The remediation of polycyclic aromatic hydrocarbon contaminated soil by immobilized microorganisms using distiller's grains.

Polycyclic aromatic hydrocarbons are a persistent organic pollutant, and their biodegradation in the soil is often limited due to the limited degradation ability of indigenous bacteria and the low activity of exogenous PAH degrading bacteria. Immobilized microbial technology can protect microorganisms from the impact of harsh environments, and distiller's grains have the potential as carriers for microbial immobilization. This study aims to use distiller's grains as a microbial carrier, investigate the feasibility of immobilized microorganisms using distiller's grains for remediation of PAH contaminated soil; explore the relationship between soil nutrient content, consumption, and PAH degradation rate; and reveal the mechanism of bioremediation from the perspective of soil enzyme activity and microbial community composition. The results showed that after 72 days of remediation, the removal rates of phenanthrene and pyrene in the treatment of immobilized microorganisms in distiller grains reached 91.78% and 58.59%, respectively. Distiller grains can serve as a carrier for microorganisms, providing them with shelter and nutrients to enhance their chance of survival. Additionally, they can regulate the composition of soil particles and improve aeration, thereby increasing the efficiency of PAH degradation in soil.

Strategy to Promote the Biodegradation of Phenanthrene in Contaminated Soil by a Novel Bacterial Consortium in Slurry Bioreactors.

Polycyclic aromatic hydrocarbons (PAHs) are typical high-risk, persistent organic pollutants. Biological slurry reactors are widely used for enhanced bioremediation. In this experiment, a highly efficient phenanthrene-degrading bacteria group was obtained through screening and domestication, and the community was named MZJ_21. After the addition of MZJ_21 to the aerobic slurry bioreactor, with the optimum conditions of the temperature, stirring speed, and aeration rate of 30 °C, 120 rpm, and 1 L/min, respectively, the phenanthrene degradation ratio reached 95.41% within 48 h. The exploration of the degradation of phenanthrene by MZJ_21 indicated that most MZJ_21 communities adsorbed on the soil particle, mainly because MZI_21 could secrete extracellular polymers, which could stably adhere MZJ_21 on the solid phase. At the same time, the distribution ratio of phenanthrene in the solid phase is increased, so that the efficient phenanthrene degradation reaction takes place in the solid phase.

Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis.

C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate ß-D-glucosidase and ß-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP-ß-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.

An atlas of bacterial secondary metabolite biosynthesis gene clusters.

Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome-sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non-ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.

Discovery of a series of 5-phenyl-2-furan derivatives containing 1,3-thiazole moiety as potent Escherichia coli ß-glucuronidase inhibitors.

Gut microbial ß-glucuronidases have drawn much attention due to their role as a potential therapeutic target to alleviate some drugs or their metabolites-induced gastrointestinal toxicity. In this study, fifteen 5-phenyl-2-furan derivatives containing 1,3-thiazole moiety (1-15) were synthesized and evaluated for their inhibitory effects against Escherichia coli ß-glucuronidase (EcGUS). Twelve of them showed satisfactory inhibition against EcGUS with IC50 values ranging from 0.25 µM to 2.13 µM with compound 12 exhibited the best inhibition. Inhibition kinetics studies indicated that compound 12 (Ki = 0.14 ± 0.01 µM) was an uncompetitive inhibitor for EcGUS and molecular docking simulation further predicted the binding model and capability of compound 12 with EcGUS. A preliminary structure-inhibitory activity relationship study revealed that the heterocyclic backbone and bromine substitution of benzene may be essential for inhibition against EcGUS. The compounds have the potential to be applied in drug-induced gastrointestinal toxicity and the findings would help researchers to design and develop more effective 5-phenyl-2-furan type EcGUS inhibitors.