Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates

Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr?1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 ± 9.2 Tg N yr?1, 18 ± 1.8 Tg C and 590 ± 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70%. It was recently established that the most commonly applied method used to measure N2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N2 fixation rate upward and may result in significantly higher estimates for the global N2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA (doi:10.1594/PANGAEA.774851)

Dust in Supernovae and Supernova Remnants I : Formation Scenarios

Supernovae are considered as prime sources of dust in space. Observations of local supernovae over the past couple of decades have detected the presence of dust in supernova ejecta. The reddening of the high redshift quasars also indicate the presence of large masses of dust in early galaxies. Considering the top heavy IMF in the early galaxies, supernovae are assumed to be the major contributor to these large amounts of dust. However, the composition and morphology of dust grains formed in a supernova ejecta is yet to be understood with clarity. Moreover, the dust masses inferred from observations in mid-infrared and submillimeter wavelength regimes differ by two orders of magnitude or more. Therefore, the mechanism responsible for the synthesis of molecules and dust in such environments plays a crucial role in studying the evolution of cosmic dust in galaxies. This review summarises our current knowledge of dust formation in supernova ejecta and tries to quantify the role of supernovae as dust producers in a galaxy.Peer reviewe

A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages

Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Cell–Matrix Interactions Improve β-Cell Survival and Insulin Secretion in Three-Dimensional Culture

Controlled matrix interactions were presented to pancreatic β-cells in three-dimensional culture within poly(ethylene glycol) hydrogels. Dispersed MIN6 β-cells were encapsulated in gel environments containing the following entrapped extracellular matrix (ECM) proteins: collagen type I, collagen type IV, fibrinogen, fibronectin, laminin, and vitronectin. In ECM-containing gels, β-cell survival was significantly better than in gels without ECM over 10 days. Correspondingly, apoptosis in encapsulated β-cells was less in the presence of each matrix protein, suggesting the ability of individual matrix interactions to prevent matrix signaling-related apoptosis (anoikis). MIN6 β-cells cultured in gels containing collagen type IV or laminin secreted more insulin in response to glucose stimulation than β-cells in all other experimental conditions. Variations in collagen type IV or laminin concentration between 10 μg/mL and 250 μg/mL did not affect insulin secretion. Finally, β-cell function in hydrogels presenting both collagen type IV and laminin revealed synergistic interactions. With a total protein concentration of 100 μg/mL, three gel compositions of varying ratios of collagen type IV to laminin (25:75, 50:50, and 75:25) were tested. In the presence of 25 μg/mL of collagen type IV and 75 μg/mL of laminin, β-cell insulin secretion was greater than with laminin or collagen type IV individually. These results demonstrate that specific, rationally designed extracellular environments promote isolated β-cell survival and function

Effects of overhead canopy on macroinvertebrate production in a Utah stream

1. Macroinvertebrate abundance and production were compared between an open and shaded site of a stream in the Wasatch Mountains, Utah. Mean biomass was significantly higher at the open site for midges (Chironomidae), 4.6x; Baetis bicaudatus, 5.7x; Baetis tricaudatus, 2.3x; Drunella coloradensis, 12x and Cinygmula sp., L6x. Abundance of most other macroinvertebrates (except black flies: Simuliidae) was also greater at the open site, but differences were not significant. Black fly biomass was 1.7x greater at the shaded site. 2. Seasonal production, estimated by the size-frequency and instantaneous growth rate methods, was greater at the open site than the shaded site for most taxa (except black flies) and reflected differences in standing crops between the sites rather than differences in rate of growth. Excluding black flies, production at the open site was twice as high as at the shaded site. 3. The greater abundance and production of most invertebrate taxa at the open site is probably associated with either higher quality food (algae and algal detritus), or a phototactic attraction to sunlit areas. 4. Sampling of large cobbles was an efficient method of sampling all taxa except Cinygmula sp. which was more abundant on smaller substrate particles