Possible roles of manganese redox chemistry in the sulfur cycle

Sulfate reducing bacteria (SRB) are very potent MnO2 reducers by virtue of their sulfide production: H2S reacts rapidly with MnO2 to yield Mn(2), elemental sulfur, and water. In manganese rich zones, Mn cycles rapidly if sulfate is present to drive the reduction and the MnO2 precipitates and sinks into anaerobic zones. The production of sulfide (by organisms requiring organic carbon compounds) to reduce manganese oxides might act to couple the carbon and sulfur cycles in water bodies in which the two cycles are physically separated. Iron has been proposed for this provision of reducing power by (Jorgensen, 1983), but since MnS is soluble and FeS is very insoluble in water, it is equally likely that manganese rather than iron provides the electrons to the more oxidized surface layers

Planetary biology and microbial ecology. Biochemistry of carbon and early life

Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described

Nucleotide sequence of the luxA gene of Vibrio harveyi and the complete amino acid sequence of the alpha subunit of bacterial luciferase

The nucleotide sequence of the 1.85-kilobase EcoRI fragment from Vibrio harveyi that was cloned using a mixed-sequence synthetic oligonucleotide probe (Cohn, D. H., Ogden, R. C., Abelson, J. N., Baldwin, T. O., Nealson, K. H., Simon, M. I., and Mileham, A. J. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 120-123) has been determined. The alpha subunit-coding region (luxA) was found to begin at base number 707 and end at base number 1771. The alpha subunit has a calculated molecular weight of 40,108 and comprises a total of 355 amino acid residues. There are 34 base pairs separating the start of the alpha subunit structural gene and a 669-base open reading frame extending from the proximal EcoRI site. At the 3' end of the luxA coding region there are 26 bases between the end of the structural gene and the start of the luxB structural gene. Approximately two-thirds of the alpha subunit was sequenced by protein chemical techniques. The amino acid sequence implied by the DNA sequence, with few exceptions, confirmed the chemically determined sequence. Regions of the alpha subunit thought to comprise the active center were found to reside in two discrete and relatively basic regions, one from around residues 100-115 and the second from around residues 280-295

Effect of spin-orbit coupling on the excitation spectrum of Andreev billiards

We consider the effect of spin-orbit coupling on the low energy excitation spectrum of an Andreev billiard (a quantum dot weakly coupled to a superconductor), using a dynamical numerical model (the spin Andreev map). Three effects of spin-orbit coupling are obtained in our simulations: In zero magnetic field: (1) the narrowing of the distribution of the excitation gap; (2) the appearance of oscillations in the average density of states. In strong magnetic field: (3) the appearance of a peak in the average density of states at zero energy. All three effects have been predicted by random-matrix theory.Comment: 5 pages, 4 figure

Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress

The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems

Carbon and nitrogen fixation and metabolite exchange in and between individual cells of Anabaena oscillarioides

Filamentous nitrogen fixing cyanobacteria are key players in global nutrient cycling, but the relationship between CO"2- and N"2-fixation and intercellular exchange of these elements remains poorly understood in many genera. Using high-resolution nanometer-scale secondary ion mass spectrometry (NanoSIMS) in conjunction with enriched H13CO"3- and 15N"2 incubations of Anabaena oscillarioides, we imaged the cellular distributions of C, N and P and 13C and 15N enrichments at multiple time points during a diurnal cycle as proxies for C and N assimilation. The temporal and spatial distributions of the newly fixed C and N were highly heterogeneous at both the intra- and inter-cellular scale, and indicative of regions performing active assimilation and biosynthesis. Subcellular components such as the neck region of heterocycts, cell division septae and putative cyanophycin granules were clearly identifiable by their elemental composition. Newly fixed nitrogen was rapidly exported from heterocysts and was evenly allocated among vegetative cells, with the exception of the most remote vegetative cells between heterocysts, which were N limited based on lower 15N enrichment. Preexisting functional heterocysts had the lowest levels of 13C and 15N enrichment, while heterocysts that were inferred to have differentiated during the experiment had higher levels of enrichment. This innovative approach, combining stable isotope labeling and NanoSIMS elemental and isotopic imaging, allows characterization of cellular development (division, heterocyst differentiation), changes in individual cell composition and cellular roles in metabolite exchange

