Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit.

[1]  J. Gat,et al.  Dissolved oxygen in the Dead Sea— seasonal changes during the holomictic stage , 1993 .

[2]  A. Post,et al.  Archaea in the Gulf of Aqaba. , 2009, FEMS microbiology ecology.

[3]  B. Schink.  The Genus Pelobacter , 1992 .

[4]  Ø. Hammer,et al.  PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS , 2001 .

[5]  M. Stein,et al.  Temporal Changes in Radiocarbon Reservoir Age in the Dead Sea-Lake Lisan System , 2004, Radiocarbon.

[6]  Martin Sauter,et al.  Using Thermal Infrared Imagery (TIR) for Illustrating the Submarine Groundwater Discharge into the Eastern Shoreline of the Dead Sea-Jordan , 2008 .

[7]  B. Spiro,et al.  The sulfur system in anoxic subsurface brines and its implication in brine evolutionary pathways: the Ca-chloride brines in the Dead Sea area , 2001 .

[8]  E. Stackebrandt,et al.  Nucleic acid techniques in bacterial systematics , 1991 .

[9]  A. Oren.  The dying Dead Sea: The microbiology of an increasingly extreme environment , 2010 .

[10]  N. Goldscheider,et al.  Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods , 2006 .

[11]  R. Amann,et al.  Community Structure, Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in Marine Arctic Sediments , 2000, Applied and Environmental Microbiology.

[12]  Dennis A. Hansell,et al.  Biogeochemistry of marine dissolved organic matter , 2002 .

[13]  D. Lovley,et al.  Fe(III) and S0 reduction by Pelobacter carbinolicus , 1995, Applied and environmental microbiology.

[14]  J. Overmann.  The Family Chlorobiaceae , 2006 .

[15]  S. Fitz-Gibbon,et al.  Amino acid signatures of salinity on an environmental scale with a focus on the Dead Sea. , 2010, Environmental microbiology.

[16]  I. Good,et al.  THE NUMBER OF NEW SPECIES, AND THE INCREASE IN POPULATION COVERAGE, WHEN A SAMPLE IS INCREASED , 1956 .

[17]  S. Bang,et al.  Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota , 2010, Environmental technology.

[18]  P. Dulski.  Interferences of oxide, hydroxide and chloride analyte species in the determination of rare earth elements in geological samples by inductively coupled plasma-mass spectrometry , 1994 .

[19]  H. Gvirtzman,et al.  Groundwater flow along and across structural folding: an example from the Judean Desert, Israel , 2005 .

[20]  Christina M. Preston,et al.  Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization , 1999, Applied and Environmental Microbiology.

[21]  K. Timmis,et al.  The Enigma of Prokaryotic Life in Deep Hypersaline Anoxic Basins , 2005, Science.

[22]  E. Rosenthal,et al.  Rare earths and yttrium hydrostratigraphy along the Lake Kinneret–Dead Sea–Arava transform fault, Israel and adjoining territories , 2003 .

[23]  Paul Stoodley,et al.  Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities , 2008, Applied and Environmental Microbiology.

[24]  Rudolf Amann,et al.  A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. , 2011, Systematic and applied microbiology.

[25]  K. Pedersen,et al.  Distribution and metabolic diversity of microorganisms in deep igneous rock aquifers of Finland , 1999 .

[26]  M. Wagner,et al.  Filamentous “Epsilonproteobacteria” Dominate Microbial Mats from Sulfidic Cave Springs , 2003, Applied and Environmental Microbiology.

[27]  Large-scale flow of geofluids at the Dead Sea Rift , 2000 .

[28]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[29]  D A Stahl,et al.  Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology , 1990, Journal of bacteriology.

[30]  D. Closson,et al.  Salt karst and tectonics: sinkholes development along tension cracks between parallel strike‐slip faults, Dead Sea, Jordan , 2009 .

[31]  B. Wilkansky.  Life in the Dead Sea , 1936, Nature.

