Anaerobic biodegradation of phenanthrene by a newly isolated nitrate‐dependent <i>Achromobacter denitrificans</i> strain <scp>PheN1</scp> and exploration of the biotransformation processes by metabolite and genome analyses

Zhang, Zuotao; Sun, Jiao; Guo, Haijiao; Wang, Chongyang; Fang, Tingting; Rogers, Matthew J.; He, Jianzhong; Wang, Hui

doi:10.1111/1462-2920.15201

Cited by 23 publications

(4 citation statements)

References 59 publications

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“…4A ). Notably, AMGs for PAH biodegradation ( ubiE ) [ 77 ] were also identified and their relative abundance increased by 55.4-fold in the high-level BaP group (Fig. 4A, C ).…”

Section: Resultsmentioning

confidence: 99%

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

et al. 2023

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The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg−1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg−1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.

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“…4A ). Notably, AMGs for PAH biodegradation ( ubiE ) [ 77 ] were also identified and their relative abundance increased by 55.4-fold in the high-level BaP group (Fig. 4A, C ).…”

Section: Resultsmentioning

confidence: 99%

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

et al. 2023

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“…Nevertheless, we have to keep in mind that gene expression involves the coordination of multiple biological traits, such as regulators, promoters, and genes encoding lower pathways. Meanwhile, compared to aerobic bacteria-mediated PAH biodegradation, it has been reported that PAHs can also be biodegraded by anaerobic bacteria [ 86 – 88 ], fungi [ 89 ], halophilic archaea [ 71 ], and microalgae [ 90 ] via significantly different pathways. These factors were not considered in the present study, requiring more experimental evidence and studies to move forward.…”

Section: Discussionmentioning

confidence: 99%

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

Huang

Yin

et al. 2023

Environmental Microbiome

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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.

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“…It is widely distributed and has high toxic potential; therefore, it must be removed from the environment [11]. Consequently, PHE is frequently used as a model compound to study PAHs [12,13].…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network

Chen

et al. 2022

IJERPH

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Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.

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Anaerobic biodegradation of phenanthrene by a newly isolated nitrate‐dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses

Cited by 23 publications

References 59 publications

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network

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