This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.salinesystems.org The latest articles from Saline Systems (ISSN 1746-1448) published by BioMed Central The significance of the transport of nutrient-rich hypolimnetic water via the benthic boundary layer (BBL) to the productivity of Mono Lake was studied using a coupled hydrodynamic and ecological model validated against field data. The coupled model enabled us to differentiate between the role of biotic components and hydrodynamic forcing on the internal recycling of nutrients necessary to sustain primary productivity. A 4-year period (1991-1994) was simulated in which recycled nutrients from zooplankton excretion and bacterially-mediated mineralization exceeded sediment fluxes as the dominant source for primary productivity. Model outputs indicated that BBL transport was responsible for a 53% increase in the flux of hypolimnetic ammonium to the photic zone during stratification with an increase in primary production of 6% and secondary production of 5%. Although the estimated impact of BBL transport on the productivity of Mono Lake was not large, significant nutrient fluxes were simulated during periods when BBL transport was most active. http://www.salinesystems.org/content/4/1/11 Louise C Bruce, Robert Jellison, Jorg Imberger and John M Melack Saline Systems 2008, 4:11 2008-08-19 doi:10.1186/1746-1448-4-11 Saline Systems 1746-1448 4 11 2008-08-19 Background: Extracellular dissolved DNA has been demonstrated to be present in many terrestrial and aquatic environments, actively secreted, or released by decaying cells. Free DNA has the genetic potential to be acquired by living competent cells by horizontal gene transfer mediated by natural transformation. Aim of this work is to study the persistence of extracellular DNA and its biological transforming activity in extreme environments like the deep hypersaline anoxic lakes of the Mediterranean Sea. The brine lakes are separated from the upper seawater by a steep chemocline inhabited by stratified prokaryotic networks, where cells sinking through the depth profile encounter increasing salinity values and osmotic stress. Results: Seven strains belonging to different taxonomic groups isolated from the seawater-brine interface of four hypersaline lakes were grown at medium salinity and then incubated in the brines. The osmotic stress induced the death of all the inoculated cells in variable time periods, between 2 hours and 144 days, depending on the type of brine rather than the taxonomic group of the strains, i.e. Bacillaceae or gamma-proteobacteria. The Discovery lake confirmed to be the most aggressive environment toward living cells. In all the brines and in deep seawater dissolved plasmid DNA demonstrated to be substantially preserved for a period of 32 days in axenic conditions. L'Atalante and Bannock brines induced a decrease of the supercoiled form up to 70 and 40% respectively, in the other brines only minor changes in plasmid conformation were observed. Plasmid DNA after incubation in the brines demonstrated to maintain the capacity to transform naturally competent cells of Acinetobacter baylii strain BD413. Conclusions: Free dissolved DNA is likely to be released by the lysis of cells induced by osmotic stress in the deep hypersaline anoxic lakes. Naked DNA was demonstrated to be preserved and biologically active in these extreme environments, and hence could constitute a genetic reservoir of traits acquirable by horizontal gene transfer. http://www.salinesystems.org/content/4/1/10 Sara Borin, Elena Crotti, Francesca Mapelli, Isabella Tamagnini, Cesare Corselli and Daniele Daffonchio Saline Systems 2008, 4:10 2008-08-05 doi:10.1186/1746-1448-4-10 Saline Systems 1746-1448 4 10 2008-08-05 The nitrogen cycle (N-cycle), principally supported by prokaryotes, involves different redox reactions mainly focused on assimilatory purposes or respiratory processes for energy conservation. As the N-cycle has important environmental implications, this biogeochemical cycle has become a major research topic during the last few years. However, although N-cycle metabolic pathways have been studied extensively in Bacteria or Eukarya, relatively little is known in the Archaea. Halophilic Archaea are the predominant microorganisms in hot and hypersaline environments such as salted lakes, hot springs or salted ponds. Consequently, the denitrifying haloarchaea that sustain the nitrogen cycle under these conditions have emerged as an important target for research aimed at understanding microbial life in these extreme environments.The haloarchaeon Haloferax mediterranei was isolated 20 years ago from Santa Pola salted ponds (Alicante, Spain). It was described as a denitrifier and it is also able to grow using NO3-, NO2- or NH4+ as inorganic nitrogen sources. This review summarizes the advances that have been made in understanding the N-cycle in halophilic archaea using Hfx mediterranei as a haloarchaeal model. The results obtained