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

AMB Express

Volumn 2, Issue 1, 2012, Pages 1-13

  Silva, Cynthia C ^a   Hayden, Helen ^b   Sawbridge, Tim ^b   Mele, Pauline ^b   Kruger, Ricardo H ^c   Rodrigues, Marili V N ^a   Costa, Gustavo G L ^a   Vidal, Ramon O ^a   Sousa, Maíra P ^d   Torres, Ana Paula R ^d   Santiago, Vânia M J ^d   Oliveira, Valéria M ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^c UNIVERSITY OF BRASILIA   (Brazil)

^d PETROBRAS   (Brazil)

Author keywords

Fosmid library; Membrane bioreactor; Metabolic profile; Microbial diversity; Pyrosequencing

Indexed keywords

BENZOIC ACID; BIPHENYL; NAPHTHALENE; PHENOL; TOLUENE;

ARTICLE; COMAMONAS; DIAPHOROBACTER; GENE LIBRARY; GENE SEQUENCE; METAGENOME; PHYLOGENETIC TREE; PROTEOBACTERIA; PSEUDOMONAS; SLUDGE TREATMENT; THAUERA; WASTE WATER MANAGEMENT; WASTE WATER TREATMENT PLANT;

EID: 84863889305     PISSN: None     EISSN: 21910855     Source Type: Journal    
DOI: 10.1186/2191-0855-2-18     Document Type: Article

References (54)

