Biodegradation of dimethylphenols by bacteria with different ring-cleavage pathways of phenolic compounds

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands

Constructed wetlands (CWs) are well-established wastewater treatment technologies and applied for bioremediation of contaminated water. Despite the optimal performance of CWs, the understanding of the bacterial processes in the rhizosphere, where mainly microbial degradation processes take place, is still limited. In the present study, laboratory-scale CWs planted with Juncus effusus and running under controlled conditions were studied in order to evaluate removal efficiency of dimethylphenols (DMPs), also in comparison to an unplanted bed. Next to removal rates, the bacterial community structure, diversity, and distribution, their correlation with physiochemical parameters, and abundance of the phenol hydroxylase gene were determined. As a result, better removal performance of DMP isomers (3,4-, 3,5-, and 2,6-DMP added as singles compounds or in mixtures) and ammonium loads, together with a higher diversity index, bacterial number, and phenol hydroxylase gene abundance in Juncus effusus CW in comparison with the non-planted CW, indicates a clear rhizosphere effect in the experimental CWs. An enhancement in the DMP removal and the recovery of the phenol hydroxylase gene were found during the fed with the DMP mixture. In addition, the shift of bacterial community in CWs was found to be DMP isomer dependent. Positive correlations were found between the bacteria harboring the phenol hydroxylase gene and communities present with 3,4-DMP and 3,5-DMP isomers, but not with the community developed with 2,6-DMP. These results indicate that CWs are highly dynamic ecosystems with rapid changes in bacterial communities harboring functional catabolic genes.

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

BACKGROUND

Dimethylphenols (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.

RESULTS

In 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.

CONCLUSIONS

LCW 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.

Competition for electrons between pyridine and quinoline during their simultaneous biodegradation

Biodegradation of pyridine and quinoline is initiated with mono-oxygenation reactions that require an intracellular electron donor. Simultaneous biodegradation of both substrates should set up competition for the intracellular electron donor that may inhibit one or more of the mono-oxygenation steps. An internal circulation baffled biofilm reactor (ICBBR) was used to evaluate the impacts of competition during pyridine and quinoline biodegradation. Compared with independent biodegradation, pyridine and quinoline removal rates were slowed when biodegraded simultaneously, although the pyridine removal rate decreased more than for quinoline. The first mono-oxygenation of quinoline (to 2-hydroxyquinoline) always was faster than the first mono-oxygenation of pyridine (to 2-hydroxypyridine), and the difference was accentuated with pyridine and quinoline which were biodegraded simultaneously due to the competition for intracellular electron donor. Competition also existed between the second mono-oxygenations, and the removal rate of 2-hydroxypyridine was faster than the rate for 2-hydroxyquinoline, even though the rate was faster for quinoline than pyridine. Adding an exogenous electron donor accelerated all mono-oxygenations in proportion to the amount of donor added, but the increments were greater for quinoline due to its higher affinity for intracellular electron donors than pyridine. When actual coking wastewater was used as the background matrix, removals of pyridine and quinoline exhibited the same competitive trends.

Determination of biodegradability of phenolic compounds, characteristic to wastewater of the oil-shale chemical industry, on activated sludge by oxygen uptake measurement

The aim of this study was to investigate the biodegradation of phenol, o-cresol and p-cresol individually and as bi-substrate mixtures at low initial substrate concentrations. Activated sludge was taken from the Kohtla-Järve wastewater treatment plant, Estonia, which is also treating phenolic wastewater from the oil-shale chemical industry and is considered to be acclimated to the phenolic compounds. Respirometric data have been used for evaluation of the kinetic parameters describing the bio-oxidation of substrates. Activated sludge was able to degrade phenol and p-cresol faster than o-cresol, showing better affinity to p-cresol. However, at higher concentrations, phenol and p-cresol exhibited also an inhibitory effect to the microorganisms. The highest values for maximum rate of oxygen uptake (V(O2,max)) were obtained for the bi-substrate system of phenol--p-cresol among the mixtures containing both substrates at equal concentrations from 0.005 mM to 0.050 mM. Concerning the systems containing one substrate at 0.1 mM and the other substrate varied in the abovementioned range, the highest V(O2,max) values were found for phenol--o-cresol(0.1 mM). The interaction parameters indicated that phenol had a stronger inhibition effect on the biodegradation of p-cresol than p-cresol had on the biodegradation of phenol. However, the obtained interaction parameters for systems of phenol--o-cresol indicated that o-cresol had a stronger inhibition effect on the biodegradation of phenol, which in turn had a mild inhibition or even enhancing effect on the biodegradation of o-cresol. In the case of a 1:1 mixture, phenol and o-cresol had a similar mild inhibition effect on each other's biodegradation.

