Locations of the sampling sites on the west coast of the Dead Sea, showing the northern and southern spring systems.

<p>Underwater springs with the corresponding reference site are marked with blue and red circles, whereas shore springs together with their reference site are marked with green and red squares, respectively. The open-water reference site for the shore springs was used only for comparison of dissolved organic matter (DOM) and total dissolved nitrogen (TDN). The open blue circle is located in the center of an underwater spring upwelling and was sampled for DOM and TDN analysis. The contour lines on the left panel represent the yearly drop in the lake level and are a close approximation of the areal topography. The satellite image was created using Google Earth.</p

Seawater normalized (C_sw) concentrations of major ions in waters from the underwater springs (A) and from reference sites (B).

<p>The concentrations are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone-0038319-t002" target="_blank">Table 2</a> and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319.s008" target="_blank">Table S1</a>. The ions are arranged along the x-axis based on their natural behavior: heavy alkalis Cs and Rb are mainly controlled by surfaces such as those of clay minerals; K, Na, Cl and Br stand for brines and salt minerals (halides); SO₄, Ca, Sr, Mg, Ba and HCO₃ represent dissolved species from carbonate-sulfate minerals (e.g., anhydrite/gypsum, aragonite and barite). All these minerals are abundant in the Dead Sea sediments. (C) Ratios between the measured ion concentrations and those calculated by a two-component mixing model (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone-0038319-t002" target="_blank">Table 2</a> for the estimated mixing coefficients) using the Jericho 5 freshwater and either the Dead Sea pore water or the Qedem brine as end-members.</p

Water chemistry of underwater springs and auxiliary sites.

*<p>Taken from Stein et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-Stein1" target="_blank">[93]</a>;</p>†<p>Taken from Gross <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-Barkan1" target="_blank">[47]</a>;</p>#<p>Taken from Stiller and Nissenbaum <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-Stiller1" target="_blank">[76]</a>.</p><p>Classification based on REY: L- Limestone group;D1- Dead Sea group, subgroup 1;D2- Dead Sea group, subgroup 2.</p><p>Chemical composition and other characteristics of the waters from the Dead Sea, underwater springs, shore springs and additional auxiliary sites. Mixing coefficients represent the calculated percentages of brine (either porewater or the Qedem brine) admixed to the freshwater from the Jericho 5 well that best explain the measured concentrations of K, Cl and Br as well as the ratios of Cl/Br and Ca/Mg. PW/− denotes mixture of the porewater and freshwater, −/Q denotes mixture of the Qedem brine and freshwater.</p

(A) Examples of absorption spectra of green biofilm samples from spring 12.

<p>Locations where these spectra were taken are shown by arrows in panel C. Major peaks at 675 nm and 740 nm correspond to in vivo absorption maxima of chlorophyll a and bacteriochlorophyll c, respectively. (B–C) Distributions of pigments in whole-biofilm samples (B) and inbiofilm samples under the microscope(C). Pigments characteristic for cyanobacteria (chlorophyll a and phycocyanin) are shown in red, whereas the pigment characteristic for green sulfur bacteria (bacteriochlorophyll c) is shown in green. Cyanobacteria were always co-localized with the green sulfur bacteria and never detected alone.</p

Non Metric Multidimensional Scaling (NMDS) plots derived by the DICE algorithm from the (A) 454 pyrosequencing and (B) ARISA data, using stress values of 13% and 7%, respectively.

<p>Clustering of the pyrosequencing data was performed on the data matrix produced by the NGS system at a taxonomic depth of 5 (Family level). Duplicate samples represent biological replicates. Data for the 1992 and 2007 analyses where obtained from Rhodes et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-LaronneBenItzhak2" target="_blank">[31]</a> and Bodaker et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-Mller1" target="_blank">[30]</a> respectively.</p

(A) Total counts of DAPI-stained cells and (B) percentage abundance of Archaea and Bacteria within the total cell counts in water samples collected from different underwater springs and from the reference Dead Sea water.

<p>Wn denotes water sample from spring n. Error-bars indicate standard error (N = 10); NA = data not available.</p

Sketch of the northern spring system.

<p>The water seep shown on the slope of the sketch is found only in deeper parts of the southern system where water seeps through the sediment surface over a large area without defined boundaries. The shafts have steep, laminated walls (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319.s001" target="_blank">Fig. S1A</a>) and contain one or more springs (blue). Localized water sources are either directly visible on the shaft bottom (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319.s001" target="_blank">Fig. S1B</a>) or are hidden within deeper cavities (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319.s001" target="_blank">Fig. S1C</a>). In the southern spring system (not shown in the sketch) springs do not form shafts and are covered by cobbles (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319.s001" target="_blank">Fig. S1D</a>).</p

Graphical representation of the sequence frequency in the studied Dead Sea samples, showing major detected classes within the Bacterial and Archaeal domains.

<p>Classes belonging to Crenarchaea and Euryarchaea are marked by brackets 1 and 2, respectively. The Halobacteria and Thermoplasmata classes are shown also at the family level to facilitate a more specific sample comparison. The color of the symbol represents the relative frequency of the taxonomic path within the sample. The size of the symbol represents the number of OTUs at deeper phylogenetic levels within that taxonomic path (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#s2" target="_blank">Methods</a> for the definition of OTU). The shape of the symbol represents the number of sequences in the specific taxonomic path. Columns are shaded according to the sample type: blue = spring water, brown = spring sediment, grey = white biofilms from northern springs, white = white biofilms from southern springs, green = green biofilms from southern springs. Abbreviations in sample names: W = spring water. S = spring sediment, WB = white biofilm, GB = green biofilm, S-REF = reference sediment from the Dead Sea.</p

Type of samples collected from the different underwater springs and auxiliary sites, and of analyses preformed.

<p>The northern system (springs 1<b>–</b>5), southern system (springs 10–12) and auxiliary sites are shaded in light and dark grey respectively. Community analysis refers to 454 pyrosequencing and Automated Ribosomal Intergenic Spacer Analysis (ARISA), pigment analysis was done by hyper-spectral imaging. Auja and Jericho 5 wells represent waters from the Lower Judea Group Aquifer (Mekorot Co., personal comm.), whereas Mitzpe Jericho 2 and Qilt springs represent waters originating from the marly sequences of the Upper Judea Group Aquifer (Mekorot Co., personal comm.). Qedem brine represents ascending water from the deep thermal aquifer south of the sampling area <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038319#pone.0038319-LaronneBenItzhak1" target="_blank">[10]</a>. Pore water was sampled at a depth of 0.7 m below surface next to shore spring 3. The sample code field refers to the naming of the respective sample in subsequent analyses. W, S, B stand for water, sediment and biofilm respectively; w/g refers to white/green biofilms; SP# refers to the identification number of the spring.</p

Graphical representation of the sequence frequency in the studied Dead Sea samples, showing major detected phyla and families of different functional groups of Bacteria.

<p>PSB and PNSB in panel B refer to purple sulfur and non sulfur bacteria, respectively. The different genera within the families Chlorobiaceae,Campylobacteraceae and Helicobacteraceaeare shown to facilitate a more specific sample comparison. The symbols and sample naming are explained in detail in Fig. 8. Note different legends for OTU/path for each panel, and scale-bars for relative sequence frequency for several combined panels.</p