Adsorbed water and thin liquid films on Mars

At present, bulk liquid water on the surface and near-subsurface of Mars does not exist due to the scarcity of condensed- and gas-phase water, pressure and temperature constraints. Given that the nuclei of soil and ice, that is, the soil solid and ice lattice, respectively, are coated with adsorbed and/or thin liquid films of water well below 273 K and the availability of water limits biological activity, we quantify lower and upper limits for the thickness of such adsorbed/water films on the surface of the Martian regolith and for subsurface ice. These limits were calculated based on experimental and theoretical data for pure water ice and water ice containing impurities, where water ice containing impurities exhibit thin liquid film enhancements, ranging from 3 to 90. Close to the cold limit of water stability (i.e. 273 K), thin liquid film thicknesses at the surface of the Martian regolith is 0.06 nm (pure water ice) and ranges from 0.2 to 5 nm (water ice with impurities). An adsorbed water layer of 0.06 nm implies a dessicated surface as the thickness of one monolayer of water is 0.3 nm but represents 0.001–0.02% of the Martian atmospheric water vapour inventory. Taking into account the specific surface area (SSA) of surface-soil (i.e. top 1 mm of regolith and 0.06 nm adsorbed water layer), shows Martian surface-soil may contain interfacial water that represents 6–66% of the upper- and lower-limit atmospheric water vapour inventory and almost four times and 33%, the lower- and upper-limit Martian atmospheric water vapour inventory. Similarly, taking the SSA of Martian soil, the top 1 mm or regolith at 5 nm thin liquid water thickness, yields 1.10×10^(13) and 6.50×10^(13) litres of waters, respectively, 55–325 times larger than Mars’ atmospheric water vapour inventory. Film thicknesses of 0.2 and 5 nm represent 2.3×10^4 – 1.5×10^6 litres of water, which is 6.0×10^(−7) – 4.0×10^(−4)%, respectively, of a 10 pr μm water vapour column, and 3.0×10^(−6) – 4.0×10^(−4)% and 6.0×10^(−6)–8.0×10^(−4)%, respectively, of the Martian atmospheric water vapour inventory. Thin liquid film thicknesses on/in subsurface ice were investigated via two scenarios: (i) under the idealistic case where it is assumed that the diurnal thermal wave is equal to the temperature of ice tens of centimetres below the surface, allowing for such ice to experience temperatures close to 273 K and (ii) under the, likely, realistic scenario where the diurnal thermal wave allows for the maximum subsurface ice temperature of 235 K at 1 m depth between 30°N and 30°S. Scenario 1 yields thin liquid film thicknesses ranging from 11 to 90 nm; these amounts represent 4×10^(6) – 3.0×10^7 litres of water. For pure water ice, Scenario 2 reveals that the thickness of thin liquid films contained on/within Martian subsurface is less than 1.2 nm, several molecular layers thick. Conversely, via the effect of impurities at 235 K allows for a thin liquid film thickness on/within subsurface ice of 0.5 nm, corresponding to 6.0×10^4 litres of water. The existence of thin films on Mars is supported by data from the Mars Exploration Rovers (MERs) Spirit and Opportunity's Alpha Proton X-ray Spectrometer instrumentation, which have detected increased levels of bromine beneath the immediate surface, suggestive of the mobilization of soluble salts by thin films of liquid water towards local cold traps. These findings show that biological activity on the Martian surface and subsurface is not limited by nanometre dimensions of available wate

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

<p>Abstract</p> <p>Background</p> <p>Carbohydrates are a primary source of carbon and energy for many bacteria. Accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative genomic approach with experimental validation of selected bioinformatic predictions by a combination of biochemical, genetic and physiological experiments.</p> <p>Results</p> <p>We applied this integrated approach to systematically map carbohydrate utilization pathways in 19 genomes from the <it>Shewanella </it>genus. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across <it>Shewanella </it>species providing insights into their ecophysiology and adaptive evolution. Phenotypic assays revealed a remarkable consistency between predicted and observed phenotype, an ability to utilize an individual sugar as a sole source of carbon and energy, over the entire matrix of tested strains and sugars.</p> <p>Comparison of the reconstructed catabolic pathways with <it>E. coli </it>identified multiple differences that are manifested at various levels, from the presence or absence of certain sugar catabolic pathways, nonorthologous gene replacements and alternative biochemical routes to a different organization of transcription regulatory networks.</p> <p>Conclusions</p> <p>The reconstructed sugar catabolome in <it>Shewanella </it>spp includes 62 novel isofunctional families of enzymes, transporters, and regulators. In addition to improving our knowledge of genomics and functional organization of carbohydrate utilization in Shewanella, this study led to a substantial expansion of our current version of the Genomic Encyclopedia of Carbohydrate Utilization. A systematic and iterative application of this approach to multiple taxonomic groups of bacteria will further enhance it, creating a knowledge base adequate for the efficient analysis of any newly sequenced genome as well as of the emerging metagenomic data.</p