8 research outputs found

    The research area and the sediment sampling sites.

    No full text
    <p>(A) Sediment sampling area in the northern Baltic Proper (1), in the Gulf of Finland (2−9), and in Ahvenkoskenlahti Bay (10−12) in the brackish Baltic Sea. The numbers refer to samplings site as follows: 1 = AS7, 2 = JML, 3 = C63, 4 = E3, 5 = GF2F, 6 = LL3A, 7 = Bisa1, 8 = XV1, 9 = BZ1, 10 = AHLA2, 11 = AHLA 6 and 12 = AHLA9. (B) A magnification of Ahvenkoskenlahti Bay and the location of sampling sites in the estuary.</p

    HaeIII-digested terminal restriction fragments of 16S rRNA genes, which correlated with the sediment chemical parameters (Figure 3B) of the Baltic Sea and their identification.

    No full text
    <p>T-RF = terminal restriction fragment, bp = base pairs.</p>a<p>Expected T-RFs based on virtual digestion of partial (appr. 400−500 bp) 16S rRNA gene sequences.</p>b<p>Observed T-RFs (27−700 bp) produced by terminal restriction fragment length polymorphism analysis of (1) 16S rRNA gene clones and (2) 16S rRNA genes of sediment samples.</p>c<p>Shift of 10 bp between expected and observed T-RFs was due to conditions in some of the capillary gel electrophoresis runs of digested 16S rRNA gene clones. Therefore, assignments of all T-RFs with observed lengths of 27−31 bp were used to identify T-RF 30 bp in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone-0067061-g003" target="_blank">Figure 3B</a>, derived from the sediment samples.</p>d<p><i>Bacteroidetes</i> incertae sedis.</p

    Effects of individual chemical parameters used in CAP analysis on bacteria community composition in the brackish sediment samples.

    No full text
    <p>The distance-based multivariate multiple regression analysis was performed on terminal restriction fragments of bacterial 16S rRNA genes produced by HaeIII and sediment chemical parameters.</p>1<p>Proportion of each chemical parameter in the variation in bacterial communities.</p>2<p>Cumulative proportion of chemical parameter in the variation in bacterial communities.</p

    Proportional effects of sediment chemical and spatial factors as well as other properties of the sampling sites on the variation in bacterial communities in organic-rich brackish sediments.

    No full text
    <p>Chemical parameters included those used in CAP (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone-0067061-g003" target="_blank">Figure 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone.0067061.s007" target="_blank">Dataset S2</a>). Spatial parameters included geographic coordinates and sediment depth, and other properties of the sampling sites consisted of sediment accumulation rate (SAR) and water depth (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone.0067061.s004" target="_blank">Table S1</a>).</p

    Relationships between bacterial communities and chemical parameters in organic-rich brackish Baltic Sea sediments.

    No full text
    <p>(A) Structure of the bacterial community composition constrained by chemical parameters, and (B) associations of bacterial community members with chemical parameters. Constrained analysis of principal coordinates (CAP), using Bray-Curtis distance, was performed on HaeIII terminal restriction fragments (T-RFs, n = 134, refer to Dataset 1 and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone-0067061-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone.0067061.s004" target="_blank">S2</a>) of the bacterial 16S rRNA genes and chemical parameters (red arrows) of sediment samples (n = 61). The chemical parameters were: HClCa = HCl-extractable calsium, NaBDMn = redox-sensitive (NaBD-extractable) manganese, NaOHMn = NaOH-extractable manganese, NaOHiP = immobile (NaOH-extractable) inorganic phosphorus, OrgC = organic carbon, OrgN = Organic nitrogen, OrgP = organic phosphorus. Numbers (A) on the top of the symbols indicate the sampling sites (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone-0067061-g001" target="_blank">Figures 1A and 1B</a>). Numbers in parentheses (B) indicate T-RFs (in bp). The letters below the numbers (B) denote the taxonomic assignments of T-RFs as follows: A = <i>Alphaproteobacteria</i>, Ana = <i>Anaerolineaceae</i>, B = <i>Betaproteobacteria</i>, F = <i>Flavobacteria</i>, G = <i>Gammaproteobacteria</i>, N = <i>Nitrospira</i>, P = <i>Planctomycetaceae</i>, S = <i>Sphingobacteria</i>, SRB = Sulphate-reducing bacteria, V = <i>Verrucomicrobia</i>. Only T-RFs with canonical scores above 0.2 for axes 1 and 2 were included.</p

    Characteristic T-RFs of bacterial communities in the estuary, coastal and open-sea sediment samples and in the sediment samples from different depths.

    No full text
    <p>Distance-based discriminant analysis was performed on bacterial T-RF data (produced by HaeIII), which were divided into <i>a priori</i> groups of (A) estuary, coastal and open-sea sediments as well as (B) depth classes. Taxonomic assignments of T-RFs (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone.0067061.s005" target="_blank">Table S2</a>): Black numbers = <i>Alphaproteobacteria</i>, <i>Flavobacteria</i>, <i>Gammaproteobacteria</i> and/or <i>Sphingobacteria</i> (each T-RF represented more than one taxon), red numbers = <i>Chloroflexi</i> (mainly family <i>Anaerolineaceae</i>), green numbers = <i>Deltaproteobacteria</i>; sulphate reducing taxa, orange numbers = <i>Betaproteobacteria</i>, violet numers = <i>Clostridia</i>, and light blue numbers = <i>Planctomycetes</i>. Only those T-RFs that affected the differentiation of a <i>priori groups</i> (canonical scores of discriminant axes 1 and 2 were above 1.0) and which belonged to the most common bacterial groups in each <i>a priori</i> group were included.</p

    Ratios of organic carbon vs. organic nitrogen and organic carbon vs. organic phosphorus of the sediment samples.

    No full text
    <p>(A) Ratios of organic carbon vs. organic nitrogen and organic carbon vs. organic phosphorus along the continuum beginning from the Baltic Proper and western Gulf of Finland towards the eastern Gulf of Finland (sampling sites 1−9), (B) in the Ahvenkoskenlahti Bay estuary (sampling sites 10−12) and along the sediment depth. Refer to locations of the sediment sampling sites in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067061#pone-0067061-g001" target="_blank">Figures 1A and 1B</a>.</p
    corecore