Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi, Michael Gatheru; Kang, Fuxing; Goikavi, Carspar; Ling, Wanting; Gao, Yanzheng

doi:10.1016/j.ibiod.2015.06.008

Cited by 151 publications

(47 citation statements)

References 202 publications

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“…Microbial degradation of phenanthrene can proceed by three different methods: mineralization, co-metabolic transformation and oxidation. In the case of aerobic growth of sphingomonads, oxidation is the favored mechanism of phenathrene degradation (Waigi et al, 2015 ). As with other PAHs, aerobic degradation of phenanthrene is initiated by the addition of two oxygen atoms to the aromatic ring, an event that is catalyzed by an aromatic-ring dioxygenase (Figure 5A ).…”

Section: Resultsmentioning

confidence: 99%

“…This metabolite can be further degraded by two different routes: it can be processed by dioxygenases and dehydrogenases ( ortho -cleavage route) to generate o -phtalate, which is later metabolized through protocatechuate to generate tricarboxylic acid (TCA) intermediates (Figure 5 , steps 8A to 16A). Alternatively, by the meta -cleavage route, 1-hydroxy-2-naphtoic acid is decarboxylated to generate 1,2-dihydroxinaphtalene, which is further serially processed by dioxygenase, isomerase, aldolase, and dehydrogenase activities to produce salicylic acid (Figure 5 , steps 8B to 12B; Goyal and Zylstra, 1997 ; Waigi et al, 2015 ). Salicylic acid is then further processed through gentisate (steps 13C to 16C) or catechol pathways (steps 13B to 18B), to generate TCA cycle intermediates, with the catechol pathway generating the yellow colored hydroximuconic acid used for the qualitative selection of strains in our screening approach.…”

Section: Resultsmentioning

confidence: 99%

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Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

et al. 2017

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Antarctica is an attractive target for human exploration and scientific investigation, however the negative effects of human activity on this continent are long lasting and can have serious consequences on the native ecosystem. Various areas of Antarctica have been contaminated with diesel fuel, which contains harmful compounds such as heavy metals and polycyclic aromatic hydrocarbons (PAH). Bioremediation of PAHs by the activity of microorganisms is an ecological, economical, and safe decontamination approach. Since the introduction of foreign organisms into the Antarctica is prohibited, it is key to discover native bacteria that can be used for diesel bioremediation. By following the degradation of the PAH phenanthrene, we isolated 53 PAH metabolizing bacteria from diesel contaminated Antarctic soil samples, with three of these isolates exhibiting a high phenanthrene degrading capacity. In particular, the Sphingobium xenophagum D43FB isolate showed the highest phenanthrene degradation ability, generating up to 95% degradation of initial phenanthrene. D43FB can also degrade phenanthrene in the presence of its usual co-pollutant, the heavy metal cadmium, and showed the ability to grow using diesel-fuel as a sole carbon source. Microtiter plate assays and SEM analysis revealed that S. xenophagum D43FB exhibits the ability to form biofilms and can directly adhere to phenanthrene crystals. Genome sequencing analysis also revealed the presence of several genes involved in PAH degradation and heavy metal resistance in the D43FB genome. Altogether, these results demonstrate that S. xenophagum D43FB shows promising potential for its application in the bioremediation of diesel fuel contaminated-Antarctic ecosystems.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

et al. 2017

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“…This is concordant with previous results on PHE-spiked agricultural soils, where Sphingomonas became the dominant genus within 2 months, together with a significant increase in Phenylobacterium abundance compared to unspiked controls (Ding et al, 2012 ). Sphingomonads are known as active hydrocarbon degraders (Peng et al, 2008 ), often isolated from polluted sites and able to use PHE and other PAHs as sole carbon sources (reviewed in Waigi et al, 2015 ). In general, sphingomonads feature several adaptive strategies for efficient PAH degradation in oligotrophic environments, such as: (i) adhesion to hydrophobic substrates and formation of biofilm (Johnsen and Karlson, 2004 ); (ii) the presence of glycosphingolipids in their cell envelope (Kawahara et al, 1999 ), which are more hydrophobic than common membrane lipids found in other Gram-negative bacteria; and (iii) high affinity uptake systems for recalcitrant compounds (Peng et al, 2008 ).…”

Section: Discussionmentioning

confidence: 99%

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Thomas

Cébron

2016

Front. Microbiol.

