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    Genebank identifiers of the nucleotide sequences of atpA, pheS and rpoA genes, used for the phylogenetic analyses. Table S2. NCBI Refseq/Genbank assembly accession numbers for the comparative genomic analysis of Leuconostoc species (29.09.2015). Table S3. L. gelidum subsp. gasicomitatum draft genomes statistics. Figure S1. Phylogenetic tree showing the relationship of L. citreum 1300_LCIT, L. gelidum subsp. gasicomitatum 1301_LGAS and L. inhae LMG 22919 genomes to other Leuconostoc species. (PDF 406 kb

    Diversity and seasonal dynamics of bacterial community in indoor environment-0

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    He number of sequences sampled in the pooled datasets of Building 1 (A) and Building 2 (B) at the evolutionary distance of 0.03. ▲, estimated number of OTUs; -, observed number of OTUs.<p><b>Copyright information:</b></p><p>Taken from "Diversity and seasonal dynamics of bacterial community in indoor environment"</p><p>http://www.biomedcentral.com/1471-2180/8/56</p><p>BMC Microbiology 2008;8():56-56.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2323381.</p><p></p

    Neighbor-joining phylogenetic tree of the partial 16S rRNA genes from stratified Baltic Sea sediments.

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    <p>In the inverted circular tree with a stacked bar chart (sea phases), red bars indicate the abundance of a leaf (sequence) found in the Litorina Sea laminae (depths 330 and 422 cm), blue bars the abundance of a leaf found in the Late Litorina Sea laminae (depths 91 and 101 cm) and the black bars the abundance of a leaf found in the Early Litorina lamina (depth 534 cm). The leaves without bars are reference sequences obtained using the NAST tool. Reliable branches are shown in the bootstrap tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054326#pone.0054326.s005" target="_blank">Fig. S5</a>). The clone sequences were assigned to phylum or class level (Proteobacteria) or to genus level (<i>Pseudomonas</i>) by the RDP classifier with an 80% threshold. The putative JS1 clones were assigned, based on the closest sequence matches, using the RDP seqmatch tool. Scale bar represents the genetic distance, i. e. the nucleotide substitutions per site.</p

    Diversity and seasonal dynamics of bacterial community in indoor environment-3

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    (P1) represents the season and P3 represents the building. 1, Building 1; 2, Building 2; W, winter; Sp, spring; Su, summer; F, fall.<p><b>Copyright information:</b></p><p>Taken from "Diversity and seasonal dynamics of bacterial community in indoor environment"</p><p>http://www.biomedcentral.com/1471-2180/8/56</p><p>BMC Microbiology 2008;8():56-56.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2323381.</p><p></p

    Spatial structure of bacterial communities along a sediment sample covering 8000 years of Baltic Sea history.

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    <p>The piecewise Mantel correlogram was based on the Bray and Curtis dissimilarity matrix (n = 148×219) of bacterial terminal restriction fragments of the 16S rRNA genes. Autocorrelations (Mantel r) were plotted against distance classes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054326#pone.0054326.s013" target="_blank">Table S6</a>), which were based on the Euclidean distance between sampling depths. Red, green and black circles represent the distinct trends detected. Filled circle: <i>P</i><0.05. Open circle: nonsignificant value.</p

    Association between bacterial sediment communities and chemical variables in Baltic Sea laminae.

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    <p>The black-filled circles indicate the sediment samples from the Early Litorina, red from the Litorina and blue from the Late Litorina sea phases. The numbers are rounded to the nearest integer. Canonical analysis of principal coordinates was based on the Bray Curtis dissimilarity matrix (n = 32×158) of bacterial terminal restriction fragments of the 16S rRNA gene. Samples and chemical parameters (purple arrows) were plotted against canonical axis scores 1 and 2. The chemical variables chosen explained 45% of the variation. Test statistics with 9999 permutations resulted in a highly significant <i>p</i> value (<i>p</i> = 1e-04), which allows rejection of the null hypothesis that there are no relationships between the bacterial communities and chemical variables. The length of the arrow indicates the strength of the correlation between the sediment samples and chemical parameter. An arrow direction indicates the increasing concentration of the chemical parameter.</p

    Diversity and seasonal dynamics of bacterial community in indoor environment-5

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    N the individual samples are displayed. Number of clones per season in the largest phyla is indicated in the row with the name of the phylum. 1, Building 1; 2, Building 2; W, winter; Sp, spring; Su, summer; F, fall. Uncultured refers to sequences of species not yet cultured; unknown refers to a sequence similarity less than 95% to a database sequence, however if the clone was clearly affiliated to a certain group in the phylogenetic tree, it was assigned to that group. In addition to the clones listed in the figure, there was one clone in Building 2, summer sample affiliating with Planctomycetes, one clone in Building 1, spring sample affiliating with Chloroflexi, and one clone with unknown phylogenetic affiliation in Building 1, winter and fall samples. The grey shading indicates the number of clones in the sample belonging to the respective family. White indicates zero clones, the grey shadings 1, 2–5, or 6–14 clones, and black indicates 15 or more clones.<p><b>Copyright information:</b></p><p>Taken from "Diversity and seasonal dynamics of bacterial community in indoor environment"</p><p>http://www.biomedcentral.com/1471-2180/8/56</p><p>BMC Microbiology 2008;8():56-56.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2323381.</p><p></p

    Diversity and seasonal dynamics of bacterial community in indoor environment-4

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    He number of sequences sampled in the pooled datasets of Building 1 (A) and Building 2 (B) at the evolutionary distance of 0.03. ▲, estimated number of OTUs; -, observed number of OTUs.<p><b>Copyright information:</b></p><p>Taken from "Diversity and seasonal dynamics of bacterial community in indoor environment"</p><p>http://www.biomedcentral.com/1471-2180/8/56</p><p>BMC Microbiology 2008;8():56-56.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2323381.</p><p></p

    Diversity and seasonal dynamics of bacterial community in indoor environment-2

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    M. Jackknife with 100 permutations was performed to assess the reliability of the tree. Jackknife values over 50 are given at the corresponding branches. 1, Building 1; 2, Building 2; W, winter; Sp, spring; Su, summer; F, fall.<p><b>Copyright information:</b></p><p>Taken from "Diversity and seasonal dynamics of bacterial community in indoor environment"</p><p>http://www.biomedcentral.com/1471-2180/8/56</p><p>BMC Microbiology 2008;8():56-56.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2323381.</p><p></p

    Identification of insertion-tolerant regions in MuA on the basis of pentapeptide insertion analysis and alignment-based data.

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    <p>Above the amino acid sequence are shown with arrows the pentapeptide-insertion tolerant sites (activity level ≥1%) colour-coded as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037922#pone-0037922-g004" target="_blank">Figure 4</a>. The percentage range chart is shown at the lower-right. Two or three arrows per site are indicative of insertions involving more than one reading frame. Below the amino acid sequence are shown the secondary structural elements (arrows and rectangles). The elements are connected with line segments indicating the length of each PDB structure. Below the structural elements are shown the subdomains as specified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037922#pone-0037922-g003" target="_blank">Figure 3</a>. Above the bolded line, the downward black and upward white arrows represent the alignment-based insertion and deletion (indel) data, respectively (each particular indel precedes the marked amino acid). The maximum indel length at each site is indicated by a number shown above each arrow (data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037922#pone.0037922.s001" target="_blank">Figure S1</a>). The stars indicate the DDE-motif residues (D269, D336, E392).</p
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