Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches

Applied Microbiology and Biotechnology

Volumn 98, Issue 9, 2014, Pages 4209-4221

  Wang, Li Ying ^a,b   Ke, Wen Ji ^a   Sun, Xiao Bo ^a   Liu, Jin Feng ^a   Gu, Ji Dong ^b   Mu, Bo Zhong ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Aqueous and oil phases; Bacterial community; Petroleum reservoir; Pyrosequencing; Water cut

Indexed keywords

BACTERIA; CLONING; CRUDE OIL; DNA; FLOODS; GENES; HYDROCARBONS; OIL FIELDS; RNA;

AQUEOUS AND OIL PHASES; BACTERIAL COMMUNITY; HYDROCARBON DEGRADATION; PHYLOGENETIC ANALYSIS; PYROSEQUENCING; SIMULTANEOUS ANALYSIS; THERMOANAEROBACTERIUM; WATER CUTS;

PETROLEUM RESERVOIRS;

ACETIC ACID; BACTERIAL DNA; HYDROCARBON; OIL; PETROLEUM; RNA 16S; WATER; RIBOSOME DNA;

ALPHAPROTEOBACTERIA; ARCOBACTER; ARTICLE; BACTERIAL GENE; BACTERIUM DETECTION; DEGRADATION; DESULFOVIBRIO; DNA EXTRACTION; EPSILONPROTEOBACTERIA; FLOODING; GAMMAPROTEOBACTERIA; GENE LIBRARY; LIQUID; METAGENOMICS; MICROBIAL COMMUNITY; MOLECULAR CLONING; MOLECULAR PHYLOGENY; NONHUMAN; OIL FIELD; POLYMERASE CHAIN REACTION; PSEUDOMONAS; PYROSEQUENCING; SPECIES DIVERSITY; SPHINGOMONAS; THERMOANAEROBACTERIUM; THERMOTOGA; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

ALPHAPROTEOBACTERIA; ARCOBACTER; BACTERIA (MICROORGANISMS); DESULFOVIBRIO; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; PSEUDOMONAS; SPHINGOMONAS; THERMOANAEROBACTERIUM; THERMODESULFORHABDUS; THERMODESULFOVIBRIO; THERMOTOGA;

BACTERIA; BIOTA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; ENVIRONMENTAL MICROBIOLOGY; METAGENOMICS; MOLECULAR SEQUENCE DATA; PETROLEUM; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER;

EID: 84899966961     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5472-y     Document Type: Article

References (66)

