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)

Microalgae dewatering is a major obstruction to industrial-scale processing of microalgae for biofuel prodn. The dil. nature of harvested microalgal cultures creates a huge operational cost during dewatering, thereby, rendering algae-based fuels less economically attractive. Currently there is no superior method of dewatering microalgae. A technique that may result in a greater algal biomass may have drawbacks such as a high capital cost or high energy consumption. The choice of which harvesting technique to apply will depend on the species of microalgae and the final product desired. Algal properties such as a large cell size and the capability of the microalgae to autoflocculate can simplify the dewatering process. This article reviews and addresses the various technologies currently used for dewatering microalgal cultures along with a comparative study of the performances of the different technologies.

Dewatering of microalgal cultures : a major bottleneck to algae-based fuels

https://openscholar.dut.ac.za/bitstream/10321/1400/1/rawat__kumar__mutanda___bux_2013_aplplied_energy.pdf

Biodiesel from microalgae: A critical evaluation from laboratory to large scale production

Flocculation as a low-cost method for harvesting microalgae for bulk biomass production.

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.

/pdf/oil-accumulation-in-the-model-green-alga-chlamydomonas-1i155vc943.pdf

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

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

Evaluation of flocculation induced by pH increase for harvesting microalgae and reuse of flocculated medium

The production, characterization, and antioxidant capacity of the carotenoid fucoxanthin from the marine diatom Odontella aurita were investigated. The results showed that low light and nitrogen-replete culture medium enhanced the biosynthesis of fucoxanthin. The maximum biomass concentration of 6.36 g L−1 and maximum fucoxanthin concentration of 18.47 mg g−1 were obtained in cultures grown in a bubble column photobioreactor (O 3.0 cm inner diameter), resulting in a fucoxanthin volumetric productivity of 7.96 mg L−1 day−1. A slight reduction in biomass production was observed in the scaling up of O. aurita culture in a flat plate photobioreactor, yet yielded a comparable fucoxanthin volumetric productivity. A rapid method was developed for extraction and purification of fucoxanthin. The purified fucoxanthin was identified as all-trans-fucoxanthin, which exhibited strong antioxidant properties, with the effective concentration for 50% scavenging (EC50) of 1,1-dihpenyl-2-picrylhydrazyl (DPPH) radical and 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS) radical being 0.14 and 0.03 mg mL−1, respectively. Our results suggested that O. aurita can be a natural source of fucoxanthin for human health and nutrition.

https://www.mdpi.com/1660-3397/11/7/2667/pdf

Production, Characterization, and Antioxidant Activity of Fucoxanthin from the Marine Diatom Odontella aurita

Recent studies have demonstrated that microalga has been widely regarded as one of the most promising raw materials of biofuels. However, lack of an economical, efficient and convenient method to harvest microalgae is a bottleneck to boost their full-scale application. Many methods of harvesting microalgae, including mechanical, electrical, biological and chemical based, have been studied to overcome this hurdle. A new flocculation method induced by decreasing pH value of growth medium was developed for harvesting freshwater microalgae. The flocculation efficiencies were as high as 90% for Chlorococcum nivale, Chlorococcum ellipsoideum and Scenedesmus sp. with high biomass concentrations (>1g/L). The optimum flocculation efficiency was achieved at pH 4.0. The flocculation mechanism could be that the carboxylate ions of organic matters adhering on microalgal cells accepted protons when pH decreases and the negative charges were neutralized, resulting in disruption of the dispersing stability of cells and subsequent flocculation of cells. A linear correlation between biomass concentration and acid dosage was observed. Furthermore, viability of flocculated cells was determined by Evans Blue assay and few cells were found to be damaged with pH decrease. After neutralizing pH and adding nutrients to the flocculated medium, microalgae were proved to maintain a similar growth yield in the flocculated medium comparing with that in the fresh medium. The recycling of medium could contribute to the economical production from algae to biodiesel. The study provided an economical, efficient and convenient method to harvest fresh microalgae. Advantages include capability of treating high cell biomass concentrations (>1g/L), excellent flocculation efficiencies (≥ 90%), operational simplicity, low cost and recycling of medium. It has shown the potential to overcome the hurdle of harvesting microalgae to promote full-scale application to biofuels from microalgae.

/pdf/freshwater-microalgae-harvested-via-flocculation-induced-by-4bqzjweqvx.pdf

Chengwu Zhang

Papers

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

Evaluation of flocculation induced by pH increase for harvesting microalgae and reuse of flocculated medium

Production, Characterization, and Antioxidant Activity of Fucoxanthin from the Marine Diatom Odontella aurita

Freshwater microalgae harvested via flocculation induced by pH decrease

A microalgae residue based carbon solid acid catalyst for biodiesel production