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)

Silver nanoparticles as antimicrobial agent: a case study on E. coli as a model for Gram-negative bacteria

We are just beginning to understand the metabolism of heavy metals and to use their metabolic functions in biotechnology, although heavy metals comprise the major part of the elements in the periodic table. Because they can form complex compounds, some heavy metal ions are essential trace elements, but, essential or not, most heavy metals are toxic at higher concentrations. This review describes the workings of known metal-resistance systems in microorganisms. After an account of the basic principles of homoeostasis for all heavy-metal ions, the transport of the 17 most important (heavy metal) elements is compared.

Microbial heavy-metal resistance

Silver nanoparticles are nanoparticles of silver which are in the range of 1 and 100 nm in size. Silver nanoparticles have unique properties which help in molecular diagnostics, in therapies, as well as in devices that are used in several medical procedures. The major methods used for silver nanoparticle synthesis are the physical and chemical methods. The problem with the chemical and physical methods is that the synthesis is expensive and can also have toxic substances absorbed onto them. To overcome this, the biological method provides a feasible alternative. The major biological systems involved in this are bacteria, fungi, and plant extracts. The major applications of silver nanoparticles in the medical field include diagnostic applications and therapeutic applications. In most of the therapeutic applications, it is the antimicrobial property that is being majorly explored, though the anti-inflammatory property has its fair share of applications. Though silver nanoparticles are rampantly used in many medical procedures and devices as well as in various biological fields, they have their drawbacks due to nanotoxicity. This review provides a comprehensive view on the mechanism of action, production, applications in the medical field, and the health and environmental concerns that are allegedly caused due to these nanoparticles. The focus is on effective and efficient synthesis of silver nanoparticles while exploring their various prospective applications besides trying to understand the current scenario in the debates on the toxicity concerns these nanoparticles pose.

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Silver nanoparticles: mechanism of antimicrobial action, synthesis, medical applications, and toxicity effects

Biological synthesis of metallic nanoparticles.

Germanium and silver resistance, accumulation, and toxicity in microorganisms

The increased use of UV radiation as a drinking water treatment technology has instigated studies of the repair potential of microorganisms following treatment. This study challenged the repair potential of an optimally grown nonpathogenic laboratory strain of Escherichia coli after UV radiation from low- and medium-pressure lamps. Samples were irradiated with doses of 5, 8, and 10 mJ/cm(2) from a low-pressure lamp and 3, 5, 8, and 10 mJ/cm(2) from a medium-pressure UV lamp housed in a bench-scale collimated beam apparatus. Following irradiation, samples were incubated at 37 degrees C under photoreactivating light or in the dark. Sample aliquots were analyzed for up to 4 h following incubation using a standard plate count. Results of this study showed that E. coli underwent photorepair following exposure to the low-pressure UV source, but no repair was detectable following exposure to the medium-pressure UV source at the initial doses examined. Minimal repair was eventually observed upon medium-pressure UV lamp exposure when doses were lowered to 3 mJ/cm(2). This study clearly indicates differences in repair potential under laboratory conditions between irradiation from low-pressure and medium-pressure UV sources of the type used in water treatment.

Potential Repair of Escherichia coli DNA following Exposure to UV Radiation from Both Medium- and Low-Pressure UV Sources Used in Drinking Water Treatment

A watershed-scale fate and transport model has been developed for Escherichia coli and several waterborne pathogens: Cryptosporidiumspp., Giardiaspp., Campylobacter spp, and E. coli O157:H7. The objectives were to determine the primary sources of pathogenic contamination in a watershed used for drinking water supply and to gain a greater understanding of the factors that most influence their survival and transport. To predict the levels of indicator bacteria and pathogens in surface water, an existing hydrologic model, WATFLOOD, was augmented for pathogen transport and tested on a watershed in Southwestern Ontario, Canada. The pathogen model considered transport as a result of overland flow, subsurface flow to tile drainage systems, and in-stream routing. The model predicted that most microorganisms entering the stream from land-based sources enter the stream from tile drainage systems rather than overland transport. Although the model predicted overland transport to be rare, when it occurred, it corresponded to the highest observed and modeled microbial concentrations. Furthermore, rapid increases in measured E. coli concentrations during storm events suggested that the resuspension of microorganisms from stream sediments may be of equal or greater importance than land-based sources of pathogens.

Hydrologic modeling of pathogen fate and transport

This review examines interactions between bacteria and the biologically non-essential metal, silver. Aspects of silver toxicity, tolerance and accumulation (possible binding and uptake as opposed to energy-dependent transport) in bacteria are discussed. In addition, plasmid biology is examined briefly since little information is available on the exact mechanism(s) of plasmid-endoced silver resistance in bacteria.

Bacterial interactions with silver

Silver (Ag) resistance and accumulation were investigated in Ag-resistant Pseudomonas stutzeri strain AG259 and Ag-sensitive P. stutzeri strain JM303. Both strains exhibited a similar pattern of silver accumulation although to different final concentrations. Energy-dispersive X-ray analyses revealed the association of dense silver deposits with the Ag-resistant strain, but not the Ag-sensitive strain. Toluene permeabilization or incubation of cells at 2°C resulted in decreased Ag accumulation in both strains. This suggests that Ag accumulation may be energy dependent. A decrease in Ag accumulation was observed when cells were pretreated with 2,4-dinitrophenol (2,4-DNP). No decrease was observed using carbonyl cyanide m-chlorphenyl-hydrazone (CCCP). However, it was observed that both 2,4-DNP and CCCP complexed to Ag, making interpretation of accumulation results difficult. Washing of cells incubated in the presence of Ag with ethylenediaminetetraacetic acid (EDTA) or hydrochloric acid did not result in decreased Ag accumulation.

Robin M. Slawson

Papers

Germanium and silver resistance, accumulation, and toxicity in microorganisms

Potential Repair of Escherichia coli DNA following Exposure to UV Radiation from Both Medium- and Low-Pressure UV Sources Used in Drinking Water Treatment

Hydrologic modeling of pathogen fate and transport

Bacterial interactions with silver

Silver accumulation and resistance in Pseudomonas stutzeri