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)

Removal of heavy metal ions from wastewaters: A review

A review of chemical, electrochemical and biological methods for aqueous Cr(VI) reduction

Water pollution is a global problem threatening the entire biosphere and affecting the life of many millions of people around the world. Not only is water pollution one of the foremost global risk factors for illness, diseases and death, but it also contributes to the continuous reduction of the available drinkable water worldwide. Delivering valuable solutions, which are easy to implement and affordable, often remains a challenge. Here we review the current state-of-the-art of available technologies for water purification and discuss their field of application for heavy metal ion removal, as heavy metal ions are the most harmful and widespread contaminants. We consider each technology in the context of sustainability, a largely neglected key factor, which may actually play a pivotal role in the implementation of each technology in real applications, and we introduce a compact index, the Ranking Efficiency Product (REP), to evaluate the efficiency and ease of implementation of the various technologies in this broader perspective. Emerging technologies, for which a detailed quantitative analysis and assessment is not yet possible according to this methodology, either due to scarcity or inhomogeneity of data, are discussed in the final part of the manuscript.

Sustainable technologies for water purification from heavy metals: review and analysis

Chelating groups are successfully linked to graphene oxide (GO) surfaces through a silanization reaction between N-(trimethoxysilylpropyl) ethylenediamine triacetic acid (EDTA-silane) and hydroxyl groups on GO surface. EDTA-GO was found to be an ideal adsorbent for Pb(II) removal with a higher adsorption capacity. EDTA-modification enhances the adsorption capacity of GO because of the chelating ability of ethylene diamine triacetic acid. This study investigates the adsorption and desorption behaviors of heavy metal cations and the effects of solution conditions such as pH on Pb(II) removal. The adsorption capacity for Pb(II) removal was found to be 479 ± 46) mg/g at pH 6.8, and the adsorption process was completed within 20 min. The Langmuir adsorption model agrees well with the experimental data. The experimental results suggest that EDTA-GO can be reused after washed with HCl, suggesting potential applications in the environmental cleanup.

Qinhong Cai

Papers

Offshore oil spill response practices and emerging challenges.

Screening of biosurfactant producers from petroleum hydrocarbon contaminated sources in cold marine environments.

Effective removal of coordinated copper from wastewater using a new dithiocarbamate-type supramolecular heavy metal precipitant.

Oil-in-water emulsion breaking marine bacteria for demulsifying oily wastewater.

Microbial degradation of four crude oil by biosurfactant producing strain Rhodococcus sp.