Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments.

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.

Full-scale demonstration of a floating seal for enhanced biological nutrient removal in a sequencing batch reactor establishing chemical-free environment in wastewater treatment at low carbon source availability.

Due to the cyclical nature and changing water levels in the sequencing batch reactor (SBR), oxygen diffusion and utilization can be difficult to control particularly in light of the need to conserve the limited quantity of carbon source required to optimize biological nutrient removal. During the fill period, oxygen penetration may be undesirable since heterotrophic and autotrophic organisms cause a reduction in the readily biodegradable carbon source (rbCOD). This carbon source is essential and often limited in the anaerobic and anoxic periods. As a consequence, unwanted oxygen penetration can hinder efficient biological phosphorus and nitrogen removal. The purpose of the present research was to verify the advantage of a floating seal on the continuously moving surface of an SBR reactor to minimize undesirable oxygen penetration. In the floating seal-covered SBR both nitrification and denitrification efficiency proved to be higher due to insulation, and even during wintertime biological phosphorus removal met target removals without chemical dosing. The SVI values in the two SBR trains proved to be close to each other, despite the high difference in chemical dosing. Having experienced the higher efficiency of the seal-covered train, microbiome compositions of the two differently operated systems were investigated to determine potential differences via 16S rRNA gene amplicon sequencing experiments. In the samples taken from the seal-covered system, higher ratios of fermentative bacteria and phosphate accumulating organisms (PAOs) as well as glycogen accumulating organisms (GAOs) could be observed as compared to the samples deriving from the uncovered system.

Viruses with U-DNA: New Avenues for Biotechnology.

Deoxyuridine in DNA has recently been in the focus of research due to its intriguing roles in several physiological and pathophysiological situations. Although not an orthodox DNA base, uracil may appear in DNA via either cytosine deamination or thymine-replacing incorporations. Since these alterations may induce mutation or may perturb DNA-protein interactions, free living organisms from bacteria to human contain several pathways to counteract uracilation. These efficient and highly specific repair routes uracil-directed excision repair initiated by representative of uracil-DNA glycosylase families. Interestingly, some bacteriophages exist with thymine-lacking uracil-DNA genome. A detailed understanding of the strategy by which such phages can replicate in bacteria where an efficient repair pathway functions for uracil-excision from DNA is expected to reveal novel inhibitors that can also be used for biotechnological applications. Here, we also review the several potential biotechnological applications already implemented based on inhibitors of uracil-excision repair, such as Crispr-base-editing and detection of nascent uracil distribution pattern in complex genomes.