relevant in situ members of the ‘river snow’ community.

Organic-Aggregate-Attached Bacteria in Aquatic Ecosystems: Abundance, Diversity, Community Dynamics and Function

“…Using fluorescent in situ hybridization, Böckelmann et al (2000), in the Elbe River of Germany, found that the bacterial aggregate community varied over the course of the year. During all seasons, -proteobacteria constituted the numerically most important bacterial group constituting ~54% of the total DAPI-stainable cells.…”

Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria

“…In this regard, many studies have demonstrated that knowledge of the structure and dynamics of the microbial community in rivers and streams is essential, mainly due to their role in several biogeochemical cycles (Brümmer et al, 2000;Araya et al, 2003;Kostanjšek et al, 2005). This is especially important for environments modified by anthropogenic action (Böckelmanna et al, 2000;Kenzaka et al, 2001;Tiquia, 2010).…”

“…Conventional methods based on microbiological culture cannot provide a representative composition of the microbial community (Böckelmanna et al, 2000). Alternatively, molecular biology techniques can be used.…”

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“…A 0.5-liter subsample for determinations of bacterial numbers and OA abundance was fixed immediately with a final concentration of 2.0% formaldehyde. The method for collecting the aggregates was modified after Bö ckelmann et al (2000). To avoid undue influence from the planktonic bacteria in the water column, the major part of the lake water was discarded after 1-h sedimentation.…”

“…500 mm) harbor specific aggregate-adapted microbial populations. For example, Betaproteobacteria were the numerically most important bacterial group in lotic microbial aggregates (river snow) from the Elbe River (Bö ckelmann et al 2000), and in lake macroaggregates (lake snow) from the Lake Constance (Weiss et al 1996;Schweitzer et al 2001), whereas Cytophaga, Planctomyces, and Gammaproteobacteria dominated in phytodetrital macroaggregates (marine snow) from the Santa Barbara Channel (Delong et al 1993).…”