The development of a liquid formulation of Pseudoxanthomonas sp. RN402 and its application in the treatment of pyrene-contaminated soil

Journal of Applied Microbiology

Volumn 111, Issue 1, 2011, Pages 36-47

  Nopcharoenkul, W ^a   Pinphanichakarn, P ^a   Pinyakong, O ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

Author keywords

Bioremediation; Denaturing gradient gel electrophoresis; Environmental; Polymerase chain reaction; Soil

Indexed keywords

BACTERIA; BIOACTIVITY; BIODEGRADATION; BIOREMEDIATION; DEGRADATION; ELECTROPHORESIS; GLYCEROL; POLYMERASE CHAIN REACTION; PYRENE; SOIL POLLUTION;

BACTERIAL CELLS; BIO-AUGMENTATION; CONTAMINATED SOILS; DENATURING GRADIENT GEL ELECTROPHORESIS; ENVIRONMENTAL; ITS APPLICATIONS; LIQUID FORMULATIONS; PHOSPHATE BUFFERS; SOIL MICROCOSMS; SURVIVAL RATE;

SOILS;

GLYCEROL; PHOSPHATE BUFFERED SALINE; PYRENE;

BACTERIUM; BIOACTIVITY; BIODEGRADATION; BIOREMEDIATION; ELECTROKINESIS; MICROCOSM; PHOSPHATE; POLYMERASE CHAIN REACTION; PYRENE; SOIL POLLUTION; SURVIVAL;

ARTICLE; BACTERIAL SURVIVAL; BIODEGRADABILITY; GRAM NEGATIVE BACTERIUM; LIQUID; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDOXANTHOMONAS; SOIL POLLUTANT; SOIL POLLUTION;

BACTERIA (MICROORGANISMS); PSEUDOXANTHOMONAS;

EID: 79958841891     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2011.05037.x     Document Type: Article

References (66)

