@article {3093, title = {Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis.}, journal = {PLoS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0170406}, abstract = {

The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.

}, keywords = {Biofilms, Biomass, Carbon, Clostridium, Culture Media, Culture Techniques, Fimbriae, Bacterial, Flagella, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Glass, Graphite, Osmotic Pressure, RNA, Bacterial, RNA, Ribosomal, Sodium Chloride, Spores, Bacterial, Stress, Physiological}, issn = {1932-6203}, doi = {10.1371/journal.pone.0170406}, author = {Philips, Jo and Rabaey, Korneel and Lovley, Derek R and Vargas, Madeline} } @article {1422, title = {Identification and characterization of a NaCl-responsive genetic locus involved in survival during desiccation in Sinorhizobium meliloti.}, journal = {Appl Environ Microbiol}, volume = {79}, year = {2013}, month = {2013 Sep}, pages = {5693-700}, abstract = {

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci asnO and ngg by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring ngg::Tn5luxAB was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a d-alanine-d-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to \β-lactam antibiotics. asnO::Tn5luxAB is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing \β-lactam inhibitors and increased resistance to \β-lactam antibiotics may indicate that asnO is involved in the production of a \β-lactam inhibitor.

}, keywords = {Desiccation, DNA Transposable Elements, Gene Expression Regulation, Bacterial, Gene Knockout Techniques, Genes, Bacterial, Genetic Loci, Microbial Viability, Mutagenesis, Insertional, Osmotic Pressure, Sinorhizobium meliloti, Sodium Chloride, Stress, Physiological}, issn = {1098-5336}, doi = {10.1128/AEM.01037-13}, author = {Vriezen, Jan A C and de Bruijn, Frans J and N{\"u}sslein, Klaus} } @article {1207, title = {Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04, isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge.}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Aug}, pages = {4434-5}, abstract = {

Pyrococcus sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further understand the distinct characteristics of this archaeon at the genome level (polysaccharide utilization at high temperature and ATP generation by a Na(+) gradient), the genome of strain ST04 was completely sequenced and analyzed. Here, we present the complete genome sequence analysis results of Pyrococcus sp. ST04 and report the major findings from the genome annotation, with a focus on its saccharolytic and metabolite production potential.

}, keywords = {Adenosine Triphosphate, Anaerobiosis, DNA, Archaeal, Genome, Archaeal, Heterotrophic Processes, Hydrothermal Vents, Molecular Sequence Data, Pacific Ocean, Polysaccharides, Pyrococcus, Seawater, Sequence Analysis, DNA, Sodium Chloride, Sulfides}, issn = {1098-5530}, doi = {10.1128/JB.00824-12}, author = {Jung, Jong-Hyun and Lee, Ju-Hoon and Holden, James F and Seo, Dong-Ho and Shin, Hakdong and Kim, Hae-Yeong and Kim, Wooki and Ryu, Sangryeol and Park, Cheon-Seok} } @article {744, title = {Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter.}, journal = {Appl Environ Microbiol}, volume = {73}, year = {2007}, month = {2007 Jul}, pages = {4171-9}, abstract = {The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl(-) in a subsurface shale rich in CH(4) derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH(4)-producing zone lacked electron acceptors such as O(2), NO(3)(-), Fe(3+), or SO(4)(2-). Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl(-) concentrations above approximately 1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H(2)/CO(2)) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH(4)-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters.}, keywords = {Archaea, Base Sequence, Cloning, Molecular, DNA Primers, Genes, Archaeal, Genetic Variation, Geologic Sediments, Methane, Michigan, Molecular Sequence Data, Organic Chemicals, Phylogeny, RNA, Archaeal, RNA, Ribosomal, 16S, Sodium Chloride, Soil, Soil Microbiology, Water Microbiology}, issn = {0099-2240}, doi = {10.1128/AEM.02810-06}, author = {Waldron, Patricia J and Petsch, Steven T and Martini, Anna M and N{\"u}sslein, Klaus and N{\"u}slein, Klaus} } @article {568, title = {Microorganisms associated with uranium bioremediation in a high-salinity subsurface sediment.}, journal = {Appl Environ Microbiol}, volume = {69}, year = {2003}, month = {2003 Jun}, pages = {3672-5}, abstract = {Although stimulation of dissimilatory metal reduction to promote the reductive precipitation of uranium has been shown to successfully remove uranium from some aquifer sediments, the organisms in the family Geobacteraceae that have been found to be associated with metal reduction in previous studies are not known to grow at the high salinities found in some uranium-contaminated groundwaters. Studies with a highly saline uranium-contaminated aquifer sediment demonstrated that the addition of acetate could stimulate the removal of U(VI) from the groundwater. This removal was associated with an enrichment in microorganisms most closely related to Pseudomonas and Desulfosporosinus species.}, keywords = {Acetates, Biodegradation, Environmental, DNA, Ribosomal, Fresh Water, Geologic Sediments, Peptococcaceae, Polymerase Chain Reaction, Pseudomonas, RNA, Ribosomal, 16S, Sodium Chloride, Uranium, Water Pollution}, issn = {0099-2240}, author = {Nevin, Kelly P and Finneran, Kevin T and Lovley, Derek R} } @article {569, title = {Thermophily in the Geobacteraceae: Geothermobacter ehrlichii gen. nov., sp. nov., a novel thermophilic member of the Geobacteraceae from the "Bag City" hydrothermal vent.}, journal = {Appl Environ Microbiol}, volume = {69}, year = {2003}, month = {2003 May}, pages = {2985-93}, abstract = {Little is known about the microbiology of the "Bag City" hydrothermal vent, which is part of a new eruption site on the Juan de Fuca Ridge and which is notable for its accumulation of polysaccharide on the sediment surface. A pure culture, designated strain SS015, was recovered from a vent fluid sample from the Bag City site through serial dilution in liquid medium with malate as the electron donor and Fe(III) oxide as the electron acceptor and then isolation of single colonies on solid Fe(III) oxide medium. The cells were gram-negative rods, about 0.5 micro m by 1.2 to 1.5 micro m, and motile and contained c-type cytochromes. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain SS015 placed it in the family Geobacteraceae in the delta subclass of the Proteobacteria. Unlike previously described members of the Geobacteraceae, which are mesophiles, strain SS015 was a thermophile and grew at temperatures of between 35 and 65 degrees C, with an optimum temperature of 55 degrees C. Like many previously described members of the Geobacteraceae, strain SS015 grew with organic acids as the electron donors and Fe(III) or nitrate as the electron acceptor, with nitrate being reduced to ammonia. Strain SS015 was unique among the Geobacteraceae in its ability to use sugars, starch, or amino acids as electron donors for Fe(III) reduction. Under stress conditions, strain SS015 produced copious quantities of extracellular polysaccharide, providing a model for the microbial production of the polysaccharide accumulation at the Bag City site. The 16S rDNA sequence of strain SS015 was less than 94\% similar to the sequences of previously described members of the Geobacteraceae; this fact, coupled with its unique physiological properties, suggests that strain SS015 represents a new genus in the family Geobacteraceae. The name Geothermobacter ehrlichii gen. nov., sp. nov., is proposed (ATCC BAA-635 and DSM 15274). Although strains of Geobacteraceae are known to be the predominant Fe(III)-reducing microorganisms in a variety of Fe(III)-reducing environments at moderate temperatures, strain SS015 represents the first described thermophilic member of the Geobacteraceae and thus extends the known environmental range of this family to hydrothermal environments.}, keywords = {Base Composition, Cytochromes, Deltaproteobacteria, DNA, Bacterial, DNA, Ribosomal, Drug Resistance, Bacterial, Ecosystem, Electron Transport, Geologic Sediments, Hot Temperature, Hydrogen-Ion Concentration, Iron, Microscopy, Electron, Molecular Sequence Data, Oxidation-Reduction, Pacific Ocean, Phylogeny, Seawater, Sodium Chloride, Species Specificity}, issn = {0099-2240}, author = {Kashefi, Kazem and Holmes, Dawn E and Baross, John A and Lovley, Derek R} } @article {1702, title = {Effect of sodium nitrate loading on electrolyte transport by the renal tubule.}, journal = {Am J Physiol}, volume = {229}, year = {1975}, month = {1975 Sep}, pages = {746-53}, abstract = {