1. Agarry SE, Solomon BO (2008) Kinetics of batch microbial degradation of phenols by indigenous Pseudomonas fluorescenc. Int J Environ Sci Tech 5:223-232
2. Ahmed Z, Cho J, Lim B-R, Song K-G, Ahn K-H (2007) Effects of sludge retention time on membrane fouling and microbial community structure in a membrane bioreactor. J Membrane Sci 287:211-218. doi:10.1016/j. memsci.2006.10.036.
3. Amann RI, Ludwig W, Schleifer K (1995) Phylogenetic identification and in sit detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
4. Arai H, Akahira S, Ohishi T, Maeda M, Kudo T (1998) Adaptation of Comamonas testosteron TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. Microbiology 144:2895-2903. doi:10.1099/00221287-144-10-2895.
5. Aziz AK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: Rapid annotation using subsystems technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75.
6. Bae HS, Lee JM, Kim YB, Lee ST (1996) Biodegradation of the mixtures of 4-chlorophenol and phenol by Comamonas testosteron CPW301. Biodegradation 7:463-469
7. Basu A, Apte AK, Phale PS (2006) Preferential utilization of aromatic compounds over glucose by Pseudomonas putid CV86. Appl Environ Microbiol 72:2226-2230. doi:10.1128/AEM.72.3.2226-2230.2006.
8. Barrios-Martinez A, Barbot E, Marrot B, Moulin P, Roche N (2006) Degradation of synthetic phenol-containing wastewaters by MBR. Journal Membrane Science 281:288-296. doi:10.1016/j.memsci.2006.03.048.
9. Billy K, Viau E, Peccia J (2010) Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Water Res 44:4252-4260. doi:10.1016/j.watres.2010.05.039.
10. Braile PM (1979) Manual of Industrial Wastewater Treatment. CETESB, São Paulo, 1
11. Breinig S, Schiltz E, Fuchs G (2000) Genes Involved in Anaerobic Metabolism of Phenol in the Bacterium Thauera aromatic. J Bacteriol 182:5849-5863. doi:10.1128/JB.182.20.5849-5863.2000.
12. Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP (2009) Microbial community structure in the North Pacific Ocean. ISME J 3:1374-1386. doi:10.1038/ismej.2009.86.
13. Chang BV, Chiang F, Yuan SY (2005) Biodegradation of nonylphenol in sewage sludge. Chemosphere 60:1652-1659. doi:10.1016/j.chemosphere.2005.02.042.
14. Gonzalez G, Herrera G, García MT, Peña M (2001) Biodegradation of phenolic industrial wastewater in a fluidized bed bioreactor with immobilized cells of Pseudomonas putid. Biores Technol 80:17-142
15. Handelsman J (2004) Metagenomics: Application of Genomics to Uncultured microorganisms. Microbiol Mol Biol Rev 68:669-685. doi:10.1128/MMBR.68.4.669-685.2004.
16. Harayama S, Kok M, Neidle EL (1992) Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol 46:565-601. doi:10.1146/annurev.mi.46.100192.003025.
17. Henze M, Harremoes P, la Cour JJ, Arvin E (1997) Wastewater treatment. Berlin: Springer, 2 Environmental Engineering
18. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377-386. doi:10.1101/gr.5969107.
19. Jiang Y, Wen JP, Li HM, Yang SL, Hu ZD (2005) The biodegradation of phenol at high initial concentration by the yeast Candida tropicali. Biochem Eng J 24:243-247. doi:10.1016/j.bej.2005.02.016.
20. Kim M-K, Harwood CS (1991) Regulation of benzoate-CoA ligase in Rhodopseudomonas palustri. FEMS Microbiol Let 83:199-203
21. Kraigher B, Kosjek T, Heath E, Kompare B, Mandic-Muleca I (2008) Influence of pharmaceutical residues on the structure of activated sludge bacterial communities in wastewater treatment bioreactors. Water Res 42:4578-4588. doi:10.1016/j.watres.2008.08.006.
22. Lack A, Fuchs G (1994) Evidence that phenol phosphorylation to phenylphosphate is the first step in anaerobic phenol metabolism in a denitrifying Pseudomona sp. Arch Microbiol 161:132-139
23. Li X, Ma H, Wang Q, Matsumoto S, Maeda T, Ogawa HI (2009) Isolation, identification of sludge-lysing strain and its utilization in thermophilic aerobic digestion for waste activated sludge. Bioresource Technology 100:2475-2481. doi:10.1016/j.biortech.2008.12.019.
24. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35:e120. doi:10.1093/nar/gkm541.
25. Madigan M, Martinko J, Dunlap P, Clark D (2008) Brock Biology of Microorganisms. New York, USA: Pearson Higher Education, 12
26. Manefield M, Whiteley AS, Griffiths GI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Applied Environment and Microbiology 68:5367-5373. doi:10.1128/AEM.68.11.5367-5373.2002.
27. Mariano JB (2001) Environmental impacts of petroleum refining. COPPE/UFRJ, Rio de Janeiro, RJ, Brazil: MSc These
28. Merimaa M, Heinaru E, Liivak M, Vedler E, Heinaru A (2006) Grouping of phenol hydroxylase and catechol 2,3-dioxygenase genes among phenol-and pcresol-degrading Pseudomonas species and biotypes. Arch Microbiol 186:287-296. doi:10.1007/s00203-006-0143-3.
29. Marques S, Ramos JL (1993) Transcriptional control of the Pseudomonas putid TOL plasmid catabolic pathways. Mol Microbiol 9:923-929. doi:10.1111/j.1365-2958.1993.tb01222.x.
