Degenerate primers as biomarker for gene-targeted metagenomics of the catechol 1, 2-dioxygenase-encoding gene in microbial populations of petroleum-contaminated environments

Annals of Microbiology

Volumn 66, Issue 3, 2016, Pages 1127-1136

  Nafian, Fatemeh ^a,b   Gharavi, Sara ^a   Soudi, Mohammad Reza ^a  

^a ALZAHRA UNIVERSITY   (Iran)

^b TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

Biomarker; Bioremediation; Catechol 1,2 dioxygenase; Metagenomics; Petroleum contaminated soil

Indexed keywords

EID: 84957954308     PISSN: 15904261     EISSN: 18692044     Source Type: Journal    
DOI: 10.1007/s13213-016-1197-3     Document Type: Article

References (59)

1. Bagneris C, Cammack R, Mason R (2005) Subtle difference between benzene and toluene dioxygenases of Pseudomonas putida. Appl Environ Microbiol 71:1570–1580
2. Boone DR, Castenholz RW, Garrity GM, Brenner DJ, Krieg NR, Staley JT (2005) Bergey's manual of systematic bacteriology. Springer Science & Business Media, New York
3. Brennerova M, Josefiova J, Brenner V, Pieper D (2009) Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ Microbiol 11:2216–2227
4. Chen Y, Liu H, Chen H (2003) Characterization of phenol biodegradation by Comamonas testosteroni zd4-1 and Pseudomonas aeruginosa zd4-3. Biomed Environ Sci 16:163–172
5. Committee on Metagenomics: Challenges and Functional Applications (2007) The new science of metagenomics: revealing the secrets of our microbial planet, 1st edn. National Academies Press, Washington D.C.
6. Cowan D, Stafford W (2007) Metagenomic methods for the identification of active micro-organisms and genes in biodegradation processes. Univ West Cape Res Repository 3:1–19
7. Daniel R (2004) The soil metagenome: a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:199–204
8. Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478
9. Delmont T, Clark I, Simonet P, Vogel T (2011a) Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods 86:397–400
10. Delmont T, Robe P, Cecillon S, Clark I, Constancias F (2011b) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77:1315–1324
11. Enan R (2006) Isolation and molecular characterization of phenol degrading Gram-positive bacteria from oil contaminated soil. Res J Microbiol 4:307–318
12. Eyers L, Schuler L, Stenuit B, Agathos N, Fantroussi S (2004) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Microbiol Biotechnol 66:123–130
13. Fernández-Arrojo L, Guazzaroni ME, López-Cortés N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21:725–733
14. Folsom J, Richards L, Pitts B, Roe F, Ehrlich G, Parker A, Mazurie A, Stewart P (2010) Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. BMC Microbiol 10:294–301
15. Geng A, Soh A, Lim C, Loke L (2006) Isolation and characterization of phenol degrading bacterium from an industrial active sludge. Appl Microbiol Cell Physiol 71:728–735
16. Gibson D, Parales R (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236–243
17. Giegerich R, Meyer F, Schleiermacher C (1996) GeneFisher software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol 4:68–77
18. Grimm A, Harwood C (1999) NahY a catabolic plasmid encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J Bacteriol 181:3310–3316
19. Handelsman J, Rondon R, Brady F, Clardy J, Goodman R (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:245–249
20. Heuer H, Krsek M, Baker P, Smalla K, Wellington M (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241
21. Hirsch R, Mauchline H, Clark M (2010) Culture independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42:878–887
22. Hosokawa R, Nagai M, Morikawa M, Okuyama H (2009) Autochthonous bioaugmentation and its possible application to oil spills. World J Microbiol Biotechnol 25:1519–1528
23. Iwai S, Chai B, Sul W, Cole J, Hashsham J, Tiedje J (2010) Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4:279–285
24. Iwai S, Chai B, Jesus E, Penton R, Lee T, Cole J, Tiedje J (2011) In: de Bruijn FJ (ed) Handbook of molecular microbial ecology 1: metagenomics and complementary approaches. Wiley Blackwell, Hoboken, pp 235–243
25. Jiang L, Ruan Q, Li R, Li T (2013) Biodegradation of phenol by using free and immobilized cells of Acinetobacter sp. BS8Y J Basic Microbiol 53(3):224–30
26. Jorgensen S (2008) Advances in monitoring of catabolic genes during bioremediation. Indian J Microbiol 48:152–155
27. Kakirde K, Parsley L, Liles M (2010) Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem 42:1911–1923
28. Khara P, Roy M, Chakraborty J, Ghosal D, Dutta K (2014) Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB. FEBS Open Biol 4:290–300
29. Kumar A, Kumar S, Kuma S (2005) Biodegradation kinetics of phenol and catechol using Pseudomonas putida MTCC 1194. Biochem Eng J 22:151–159
30. Liang R, Wu X, Dai Q, Jin D, Wang Y (2010) Genetic diversity of phthalic acid esters degrading bacteria isolated from different geographical regions of China. Antonie Van Leeuwenhoek 97:79–89
31. Linhart C, Shamir R (2005) The degenerate primer design problem: theory and applications. Bioinformatics 18:172–180
32. Lisek A, Sas Paszt L, Trzciński P (2014) Identification and assessment of genetic similarity of soil bacterial isolates of Pseudomonas spp. using molecular techniques. Pol J Microbiol 63(3):291–8
33. Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516
34. Louws FJ, Fulbright DW, Stephens CT, de Bruijn FJ (1994) Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl Environ Microbiol 60(7):2286–95
35. Malik S, Beer M, Megharaj M (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34:265–276
36. Manickam N, Pathak A, Saini S, Mayilraj S, Shanker R (2010) Metabolic profiles and phylogenetic diversity of microbial communities from chlorinated pesticides contaminated sites of different geographical habitats of India. J Appl Microbiol 109:1458–1468
37. Mocali S, Bendetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497–505
38. Morimoto S, Fujii T (2009) A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl Microbiol Biotechnol 83:389–396
39. Mrozik A, Piotrowska-Seget Z (2010) Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol Res 165:363–375
40. Newton CR, Graham A (1996) PCR: introduction to biotechniques. 2nd edn. Bios Scientific Publishers, Milton Park
41. Parales E, Lee K, Resnick S, Jiang H, Lessner D, Gibson D (2000) Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J Bacteriol 182:1641–1649
42. Prakash T, Taylor T (2012) Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 10:1–17
43. Rondon M, August P, Bettermann A, Brady S (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 6:2541–2547
44. Sambrook J, Russel D (2001) Molecular cloning. 3rd edn. Cold Spring Harbor Laboratory Press, New York
45. SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460–1465
46. Sei K, Asano K, Tateishi N, Mori K, Ike M, Fujita M (1999) Design of PCR primers and gene probes for the general detection of bacterial populations capable of degrading aromatic compounds via catechol cleavage pathways". J Biosci Bioeng 88:542–550
47. Silva C, Hayden H, Sawbridge T, Mele P, Paula S, Silva L, Vidigal P, Vicentini R, Sousa M, Torres A, Santiago M, Oliveira V (2013) Identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater. PLoS One 4:1–11
48. Steele L, Streit R (2005) Metagenomics: advances in ecology and biotechnology. FEMS Microbiol Lett 247:105–111
49. Stenuit B, Eyers L, Schuler L, Agathos S, George I (2008) Emerging high-throughput approaches to analyse bioremediation of sites contaminated with hazardous and/or recalcitrant wastes. Biotechnol Adv 26:561–575
50. Suenaga H, Watanabe T, Sato M, Furukawa K (2002) Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J Bacteriol 184:3682–3688
51. Suenaga H, Mizuta S, Miyazaki K, Yaoi K (2014) Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches. FEMS Microbiol Ecol 90(2014):367–379
52. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
53. Tancsics A, Szoboszlay S, Kriszt B, Kukolya J, Baka E, Marialigeti K, Revesz S (2008) Applicability of the functional gene catechol 1 2-dioxygenase as a biomarker in the detection of BTEX-degrading Rhodococcus species. J Appl Microbiol 105:1026–1033
54. Uhlik O, Jecna K, Leigh M, Mackova M, Macek T (2009) DNA based stable isotope probing: a link between community structure and function. Sci Total Environ 407:3611–3619
55. Vardar G, Wood K (2005) Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation. Appl Microbiol Biotechnol 68:510–517
56. Warnecke F, Hugenholtz P (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8:231
57. Watanabe K, Teramoto M, Futamata H, Harayama S (1998) Molecular detection isolation and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol 11:4396–4402
58. Webster R (2008) Soil sampling and methods of analysis - edited by M.R. Carter & E.G. Gregorich. Eur J Soil Sci 59:1010–1011. doi:10.1111/j.1365-2389.2008.01052_5.x
59. Witzig R, Junca H, Hecht J, Pieper D (2006) Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases. Appl Environ Microbiol 72:3504–3514