Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Smith, Renee J ^a   Jeffries, Thomas C ^b   Adetutu, Eric M ^a   Fairweather, Peter G ^a   Mitchell, James G ^a  

^a FLINDERS UNIVERSITY   (Australia)

^b UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACID; HYDROCARBON;

ARTICLE; BACTERIOPHAGE; BIODEGRADATION; CANONICAL ANALYSIS; CARBON METABOLISM; CELL MOTILITY; CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; GENETIC ASSOCIATION; GEOGRAPHIC DISTRIBUTION; IRON METABOLISM; METAGENOME; MULTIVARIATE ANALYSIS; NONHUMAN; SEDIMENT; SIGNAL TRANSDUCTION; SPOROGENESIS; TRANSPORT KINETICS; VIRULENCE;

HYDROCARBONS; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS;

EID: 84896728211     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081910     Document Type: Article

References (67)

1. Falkowski PG, Fenchel T, Delong EF (2008) The Microbial Engines That Drive Earth's Biogeochemical. Cycles - Microbial Ecology 320: 1034-1039. (Pubitemid 351929518)
2. Chapin FS III, Walker BH, Hobbs RJ, Hooper DU, Lawton JH et al. (1997) Biotic control over the functioning of ecosystems. Science 277: 500-504. doi:10.1126/science.277.5325.500. (Pubitemid 27368987)
3. Karl DM (2002) Nutrient dynamics in the deep blue sea. Trends Microbiol 10: 410 - 418. doi:10.1016/S0966-842X(02)02430-7. PubMed: 12217506.
4. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-633. doi:10.1038/nature06810. PubMed: 18337718.
5. Brown JH, Gillooly JF, Allen AP, Savage VM (1771-1789) West GB (2004) Toward a metabolic theory of ecology. Ecology 85.
6. Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L et al. (2010) Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.ISME J 4: 660-672. doi:10.1038/ismej.2009.154. PubMed: 20182523.
7. Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G et al. (2011) Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Appl Environ Microbiol 77: 7962-7974. doi:10.1128/AEM.05402-11. PubMed: 21948834.
8. Smith RJ, Jeffries TC, Roudnew B, Fitch AJ, Seymour JR et al. (2012) Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems. Environ Microbiol 14: 240-253. PubMed: 22004107.
9. Henriques IDS, Aga DS, Mendes P, Connor SKO, Love NG (2007) Metabolic Footprinting: A New Approach to Identify Physiological Changes in Complex Microbial Communities upon Exposure to Toxic Chemicals. Environ Sci Technol 41: 3945-3951. doi:10.1021/es062796t. PubMed: 17612173. (Pubitemid 46903204)
10. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO et al. (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A 106: 1374 - 1379. doi: 10.1073/pnas.0808022106. PubMed: 19164758.
11. Röling WFM, Ferrer M, Golyshin PN (2010) Systems approaches to microbial communities and their functioning. Curr Opin Biotechnol 21: 532-538. doi:10.1016/j.copbio.2010.06.007. PubMed: 20637597.
12. Schimel J, Balser TC, Wallenstein M (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88: 1386-1394. doi:10.1890/06-0219. PubMed: 17601131. (Pubitemid 351345214)
13. Steube C, Richter S, Griebler C (2009) First attempts towards an integrative concept for the ecological assessment of groundwater ecosystems. Hydrogeol J 17: 23-35. doi:10.1007/s10040-008-0346-6.
14. Head IM, Jones DM, Röling WFM (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4: 173-182. doi:10.1038/nrmicro1348. PubMed: 16489346.
15. Mailaa MP, Cloeteb TE (2005) The use of biological activities to monitor the removal of fuel contaminants - perspective for monitoring hydrocarbon contamination: a review. Int Biodeterior 55: 1-8. doi: 10.1016/j.ibiod.2004.10. 003.
16. Avidano L, Gamalero E, Cossa GP, Carraro E (2005) Characterization of soil health in an Italian polluted site by using microorganisms as bioindicators. Appl Soil Ecol 30: 21-33. doi:10.1016/j.apsoil.2005.01.003. (Pubitemid 40938501)
17. Anderson T (2003) Microbial eco-physiological indicators to asses soil quality. Agric Ecosyst Environ 98: 285-293. doi:10.1016/S0167-8809(03)00088-4.
18. Bonjoch X, Ballesté E, Blanch AR (2004) Multiplex PCR with 16S rRNA Gene-Targeted Primers of Bifidobacterium spp. To Identify Sources of Fecal Pollution. Appl Environ Microbiol 70: 3171-3175. doi:10.1128/AEM.70.5.3171-3175. 2004. PubMed: 15128586. (Pubitemid 38657843)
19. Wooley JC, Ye Y (2010) Metagenomics: Facts and Artifacts, and Computational Challenges. J Comput Sci Technol 25: 71-81. doi: 10.1007/s11390-010-9306-4.
20. Buyer JS, Drinkwater LE (1997) Comparison of substrate utilization assay and fatty acid analysis of soil microbial communities. J Microbiol Methods 30: 3-11. doi:10.1016/S0167-7012(97)00038-9. (Pubitemid 27387550)
21. Hernesmaa A, Björklöf K, Kiikkilä O, Fritze H, Haahtela K et al. (2005) Structure and function of microbial communities in the rhizosphere of Scots pine after tree-felling. Soil Biol Biochem 37: 777-785. doi: 10.1016/j.soilbio.2004.10.010.
22. Williams BK, Titus K (1988) Assessment of sampling stability in ecological applications of discriminant analysis. Ecology 69: 1275-1285. doi:10.2307/1941283. (Pubitemid 20418156)
23. Pelz O, Tesar M, Wittich RM, Moore ERB, Timmis KN et al. (1999) Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ Microbiol 1: 167-174. doi:10.1046/j.1462-2920.1999.00023.x. PubMed: 11207732. (Pubitemid 129640039)
24. Anderson MJ, Willis TJ (2003) Canonical analysis of principle coordinates: A useful method of constrained ordination for ecology. Ecology 84: 511-525. Available online at: doi: 10.1890/0012-9658(2003)084[0511:CAOPCA]2.0. CO;2
25. Bastias BA, Huang ZQ, Blumfield T, Xu Z, Cairney JWG (2006) Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest. Soil Biol Biochem 38: 3492-3501. doi:10.1016/j.soilbio.2006.06.007. (Pubitemid 44604396)
26. Cookson WR, Osman M, Marschner P, Abaye DA, Clark I et al. (2007) Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature. Soil Biol Biochem 39: 744-756. doi:10.1016/j.soilbio.2006.09.022. (Pubitemid 44909229)
27. Lear G, Lewis GD (2009) Impact of catchment land use on bacterial communities within stream biofilms. Ecol Indic 9: 848 - 855. doi: 10.1016/j.ecolind.2008.10.001.
28. Baker KL, Langenheder S, Nicol GW, Ricketts D, Killham K et al. (2009) Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies. Soil Biol Biochem 41: 2292-2298. doi:10.1016/j.soilbio.2009.08.010.
29. Singleton I (1994) Microbial Metabolism of Xenobiotics: Fundamental and Applied Research. J Chem Technol Biotechnol 59: 9-23. doi: 10.1002/jctb. 280590104.
30. Chikere CB, Okpokwasili GC, Chikere BO (2011) Monitoring of microbial hydrocarbon remediation in the soil. 3 Biotech 1: 117-138
31. Liang Y, Van Nostrand JD, Deng Y, He Z, Wu L et al. (2011) Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.ISME J 5: 403-413. doi:10.1038/ismej.2010.142. PubMed: 20861922.
32. Viñas M, Sabaté J, José Espuny M, Solanas AM (2005) Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil. Appl Environ Microbiol 71: 7008-7018. doi:10.1128/AEM.71.11.7008-7018.2005. PubMed: 16269736. (Pubitemid 43194190)