1. Abadias, M., Usall, J., Teixidó, N. and Viñas, I. (2003) Liquid formulation of the postharvest biocontrol agent Candida sake CPA-1 in isotonic solutions. Phytopathology 93, 436-442.
2. Albareda, M., Rodríguez-Navarro, D.N., Camacho, M. and Temprano, F.J. (2008) Alternatives to peat as a carrier for rhizobia inoculants: solid and liquid formulations. Soil Biol Biochem 40, 2771-2779.
3. Amann, R., Ludwig, W. and Schleifer, K. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169.
4. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K. (1993) Current Protocols in Molecular Biology. New York: John Wiley & Sons, Inc.
5. Bach, Q.D., Kim, S.J., Choi, S.C. and Oh, Y.S. (2005) Enhancing the intrinsic bioremediation of PAH-contaminated anoxic estuarine sediments with biostimulating agents. J Microbiol 43, 319-324.
6. Baldwin, B.R., Nakatsu, C.H. and Nies, L. (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microbiol 69, 3350-3358.
7. Boldrin, B., Tiehm, A. and Fritzsche, C. (1993) Degradation of phenanthrene, fluorene, fluoranthene, and pyrene by a Mycobacterium sp. Appl Environ Microbiol 59, 1927-1930.
8. Cébron, A., Norini, M.P., Beguiristain, T. and Leyval, C. (2008) Real-time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from gram positive and gram negative bacteria in soil and sediment samples. J Microbiol Meth 73, 148-159.
9. Cerniglia, C.E. (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3, 351-368.
10. Churchill, S.A., Harper, J.P. and Churchill, P.F. (1999) Isolation and characterization of a Mycobacterium species capable of degrading three- and four-ring aromatic and aliphatic hydrocarbons. Appl Environ Microbiol 65, 549-552.
11. Churchill, P.F., Morgan, A.C. and Kitchens, E. (2008) Characterization of a pyrene-degrading Mycobacterium sp. strain CH-2. J Environ Sci Health B 43, 698-706.
12. Cunliffe, M., Kawasaki, A., Fellows, E. and Kertesz, M.A. (2006) Effect of inoculum pretreatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol 58, 364-372.
13. Dominguez, R., da Silva, M., McGuire, T., Adamson, D., Newell, C. and Alvarez, P. (2008) Aerobic bioremediation of chlorobenzene source-zone soil in flow-through columns: performance assessment using quantitative PCR. Biodegradation 19, 545-553.
14. Gutierrez, C., Abee, T. and Booth, I.R. (1995) Physiology of the osmotic stress response in microorganisms. Int J Food Microbiol 28, 233-244.
15. Habe, H., Kanemitsu, M., Nomura, M., Takemura, T., Iwata, K., Nojiri, H., Yamane, H. and Omori, T. (2004) Isolation and characterization of an alkaliphilic bacterium utilizing pyrene as a carbon source. J Biosci Bioeng 98, 306-308.
16. Haritash, A.K. and Kaushik, C.P. (2009) Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J Hazard Mater 169, 1-15.
17. Jameson, C.W. (2004) Report on carcinogens-history and process. Chem Health Saf 12, 9-14.
18. Johnsen, A.R., Bendixen, K. and Karlson, U. (2002) Detection of microbial growth on polycyclic aromatic hydrocarbons in microtiter plates by using the respiration indicator WST-1. Appl Environ Microbiol 68, 2683-2689.
19. Johnsen, A.R., Schmidt, S., Hybholt, T.K., Henriksen, S., Jacobsen, C.S. and Andersen, O. (2007) Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria. Appl Environ Microbiol 73, 1474-1480.
20. Kalendar, R., Lee, D. and Schulman, A.H. (2009) FastPCR software for PCR primer and probe design and repeat search. Genes Genomes Genomics 3, 1-14.
21. Kao, C.M., Chen, C.S., Tsa, F.Y., Yang, K.H., Chien, C.C., Liang, S.H., Yang, C.A. and Chen, S.C. (2010) Application of real-time PCR, DGGE fingerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume. J Hazard Mater 178, 409-416.
22. Karabika, E., Kallimanis, A., Dados, A., Pilidis, G., Drainas, C. and Koukkou, A. (2009) Taxonomic identification and use of free and entrapped cells of a new Mycobacterium sp., strain Spyr1 for degradation of polycyclic aromatic hydrocarbons (PAHs). Appl Biochem Biotechnol 159, 155-167.
23. Khan, A.A., Wang, R.F., Cao, W.W., Doerge, D.R., Wennerstrom, D. and Cerniglia, C.E. (2001) Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67, 3577-3585.
24. Kim, W.S., Park, J.H., Ren, J., Su, P. and Dunn, N.W. (2001) Survival response and rearrangement of plasmid DNA of Lactococcus lactis during long-term starvation. Appl Environ Microbiol 67, 4594-4602.
25. Klankeo, P., Nopcharoenkul, W. and Pinyakong, O. (2009) Two novel pyrene-degrading Diaphorobacter sp. and Pseudoxanthomonas sp. isolated from soil. J Biosci Bioeng 108, 488-495.
26. Kouzuma, A., Pinyakong, O., Nojiri, H., Omori, T., Yamane, H. and Habe, H. (2006) Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4. Microbiology 152, 2455-2467.
27. Lee, S.H., Lee, S., Kim, D.Y. and Kim, J.G. (2007) Degradation characteristics of waste lubricants under different nutrient conditions. J Hazard Mater 143, 65-72.
28. Li, L., Ye, Y., Pan, L., Zhu, Y., Zheng, S. and Lin, Y. (2009) The induction of trehalose and glycerol in Saccharomyces cerevisiae in response to various stresses. Biochem Biophys Res Commun 387, 778-783.
29. Liu, Y., Zhang, J. and Zhang, Z. (2004) Isolation and characterization of polycyclic aromatic hydrocarbons-degrading Sphingomonas sp. strain ZL5. Biodegradation 15, 205-212.
30. Liu, J., Tian, S.P., Li, B.Q. and Qin, G.Z. (2009) Enhancing viability of two biocontrol yeasts in liquid formulation by applying sugar protectant combined with antioxidant. Biol Control 54, 817-824.
31. Lui, P. and Zhang, C.K. (2007) Detection and quantification of phnE gene from oil-contaminated soil samples by competitive quantitative PCR. Microbiol Res 162, 335-340.
32. Mahanty, B., Pakshirajan, K. and Dasu, V. (2006) Production and properties of a biosurfactant applied to polycyclic aromatic hydrocarbon solubilization. Appl Biochem Biotechnol 134, 129-141.
33. Manikandan, R., Saravanakumar, D., Rajendran, L., Raguchander, T. and Samiyappan, R. (2010) Standardization of liquid formulation of Pseudomonas fluorescens Pf1 for its efficacy against Fusarium wilt of tomato. Biol Control 54, 83-89.
34. Melin, P., Håkansson, S., Eberhard, T.H. and Schnürer, J. (2006) Survival of the biocontrol yeast Pichia anomala after long-term storage in liquid formulations at different temperatures, assessed by flow cytometry. J Appl Microbiol 100, 264-271.
35. Melin, P., Schnürer, J. and Håkansson, S. (2011) Formulation and stabilisation of the biocontrol yeast Pichia anomala. Antonie Van Leeuwenhoek 99, 107-112.
36. Mrozik, A. and Piotrowska-Seget, Z. (2010) Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol Res 165, 363-375.
37. Muyzer, G., de Waal, E.C. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59, 695-700.
38. Nancharaiah, Y.V., Joshi, H.M., Hausner, M. and Venugopalan, V.P. (2008) Bioaugmentation of aerobic microbial granules with Pseudomonas putida carrying TOL plasmid. Chemosphere 71, 30-35.
39. Nyyssönen, M., Kapanen, A., Piskonen, R., Lukkari, T. and Itävaara, M. (2009) Functional genes reveal the intrinsic PAH biodegradation potential in creosote-contaminated groundwater following in situ biostimulation. Appl Microbiol Biotechnol 84, 169-182.
40. Obayori, O., Ilori, M., Adebusoye, S., Oyetibo, G. and Amund, O. (2008) Pyrene-degradation potentials of Pseudomonas species isolated from polluted tropical soils. World J Microbiol Biotechnol 24, 2639-2646.
41. Patiño-Vera, M., Jiménez, B., Balderas, K., Ortiz, M., Allende, R., Carrillo, A. and Galindo, E. (2005) Pilot-scale production and liquid formulation of Rhodotorula minuta, a potential biocontrol agent of mango anthracnose. J Appl Microbiol 99, 540-550.
42. Phrommanich, S., Suanjit, S., Upatham, S., Grams, S.V., Kruatrachue, M., Pokethitiyook, P., Korge, G. and Hofmann, A. (2009) Quantitative detection of the oil-degrading bacterium Acinetobacter sp. strain MUB1 by hybridization probe based real-time PCR. Microbiol Res 164, 486-492.
43. Pinyakong, O., Habe, H., Supaka, N., Pinpanichkarn, P., Juntongjin, K., Yoshida, T., Furihata, K., Nojiri, H. et al. (2000) Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2. FEMS Microbiol Lett 191, 115-121.
44. Pizzul, L., Sjögren, Å., Castillo, M.D. and Stenström, J. (2007) Degradation of polycyclic aromatic hydrocarbons in soil by a two-step sequential treatment. Biodegradation 18, 607-616.
45. Quan, X.C., Tang, H., Xiong, W.C. and Yang, Z.F. (2010) Bioaugmentation of aerobic sludge granules with a plasmid donor strain for enhanced degradation of 2, 4-dichlorophenoxyacetic acid. J Hazard Mater 179, 1136-1142.
46. Rehmann, K., Noll, H.P., Steinberg, C.E.W. and Kettrup, A.A. (1998) Pyrene degradation by Mycobacterium sp. strain KR2. Chemosphere 36, 2977-2992.
47. Robles-Gonzalez, I., Fava, F. and Poggi-Varaldo, H. (2008) A review on slurry bioreactors for bioremediation of soils and sediments. Microb Cell Fact 7, 5.
48. Romine, M.F., Stillwell, L.C., Wong, K.K., Thurston, S.J., Sisk, E.C., Sensen, C., Gaasterland, T., Fredrickson, J.K. et al. (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181, 1585-1602.
49. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press.
50. Sayler, G., Layton, A., Lajoie, C., Bowman, J., Tschantz, M. and Fleming, J. (1995) Molecular site assessment and process monitoring in bioremediation and natural attenuation. Appl Biochem Biotechnol 54, 277-290.
51. Schneider, J., Grosser, R., Jayasimhulu, K., Xue, W. and Warshawsky, D. (1996) Degradation of pyrene, benz[a]anthracene, and benzo[a]pyrene by Mycobacterium sp. strain RJGII-135, isolated from a former coal gasification site. Appl Environ Microbiol 62, 13-19.
52. Shannon, K.E., Lee, D.Y., Trevors, J.T. and Beaudette, L.A. (2007) Application of real-time quantitative PCR for the detection of selected bacterial pathogens during municipal wastewater treatment. Sci Total Environ 382, 121-129.
53. Shi, Z., Tian, L. and Zhang, Y. (2010) Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation. Acta Ecol Sin 30, 292-295.
54. Sho, M., Hamel, C. and Greer, C.W. (2004) Two distinct gene clusters encode pyrene degradation in Mycobacterium sp. strain S65. FEMS Microbiol Ecol 48, 209-220.
55. Springael, D. and Top, E.M. (2004) Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends Microbiol 12, 53-58.
56. Tathong, S. (2008) Assessment of bioremediation potential of wastewater from petrol station. Science Program Environmental Management. In Science Program Environmental Management (Interdisciplinary Program). Bangkok: Graduate School Chulalongkorn University.
57. Tittabutra, P., Payakaponga, W., Teaumroonga, N., Singletonb, W.P. and Boonkerda, N. (2007) Growth, survival and field performance of bradyrhizobial liquid inoculant formulations with polymeric additives. ScienceAsia 33, 069-077.
58. Torres, R., Usall, J., Teixidó, N., Abadias, M. and Viñas, I. (2003) Liquid formulation of the biocontrol agent Candida sake by modifying water activity or adding protectants. J Appl Microbiol 94, 330-339.
59. Venkata, M.S., Prasanna, D., Purushotham, R.B. and Sarma, P.N. (2008) Ex situ bioremediation of pyrene contaminated soil in bio-slurry phase reactor operated in periodic discontinuous batch mode: influence of bioaugmentation. Int Biodeterior Biodegradation 62, 162-169.
60. Vidali, M. (2001) Bioremediation: an overview. Pure Appl Chem 73, 1163.
61. Vila, J., Lopez, Z., Sabate, J., Minguillon, C., Solanas, A.M. and Grifoll, M. (2001) Identification of a novel metabolite in the degradation of pyrene by Mycobacterium sp. strain AP1: actions of the isolate on two- and three-ring polycyclic aromatic hydrocarbons. Appl Environ Microbiol 67, 5497-5505.
62. Walter, U., Beyer, M., Klein, J. and Rehm, H.J. (1991) Degradation of pyrene by Rhodococcus sp. UW1. Appl Microbiol Biotechnol 34, 671-676.
63. Watanabe, K., Miyashita, M. and Harayama, S. (2000) Starvation improves survival of bacteria introduced into activated sludge. Appl Environ Microbiol 66, 3905-3910.
64. Zancan, P. and Sola-Penna, M. (2005) Trehalose and glycerol stabilize and renature yeast inorganic pyrophosphatase inactivated by very high temperatures. Arch Biochem Biophys 444, 52-60.
65. Zeng, J., Lin, X., Zhang, J. and Li, X. (2010) Isolation of polycyclic aromatic hydrocarbons (PAHs) degrading Mycobacterium spp. and the degradation in soil. J Hazard Mater 183, 718-723.
66. Zhou, H., Wong, A., Yu, R., Park, Y., Wong, Y. and Tam, N. (2009) Polycyclic aromatic hydrocarbon induced structural shift of bacterial communities in mangrove sediment. Microbial Ecol 58, 153-160.