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Over the last decades, understanding of the effects of plants on soil microbiomes has greatly advanced. However, knowledge on the assembly of rhizospheric communities in aged-contaminated industrial soils is still limited, especially with regard to transcriptionally active microbiomes and their link to the quality or quantity of carbon sources. We compared the short-term (2–10 days) dynamics of bacterial communities and potential PAH-degrading bacteria in bare or ryegrass-planted aged-contaminated soil spiked with phenanthrene, put in relation with dissolved organic carbon (DOC) sources and polycyclic aromatic hydrocarbon (PAH) pollution. Both resident and active bacterial communities (analyzed from DNA and RNA, respectively) showed higher species richness and smaller dispersion between replicates in planted soils. Root development strongly favored the activity of Pseudomonadales within the first 2 days, and of members of Actinobacteria, Caulobacterales, Rhizobiales, and Xanthomonadales within 6–10 days. Plants slowed down the dissipation of phenanthrene, while root exudation provided a cocktail of labile substrates that might preferentially fuel microbial growth. Although the abundance of PAH-degrading genes increased in planted soil, their transcription level stayed similar to bare soil. In addition, network analysis revealed that plants induced an early shift in the identity of potential phenanthrene degraders, which might influence PAH dissipation on the long-term.

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“…Microbial degradation or mineralization depends on the metabolic potential of microorganisms to detoxify or transform these pollutants. Several enzyme-catalyzed metabolic reactions in the biodegradation process include the addition of oxygen to double bonds, dehalogenation, ring cleavage, and the addition of hydroxyl groups to the benzene ring (17)(18)(19). Some functional genes have been identified and linked to the initial metabolic process of PAH and PCB degradation, including PAH ring-hydroxylating dioxygenase (PAH-RHD) (20) and biphenyl dioxygenase (bphA) genes (11).…”

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confidence: 99%

Stable-Isotope Probing-Enabled Cultivation of the Indigenous Bacterium Ralstonia sp. Strain M1, Capable of Degrading Phenanthrene and Biphenyl in Industrial Wastewater

Luo

Zhang

et al. 2019

Appl Environ Microbiol

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To identify and obtain the indigenous degraders metabolizing phenanthrene (PHE) and biphenyl (BP) from the complex microbial community within industrial wastewater, DNA-based stable-isotope probing (DNA-SIP) and cultivation-based methods were applied in the present study. DNA-SIP results showed that two bacterial taxa (Vogesella and Alicyclobacillus) were considered the key biodegraders responsible for PHE biodegradation only, whereas Bacillus and Cupriavidus were involved in BP degradation. Vogesella and Alicyclobacillus have not been linked with PHE degradation previously. Additionally, DNA-SIP helped reveal the taxonomic identity of Ralstonia-like degraders involved in both PHE and BP degradation. To target the separation of functional Ralstonia-like degraders from the wastewater, we modified the traditional cultivation medium and culture conditions. Finally, an indigenous PHE- and BP-degrading strain, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by enrichment of the 16S rRNA gene and distinctive dioxygenase genes in the DNA-SIP experiment. Our study has successfully established a program for the application of DNA-SIP in the isolation of the active functional degraders from an environment. It also deepens our insight into the diversity of indigenous PHE- and BP-degrading communities. IMPORTANCE The comprehensive treatment of wastewater in industrial parks suffers from the presence of multiple persistent organic pollutants (POPs), such as polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), which reduce the activity of activated sludge and are difficult to eliminate. Characterizing and applying active bacterial degraders metabolizing multiple POPs therefore helps to reveal the mechanisms of synergistic metabolism and to improve wastewater treatment efficiency in industrial parks. To date, SIP studies have successfully investigated the biodegradation of PAHs or PCBs in real-world habitats. DNA-SIP facilitates the isolation of target microorganisms that pose environmental concerns. Here, an indigenous phenanthrene (PHE)- and biphenyl (BP)-degrading strain in wastewater, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by DNA-SIP. Our study provides a routine protocol for the application of DNA-SIP in the isolation of the active functional degraders from an environment.

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Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Cited by 151 publications

References 202 publications

Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Stable-Isotope Probing-Enabled Cultivation of the Indigenous Bacterium Ralstonia sp. Strain M1, Capable of Degrading Phenanthrene and Biphenyl in Industrial Wastewater

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