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Thureborn P, Hu YOO, Franzetti A, Sjöling S, Lundin D. (2016) Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea. PeerJ Preprints4:e2051v1https://doi.org/10.7287/peerj.preprints.2051v1
Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.
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Table 1. Sequencing output and Shannon diversity
Number of sequence reads per sequence dataset that match OTU seed sequences, excluding chloroplast OTUs. Shannon diversity calculated as the mean of 50 subsampling iterations to 4,411 observations per sample (size of the totalDNA sample). In parentheses, values after subsampling to 22,350 (size of the rDNA sample).
Figure 2. Distribution of ratios between totalRNA and rDNA in OTUs among the major bacterial phyla and proteobacterial classes
A) Distributions of ratios between 0 and 100; and B) zoom in on ratios between 0 and 10. Taxa with a distribution of ratios significantly greater or lower than the community median (0.47) are indicated with green and yellow triangles, respectively. Taxa with a ratio not significantly higher nor lower than the community median (sign test, p < 0.05) are indicated by a blue circle. The community median (0.47) is indicated by a solid black line and interquartile limits are indicated by dashed lines. Only taxa with a frequency of at least 1% in one of the datasets are shown.
Figure 3. rDNA abundances as a function of totalRNA/rDNA ratios for the most abundant phyla and proteobacterial classes
For clarity, ratios were grouped into percentiles for which relative abundances were calculated by summing all OTUs’ relative abundances. Each symbol is one ratio percentile, plotted on the x-axes at the top totalRNA/rDNA ratio within the percentile. Taxa with a distribution of ratios among OTUs significantly higher than the community median are indicated in green; taxa significantly lower are indicated in yellow. In each taxon, the top two orders are indicated with colour and shape, excluding orders with a relative abundance lower than 0.5 %; all other orders are grouped in “Minor orders”. A linear model fitted to logarithms of each OTUs rDNA and totalRNA/rDNA ratio is shown. Community-wide median (solid line) and interquartile ranges (dashed lines) are indicated. Note that both the x-axes and y-axes are logarithmic.
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