Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach
Abstract Background Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation ge...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | Environmental Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40793-023-00497-7 |
| _version_ | 1797831874510323712 |
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| author | Yue Huang Liguan Li Xiaole Yin Tong Zhang |
| author_facet | Yue Huang Liguan Li Xiaole Yin Tong Zhang |
| author_sort | Yue Huang |
| collection | DOAJ |
| description | Abstract Background Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear. Results Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway. Conclusions Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants. |
| first_indexed | 2024-04-09T13:58:42Z |
| format | Article |
| id | doaj.art-4147d42228094e409092e31b3dde82eb |
| institution | Directory Open Access Journal |
| issn | 2524-6372 |
| language | English |
| last_indexed | 2024-04-09T13:58:42Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Environmental Microbiome |
| spelling | doaj.art-4147d42228094e409092e31b3dde82eb2023-05-07T11:24:51ZengBMCEnvironmental Microbiome2524-63722023-04-0118111310.1186/s40793-023-00497-7Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approachYue Huang0Liguan Li1Xiaole Yin2Tong Zhang3Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongAbstract Background Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear. Results Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway. Conclusions Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.https://doi.org/10.1186/s40793-023-00497-7PAHBiodegradationDatabase miningFunctional geneGenome-centric analysisGenotype–phenotype relationship |
| spellingShingle | Yue Huang Liguan Li Xiaole Yin Tong Zhang Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach Environmental Microbiome PAH Biodegradation Database mining Functional gene Genome-centric analysis Genotype–phenotype relationship |
| title | Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach |
| title_full | Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach |
| title_fullStr | Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach |
| title_full_unstemmed | Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach |
| title_short | Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach |
| title_sort | polycyclic aromatic hydrocarbon pah biodegradation capacity revealed by a genome function relationship approach |
| topic | PAH Biodegradation Database mining Functional gene Genome-centric analysis Genotype–phenotype relationship |
| url | https://doi.org/10.1186/s40793-023-00497-7 |
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