pahE , a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

Abstract

The characterization of native polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is significant for understanding the PAH degradation process in the natural environment and developing effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employpahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and nonspecificity ofpahAcresult in a misestimation of PAH-degrading bacteria. Here, we propose a PAH hydratase-aldolase-encoding gene,pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper pathway of PAH degradation indicated thatpahEevolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except for the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed thatpahEcan specifically distinguish PAH-degrading bacteria, whilepahAccannot. Illumina sequencing ofpahEandpahAcamplicons showed more genotypes and higher specificity and resolution forpahE. Novel reads were also discovered among thepahEamplicons, suggesting the presence of novel PAH-degrading populations. These results suggest thatpahEis a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCEPAH contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for PAH pollution bioremediation. However, the nonspecificity ofpahAcas a functional marker of PAH-degrading bacteria has resulted neither in a reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introducedpahEencoding the PAH hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.

Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders

“…Microorganisms present in contaminated environments often manifest the environmental adaptability required for effective remediation of contaminants [ 24 , 25 , 26 ]. Hence, petroleum-contaminated sites are often the first point of recourse in the search for organisms with the ability for organic pollutant degradation.…”

High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments

“…The Pearson correlation among azo dye degrading related genes (Table 3) showed azoR genes had a significant positive correlation with nahAb, nahAc, nahAa, nahD, tyrosinase and glutamine synthetase. These results suggest azoR and the naphthalene degradation genes probably evolved closely [60]. Except nahP and nahF, there were significant positive correlation between nahAa, nahAb, nahAc, nahC, and nahD.…”

Metagenomic insight into the plant growth-promoting potential of a diesel-degrading bacterial consortium for enhanced rhizoremediation application

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