conjugal vectors for cloning expression and insertional mutagenesis in gram negative bacteria

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Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

BACKGROUND: Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth

Citizen-Science for the Future: Advisory Case Studies From Around the Globe

The democratization of ocean observation has the potential to add millions of observations every day. Though not a solution for all ocean monitoring needs, citizen scientists offer compelling examples showcasing their ability to augment and enhance traditional research and monitoring. Information they are providing is increasing the spatial and temporal frequency and duration of sampling, reducing time and labor costs for academic and government monitoring programs, providing hands-on STEM learning related to real-world issues and increasing public awareness and support for the scientific process. Examples provided here demonstrate the wide range of people who are already dramatically reducing gaps in our global observing network while at the same time providing unique opportunities to meaningfully engage in ocean observing and the research and conservation it supports. While there are still challenges to overcome before widespread inclusion in projects requiring scientific rigor, the growing organization of international citizen science associations is helping to reduce barriers. The case studies described support the idea that citizen scientists should be part of an effective global strategy for a sustained, multidisciplinary and integrated observing system

Global biogeography of SAR11 marine bacteria

The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the worldĝ€™s oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the data set enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterization of the distribution of SAR11, from waters spanning temperatures ĝ̂'2 to 30°C. Our data show a stable co-occurrence of phylotypes within both ĝ€̃ tropicalĝ€™ (>20°C) and ĝ€̃ polarĝ€™ (<10°C) biomes, highlighting ecological niche differentiation between major SAR11 subgroups. All phylotypes display transitions in abundance that are strongly correlated with temperature and latitude. By assembling SAR11 genomes from Antarctic metagenome data, we identified specific genes, biases in gene functions and signatures of positive selection in the genomes of the polar SAR11ĝ€"genomic signatures of adaptive radiation. Our data demonstrate the importance of adaptive radiation in the organismĝ€™s ability to proliferate throughout the worldĝ€™s oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes. © 2012 EMBO and Macmillan Publishers Limited All rights reserved

Modeling the cosmological co-evolution of supermassive black holes and galaxies: I. BH scaling relations and the AGN luminosity function

We model the cosmological co-evolution of galaxies and their central supermassive black holes (BHs) within a semi-analytical framework developed on the outputs of the Millennium Simulation. This model, described in detail in Croton et al. (2006) and De Lucia & Blaizot (2007), introduces a `radio mode' feedback from Active Galactic Nuclei (AGN) at the centre of X-ray emitting atmospheres in galaxy groups and clusters. Thanks to this mechanism, the model can simultaneously explain: (i) the low observed mass drop-out rate in cooling flows; (ii) the exponential cut-off in the bright end of the galaxy luminosity function; and (iii) the bulge-dominated morphologies and old stellar ages of the most massive galaxies in clusters. This paper is the first of a series in which we investigate how well this model can also reproduce the physical properties of BHs and AGN. Here we analyze the scaling relations, the fundamental plane and the mass function of BHs, and compare them with the most recent observational data. Moreover, we extend the semi-analytic model to follow the evolution of the BH mass accretion and its conversion into radiation, and compare the derived AGN bolometric luminosity function with the observed one. While we find for the most part a very good agreement between predicted and observed BH properties, the semi-analytic model underestimates the number density of luminous AGN at high redshifts, independently of the adopted Eddington factor and accretion efficiency. However, an agreement with the observations is possible within the framework of our model, provided it is assumed that the cold gas fraction accreted by BHs at high redshifts is larger than at low redshifts.Comment: 15 pages, 7 figures, MNRAS submitte

Modeling the cosmological co-evolution of supermassive black holes and galaxies: II. The clustering of quasars and their dark environment

We use semi-analytic modeling on top of the Millennium simulation to study the joint formation of galaxies and their embedded supermassive black holes. Our goal is to test scenarios in which black hole accretion and quasar activity are triggered by galaxy mergers, and to constrain different models for the lightcurves associated with individual quasar events. In the present work we focus on studying the spatial distribution of simulated quasars. At all luminosities, we find that the simulated quasar two-point correlation function is fit well by a single power-law in the range 0.5 < r < 20 h^{-1} Mpc, but its normalization is a strong function of redshift. When we select only quasars with luminosities within the range typically accessible by today's quasar surveys, their clustering strength depends only weakly on luminosity, in agreement with observations. This holds independently of the assumed lightcurve model, since bright quasars are black holes accreting close to the Eddington limit, and are hosted by dark matter haloes with a narrow mass range of a few 10^12 h^{-1} M_sun. Therefore the clustering of bright quasars cannot be used to disentangle lightcurve models, but such a discrimination would become possible if the observational samples can be pushed to significantly fainter limits. Overall, our clustering results for the simulated quasar population agree rather well with observations, lending support to the conjecture that galaxy mergers could be the main physical process responsible for triggering black hole accretion and quasar activity.Comment: 17 pages, 16 figures, to be published on MNRA

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, freeliving bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages. comparative genomics | marine microbiology | microbial ecology | microbial microevolution | operational taxonomic uni

The Ocean Sampling Day Consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits