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

<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.

<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

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

<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

Bacterial taxa of brackish sediments from the organic-rich Gulf of Finland of the northeastern Baltic sea.

<p>The 16S rRNA genes were cloned from the surface sediments of the estuary (10), eastern coastal (7) and western open-sea sites (4).</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.

<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

The research area and the sediment sampling sites.

<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

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

<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.

<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.

<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

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.

<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