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 synthetic dyes from wastewaters: a review.

A variety of synthetic dyestuffs released by the textile industry pose a threat to environmental safety. Azo dyes account for the majority of all dyestuffs, produced because they are extensively used in the textile, paper, food, leather, cosmetics and pharmaceutical industries. Existing effluent treatment procedures are unable to remove recalcitrant azo dyes completely from effluents because of their color fastness, stability and resistance to degradation. Bacterial decolorization and degradation of azo dyes under certain environmental conditions has gained momentum as a method of treatment, as these are inexpensive, eco-friendly and can be applied to wide range of such dyes. This review mainly focuses on the different mechanisms of decolorization and discusses the effect of various physicochemical parameters on the dye removal efficiency of different bacteria. The enzymatic mechanisms involved in the bacterial degradation of azo dyes, the identification of metabolites by using various analytical techniques, and the nature of their toxicity has been investigated. This review provides an overview of bacterial decolorization/degradation of azo dyes and emphasizes the application of these processes for the treatment of azo dye-containing wastewaters.

Bacterial decolorization and degradation of azo dyes: a review.

Industrial and biotechnological applications of laccases: a review.

Decolorization of dye wastewaters by biosorbents: A review

Glucoamylase production by solid-state fermentation using rice flake manufacturing waste products as substrate

Statistical screening of medium components by Plackett-Burman design for lactic acid production by Lactobacillus sp. KCP01 using date juice.

Summary Production of a-amylase under solid-state fermentation by Bacillus cereus MTCC 1305 has been investigated using wheat bran and rice flake manufacturing waste as substrates. With wheat bran, highest enzyme production expressed as units per mass of dry substrate ((94±2) U/g) was observed. Production parameters were optimized as inoculum size 10 % (volume per mass) and substrate:moisture ratio 1:1. Among different carbon sources supplemented, glucose (0.04 g/g) showed enhanced enzyme production ((122±5) U/g). Supplementation of different nitrogen sources (0.02 g/g) showed decline in enzyme production. Optimum a-amylase enzyme activity was observed at 55 °C and pH=5. At 75 °C, enzyme showed 90 % activity compared to 55 °C.

/pdf/a-amylase-production-by-bacillus-cereus-mtcc-1305-using-l33tfknvba.pdf

α-Amylase Production by Bacillus cereus MTCC 1305 Using Solid-State Fermentation

Decolorization of synthetic dyes by Irpex lacteus in liquid cultures and packed-bed bioreactor

Indole-3-acetic acid (IAA) production was monitored in nine plant growth-promoting rhizobacteria isolated from the rhizospheric soil of alfalfa (Medicago sativa). The isolate producing maximum amount of IAA was identified as Pseudomonas putida UB1 by 16S rRNA partial gene sequencing. Further investigations were carried out for optimal l-tryptophan concentration and other growth parameters for IAA production by P. putida. IAA production increased when the l-tryptophan medium for IAA production was supplemented with sucrose 0.5 %, (NH4)2SO4 10 mg/ml, and tryptophan 0.2 mg/ml at pH 7.5. Maximum IAA production was achieved at 96 h. Production of IAA was confirmed by extraction of crude IAA and subsequent thin-layer chromatography analysis. The specific spot from the extracted IAA was found to correspond with a spot of standard IAA with the same R
 f value (0.36). The crude IAA was further purified by passing it through a silica gel column. P. putida UB1 and its purified IAA were demonstrated to show stimulatory effect on mustard (Brassica nigra) plants in vitro with their incorporation in MS medium as a novel approach.

https://link.springer.com/content/pdf/10.1007%2Fs40003-013-0065-7.pdf

Optimization of Indole Acetic Acid Production by Pseudomonas putida UB1 and its Effect as Plant Growth-Promoting Rhizobacteria on Mustard (Brassica nigra)

Kamlesh C. Patel

Papers

Glucoamylase production by solid-state fermentation using rice flake manufacturing waste products as substrate

Statistical screening of medium components by Plackett-Burman design for lactic acid production by Lactobacillus sp. KCP01 using date juice.

α-Amylase Production by Bacillus cereus MTCC 1305 Using Solid-State Fermentation

Decolorization of synthetic dyes by Irpex lacteus in liquid cultures and packed-bed bioreactor

Optimization of Indole Acetic Acid Production by Pseudomonas putida UB1 and its Effect as Plant Growth-Promoting Rhizobacteria on Mustard (Brassica nigra)