1. Abbasnezhad H, Foght JM, Gray MR (2011) Adhesion to the hydrocarbon phase increases phenanthrene degradation by Pseudomonas fluorescens LP6a. Biodegradation 22(3):485-496. doi:10.1007/s10532-010-9421-5
2. 2 by a new type of sulfate-reducing bacterium. Arch Microbiol 156(1):5-14. doi:10.1007/BF00418180
3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402. doi:10.1093/nar/25.17.3389 (Pubitemid 27359211)
4. Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF (2011) CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinforma 12:356. doi:10.1186/1471-2105-12-356
5. Ashelford KE, Chuzhanova NA FJC, Jones AJ, Weightman AJ (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71(12):7724-7736. doi:10.1128/AEM.71.12.7724-7736.2005 (Pubitemid 41803890)
6. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ,Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72(9):5734-5741. doi:10.1128/aem.00556- 06 (Pubitemid 44414595)
7. Beeder J, Torsvik T, Lien T (1995) Thermodesulforhabdus norvegicus gen. nov., sp. nov., a novel thermophilic sulfate-reducing bacterium from oil field water. Arch Microbiol 164(5):331-336. doi:10.1007/bf02529979
8. Brown L (2013) The use of microorganisms to enhance oil recovery. In: James S (ed) Enhanced oil recovery field case studies. Gulf Professional Publishing, Boston, pp 561-580
9. Callbeck CM, Dong X, Chatterjee I, Agrawal A, Caffrey SM, Sensen CW, Voordouw G (2011) Microbial community succession in a bioreactormodeling a souring low-temperature oil reservoir subjected to nitrate injection. Appl Microbiol Biotechnol 91(3):799-810. doi:10.1007/s00253-011-3287-2
10. Cephas KD, Kim J, Mathai RA, Barry KA, Dowd SE, Meline BS, Swanson KS (2011) Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing. PLoS ONE 6(8):e23503. doi:10.1371/journal.pone.0023503
11. Chen H, Boutros P (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinforma 12(1):35. doi:10.1186/1471-2105-12-35
12. Davidova IA, Suflita JM (2005) Enrichment and isolation of anaerobic hydrocarbon-degrading bacteria.Methods Enzymol 397:17-34. doi:10.1016/s0076- 6879(05)97002-x (Pubitemid 41562892)
13. Ehrenreich P, Behrends A, Harder J, Widdel F (2000) Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria. Arch Microbiol 173(1):58-64. doi:10.1007/s002030050008 (Pubitemid 30060681)
14. Fedorovich V, Knighton MC, Pagaling E, Ward FB, Free A, Goryanin I (2009) Novel electrochemically active bacterium phylogenetically related to Arcobacter butzleri, isolated from a microbial fuel cell. Appl Environ Microbiol 75(23):7326-7334. doi:10.1128/aem.01345-09
15. Fry JC, Horsfield B, Sykes R, Cragg BA, Heywood C, Kim GT, Mangelsdorf K, Mildenhall DC, Rinna J, Vieth A, Zink K-G, Sass H, Weightman AJ, Parkes RJ (2009) Prokaryotic populations and activities in an interbedded coal deposit, including a previously deeply buried section (1.6-2.3 km) above-150 ma basement rock. Geomicrobiol J 26(3):163-178. doi:10.1080/01490450902724832
16. Gieg LM, Duncan KE, Suflita JM (2008) Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol 74(10):3022-3029. doi:10.1128/aem.00119-08 (Pubitemid 351747006)
17. Grabowski A, Nercessian O, Fayolle F, Blanchet D, Jeanthon C (2005) Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiol Ecol 54(3):427-443. doi:10.1016/j.resmic.2005.03.009 (Pubitemid 41416859)
18. Gray ND, Sherry A, Grant RJ, Rowan AK, Hubert CRJ, Callbeck CM, Aitken CM, Jones DM, Adams JJ, Larter SR, Head IM (2011) The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol 13(11):2957-2975. doi:10.1111/j.1462-2920. 2011.02570.x
19. Guan J, Xia L-P, Wang L-Y, Liu J-F, Gu J-D, Mu B-Z (2013) Diversity and distribution of sulfate-reducing bacteria in four petroleum reservoirs detected by using 16S rRNA and dsrAB genes. Int Biodeterior Biodegrad 76:58-66. doi:10.1016/j.ibiod.2012.06.021
