New insights into biodegradation of environmental pollutants through metagenomics and bioinformatics

Abstract

This study was conducted to investigate the biodegradation of artificial sweeteners and polycyclic aromatic hydrocarbons (PAHs) as a mix of emerging and well-document contaminants. The major objectives of this study were (1) to investigate the bacterial population responsible for sucralose biodegradation and its degradation pathways; (2) to explore the biodegradation of acesulfame by enriched consortia and pure cultures under aerobic and anoxic conditions, respectively; (3) to establish a comprehensive PAHs-degrading genes database and investigate its distribution in the public database.

Genome-resolved metagenomic analysis of sucralose-degrading consortia deciphered that the function of sucralose biodegradation was driven by some novel bacteria (at genus level), and the strains in a few families (Polyangiaceae, UBA11579, Xanthobacteraceae, and Kaistiaceae) were involved in the biodegradation process. The sucralose was degraded completely and 5 biotransformation products were determined by UPLC-QTOF-MS, of which TP-381P was the principal intermediate towards the dechlorination of sucralose.

Two aerobic acesulfame-degrading bacterial strains were obtained from the enriched consortia, namely, Chelatococcus sp. YT9 and Chelatococcus sp. HY11. The biodegradation of acesulfame by YT9 fit well using the Michaelis-Menten kinetics model under environmentally relevant concentrations showing a maximum degradation rate (Vmax) of 24.60 mg ACE/g VSS·h-1 and a Km value of 2.47  10-7 mol/L, respectively. Meanwhile, the anoxic acesulfame biodegradation was first evidenced by the enriched consortia inoculated with activated sludge. Three new acesulfame degraders affiliated with Shinella were isolated, characterized, and sequenced. All these three isolates were capable of degrading acesulfame completely under both aerobic and anoxic conditions with the maximum degradation rates of 30.3 mg ACE/g VSS·h-1 and 8.92 mg ACE/g VSS·h-1 following the zero-order and modified Gompertz model kinetics, respectively. Furthermore, the genome-centric profiles of aerobic and anoxic acesulfame-degrading consortia illustrated that metagenome-assembled genomes from the order Hyphomicrobiales played an important role in acesulfame biodegradation.

As a typical conventional pollutant group, PAHs’ biodegradation still gets a lot of attention now. The established PAHs-degrading genes database was comprised of 1186 accurate protein sequences from 16 kinds of degradation genes, which could be divided into three types of mechanisms of aerobic PAHs biodegradation. The database was applied in a genome-centric interpterion of 47 identified PAHs-degrading bacteria, implying that genes encoding hydratase-aldolase may be a potential superior biomarker for the identification of PAHs degraders in complex environments. Additionally, the investigation of PAHs-degrading genes distribution demonstrated that nah genes were the most ubiquitous genes, especially in Gram-negative strains of Proteobacteria, while nar and nid genes clusters were conservative in Gram-positive and Mycobacteriaceae strains, respectively. A few strains, affiliated with the genera without reported PAHs degraders before, also bore a complete PAH-catabolic gene cluster and were potentially capable of PAHs biodegradation. Furthermore, a random forest analysis was employed to develop a reliable method for rapidly identifying PAHs degraders based on their genomes, suggesting that 29 bacterial strains were newly predicted as potential PAHs degraders in the complete genome database.