33. Röling WFM, Milner MG, Martin Jones D, Lee K, Daniel F et al. (2002) Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation. Appl Environ Microbiol 68: 5537-5548. doi:10.1128/AEM. 68.11.5537-5548.2002. PubMed: 12406747.
34. Singh AK, Sherry A, Gray ND, Jones MD, Röling WFM, et al. (2011) Dynamics of Alcanivorax spp. in Oil-Contaminated Intertidal Beach Sediments Undergoing Bioremediation. Appl Microbiol Mol Biol DOI 10.1007/978-90-481-9252- 6-24: 199-209
35. Xu R, Obbard JP, Tay ETC (2003) Optimization of slow-release fertilizer dosage for bioremediation of oil-contaminated beach sediment in a tropical environment. World J Microbiol Biotechnol 19: 719-725. doi:10.1023/A: 1025116421986. (Pubitemid 37089981)
36. Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18: 257-266. doi:10.1016/j.copbio.2007.04.006. PubMed: 17493798. (Pubitemid 46880285)
37. Walworth J, Pond A, Snape I, Rayner J, Ferguson S et al. (2007) Nitrogen requirements for maximizing petroleum bioremediation in a sub-Antarctic soil. Cold Reg Sci Technol 48: 84-91. doi:10.1016/j.coldregions.2006.07.001. (Pubitemid 46477797)
38. Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23: 1-8. doi:10.1016/j.copbio.2011.12.020. PubMed: 22244690.
39. Kennedy J, Flemer B, Jackson SA, Lejon DPH, Morrissey JP et al. (2010) Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial. Metabolism - Mar Drugs 8: 608-628. doi:10.3390/md8030608.
40. Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils. PLOS ONE 7: 1-10. PubMed: 22253877.
41. Meyer F, Paarmann D, D'Souza M, Olsem R, Glass EM et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 1-8. doi:10.1186/1471-2105-9-S10-O1. PubMed: 18173834.
42. Clarke A, Gorley R (2006) PRIMER v6: User Manula/Tutorial. Plymouth, UK: PRIMER-E.
43. Clarke KR (1993) Nonparametric multivariate analysis of changes in community structure. Aust J Ecol 18: 117-143. doi:10.1111/j.1442-9993.1993. tb00438.x.
44. Anderson MJ, Robinson J (2001) Permutation tests for linear models. Aust NZ J Stat 43: 75-88. doi:10.1111/1467-842X.00156.
45. Anderson MJ, Gorley RN, Clarke KR (2008) PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods. PRIMER-E, Plymouth, UK.
46. Clarke KR, Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd Edition. PRIMER-E Ltd.
47. Langworthy DE, Stapleton RD, Sayler GS, Findlay RH (1998) Genotypic and Phenotypic Responses of a Riverine Microbial Community to Polycyclic Aromatic Hydrocarbon Contamination. Appl Environ Microbiol 64: 3422 - 3428. PubMed: 9726892
48. Siciliano SD, Germida JJ, Banks K, Greer CW (2003) Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field. Trial - Appl Environ Microbiol 69: 483-489. (Pubitemid 36077511)
49. Watanabe K (2001) Microorganisms relevant to bioremediation. Curr Opin Biotechnol 12: 237-241. doi:10.1016/S0958-1669(00)00205-6. PubMed: 11404100.
50. Jeffries TC, Seymour JR, Gilbert JA, Dinsdale EA, Newton K, et al. (2011) Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats. PLoS ONE 6: e2517325110.21371/journal.pone.0025173
51. Wu Y, Luo Y, Zou D, Ni J, Liu W et al. (2008) Bioremediation of polycyclic aromatic hydrocarbons contaminated soil with Monilinia sp.: degradation and microbial community analysis. Biodegradation 19: 247-257. doi:10.1007/s10532-007-9131-9. PubMed: 17541708. (Pubitemid 351311403)
