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)

https://cyberleninka.org/article/n/567486.pdf

A review on polycyclic aromatic hydrocarbons: Source, environmental impact, effect on human health and remediation

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times ( 2 S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.

Recent Advances in Petroleum Microbiology

In the last few decades, pharmaceuticals, credited with saving millions of lives, have emerged as a new class of environmental contaminant. These compounds can have both chronic and acute harmful effects on natural flora and fauna. The presence of pharmaceutical contaminants in ground waters, surface waters (lakes, rivers, and streams), sea water, wastewater treatment plants (influents and effluents), soils, and sludges has been well doccumented. A range of methods including oxidation, photolysis, UV-degradation, nanofiltration, reverse osmosis, and adsorption has been used for their remediation from aqueous systems. Many methods have been commercially limited by toxic sludge generation, incomplete removal, high capital and operating costs, and the need for skilled operating and maintenance personnel. Adsorption technologies are a low-cost alternative, easily used in developing countries where there is a dearth of advanced technologies, skilled personnel, and available capital, and adsorption appears to be the most broadly feasible pharmaceutical removal method. Adsorption remediation methods are easily integrated with wastewater treatment plants (WWTPs). Herein, we have reviewed the literature (1990-2018) illustrating the rising environmental pharmaceutical contamination concerns as well as remediation efforts emphasizing adsorption.

Pharmaceuticals of Emerging Concern in Aquatic Systems: Chemistry, Occurrence, Effects, and Removal Methods.

Effects of plants and microorganisms in constructed wetlands for wastewater treatment.

A serine protease from the keratin-degrading Streptomyces pactum DSM 40530 was purified by casein agarose affinity chromatography. The enzyme had a molecular weight of 30,000 and an isoelectric point of 8.5. The proteinase was optimally active in the pH range from 7 to 10 and at temperatures from 40 to 75 degrees C. The enzyme was specific for arginine and lysine at the P1 site and for phenylalanine and arginine at the P1' site. It showed a high stereoselectivity and secondary specificity with different synthetic substrates. The keratinolytic activity of the purified proteinase was examined by incubation with the insoluble substrates keratin azure, feather meal, and native and autoclaved chicken feather downs. The S. pactum proteinase was significantly more active than the various commercially available proteinases. After incubation with the purified proteinase, a rapid disintegration of whole feathers was observed. But even after several days of incubation with repeated addition of enzymes, less than 10% of the native keratin substrate was solubilized. In the presence of dithiothreitol, degradation was more than 70%.

Characterization of a keratinolytic serine proteinase from Streptomyces pactum DSM 40530.

Odor compounds in waste gas emissions from agricultural operations and food industries.

Pyrazines are a class of compounds that occur almost ubiquitously in nature. Pyrazines can be synthesised chemically or biologically, and are used as flavouring additives. The major formation of pyrazines occurs during heating of food. There is very little information available on the degradation of these compounds. In humans and animals, pyrazines are excreted as glucuronates or bound to glutathione via the kidney after hydroxylation, but the pyrazine ring is not cleaved. Bacteria have been isolated, which are able to use various substituted pyrazines as a sole carbon and energy source. In a few cases, the initial metabolites have been characterised; however, the mechanism of ring cleavage and the further degradation pathways are still unknown and await further investigation.

Pyrazines: occurrence, formation and biodegradation

Pseudomonas sp. CBS3 converted various nitro-aromatic compounds under aerobic resting-cell conditions to the corresponding amino compounds. Mononitro-compounds were reduced to anilines. 1-Chloro-2,4-dinitrobenzene was reduced via the two possible chloronitroanilines to 4-chloro-1,3-diaminobenzene. In the case of 2,4,6-trinitrotoluene, two monoaminodinitrotoluenes and one diaminomononitrotoluene were obtained. In addition to the reduction, in most cases the amines were partially acetylated. In experiments under an argon atmosphere conversion of the nitro-compounds was as fast as under aerobic conditions. Cells of Pseudomonas sp. CBS3 cultivated on complex medium showed higher nitro-reducing activity than those cultivated on mineral salts medium with 4-chlorobenzoate as substrate, which is normally used as medium for this strain. Several other Pseudomonas species (ATCC 4359, ATCC 23937, ATCC 15005, ATCC 17933) also showed nitro-reducing activities. In crude cell-free extracts of Pseudomonas sp. CBS3 an enzyme catalysing the reduction of nitro-aromatics was detected. The enzyme was inactivated by dialysis and was reactivated by the addition of NADH or NADPH. NADPH was the more efficient co-substrate.

Reduction of nitroaromatic compounds by different Pseudomonas species under aerobic conditions

https://www.jbc.org/content/278/48/47545.full.pdf

Rudolf Müller

Papers

Characterization of a keratinolytic serine proteinase from Streptomyces pactum DSM 40530.

Odor compounds in waste gas emissions from agricultural operations and food industries.

Pyrazines: occurrence, formation and biodegradation

Reduction of nitroaromatic compounds by different Pseudomonas species under aerobic conditions

Phenol Hydroxylase from Bacillus thermoglucosidasius A7, a Two-protein Component Monooxygenase with a Dual Role for FAD *