Archaeal diversity in the Dead Sea: Microbial survival under increasingly harsh conditions

The Dead Sea is rapidly drying out. The lake is supersaturated with NaCl, and precipitated of halite from the water column has led to a decrease in sodium content, while concentrations of magnesium and calcium greatly increased, making the lake an ever more extreme environment for microbial life. In the past decades, blooms of algae (Dunaliella) and halophilic Archaea were twice observed in the lake (1980-1982 and 1992-1995), triggered by massive inflow of freshwater floods, but no conditions suitable for renewed microbial growth have occurred since. To examine whether the Death Sea in its current state (density 1.24 g ml-1, water activity about 0.67) still supports life of halophilic Archaea, we collected particulate matter from a depth of 5 m at an offshore station by means of tangential filtration. Presence of bacterioruberin carotenoids, albeit at low concentrations, in the particulate material showed the members of the Halobactericacae were still present in the lake\u27s water column. Amplification of 16S rRNA genes from the biomass yielded genes with less than 95% identify with environmental sequences reported from other environments and only 85-95% identity with cultivated Halobacteriaceae. It is thus shown that the Dead Sea, in spite of the ever more adverse conditions to life, supports a unique and varied community of halophilic Archaea. We have also isolated a number of strains of Halobacteriaceae from the samples collected, and their characterization is currently in progress

Differences in lateral gene transfer in hypersaline versus thermal environments

<p>Abstract</p> <p>Background</p> <p>The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.</p> <p>Results</p> <p>We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.</p> <p>Conclusions</p> <p>Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.</p

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

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a w) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a w. Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a w). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 a w for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a w for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life

Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 77 (2011): 7647-7655, doi:10.1128/AEM.05565-11.The leaf surfaces of Tamarix, a salt secreting desert tree, harbor a diverse community of microbial epiphytes. This ecosystem presents a unique set of ecological characteristics and imposes a set of extreme stress conditions. The composition of the microbial community along ecological gradients was studied from analyses of microbial richness and diversity in the phyllosphere of three Tamarix species in the Mediterranean and Dead Sea regions in Israel, and in two locations in the USA. Over 200,000 sequences of the 16S-V6 and 18S-V9 hypervariable regions revealed a diverse community, with 788 bacterial and 64 eukaryotic genera, but only one archaeal genus. Both geographic location and tree species were determinants of microbial community structures, with the former being more dominant. Tree leaves of all three species in the Mediterranean region were dominated by Halomonas and Halobacteria, whereas trees from the Dead Sea area were dominated by Actinomycetales and Bacillales. Our findings demonstrate that microbial phyllosphere communities on different Tamarix species are highly similar in the same locale, whereas trees of the same species that grow in different climatic regions host distinct microbial communities.Research was supported in part by the US-Israel Binational Science Foundation grant number 2006324 to SB and SEL. OF and SB are indebted to the Gruss-Lipper Family Foundation for summer research fellowships (2009 and 2010) at the Marine Biology Laboratory (Woods Hole, MA, USA) that supported pyrosequencing and data analysis