52. Liang Y, Nostrand JD, Wang J, Zhang X, Zhou J et al. (2009) Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. Chemosphere 75: 193-199. doi:10.1016/j.chemosphere.2008.12.007. PubMed: 19144375.
53. Ford TE (2000) Response of marine microbial communities to anthropogenic stress. J Aquat Ecosyst Stress and Recovery 7: 75-89. doi:10.1023/A: 1009971414055.
54. Suenaga H, Ohnuki T, Miyazaki K (2007) Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 9: 2289-2297. doi:10.1111/j.1462-2920.2007.01342.x. PubMed: 17686025. (Pubitemid 47224882)
55. Schneiker S, Martins dos Santos VAP, Bartels D, Bekel T, Brecht M et al. (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24: 997-1004. doi:10.1038/nbt1232. PubMed: 16878126. (Pubitemid 44215394)
56. Ron EZ, Rosenberg E (2002) Biosurfactants and oil bioremediation. Curr Opin Biotechnol 13: 249-252. doi:10.1016/S0958-1669(02)00316-6. PubMed: 12180101. (Pubitemid 35299545)
57. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F et al. (2008) Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 32: 927-955. doi:10.1111/j.1574-6976.2008.00127.x. PubMed: 18662317.
58. Ortega-Calvo JJ, Marchenko AI, Vorobyov AV, Borovick RV (2003) Chemotaxis in polycyclic aromatic hydrocarbon-degrading bacteria isolated from coal-tar- and oil-polluted rhizospheres. FEMS Microbiol Ecol 44: 373-381. doi:10.1016/S0168-6496(03)00092-8. PubMed: 19719618. (Pubitemid 36556212)
59. Fernández-Luqueño F, Valenzuela-Encinas C, Marsch R, Martínez-Suárez C, Vázquez-Núñez E et al. (2011) Microbial communities to mitigate contamination of PAHs in soil-possibilities and challenges: a review. Environ Sci Poll R 18: 12-30. doi:10.1007/s11356-010-0371-6.
60. Venkata Mohan S, Kisa T, Ohkuma T, Kanaly RA, Shimizu Y (2006) Bioremediation technologies for treatment of PAH-contaminated soil and strategies to enhance process efficiency. Rev Environ Sci Biotechnol 5: 347-374. doi:10.1007/s11157-006-0004-1. (Pubitemid 44601263)
61. Hamamura N, Olson SH, Ward DM, Inskeep WP (2006) Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils. Appl Environ Microbiol 72: 6316-6324. doi:10.1128/AEM.01015-06. PubMed: 16957258. (Pubitemid 44414665)
62. Yergeau E, Arbour M, Brousseau R, Juck D, Lawrence JR et al. (2009) Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments. Appl Environ Microbiol 75: 6258-6267. doi:10.1128/AEM.01029-09. PubMed: 19684169.
63. Beller HR, Grbiæ-Galiæ D, Reinhard M (1992) Microbial Degradation of Toluene under Sulfate-Reducing Conditions and the Influence of Iron on the Process. Appl Environ Microbiol 58: 786-793. PubMed: 1575481. (Pubitemid 23399995)
64. Haberl H, Erb KH, Krausmann F, Gaube V, Bondeau A, et al. (2007) Quantifying and mapping the human appropriation of net primary production in earth's terrestrial ecosystems. Proc Natl Acad Sci USA 104: 12942-12947 (Pubitemid 47255259)
65. Barnosky AD, Hadly EA, Bascompte J, Berlow EL, Brown JH et al. (2012) Approaching a state shift in Earth's biosphere. Nature 486: 52-58. doi:10.1038/nature11018. PubMed: 22678279.
66. Delille D, Delille B (2000) Field observations on the variability of crude oil impact on indigenous hydrocarbon-degrading bacteria from sub-Antarctic intertidal sediments. Marine. Environ Rev 49: 403-417. (Pubitemid 30246040)
67. Urich T, Lanzén A, Qi J, Huson DH, Schleper C et al. (2008) Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the meta-Transcriptome. PLOS ONE 3: 1-13. PubMed: 18575584.