Multivariate analysis of microbial communities in the River Elbe (Germany) on different phylogenetic and spatial levels of resolution

Abstract

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.

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments

“…We provide additional evidence that molecular techniques, such as TRFLP, were useful in testing hypotheses on seasonal community composition and physicochemical parameters (Battin, 2000;Feris et al, 2003a;Findlay et al, 2003). Some evidence suggests a clear separation in microbial community composition between sediment, river, and hyporheic water (Kloep et al, 2006), however, we show that the use of colonization corers to collect integrated sediment samples reflect the subsurface dynamics that occurred at each site. This approach ensures that the communities described using molecular techniques accurately represent bacteria that have colonized the cores as opposed to lysed or dead bacterial cells among the sediments.…”

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

“…Whole-cell hybridization techniques have routinely been applied for the molecular characterization of complex microbial communities for more than a decade, and they also provide quantitative data on the cellular level in terms of relative or even absolute abundances of selected populations (3). Recently, FISH analysis was also adapted to the characterization of microbial communities in lotic freshwater sediments (15,17). Moreover, identical RNA-targeting probes can be used in both formats, enabling high comparability of the two data sets.…”

Microbial leaf degraders in boreal streams: bringing together stochastic and deterministic regulators of community composition

“…, 2005), in the hyporheic zone (Feris et al. , 2004; Kloep et al. , 2006) or on leaf litter (this study).…”

“…However, the catchment influence is often masked by in‐stream variation of microbial communities among habitats. Thus, bacterial community structure in river sediments strongly varies with sediment depth, clearly indicating habitat‐specific impacts while, on a large‐scale over several hundred kilometres, variation in bacterial community structure in the upper sediment layer was minor (Kloep et al. , 2006).…”

“…, 2008). Accordingly, bacterial communities of separate but similar habitats within a catchment may be very similar, as in the sediments along the river continuum (Kloep, Manz & Röske, 2006), and in fine benthic organic matter in streams of a forested catchment (Fierer et al. , 2007).…”