show that this microorganism could be very attractive for bioremediation applications in those areas where high salt, nitrate and nitrite concentrations are found in ground waters and soils. http://www.salinesystems.org/content/4/1/9 María José Bonete, Rosa María Martínez-Espinosa, Carmen Pire, Basilio Zafrilla and David J Richardson Saline Systems 2008, 4:9 2008-07-01 doi:10.1186/1746-1448-4-9 Saline Systems 1746-1448 4 9 2008-07-01 Background: The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored. Results: Eighty nine isolates were obtained from the sediments of four deep-sea, hypersaline anoxic brine lakes in the Eastern Mediterranean Sea: l'Atalante, Bannock, Discovery and Urania basins. This culture collection was dominated by representatives of the genus Bacillus and close relatives (90% of all isolates) that were investigated further. Physiological characterization of representative strains revealed large versatility with respect to enzyme activities or substrate utilization. Two third of the isolates did not grow at in-situ salinities and were presumably present as endospores. This is supported by high numbers of endospores in Bannock, Discovery and Urania basins ranging from 3.8 × 105 to 1.2 × 106 g-1 dw sediment. However, the remaining isolates were highly halotolerant growing at salinities of up to 30% NaCl. Some of the novel isolates affiliating with the genus Pontibacillus grew well under anoxic conditions in sulfidic medium by fermentation or anaerobic respiration using dimethylsulfoxide or trimethylamine N-oxide as electron acceptor. Conclusion: Some of the halophilic, facultatively anaerobic relatives of Bacillus appear well adapted to life in this hostile environment and suggest the presence of actively growing microbial communities in the NaCl-rich, deep-sea brine-lake sediments. http://www.salinesystems.org/content/4/1/8 Andrea M Sass, Boyd A McKew, Henrik Sass, Jörg Fichtel, Kenneth N Timmis and Terry J McGenity Saline Systems 2008, 4:8 2008-06-09 doi:10.1186/1746-1448-4-8 Saline Systems 1746-1448 4 8 2008-06-09 Background: In spite of considerable efforts over past decades we still know relatively little regarding the biogeography of rotifers of inland waters in México. To help rectify this we undertook an extensive survey of the rotifer fauna of 48 water bodies in the Chihuahuan Desert of México. Results: Of the sites surveyed, 21 had salinities ≥ 2000 μS cm-1 and in these we found 57 species of monogonont rotifers and several bdelloids. Species richness in the saline sites varied widely, with a range in species richness of 1 to 27 and a mean (± 1SD) = 8.8 (± 6.2). Collectively all sites possess relatively high percent single- and doubletons, 33.3 and 21.7%, respectively. Simpson's Asymmetric Index indicated that similarity in rotifer species composition varied widely among a set of 10 sites. These were selected because they were sampled more frequently or represent unusual habitats. These SAI values ranged from 0.00 (complete dissimilarity) to 1.00 (complete similarity). The Jaccard Index varied between 0.00 and 0.35. This observation probably reflects similarities and differences in water chemistry among these sites. Inland saline systems differed in their chemical composition by region. Conductivity was related to hardness and alkalinity. In addition, hardness was positively associated with chloride and sulfate. RDA showed that several species were positively associated with chloride concentration. Other factors that were significantly associated with rotifer species included the presence of macrophytes, nitrate content, oxygen concentration, TDS, latitude and whether the habitat was a large lake or reservoir. Conclusion: This study illustrates the diversity of the rotiferan fauna of inland saline systems and the uniqueness among waterbodies. Conservation of these systems is needed to preserve these unique sources of biodiversity that include rotifers and the other endemic species found in association with them. http://www.salinesystems.org/content/4/1/7 Elizabeth J Walsh, Thomas Schröder, Robert L Wallace, Judith V Ríos-Arana and Roberto Rico-Martínez Saline Systems 2008, 4:7 2008-06-04 doi:10.1186/1746-1448-4-7 Saline Systems 1746-1448 4 7 2008-06-04 Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications.Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics. http://www.salinesystems.org/content/4/1/6 Matthias Kurz Saline Systems 2008, 4:6 2008-06-03 doi:10.1186/1746-1448-4-6 Saline Systems 1746-1448 4 6 2008-06-03 The consistent use of the taxonomic system of binomial nomenclature (genus and species) was first popularized by Linnaeus nearly three-hundred years ago to classify mainly plants and animals. His main goal was to give labels that would ensure that biologists could agree on which organism was under investigation. One-hundred fifty years later, Darwin considered the term species as one of convenience and not essentially different from variety. In the modern era, exploration of the world's niches together with advances in genomics have expanded the number of named species to over 1.8 million, including many microorganisms. However, even this large number excludes over 90% of microorganisms that have yet to be cultured or classified. In naming new isolates in the microbial world, the challenge remains the lack of a universally held and evenly applied standard for a species. The definition of species based on the capacity to form fertile offspring is not applicable to microorganisms and 70% DNA-DNA hybridization appears rather crude in light of the many completed genome sequences. The popular phylogenetic marker, 16S rRNA, is tricky for classification since it does not provide multiple characteristics or phenotypes used classically for this purpose. Using most criteria, agreement may usually be found at the genus level, but species level distinctions are problematic. These observations lend credence to the proposal that the species concept is flawed when applied to prokaryotes. In order to address this topic, we have examined the taxonomy of extremely halophilic Archaea, where the order, family, and even a genus designation have become obsolete, and the naming and renaming of certain species has led to much confusion in the scientific community. http://www.salinesystems.org/content/4/1/5 Priya DasSarma and Shiladitya DasSarma Saline Systems 2008, 4:5 2008-05-16 doi:10.1186/1746-1448-4-5 Saline Systems 1746-1448 4 5 2008-05-16 The moderate halophile Halobacillus halophilus is the paradigm for chloride dependent growth in prokaryotes. Recent experiments shed light on the molecular basis of the chloride dependence that is reviewed here. In the presence of moderate salinities Halobacillus halophilus mainly accumulates glutamine and glutamate to adjust turgor. The transcription of glnA2 (encoding a glutamine synthetase) as well as the glutamine synthetase activity were identified as chloride dependent steps. Halobacillus halophilus switches its osmolyte strategy and produces proline as the main compatible solute at high salinities. Furthermore, Halobacillus halophilus also shifts its osmolyte strategy at the transition from the exponential to the stationary phase where proline is exchanged by ectoine. Glutamate was found as a “second messenger” essential for proline production. This observation leads to a new model of sensing salinity by sensing the physico-chemical properties of different anions. http://www.salinesystems.org/content/4/1/4 Stephan H Saum and Volker Müller Saline Systems 2008, 4:4 2008-04-28 doi:10.1186/1746-1448-4-4 Saline Systems 1746-1448 4 4 2008-04-28 Background: The Northern Great Plains of Canada are home to numerous permanent and ephemeral athalassohaline lakes. These lakes display a wide range of ion compositions, salinities, stratification patterns, and ecosystems. Many of these lakes are ecologically and economically significant to the Great Plains Region. A survey of the physical characteristics and chemistry of 19 lakes was carried out to assess their suitability for testing new tools for determining past salinity from the sediment record. Results: Data on total dissolved solids (TDS), specific conductivity, temperature, dissolved oxygen (DO), and pH were measured in June, 2007. A comparison of these data with past measurements indicates that salinity is declining at Little Manitou and Big Quill Lakes in the province of Saskatchewan. However salinity is rising at other lakes in the region, including Redberry and Manito Lakes. Conclusion: The wide range of salinities found across a small geographic area makes the Canadian saline lakes region ideal for testing salinity proxies. A nonlinear increase in salinity at Redberry Lake is likely influenced by its morphometry. This acceleration has ecological implications for the migratory bird species found within the Redberry Important Bird Area. http://www.salinesystems.org/content/4/1/3 Jeff S Bowman and Julian P Sachs Saline Systems 2008, 4:3 2008-04-22 doi:10.1186/1746-1448-4-3 Saline Systems 1746-1448 4 3 2008-04-22 Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100–150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine, ectoine and other amino acid derivatives, sugars and sugar alcohols. The 'high-salt-in strategy' is not limited to the Halobacteriaceae. The Halanaerobiales (Firmicutes) also accumulate salt rather than organic solutes. A third, phylogenetically unrelated organism accumulates KCl: the red extremely halophilic Salinibacter (Bacteroidetes), recently isolated from saltern crystallizer brines. Analysis of its genome showed many points of resemblance with the Halobacteriaceae, probably resulting from extensive horizontal gene transfer. The case of Salinibacter shows that more unusual types of halophiles may be waiting to be discovered. http://www.salinesystems.org/content/4/1/2 Aharon Oren Saline Systems 2008, 4:2 2008-04-15 doi:10.1186/1746-1448-4-2 Saline Systems 1746-1448 4 2 2008-04-15