[32]  B. Elazari-Volcani.  Bacteria in the Bottom Sediments of the Dead Sea , 1943, Nature.

[33]  B. Lazar,et al.  Dynamics of the carbon dioxide system in the Dead Sea , 2001 .

[34]  T. Schmidt,et al.  Archaeal nucleic acids in picoplankton from great lakes on three continents , 2003, Microbial Ecology.

[35]  R. Amann,et al.  A CARD-FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae. , 2006, Journal of microbiological methods.

[36]  Abdelkarim Saudi,et al.  GEOTHERMAL ENERGY RESOURCES IN JORDAN, COUNTRY UPDATE REPORT , 2000 .

[37]  Rarefaction and Taxonomic Diversity , 1982 .

[38]  P. Dulski.  Reference Materials for Geochemical Studies: New Analytical Data by ICP‐MS and Critical Discussion of Reference Values , 2001 .

[39]  O Hammer-Muntz,et al.  PAST: paleontological statistics software package for education and data analysis version 2.09 , 2001 .

[40]  D. Bryant,et al.  Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria , 2004, Archives of Microbiology.

[41]  J. Gat,et al.  The Dead Sea , 1983 .

[42]  S. Dowd,et al.  Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. , 2008, Foodborne pathogens and disease.

[43]  D. Lane.  16S/23S rRNA sequencing , 1991 .

[44]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[45]  M. J. Baedecker,et al.  Organic geochemistry of Dead Sea sediments , 1972 .

[46]  K. Johannesson,et al.  Rare earth element fractionation and concentration variations along a groundwater flow path within a shallow, basin-fill aquifer, southern Nevada, USA , 1999 .

[47]  A. Oren.  Halophilic Microorganisms and their Environments , 2002, Cellular Origin, Life in Extreme Habitats and Astrobiology.

[48]  R. Hannigan,et al.  The development of middle rare earth element enrichments in freshwaters: weathering of phosphate minerals , 2001 .

[49]  Joel D. Cline,et al.  SPECTROPHOTOMETRIC DETERMINATION OF HYDROGEN SULFIDE IN NATURAL WATERS1 , 1969 .

[50]  Itai Sharon,et al.  Comparative community genomics in the Dead Sea: an increasingly extreme environment , 2010, The ISME Journal.

[51]  A. Agnon,et al.  Earthquake-induced barium anomalies in the Lisan Formation, Dead Sea Rift valley, Israel , 2009 .

[52]  L. Forney,et al.  Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA , 1997, Applied and environmental microbiology.

[53]  Nissenbaum.  Geochemical investigation of phosphorus and nitrogen in the hypersaline Dead Sea Stiller, ARIE , 1999 .

[54]  Detection of Euryarchaeota and Crenarchaeota in an oxic basalt aquifer. , 2003, FEMS microbiology ecology.

[55]  B. Elazari-Volcani.  Algæ in the Bed of the Dead Sea , 1940, Nature.

[56]  M. Stiller,et al.  Iron in the Dead Sea , 1984 .

[57]  A. Oren,et al.  Biological effects of dilution of Dead Sea brine with seawater: implications for the planning of the Red Sea–Dead Sea “Peace Conduit” , 2004 .

[58]  B. Jørgensen,et al.  Adaptation to Hydrogen Sulfide of Oxygenic and Anoxygenic Photosynthesis among Cyanobacteria , 1986, Applied and environmental microbiology.

[59]  Yanan Shen,et al.  The antiquity of microbial sulfate reduction , 2004 .

[60]  E. Usdowski.  Das geochemische Verhalten des Strontiums bei der Genese und Diagenese von Ca-Karbonat- und Ca-Sulfat-Mineralen , 1973 .

[61]  K. Bosecker,et al.  Bioleaching: metal solubilization by microorganisms , 1997 .

