The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Cause, conseguenze e strategie di mitigazione Proponiamo il primo di una serie di articoli in cui affronteremo l’attuale problema dei mutamenti climatici. Presentiamo il documento redatto, votato e pubblicato dall’Ipcc - Comitato intergovernativo sui cambiamenti climatici - che illustra la sintesi delle ricerche svolte su questo tema rilevante.

/pdf/climate-change-2007-the-physical-science-basis-1x93ttz9jt.pdf

Climate Change 2007: The Physical Science Basis.

Evolution of Protein Molecules

Microbes are the unseen majority in soil and comprise a large portion of lifes genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5‐20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

/pdf/the-unseen-majority-soil-microbes-as-drivers-of-plant-1yjo7xbywu.pdf

The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

/pdf/microbial-diversity-in-the-deep-sea-and-the-underexplored-mh8sm5okzt.pdf

Microbial diversity in the deep sea and the underexplored “rare biosphere”

Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (for example, methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites. 

/pdf/a-phylogenetic-and-proteomic-reconstruction-of-eukaryotic-18x4g6en.pdf

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Translation factor a/eIF5A is highly conserved in Eukarya and Archaea. The eukaryal eIF5A protein is required for transit of ribosomes across consecutive proline codons, whereas the function of the archaeal orthologue remains unknown. Here, we provide a first hint for an involvement of Sulfolobus solfataricus (Sso) aIF5A in translation. CRISPR-mediated knock down of the aif5A gene resulted in strong growth retardation, underlining a pivotal function. Moreover, in vitro studies revealed that Sso aIF5A is endowed with endoribonucleolytic activity. Thus, aIF5A appears to be a moonlighting protein that might be involved in protein synthesis as well as in RNA metabolism.

Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus.

The “Double‐RNA” Approach to Simultaneously Assess the Structure and Function of a Soil Microbial Community

The present invention relates to a device for the isolation and/or purification of nucleic acid molecules suitable to bind and/or inactivate inhibitors of the activity of reagents or enzymes used for DNA manipulation and to separate a plurality of nucleic acid molecules with respect to their size. Moreover, the invention relates to a method for the isolation of a nucleic acid molecule comprising applying a sample to the device of the invention wherein said nucleic acid molecule preferably represents a fraction of the metagenome of a given habitat. Furthermore, the invention relates to a method for the generation of at least one gene library comprising nucleic acid molecules isolated by the method of the invention and to a nucleic acid molecule isolated by the method of the invention.

Isolation and cloning of DNA from uncultivated organisms

The organization of the genes for the large components of DNA-dependent RNA polymerase in archaebacteria resembles that in eubacteria.

Christa Schleper

Papers

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus.

The “Double‐RNA” Approach to Simultaneously Assess the Structure and Function of a Soil Microbial Community

Isolation and cloning of DNA from uncultivated organisms

Phylogeny of DNA-Dependent RNA Polymerases: Testimony for the Origin of Eukaryotes