Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.

[1]  J. E. Grimley,et al.  Under the microscope. , 1976, Journal Of The Macomb Dental Society.

[2]  V. Torsvik,et al.  High diversity in DNA of soil bacteria , 1990, Applied and environmental microbiology.

[3]  C. Harwood,et al.  Regulation of benzoate-CoA ligase in Rhodopseudomonas palustris , 1991 .

[4]  S. Harayama,et al.  Functional and evolutionary relationships among diverse oxygenases. , 1992, Annual review of microbiology.

[5]  J. Ramos,et al.  Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways , 1993, Molecular microbiology.

[6]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[7]  W. Rulkens,et al.  Environmental engineering series: Wastewater treatment, M. Henze, P. Harremoës, J. de la Cour, E. Arvin. , 1995 .

[8]  M. Madigan,et al.  Brock Biology of Microorganisms , 1996 .

[9]  T. Kudo,et al.  Adaptation of Comamonas testosteroni TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. , 1998, Microbiology.

[10]  G. Fuchs,et al.  Genes Involved in Anaerobic Metabolism of Phenol in the Bacterium Thauera aromatica , 2000, Journal of bacteriology.

[11]  G. González,et al.  Biodegradation of phenolic industrial wastewater in a fluidized bed bioreactor with immobilized cells of Pseudomonas putida. , 2001, Bioresource technology.

[12]  E. Stackebrandt,et al.  Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. , 2002, Archives of Microbiology.

[13]  Mark J. Bailey,et al.  RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny , 2002, Applied and Environmental Microbiology.

[14]  P. Stepnowski,et al.  Enhanced photo-degradation of contaminants in petroleum refinery wastewater. , 2002, Water research.

[15]  Anthony V. Palumbo,et al.  Spatial and Resource Factors Influencing High Microbial Diversity in Soil , 2002, Applied and Environmental Microbiology.

[16]  H. Yukawa,et al.  Aerobic and Anaerobic Toluene Degradation by a Newly Isolated Denitrifying Bacterium, Thauera sp. Strain DNT-1 , 2004, Applied and Environmental Microbiology.

[17]  James M. Lee,et al.  Biodegradation of the mixtures of 4-chlorophenol and phenol by Comamonas testosteroni CPW301 , 2004, Biodegradation.

[18]  J. Handelsman.  Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[19]  M. Bailey,et al.  N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge. , 2004, Environmental microbiology.

[20]  G. Fuchs,et al.  Evidence that phenol phosphorylation to phenylphosphate is the first step in anaerobic phenol metabolism in a denitrifying Pseudomonas sp. , 2004, Archives of Microbiology.

[21]  J. Wen,et al.  The biodegradation of phenol at high initial concentration by the yeast Candida tropicalis , 2005 .

[22]  B. Chang,et al.  Biodegradation of nonylphenol in sewage sludge. , 2005, Chemosphere.

[23]  J. Sonibare,et al.  Evaluation of microbial systems for bioremediation of petroleum refinery effluents in Nigeria , 2005 .

[24]  W. Verstraete,et al.  H2S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter , 2006, Applied Microbiology and Biotechnology.

[25]  M. Merimaa,et al.  Grouping of phenol hydroxylase and catechol 2,3-dioxygenase genes among phenol- and p-cresol-degrading Pseudomonas species and biotypes , 2006, Archives of Microbiology.

[26]  P. Phale,et al.  Preferential Utilization of Aromatic Compounds over Glucose by Pseudomonas putida CSV86 , 2006, Applied and Environmental Microbiology.

[27]  P. Moulin,et al.  Degradation of synthetic phenol-containing wastewaters by MBR , 2006 .

[28]  F. Bushman,et al.  Short pyrosequencing reads suffice for accurate microbial community analysis , 2007, Nucleic acids research.

[29]  K. Ahn,et al.  Effects of sludge retention time on membrane fouling and microbial community structure in a membrane bioreactor , 2007 .

[30]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[31]  Y. Watanabe,et al.  Bacterial community structures in MBRs treating municipal wastewater: relationship between community stability and reactor performance. , 2007, Water research.

[32]  G. Casella,et al.  Pyrosequencing enumerates and contrasts soil microbial diversity , 2007, The ISME Journal.

[33]  Alexander F. Auch,et al.  MEGAN analysis of metagenomic data. , 2007, Genome research.

[34]  A. Fodor,et al.  Molecular Diversity of a North Carolina Wastewater Treatment Plant as Revealed by Pyrosequencing , 2008, Applied and Environmental Microbiology.

[35]  Alexander Goesmann,et al.  Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. , 2008, Journal of Biotechnology.

[36]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[37]  K. Jayachandran,et al.  Biodegradation of phenol , 2008 .

[38]  H. Furumai,et al.  Analysis of the phylogenetic diversity of estrone-degrading bacteria in activated sewage sludge using microautoradiography-fluorescence in situ hybridization. , 2008, Systematic and applied microbiology.

[39]  A. Goesmann,et al.  Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. , 2008, Journal of biotechnology.

[40]  I. Mandic-Mulec,et al.  Influence of pharmaceutical residues on the structure of activated sludge bacterial communities in wastewater treatment bioreactors. , 2008, Water research.

[41]  Karl-Erich Jaeger,et al.  Advances in Recovery of Novel Biocatalysts from Metagenomes , 2008, Journal of Molecular Microbiology and Biotechnology.

[42]  Cristiano Piacsek Borges,et al.  The effects of long-term feeding of high organic loading in a submerged membrane bioreactor treating oil refinery wastewater , 2008 .

[43]  S. Agarry,et al.  Kinetics of batch microbial degradation of phenols by indigenous Pseudomonas fluorescence , 2008 .

[44]  G. R. D. Oliveira,et al.  Activated sludge system microbiology and its relationship with the industrial effluents treatment: the experience of the Cetrel , 2009 .

[45]  Yoshihiro Yamanishi,et al.  E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs , 2009, Bioinform..

[46]  Prathap Parameswaran,et al.  Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. , 2009, Water research.

[47]  Qunhui Wang,et al.  Isolation, identification of sludge-lysing strain and its utilization in thermophilic aerobic digestion for waste activated sludge. , 2009, Bioresource technology.

[48]  J. Bunge,et al.  Microbial community structure in the North Pacific ocean , 2009, The ISME Journal.

[49]  V. M. Oliveira,et al.  Investigation of bacterial diversity in membrane bioreactor and conventional activated sludge processes from petroleum refineries using phylogenetic and statistical approaches. , 2010, Journal of microbiology and biotechnology.

[50]  K. Bibby,et al.  Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. , 2010, Water research.

[51]  V. M. Oliveira,et al.  Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load. , 2010, Journal of microbiology and biotechnology.