[62]  J. Guttman,et al.  Hydrochemical processes in the lower Jordan valley and in the Dead Sea area , 2007 .

[63]  A. Starinsky,et al.  Geochemical History of the Dead Sea , 2009 .

[64]  G. Garrity.  Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[65]  B. Roe,et al.  Survey of Archaeal Diversity Reveals an Abundance of Halophilic Archaea in a Low-Salt, Sulfide- and Sulfur-Rich Spring , 2004, Applied and Environmental Microbiology.

[66]  J. Ganor,et al.  Kinetics of gypsum nucleation and crystal growth from Dead Sea brine , 2009 .

[67]  K. Schleifer,et al.  Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium , 1996, Archives of Microbiology.

[68]  W. Sand,et al.  Sulfur chemistry, biofilm, and the (in)direct attack mechanism — a critical evaluation of bacterial leaching , 1995, Applied Microbiology and Biotechnology.

[69]  J. Ehrenfeld,et al.  Ammonium oxidation coupled to dissimilatory reduction of iron under anaerobic conditions in wetland soils , 2005 .

[70]  M. Borghini,et al.  Unveiling microbial life in new deep-sea hypersaline Lake Thetis. Part I: Prokaryotes and environmental settings. , 2011, Environmental microbiology.

[71]  T. Hansen.  Bergey's Manual of Systematic Bacteriology , 2005 .

[72]  D. Graças,et al.  Microbial Diversity of an Anoxic Zone of a Hydroelectric Power Station Reservoir in Brazilian Amazonia , 2011, Microbial Ecology.

[73]  Karsten Pedersen,et al.  Distribution and activity of bacteria in deep granitic groundwaters of southeastern sweden , 1990, Microbial Ecology.

[74]  B. Patel,et al.  Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. , 1997, International journal of systematic bacteriology.

[75]  Daniel S. Jones,et al.  Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. , 2007, Environmental microbiology.

[76]  B. Elazari-Volcani.  A Ciliate from the Dead Sea , 1944, Nature.

[77]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[78]  T. Reinthaler,et al.  Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean , 2004, Applied and Environmental Microbiology.

[79]  D. Ionescu,et al.  Fatty acid analysis of a layered community of cyanobacteria developing in a hypersaline gypsum crust , 2005 .

[80]  A. Ramette.  Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities , 2009, Applied and Environmental Microbiology.

[81]  C. Siebert,et al.  Lake Tiberias and its dynamic hydrochemical environment , 2009 .

[82]  E. Donati,et al.  The role of Acidithiobacillus Caldud in the bioleaching of metal sulfides , 2002 .

[83]  J. Gat,et al.  Changes in the thermo-haline structure of the Dead Sea: 1979–1984 , 1987 .

[84]  F. Widdel,et al.  Anaerobic, nitrate-dependent microbial oxidation of ferrous iron , 1996, Applied and environmental microbiology.

[85]  A. Oren,et al.  Dynamics of a bloom of halophilic archaea in the Dead Sea , 1995, Hydrobiologia.

[86]  C. Siebert.  Saisonale chemische Variationen des See Genezareth, seiner Zuflüsse und deren Ursachen , 2006 .

[87]  P. Bennett,et al.  Microbial contributions to cave formation: New insights into sulfuric acid speleogenesis , 2004 .

[88]  B. Elazari-Volcani.  A Dimastigamœba in the Bed of the Dead Sea , 1943, Nature.

[89]  E. Delong.  Archaea in coastal marine environments. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[90]  J. Gat,et al.  The Dead Sea: Deepening of the Mixolimnion Signifies the Overture to Overturn of the Water Column , 1979, Science.

[91]  M. Bau.  Scavenging of dissolved yttrium and rare earths by precipitating iron oxyhydroxide: experimental evidence for Ce oxidation, Y-Ho fractionation, and lanthanide tetrad effect , 1999 .

[92]  Frede Thingstad,et al.  Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. , 2002, Environmental microbiology.