Aerobic Degradation of Aromatic Hydrocarbons

Pérez‐Pantoja, Danilo; González, Bernardo; Pieper, Dietmar H.

doi:10.1007/978-3-319-50418-6_10

Cited by 16 publications

(23 citation statements)

References 187 publications

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“…ISTKB genome and in expression profile. These enzymes help in activation and decarboxylation of aromatic compounds (hydroxycinnamates, carboxyvanillin) and play an important role in diversion of substrate towards central degradation [ 42 – 44 ]. The expression of both protocatechuate 3,4-dioxygenase and protocatechuate 4,5-dioxygenase on both KL–VA indicated that this strain has both functional ortho and meta cleavage pathway for degradation of lignin and its derivatives.…”

Section: Discussionmentioning

confidence: 99%

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Kumar

Verma

Gazara

et al. 2018

Biotechnol Biofuels

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BackgroundLignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization.ResultsGenomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase–peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL–VA.ConclusionsThe unusual aerobic ‘-CoA’-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4–5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain’s robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1148-2) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Kumar

Verma

Gazara

et al. 2018

Biotechnol Biofuels

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“…Screening of catabolic genes using degenerated primers and PCR led to the detection of the fragment of the phenol hydroxylase large subunit [ 38 , 39 ]. The phenol hydroxylases comprise related family of enzymes capable to hydroxylate mainly phenols and their methyl-substituted derivatives to the corresponding catechols [ 40 , 41 ]. Some phenol hydroxylases families have showed also the ability to transform toluene or benzene [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

“…CF600 and Pseudomonas putida P35X [ 10 , 29 ], Pseudomonas aeruginosa T1 [ 30 ] and Comamonas testosteroni JH5 [ 26 ]. Furthermore, phenol hydroxylases are reported to be of broad substrate specificity and to transform, phenol, 2-methylphenols, 2,4 and 3,4-DMP, o -cresol, m -cresol [ 28 , 40 , 47 , 48 ], and are able to transform 2,4-DMP and 2,5-DMP [ 47 ]. Based on our findings, it is assumed that phenol hydroxylase of Delftia sp.…”

Section: Discussionmentioning

confidence: 99%

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Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation

et al. 2018

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BackgroundDimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems.ResultsIn this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols.ConclusionsLCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1255-z) contains supplementary material, which is available to authorized users.

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“…While aromatic compounds are readily degraded, they do not degrade as quickly as alkanes under aerobic conditions (Head et al ., ), and persistence in the environment may confer greater long‐term environmental significance (Menzie and Coleman, ). Biodegradation of aromatic hydrocarbons occurs through activation of the aromatic ring by mono‐ or dioxygenases (reviewed in, Gibson and Parales ; Leahy et al ., ; Pérez‐Pantoja et al ., ) and further degrdation of these active compounds by catechol–dioxygenases (Cerniglia, ), including catechol 2,3‐dioxygenase (encoded by c23o ). This enzyme is thought to control the rate limiting step in aerobic degradation of both monocyclic (MAH) and polycyclic (PAH) hydrocarbons, and is the most widespread of ring cleavage enzymes (Okuta et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep‐sea sediments of the Great Australian Bight, Australia

Kamp

Hook

Williams

et al. 2019

Environmental Microbiology

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Summary Exploratory drilling for deep‐sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional ‘ecotypes’ related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep‐sea ecosystem.

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Aerobic Degradation of Aromatic Hydrocarbons

Cited by 16 publications

References 187 publications

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep‐sea sediments of the Great Australian Bight, Australia

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