Genomic-assisted determination of the natural nutrient requirements of the cosmopolitan marine bacterium 'Candidatus Pelagibacter ubique'

To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining tools were developed, and all major biosynthetic and energy pathways were reconstructed from a genome annotation. Analysis of the genomic data suggested 'Cand. P. ubique' might be limited by the availability of reduced sulfur, since genes cysDNCHIJ, used for assimilatory sulfate reduction, were missing. When reduced sulfur in the form of 3-dimethylsulfoniopropionate (DMSP), methionine, or cysteine was added to filtered, autoclaved seawater containing all other nutrients in excess, maximum cell yield increased an order of magnitude. But, increasing DMSP additions from 50 nM to 10 μM did not lead to higher cell densities at a normal growth rate; instead, cultures increased in cell density from 3.03 x 10⁶ cells ml⁻¹ to 2.1 x 10⁷ cells ml⁻¹, at a growth rate of 0.110 d⁻¹ instead of 0.664 d⁻¹. An additional hypothesis was that, due to the inefficiency with which threonine degradation to glycine compensates for missing serBC genes, and the presence of a glycine-activated riboswitch on malate synthase, the growth rate using DMSP as a sole sulfur source would be improved by addition of glycine betaine because glycine can be used as a methyl acceptor to regenerate methyl carriers needed to demethylate DMSP. When glycine betaine was added to filtered, autoclaved seawater containing DMSP and all other nutrients in excess, growth rate increased.Keywords: sulfate, genomic

Investing in Mobility: Freight Transport in the Hudson Region

Proposes a framework for assessing alternative investments in freight rail, highway, and transit capacity that would increase the ability to improve mobility and air quality in the New York metropolitan area

Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features

Unicellular nitrogen-fixing cyanobacteria are important components of marine phytoplankton. Although non-nitrogen-fixing marine phytoplankton generally exhibit high gene sequence and genomic diversity, gene sequences of natural populations and isolated strains of Crocosphaera watsonii, one of the two most abundant open ocean unicellular cyanobacteria groups, have been shown to be 98–100% identical. The low sequence diversity in Crocosphaera is a dramatic contrast to sympatric species of Prochlorococcus and Synechococcus, and raises the question of how genome differences can explain observed phenotypic diversity among Crocosphaera strains. Here we show, through whole genome comparisons of two phenotypically different strains, that there are strain-specific sequences in each genome, and numerous genome rearrangements, despite exceptionally low sequence diversity in shared genomic regions. Some of the strain-specific sequences encode functions that explain observed phenotypic differences, such as exopolysaccharide biosynthesis. The pattern of strain-specific sequences distributed throughout the genomes, along with rearrangements in shared sequences is evidence of significant genetic mobility that may be attributed to the hundreds of transposase genes found in both strains. Furthermore, such genetic mobility appears to be the main mechanism of strain divergence in Crocosphaera which do not accumulate DNA microheterogeneity over the vast majority of their genomes. The strain-specific sequences found in this study provide tools for future physiological studies, as well as genetic markers to help determine the relative abundance of phenotypes in natural populations

Agricultural Land Use Planning and Groundwater Quality

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75123/1/j.1468-2257.1983.tb00394.x.pd

nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2-fixing community dynamics

A dataset of 87 020 nifH reads and 16 782 unique nifH protein sequences obtained over 2 years from four locations across a gradient of agricultural soil types in Argentina were analysed to provide a detailed and comprehensive picture of the diversity, abundance and responses of the N2-fixing community in relation to differences in soil chemistry and agricultural practices. Phylogenetic analysis revealed an expected high proportion of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria, mainly relatives to Bradyrhizobium and Methylosinus/Methylocystis, but a surprising paucity of Gammaproteobacteria. Analysis of variance and stepwise regression modelling suggested location and treatment-specific influences of soil type on diazotrophic community composition and organic carbon concentrations on nifH diversity. nifH gene abundance, determined by quantitative real-time polymerase chain reaction, was higher in agricultural soils than in non-agricultural soils, and was influenced by soil chemistry under intensive crop rotation but not under monoculture. At some locations, sustainable increased crop yields might be possible through the management of soil chemistry to improve the abundance and diversity of N2-fixing bacteriaFil: Collavino, Mónica Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Nordeste. Instituto de Botánica del Nordeste (i); Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Tripp, H. James. University of California. Department of Ocean Sciences; Estados UnidosFil: Frank, Ildiko E.. University of California. Department of Ocean Sciences; Estados UnidosFil: Vidoz, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Nordeste. Instituto de Botánica del Nordeste (i); ArgentinaFil: Calderoli, Priscila Anabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Donato, Mariano Humberto. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Laboratorio de Sistemática y Biología Evolutiva; ArgentinaFil: Zehr, Jonathan P.. University of California. Department of Ocean Sciences; Estados UnidosFil: Aguilar, Orlando Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Biotecnología y Biología Molecular; Argentin

The significance of 'the visit' in an English category-B prison: Views from prisoners, prisoners' families and prison staff

A number of claims have been made regarding the importance of prisoners staying in touch with their family through prison visits, firstly from a humanitarian perspective of enabling family members to see each other, but also regarding the impact of maintaining family ties for successful rehabilitation, reintegration into society and reduced re-offending. This growing evidence base has resulted in increased support by the Prison Service for encouraging the family unit to remain intact during a prisoner’s incarceration. Despite its importance however, there has been a distinct lack of research examining the dynamics of families visiting relatives in prison. This paper explores perceptions of the same event – the visit – from the families’, prisoners’ and prison staffs' viewpoints in a category-B local prison in England. Qualitative data was collected with 30 prisoners’ families, 16 prisoners and 14 prison staff, as part of a broader evaluation of the visitors’ centre. The findings suggest that the three parties frame their perspective of visiting very differently. Prisoners’ families often see visits as an emotional minefield fraught with practical difficulties. Prisoners can view the visit as the highlight of their time in prison and often have many complaints about how visits are handled. Finally, prison staff see visits as potential security breaches and a major organisational operation. The paper addresses the current gap in our understanding of the prison visit and has implications for the Prison Service and wider social policy

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth\u27s subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2‐saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications

nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N₂-fixing community dynamics

A dataset of 87 020 nifH reads and 16 782 unique nifH protein sequences obtained over 2 years from four locations across a gradient of agricultural soil types in Argentina were analysed to provide a detailed and comprehensive picture of the diversity, abundance and responses of the N₂-fixing community in relation to differences in soil chemistry and agricultural practices. Phylogenetic analysis revealed an expected high proportion of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria, mainly relatives to Bradyrhizobium and Methylosinus/Methylocystis, but a surprising paucity of Gammaproteobacteria. Analysis of variance and stepwise regression modelling suggested location and treatment-specific influences of soil type on diazotrophic community composition and organic carbon concentrations on nifH diversity. nifH gene abundance, determined by quantitative real-time polymerase chain reaction, was higher in agricultural soils than in non-agricultural soils, and was influenced by soil chemistry under intensive crop rotation but not under monoculture. At some locations, sustainable increased crop yields might be possible through the management of soil chemistry to improve the abundance and diversity of N₂-fixing bacteria.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia MolecularFacultad de Ciencias Naturales y MuseoLaboratorio de Sistemática y Biología Evolutiv

Mycotoxins in Feed and Food Crops.

20 p