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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Available from: Richard Christen, Oct 09, 2015
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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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    ABSTRACT: We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.
    The ISME Journal 04/2014; 8(11). DOI:10.1038/ismej.2014.67 · 9.30 Impact Factor
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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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    ABSTRACT: This study analyzed the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose or xylan) by barcoded 454 pyrosequencing of the bacterial and archaeal 16S rRNA genes in the DNA and RNA. The number of operational taxonomic units at 97% similarity for bacteria and archaea ranged from 162-261 and 31-166, respectively. Principal coordinates analysis and Venn diagram revealed that there were significant differences in the microbial community structure between the active members transforming each substrate and the inoculum. The active bacterial populations detected were those required for the hydrolysis of the amended substrate. The active archaeal populations were methanogens but the ratio of Methanosarcinales and Methanomicrobiales varied between the cultures. Overall, results of this study showed that a subset of the populations became active and altered in relative abundance during methane production according to the amended substrate.
    Bioresource Technology 09/2013; 148C:517-524. DOI:10.1016/j.biortech.2013.09.017 · 4.49 Impact Factor
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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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    ABSTRACT: Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high NA yield, quality, purity, representativeness of microbial community and processing time efficiency). The PowerSoil RNA Isolation Kit was the only method which resulted in amplifiable RNA of good quality (ie intact 16S/23S rRNA). Sample homogenization and hot chemical (SDS) cell lysis combined with mechanical (bead-beating) lysis in presence of a DNA competitor (skim milk) contributed to improving substantially (around 23 times) the DNA yield of the PowerSoil DNA Isolation Kit. Apart from presenting NA extraction strategies for optimizing extraction parameters with corrosion samples from carbon steel, this study proposes DNA and RNA extraction procedures suited for comparative molecular analysis of total and active fractions of bacterial communities associated with carbon steel corrosion events, thereby contributing to improved MIC diagnosis and control.
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