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)

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants However, the study of such microbial populations requires a more advanced and multifaceted approach Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments

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Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities.

Pesticides are xenobiotic molecules necessary to control pests in agriculture, home, and industry. However, water and soil can become contaminated as a consequence of their extensive use. Therefore, because of its eco-friendly characteristics and efficiency, bioremediation of contaminated sites is a powerful tool with advantages over other kinds of treatments. For an efficient pesticides bioremediation, it is necessary to take into account different aspects related to the microbial metabolism and physiology. In this respect, OMICs studies such as genomics, transcriptomics, proteomics, and metabolomics are essential to generate relevant information about the genes and proteins involved in pesticide degradation, the metabolites generated by microbial pesticide degradation, and the cellular strategies to contend against stress caused by pesticide exposition. Pesticides as organochlorines and organophosphorus are the more commonly studied using OMIC approaches. To date, many genomes of microorganisms capable of degrading pesticides have been published, mainly bacterial strains from Burkholderia, Pseudomonas, and Rhodococcus genera. Following the genomic reports, transcriptomic studies, using microarrays and more recently next-generation sequencing technology RNA-Seq, in pesticide microbial degradation are the most numerous. Proteomics, metabolomics, as well as studies that combine different OMIC are gained interest. This review aims to describe a brief overview of pesticide biodegradation mechanisms; new tools to study microorganisms in natural environments; basic concepts of the OMICs approaches; as well as advances in methodologies associated with the analysis of that tools. Additionally, the most recent reports on genomics, transcriptomics, proteomics, and metabolomics during the degradation of pesticides are also analyzed.

Omics Approaches to Pesticide Biodegradation.

Surfactant is a special kind of amphiphilic compound composed of water-loving and hating parts. The remarkable physical properties like interfacial tension, wettability, emulsifying and dispersing ability make the surfactant accessible for numerous applications from laboratory to commercial products. In recent years, the commercial applications of surfactant have led to greater relevance on account of the environmental concerns and market pressures of this compound. The utility of surfactants in global market increases steadily since its formulation with several beneficial aspects in pharmaceutical, detergent, cosmetic, paint, food science, gas hydrate, nanotechnology, petroleum recovery, bioremediation, chemical transformation and drug delivery. This review briefly discusses the applied aspect of surfactants in diverse area as well as catalytic effect of micelle in organic reactions from the recent literature survey. The trend of increasing use of bioderived surfactants in the modern field of research is also considered in this report. The recent advancement of surfactant-based organic transformations has been emphasized with the role of surfactant aggregates in course of different organic reactions.

Surfactant for better tomorrow: applied aspect of surfactant aggregates from laboratory to industry

Kinetic study of nickel-glycylglycine with ninhydrin in alkanediyl-α,ω-gemini (m-s-m type) surfactant system

Effect of CPC micelle on N-hetero-aromatic base promoted room temperature permanganate oxidation of 2-butanol in aqueous medium

Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other Rhodococcus sp. A novel 4-NP catabolic 43 gene cluster "nph" was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many nph cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the nph cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the nph gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the nph cluster, for potential exploitation in bioremediation.

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Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1.

A halotolerant 4-nitrophenol (4-NP) degrading bacterial strain designated as BUPNP2 was isolated by enrichment culture technique from the rhizospheric soil of rice plants (Oryzae sativa) of an agricultural field located in Memari within Burdwan district of West Bengal, India. It was identified as a member of genus Bacillus by 16S rRNA gene based molecular phylogenetic approach. The strain was capable of degrading 4-NP (0.3 mM) as sole source of carbon through 4-nitrocatechol (4-NC) as intermediate. The strain also tolerated up to 12 % NaCl (w/v). The degradation capacity of 4-NP was enhanced by this strain up to 0.6 mM in presence of cellulose, starch and glucose. The strain could tolerate several heavy metals such as cadmium, chromium, iron, lead, nickel and zinc and it was degrading 4-NP in presence of each of these heavy metals. Glucose, starch and cellulose also enhanced 4-NP degradation capacity of the strain even in presence of each of these heavy metals. The strain BUPNP2 also possessed important plant growth promoting (PGP) traits such as production of siderophore, indole acetic acid (IAA), ammonia; phosphate solubilization along with protease, lipase, amylase and cellulase activities. Thus, the halotolerant strain BUPNP2 has biotechnological potential and can be utilized for bioremediation of heavy metal infested 4-NP contaminated agricultural soil (common in industrial belt) where it might also help in plant growth promotion.

Degradation of 4-nitrophenol in presence of heavy metals by a halotolerant Bacillus sp. strain BUPNP2, having plant growth promoting traits

A bacterial strain, designated as MemCl4, capable of utilizing chlorpyrifos as sole source of carbon was isolated by enrichment culture from an agricultural soil sample of Burdwan District, West Bengal, India. It was identified as Acinetobacter sp. by using phenotypic and 16S rRNA gene-based molecular phylogenetic approach. The strain could degrade 98 % of chlorpyrifos within 144 h. Through thin layer chromatography, high-performance liquid chromatography and gas chromatography–mass spectrometry analyses, 3,5,6 trichloro-2-pyridinol (TCP) was identified as the only major intermediate during such degradation. The strain could also utilize TCP as sole source of carbon for growth. Degradation studies indicated utilization of chlorpyrifos with formation TCP, followed by decrease in amount of TCP with gradual passage of time. This indicated evidence of mineralization of both chlorpyrifos and TCP by the strain. The Gram-negative and esterase-positive strain was capable of tolerating various heavy metal salts such as arsenite, arsenate, cadmium, chromium, copper, iron, lead, nickel and zinc on sucrose low-phosphate medium. The strain MemCl4 might be considered biotechnologically potential for bioremediation and or restoration of chlorpyrifos-contaminated agricultural fields. This is the first report of a chlorpyrifos-degrading, heavy metal-tolerant bacterium belonging to the genus Acinetobacter, to the best of our knowledge. The strain, however, could not degrade chlorpyrifos in the presence of two heavy metal salts tested (viz. arsenate and zinc sulfate).

Evidence of biodegradation of chlorpyrifos by a newly isolated heavy metal-tolerant bacterium Acinetobacter sp. strain MemCl4

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Kriti Sengupta

Papers

Effect of CPC micelle on N-hetero-aromatic base promoted room temperature permanganate oxidation of 2-butanol in aqueous medium

Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1.

Degradation of 4-nitrophenol in presence of heavy metals by a halotolerant Bacillus sp. strain BUPNP2, having plant growth promoting traits

Evidence of biodegradation of chlorpyrifos by a newly isolated heavy metal-tolerant bacterium Acinetobacter sp. strain MemCl4

Biodegradation of 4-nitrophenol by a Rhodococcus species and a preliminary insight into its toxicoproteome based on mass spectrometry analysis