Effects of sodium nitrate were compared with sodium chloride loading on transport of electrolytes by the nephron. Maximal levels of free water clearance/clomerular filtration rate (CH2O/GFR) averaged 8.4\% with nitrate loading and 14.4\% with saline loading. Since ethacrynic acid and chlorothiazide exert their major natriuretic effect in the distal nephron, the increment in Na ad Cl reabsorbed beyond the proximal tubule. The administration of these agents resulted in an increase in fractional sodium excretion (CNa/GFR) of 21.1\%, urinary sodium excretion (UNaV) of 1,126 mueq/min, and urinary chloride excretion (UClV) of 848 mueq/min during nitrate loading compared with an increase in CNa/GFR of 37.6\%, UNaV of 2,362 mueq/min, and UClV of 2,397 mueq/min during saline loading. The smaller diuretic-induced increment in Na and Cl excretion in the nitrate studies suggests, as do the hydrated studies, that less Cl and Na are reabsorbed in the distal nephron during nitrate than saline loading. At every level of UNaV, fractional bicarbonate reabsorption was higher, urine pH was lower, and urinary potassium excretion (UKV) was higher in the nitrate studies. Thus, compared with saline loading, sodium nitrate decreases chloride and sodium reabsorption in the distal nephron. The higher hydrogen and potassium secretion in the nitrate studies may be consequent to the decreased ability of the distal nephron to reabsorb chloride.

}, keywords = {Animals, Bicarbonates, Biological Transport, Chlorides, Chlorothiazide, Diuresis, Dogs, Electrolytes, Ethacrynic Acid, Glomerular Filtration Rate, Hydrogen-Ion Concentration, Kidney Tubules, Nitrates, Potassium, Sodium, Sodium Chloride, Urine}, issn = {0002-9513}, author = {Kahn, T and Bosch, J and Levitt, M F and Goldstein, M H} } @article {1712, title = {Evaluation of amplitude and frequency changes of miniature potentials with a poor signal-to-noise ratio.}, journal = {Comp Biochem Physiol C}, volume = {52}, year = {1975}, month = {1975 Oct 1}, pages = {11-6}, keywords = {Animals, Gallamine Triethiodide, Grasshoppers, Muscle Contraction, Potentiometry, Sodium Chloride, Strychnine, Sucrose}, issn = {0306-4492}, author = {Huijbregts, L A and Schreurs, M} }