Biodegradation of phenolic mixtures in a sequencing batch reactor. A kinetic study

GOAL, SCOPE AND BACKGROUND

In this study, attention was focused on substituted phenols because of their widespread presence in industrial effluents originating from many different sources: they are major constituents of wastewater from coal conversion processes, coke ovens, petroleum refineries and petrochemical industries, resin and fibreglass manufacturing and herbicide production. Moreover, for their characteristics of toxicity to humans and aquatic life (1 mgl(-1) is enough to detect the effects), they are included in the USEPA list of priority pollutants. Toxicity is higher in substituted phenols and is dependent on the nature and numbers of substituent groups. Objective of the present paper is to give a contribution to the modelling of phenolic mixture biodegradation by kinetic studies in which the different compounds are followed separately: this can be easily attained with an experimental apparatus such as the Sequencing Batch Reactor (SBR). Two substituted phenols, 4-nitrophenol (4NP) and 3,4-dimethylphenol (3,4DMP), were utilized as substrates and their degradation kinetics were investigated to evaluate the process parameters both in single compound and in mixture tests.

METHODS

Single compound and mixture kinetic tests have been carried out during the reaction phase of the working cycle of the SBR reactor. The single substrates and their mixture were utilized as sole carbon and energy sources. Moreover, in order to verify data reproducibility, all kinetic tests have been carried out in at least two replicates under the same operating conditions.

RESULTS AND DISCUSSION

Kinetic data showed the presence of substrate inhibition, to model this experimental evidence the Haldane equation, that is usually employed for substrate inhibited kinetics, was rearranged in a different form with parameters which have a precise meaning in relation to the process kinetics and, at the same time, make the integration procedure easier. The derivation of the equation is shown in an Appendix at the end of the paper. Kinetic parameters obtained are suitable for application. It was observed that the 4-nitrophenol removal rate in single compound tests is significantly higher than the 3,4-dimethylphenol removal rate in the whole range of investigated concentrations (up to 80 mg COD l(-1)). A faster 4-nitrophenol biodegradation was also observed in mixture tests. Moreover, it is worth noting that the two compounds were simultaneously degraded and no diauxic growth was observed. The comparison between single compound and mixture degradation kinetics showed that the 4-nitrophenol degradation rate was comparable in the two cases while a significantly beneficial effect (by increase by about 80% of the maximum removal rate) was detected for 3,4-dimethylphenol degradation in the mixture.

CONCLUSIONS

Results of this study showed that the biodegradation kinetics of substituted phenols in mixture can be significantly different from that observed in single compound tests: in fact, the presence of a faster degradable compound (the 4NP) seems to exert a positive effect on the removal of a slower degradable compound (the 3,4DMP). The higher removal rate detected for 4NP, both in single compound and mixture tests, confirmed the key role of the biomass acclimatization in determining the biodegradation kinetics of xenobiotic compounds. The experimental approach and the original method applied for data analysis are of general validity and can be extended to the investigation of different classes of compounds.

RECOMMENDATIONS AND PERSPECTIVES

A relevant aspect related to the process applicability is the demonstrated possibility of easily adapting an enriched culture grown on a specific xenobiotic (in our case the 4NP) for the removal of similar single compounds or in mixtures. When biological process are considered for xenobiotic removal, this suggests a possible strategy of developing enriched cultures on target compounds that can be efficiently utilized on more complex matrices with reduced start up and acclimatization periods.

Intradiol pathway of para-cresol conversion by Rhodococcus opacus 1CP

The growth of Rhodococcus opacus 1CP in medium with different concentrations of p-cresol as the sole source of carbon and energy was studied. It was shown that the optimal concentration of p-cresol was 600 mg/L. The ability of this strain to transform practically all amounts of p-cresol to 4-methylcatechol followed by its utilization through ortho-pathway was shown. New enzymes (4-methylcatechol 1,2-dioxygenase, catechol 1,2-dioxygenase, and methylmuconate cycloisomerase) were purified to homogeneity and characterized. Based on the data obtained on p-cresol degradation, formation of intermediates, and the enzymes participating in this pathway, we suggest an ortho-pathway of p-cresol degradation by R. opacus 1CP through 4-methylcatechol and 3-methyl-cis, cis-muconate.

Biodegradation efficiency of functionally important populations selected for bioaugmentation in phenol- and oil-polluted area

Denaturing gradient gel electrophoresis of amplified fragments of genes coding for 16S rRNA and for the largest subunit of multicomponent phenol hydroxylase (LmPH) was used to monitor the behaviour and relative abundance of mixed phenol-degrading bacterial populations (Pseudomonas mendocina PC1, P. fluorescens strains PC18, PC20 and PC24) during degradation of phenolic compounds in phenolic leachate- and oil-amended microcosms. The analysis indicated that specific bacterial populations were selected in each microcosm. The naphthalene-degrading strain PC20 was the dominant degrader in oil-amended microcosms and strain PC1 in phenolic leachate microcosms. Strain PC20 was not detectable after cultivation in phenolic leachate microcosms. Mixed bacterial populations in oil-amended microcosms aggregated and formed clumps, whereas the same bacteria had a planktonic mode of growth in phenolic leachate microcosms. Colony hybridisation data with catabolic gene specific probes indicated that, in leachate microcosms, the relative proportions of bacteria having meta (PC1) and ortho (PC24) pathways for degradation of phenol and p-cresol changed alternately. The shifts in the composition of mixed population indicated that different pathways of metabolism of aromatic compounds dominated and that this process is an optimised response to the contaminants present in microcosms.