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Supplemental Information

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).

DOI: 10.7287/peerj.preprints.2051v1/supp-1

Table 2. Significant log/log Pearson correlations between rDNA abundance and totalRNA/rDNA ratios

Taxa ordered after their Pearson’s R value from strongest to weakest correlation.

DOI: 10.7287/peerj.preprints.2051v1/supp-2

Figure 1. Distribution of major taxonomic groups among amplicon OTUs

Distribution of phyla and proteobacterial classes in the three datasets, counted in rDNA amplicon OTUs.

DOI: 10.7287/peerj.preprints.2051v1/supp-3

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.

DOI: 10.7287/peerj.preprints.2051v1/supp-4

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.

DOI: 10.7287/peerj.preprints.2051v1/supp-5

Figure 4. TotalRNA/rDNA ratio medians and rDNA abundances per family

Families larger than 1 % in either the totalRNA or the rDNA datasets are presented with their median totalRNA/rDNA ratios and rDNA relative abundances. Note that both scales are logarithmic.

DOI: 10.7287/peerj.preprints.2051v1/supp-6

Figure 5. Ab initio identified 16S sequences

A) Proportion of phyla and proteobacterial classes in amplicon-independent totalRNA and totalDNA analysis. B) TotalRNA/totalDNA ratios for orders appearing in the totalDNA dataset.

DOI: 10.7287/peerj.preprints.2051v1/supp-7

Supplementary Table S1. OTU table

OTUs defined in the rDNA dataset and quantified in the totalDNA and totalRNA datasets.

DOI: 10.7287/peerj.preprints.2051v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Petter Thureborn conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Yue O.O. Hu performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Andrea Franzetti analyzed the data, wrote the paper, reviewed drafts of the paper.

Sara Sjöling conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Daniel Lundin conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

ENA PRJEB13658

Data Deposition

The following information was supplied regarding data availability:

Raw data details supplied under DNA sequencing clause.

Funding

The work was funded by the Foundation for Baltic and East European Studies 1169/42/2007:17 (www.ostersjostiftelsen.se) to SS, Britt-Marie Sjöberg and Anthony Poole, the EU Metaexplore project (KBBE-222625) to SS and Stockholm Läns Landsting to SS and PT. YOOH was supported by a scholarship from the China Scholarship Council (CSC#201206950024). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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