30. Mechichi T, Stackebrandt E, Gadon N, Fuchs G (2002) Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetic sp. nov., Thauera aminoaromatic sp. nov., and Azoarcus buckeli sp. nov. Arch Microbiol 178:26-35. doi:10.1007/s00203-002-0422-6.
31. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The Metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:10.1186/1471-2105-9-386.
32. Miura Y, Hiraiwa MN, Ito T, Itonaga T, Watanabe Y, Okabe S (2007) Bacterial community structures in MBRs treating municipal wastewater: Relationship between community stability and reactor performance. Water Res 41:627-637. doi:10.1016/j.watres.2006.11.005.
33. Nair CI, Jayachandran K, Shashidhar S (2008) Biodegradation of phenol. African J Biotechnol 7:4951-4958
34. Ojumu TV, Bello OO, Sonibare JA, Solomon BO (2005) Evaluation of microbial systems for bioremediation of petroleum refinery effluents in Nigeria. African J Biotechnol 4:31-35
35. Oliveira GSS, Araújo CVM, Fernandes JGS (2009) Activated sludge system microbiology and its relationship with the industrial effluents treatment: the experience of the Cetrel. Eng Sanit Ambient 14:183-192
36. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283-290
37. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM (2009) Molecular diversity of a north carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 175:1688-1696
38. Schlüter A, Krause L, Szczepanowski R, Goesmann A, Pühler A (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. J Biotechnol 136:65-72. doi:10.1016/j.jbiotec.2008.03.017.
39. Sercu B, Boon N, Verstraete W, van Langenhove H (2006) H2S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter. Appl Microbiol Biotechnol 72:1090-1098. doi:10.1007/s00253-006-0382-x.
40. Shinoda Y, Sakai Y, Uenishi H, Uchihashi Y, Hiraishi A, Yukawa H, YurimotoH KN (2004) Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauer sp. strain DNT-1. Appl Environ Microbiol 70:1385-1392. doi:10.1128/AEM.70.3.1385-1392.2004.
41. Silva CC, Jesus EC, Torres APR, Sousa MP, Santiago VMJ, Oliveira VM (2010) Investigation of bacterial diversity in membrane bioreactor and conventional activated sludge processes from petroleum refineries using phylogenetic and statistical approaches. J Microbiol Biotechnol 20:447-459
42. Silva CC, Viero AF, Dias ACF, Andreote FD, Jesus EC, De Paula SO, Torres APR, Santiago VMJ, Oliveira VM (2010) Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load. J Microbiol Biotechnol 20:17-25
43. Sleator RD, Shortall C, Hill C (2008) Under the microscope: Metagenomics. Let Appl Microbiol 47:361-366. doi:10.1111/j.1472-765X.2008.02444.x.
44. Standard Methods for the Examination of Water and Wastewater (1998) American Public Health Association and American Water Works Association and Water Pollution Control Federation. USA: Washington, 20
45. Steele HL, Jaeger K-E, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16:25-37. doi:10.1159/000142892.
46. Stepnowski P, Siedlecka EM, Behrend P, Jastorff B (2002) Enhanced photodegradation of contaminants in petroleum refinery wastewater. Water Res 36:2167-2172. doi:10.1016/S0043-1354(01)00450-X.
47. Szczepanowski R, Bekel T, Goesmann A, Krause L, Krömeke H, Kaiser O, Eichler W, Pühler A, Schlüter A (2008) Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analyzed by the 454-pyrosequencing technology. J Biotechnol 136:54-64. doi:10.1016/j.jbiotec.2008.03.020.
48. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782-787
49. Valle A, Bailey MJ, Whiteley AS, Manefield M (2004) N-acyl-L-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge. Environmental Microbiology 6:424-433. doi:10.1111/j.1462-2920.2004.00581.x.
50. Viero AF, Melo TM, Torres APR, Ferreira NR, Sant'Anna GL Jr, Borges CP, Santiago VMJ (2008) The effects of long-term feeding of high organic loading in a submerged membrane bioreactor treating oil refinery wastewater. J Membrane Sci 319:223-230. doi:10.1016/j.memsci.2008.03.038.
51. Yamanishi Y, Hattori M, Kotera M, Goto S, Kanehisa M (2009) E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrateproduct pairs. Bioinformatics 25:179-182. doi:10.1093/bioinformatics/btp223.
52. Zang K, Kurisu F, Kasuga I, Furumai H, Yagi O (2008) Analysis of the phylogenetic diversity of estrone-degrading bacteria in activated sewage sludge using microautoradiography-fluorescence in situ hybridization. Systematic Appl Microbiol 31:206-214. doi:10.1016/j.syapm.2008.03.005.
53. Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE (2009) Focused-pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. Water Res 43:4517-4526. doi:10.1016/j.watres.2009.07.034.
54. Zhou J, Xia B, Treves DS, Wu L-Y, Marsh TL, O'Neill RV, Palumbo AV, Tiedje JM (2001) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326-334