Substrate specificities of aromatic ring-hydroxylating oxygenases of an uncultured gammaproteobacterium from chronically-polluted subantarctic sediments

Musumeci, Matías A.; Loviso, Claudia L.; Lozada, Mariana; Ferreira, Flavia Vanina; Dionisi, Hebe M.

doi:10.1016/j.ibiod.2018.12.005

Cited by 13 publications

(5 citation statements)

References 62 publications

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“…This suggests that whilst enzymes capable of the hydrolysis of PET, PETases, are generally present in relatively low abundances [ 19 ], the enzymes involved in the metabolisation of PET degradation sub-products may be more widely distributed in the marine environment. Whilst we tend to assign enzymes to very specific substrates, it is not new that some oxygenases may display a broader substrate specificity [ 65 ], especially those with larger catalytic pockets [ 66 ]. The enzymes identified in this study are, hence, excellent candidates for further substrate specificity evaluation.…”

Section: Discussionmentioning

confidence: 99%

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

et al. 2021

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Background Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. Results We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. Conclusions Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris.

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Section: Discussionmentioning

confidence: 99%

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

et al. 2021

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“…Additionally, Khara et al [48] showed that the αand β-subunit structures of Rieske oxygenase can affect the substrate specificity of the enzyme, and reported that the specificity relies on the properties of the catalytic subunit, specifically, the volume, size and shape. In addition, many factors influence enzymatic reactions, including the structure of the catalytic center, entry and exit channels of substrates, and the physicochemical properties of size, geometry and hydrophobicity of the ligands [49]. Furthermore, the unique loop structure linking the αand βsubunits in Rieske oxygenase plays a significant role in maintaining its structural stability and catalytic activity, and is important for NADPH binding and screening substrates [50].…”

Section: Discussionmentioning

confidence: 99%

Crude Oil Degradation by a Novel Strain Pseudomonas aeruginosa AQNU-1 Isolated from an Oil-Contaminated Lake Wetland

et al. 2022

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In this study, a novel crude oil degrading bacterium was isolated from an oil-contaminated freshwater lake using crude oil as the sole carbon source. The strain was named Pseudomonas aeruginosa AQNU-1 based on the analyses of its morphological characteristics and 16S rRNA gene sequencing. Gas chromatography-mass spectrometry (GC-MS) was carried out to investigate the degradation of crude oil fractions under dynamic (37 °C, 180 r/min) and static (37 °C, 0 r/min) cultivation over three months of continuous enrichment in the laboratory. It was found that strain AQNU-1 exhibited stronger biodegradation efficiency for n-alkanes of C13–C35 under dynamic cultivation with degradation ratios of 87–100% compared to ratios of 74–100% under static cultivation. Furthermore, this strain could fully utilize alkylcyclohexane (M/Z 82), alkylbenzene (M/Z 92) and alkyltoluene (M/Z 106) in crude oil under both conditions. It also had better biodegradability of partial aromatic compounds in the crude oil, showing differences within compound families of aromatic hydrocarbons. Further, the potential degradation ability of this isolated strain decreased with increasing molecular weight, with the dynamic condition performing better in general. These results suggest that the isolated strain has great potential to assimilate indigestible crude-oil contaminants under different hydrological conditions, providing a valuable microbiological resource for in situ remediation of natural wetlands.

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“…This suggests that while enzymes capable of the hydrolysis of PET, PETases, are generally present in relatively low abundances [19], the enzymes involved in the metabolisation of PET degradation sub-products may be more widely distributed in the marine environment. While we tend to assign enzymes to very speci c substrates, it is not new that some oxygenases may display a broader substrate speci city [60], especially those with larger catalytic pockets [61]. The enzymes identi ed in this study are, hence, excellent candidates for further substrate speci city evaluation.…”

Section: Discussionmentioning

confidence: 90%

A Multi-OMIC Characterisation of Biodegradation and Microbial Community Succession Within the PET Plastisphere

Wright

Bosch

Langille

et al. 2020

Preprint

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BackgroundPlastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the Plastisphere. Members of the Plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine Plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here we obtained a microbial community from marine plastic debris and analysed the community succession across six weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the Plastisphere. ResultsWe found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the Plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that while Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. ConclusionsOverall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the Plastisphere of marine plastic debris.

show abstract

Substrate specificities of aromatic ring-hydroxylating oxygenases of an uncultured gammaproteobacterium from chronically-polluted subantarctic sediments

Cited by 13 publications

References 62 publications

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

Crude Oil Degradation by a Novel Strain Pseudomonas aeruginosa AQNU-1 Isolated from an Oil-Contaminated Lake Wetland

A Multi-OMIC Characterisation of Biodegradation and Microbial Community Succession Within the PET Plastisphere

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