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)

In late May, 2007, a drinking water crisis took place in Wuxi, Jiangsu Province, China, following a massive bloom of the toxin producing cyanobacteria Microcystis spp. in Lake Taihu, China’s third largest freshwater lake. Taihu was the city’s sole water supply, leaving approximately two million people without drinking water for at least a week. This cyanobacterial bloom event began two months earlier than previously documented for Microcystis blooms in Taihu. This was attributed to an unusually warm spring. The prevailing wind direction during this period caused the bloom to accumulate at the shoreline near the intake of the water plant. Water was diverted from the nearby Yangtze River in an effort to flush the lake of the bloom. However, this management action was counterproductive, because it produced a current which transported the bloom into the intake, exacerbating the drinking water contamination problem. The severity of this microcystin toxin containing bloom and the ensuing drinking water crisis were attributable to excessive nutrient enrichment; however, a multi-annual warming trend extended the bloom period and amplified its severity, and this was made worse by unanticipated negative impacts of water management. Long-term management must therefore consider both the human and climatic factors controlling these blooms and their impacts on water supply in this and other large lakes threatened by accelerating eutrophication.

A Drinking Water Crisis in Lake Taihu, China: Linkage to Climatic Variability and Lake Management

A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp.

When cultivated under stress conditions, many microalgae species accumulate both starch and oil (triacylglycerols). The model green microalga Chlamydomonas reinhardtii has recently emerged as a model to test genetic engineering or cultivation strategies aiming at increasing lipid yields for biodiesel production. Blocking starch synthesis has been suggested as a way to boost oil accumulation. Here, we characterize the triacylglycerol (TAG) accumulation process in Chlamydomonas and quantify TAGs in various wild-type and starchless strains. In response to nitrogen deficiency, Chlamydomonas reinhardtii produced TAGs enriched in palmitic, oleic and linoleic acids that accumulated in oil-bodies. Oil synthesis was maximal between 2 and 3 days following nitrogen depletion and reached a plateau around day 5. In the first 48 hours of oil deposition, a ~80% reduction in the major plastidial membrane lipids occurred. Upon nitrogen re-supply, mobilization of TAGs started after starch degradation but was completed within 24 hours. Comparison of oil content in five common laboratory strains (CC124, CC125, cw15, CC1690 and 11-32A) revealed a high variability, from 2 μg TAG per million cell in CC124 to 11 μg in 11-32A. Quantification of TAGs on a cell basis in three mutants affected in starch synthesis (cw15sta1-2, cw15sta6 and cw15sta7-1) showed that blocking starch synthesis did not result in TAG over-accumulation compared to their direct progenitor, the arginine auxotroph strain 330. Moreover, no significant correlation was found between cellular oil and starch levels among the twenty wild-type, mutants and complemented strains tested. By contrast, cellular oil content was found to increase steeply with salt concentration in the growth medium. At 100 mM NaCl, oil level similar to nitrogen depletion conditions could be reached in CC124 strain. A reference basis for future genetic studies of oil metabolism in Chlamydomonas is provided. Results highlight the importance of using direct progenitors as control strains when assessing the effect of mutations on oil content. They also suggest the existence in Chlamydomonas of complex interplays between oil synthesis, genetic background and stress conditions. Optimization of such interactions is an alternative to targeted metabolic engineering strategies in the search for high oil yields.

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Oil accumulation in the model green alga Chlamydomonas reinhardtii : characterization, variability between common laboratory strains and relationship with starch reserves

Blue-green algae are found in lakes, ponds, rivers and brackish waters throughout the world. In case of excessive growth such as bloom formation, these bacteria can produce inherent toxins in quantities causing toxicity in mammals, including humans. These cyanotoxins include cyclic peptides and alkaloids. Among the cyclic peptides are the microcystins and the nodularins. The alkaloids include anatoxin-a, anatoxin-a(S), cylindrospermopsin, saxitoxins (STXs), aplysiatoxins and lyngbyatoxin. Both biological and chemical methods are used to determine cyanotoxins. Bioassays and biochemical assays are nonspecific, so they can only be used as screening methods. HPLC has some good prospects. For the subsequent detection of these toxins different detectors may be used, ranging from simple UV-spectrometry via fluorescence detection to various types of MS. The main problem in the determination of cyanobacterial toxins is the lack of reference materials of all relevant toxins. In general, toxicity data on cyanotoxins are rather scarce. A majority of toxicity data are known to be of microcystin-LR. For nodularins, data from a few animal studies are available. For the alkaloids, limited toxicity data exist for anatoxin-a, cylindrospermopsin and STX. Risk assessment for acute exposure could be relevant for some types of exposure. Nevertheless, no acute reference doses have formally been derived thus far. For STX(s), many countries have established tolerance levels in bivalves, but these limits were set in view of STX(s) as biotoxins, accumulating in marine shellfish. Official regulations for other cyanotoxins have not been established, although some (provisional) guideline values have been derived for microcystins in drinking water by WHO and several countries.

Toxins of cyanobacteria

A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae

Responses of antioxidant systems in the hepatocytes of common carp (Cyprinus carpio L.) to the toxicity of microcystin-LR.

Distribution and bioaccumulation of microcystins in water columns: a systematic investigation into the environmental fate and the risks associated with microcystins in Meiliang Bay, Lake Taihu

Microcystis is a cosmopolitan genus of cyanobacteria and occurs in many different forms. Large surface blooms of the cyanobacterium are well known in eutrophic lakes throughout the globe. We evaluated the role of microcystins (MCs) in promoting and maintaining bloom-forming cell aggregates at environmentally relevant MC concentrations (0.25-10 mu g l(-1)). MCs significantly enhanced Microcystis colony sizes. Colonial diameters in microcystin-RR (MC-RR)-treated cultures (at 1 mu g l(-1)) were significantly larger than control colonies, by factors of 1.5, 2.6 and 2.7 in Microcystis wesenbergii DC-M1, M. ichthyoblabe TH-M1 and Microcystis sp. FACHB1027 respectively. Depletion of extracellular MC concentrations caused Microcystis colony size to decrease, suggesting that released MCs are intimately involved in the maintenance of Microcystis colonial size. MC-RR exposure did not influence Microcystis growth rate, but did significantly increase the production of extracellular polysaccharides (EPS). In addition, MC-RR exposure appeared to trigger upregulation of certain parts of four polysaccharide biosynthesis-related genes: capD, csaB, tagH and epsL. These results strongly indicate that induction of polysaccharides by MC-RR was the major mechanism through which MCs enhanced colony formation in Microcystis spp. Cellular release of MCs, therefore, may play a key role in the persistence of algal colonies and the dominance of Microcystis.

Lirong Song

Papers

A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae

Responses of antioxidant systems in the hepatocytes of common carp (Cyprinus carpio L.) to the toxicity of microcystin-LR.

Distribution and bioaccumulation of microcystins in water columns: a systematic investigation into the environmental fate and the risks associated with microcystins in Meiliang Bay, Lake Taihu

The role of microcystins in maintaining colonies of bloom-forming Microcystis spp.

Effects of microcystins on the growth and the activity of superoxide dismutase and peroxidase of rape (Brassica napus L.) and rice (Oryza sativa L.).