Brettar I, Christen R, HöFle MG.. Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships. ISME J 6: 195-212

Department of Vaccinology and Applied Microbiology, Helmholtz Centre of Infection Research (HZI), Braunschweig, Germany.
The ISME Journal (Impact Factor: 9.3). 06/2011; 6(1):195-212. DOI: 10.1038/ismej.2011.80
Source: PubMed


Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.

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    • "In other words, bacterial cells that contribute substantially to the DNA pool are also active, possibly indicating tight coupling between bacterial community composition and activity. This trend toward tighter coupling of bacterial presence and activity was previously attributed to decreased oxidative stress in anoxic deep water (Brettar et al., 2012) but is documented here in oxygenated deep waters. In contrast to the mid-water sample, the offshore surface and deepwater samples as well as the coastal station contain several OTUs that appear on DNA level but without counterparts in the RNA data sets, indicating some bacterial populations with attenuated activity and rRNA content, or entirely inactive populations (Supplementary Figure S3). "
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    • "The bacterial richness at 97% sequence similarity of the analyzed samples was ranked, from high to low, as food waste > AD sludge > cellulose > xylan and archaeal richness as food waste > xylan > cellulose > AD sludge (Table 1). In general, richness in archaea was lower than bacteria but the richness observed in the RNA was not significantly less than the gDNA, indicating that a significant portion of the microbial populations were metabolically active during the transformation of the amended substrates and the presence of diverse active members has previously been observed in environmental systems (Brettar et al., 2012). "
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    • "Furthermore, the stability of RNA is known to be much lower than for DNA due to major structural differences leading to different sensitivities to hydrolysis . Therefore, as exemplified by several ecological studies (eg Wrighton et al. 2008; Brettar et al. 2012), the possibility of carrying out RNA-based studies of bacterial communities associated with corrosion products may contribute to providing a more accurate and dynamic picture of the structure of bacterial communities , the dominant metabolic processes and the potential interactions with corrosion product formation and the metal surface. "
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