20. Hubert CRJ, Oldenburg TBP, Fustic M, Gray ND, Larter SR, Penn K, Rowan AK, Seshadri R, Sherry A, Swainsbury R, Voordouw G, Voordouw JK, Head IM (2012) Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil. Environ Microbiol 14(2):387-404. doi:10.1111/j.1462-2920.2011.02521.x
21. Jones DM, Head IM, Gray ND, Adams JJ, Rowan AK, Aitken CM, Bennett B, Huang H, BrownA, Bowler BFJ, Oldenburg T, Erdmann M, Larter SR (2008) Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451(7175):176-180. doi:10.1038/nature06484
22. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3(4):442-453. doi:10.1038/ismej.2008.127
23. KerteszM, Kawasaki A (2010) Hydrocarbon-degrading Sphingomonads: Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1693-1075
24. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
25. Kobayashi H, Endo K, Sakata S, Mayumi D, Kawaguchi H, Ikarashi M, Miyagawa Y, Maeda H, Sato K (2012) Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir. J Biosci Bioeng 113(2):204-210. doi:10.1016/j.jbiosc.2011.09. 015
26. Korenblum E, Souza DB, Penna M, Seldin L (2012) Molecular analysis of the bacterial communities in crude oil Samples from two Brazilian offshore petroleum platforms. Int J Microbiol 2012:156537. doi:10.1155/2012/156537
27. Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142(1):38-49. doi:10.1016/j.jbiotec.2009.02.010
28. Kryachko Y, Dong X, Sensen C, Voordouw G (2012) Compositions of microbial communities associated with oil and water in a mesothermic oil field. Anton Leeuw 101(3):493-506. doi:10.1007/s10482-011-9658-y
29. Li H, Yang S-Z, Mu B-Z, Rong Z-F, Zhang J (2006) Molecular analysis of the bacterial community in a continental high-temperature and water-flooded petroleum reservoir. FEMS Microbiol Lett 257(1):92-98. doi:10.1111/j.1574-6968. 2006.00149.x
30. Li H, Yang S-Z, Mu B-Z (2007a) Phylogenetic diversity of the Archaeal community in a continental high-temperature, water-flooded petroleum reservoir. Curr Microbiol 55(5):382-388. doi:10.1007/s00284-007-9002-y (Pubitemid 47536821)
31. Li H, Yang S-Z, Mu B-Z, Rong Z-F, Zhang J (2007b) Molecular phylogenetic diversity of themicrobial community associated with a hightemperature petroleum reservoir at an offshore oilfield. FEMS Microbiol Ecol 60(1):74-84. doi:10.1111/j.1574-6941.2006.00266.x (Pubitemid 46426574)
32. Li W, Wang L-Y, Duan R-Y, Liu J-F, Gu J-D, Mu B-Z (2012) Microbial community characteristics of petroleum reservoir production water amended with n-alkanes and incubated under nitrate-, sulfate-reducing and methanogenic conditions. Int Biodeterior Biodegrad 69:87-96. doi:10.1016/j.ibiod.2012.01.005
33. Magot M, Ollivier B, Patel BKC (2000) Microbiology of petroleum reservoirs. Antonie Van Leeuwenhoek 77(2):103-116. doi:10.1023/A:1002434330514 (Pubitemid 30160411)
34. Mbadinga S, Li K-P, Zhou L,Wang L-Y, Yang S-Z, Liu J-F, Gu J-D, Mu B-Z (2012)Analysis of alkane-dependentmethanogenic community derived from production water of a high-temperature petroleum reservoir. Appl Microbiol Biotechnol 96(2):531-542. doi:10.1007/s00253-011-3828-8
35. Mbadinga SM, Wang L-Y, Zhou L, Liu J-F, Gu J-D, Mu B-Z (2011) Microbial communities involved in anaerobic degradation of alkanes. Int Biodeterior Biodegrad 65(1):1-13. doi:10.1016/j.ibiod.2010.11.009
36. McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML (2010) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12(2):378-392. doi:10.1111/j.1462-2920.2009.02075.x
37. Mukherjee S, Bardolui NK, Karim S, Patnaik VV, Nandy RK, Bag PK (2010) Isolation and characterization of a monoaromatic hydrocarbon-degrading bacterium, Pseudomonas aeruginosa from crude oil. J Environ Sci Health A 45(9):1048-1053. doi:10.1080/10934529.2010.486328
38. Navarro-Noya Y, Suárez-Arriaga M, Rojas-Valdes A, Montoya-Ciriaco N, Gómez-Acata S, Fernández-Luqueño F, Dendooven L (2013) Pyrosequencing analysis of the bacterial community in drinking water wells. Microb Ecol 66(1):19-29. doi:10.1007/s00248-013-0222-3
39. Nazina TN, Shestakova NM, Pavlova NK, Tatarkin YV, Ivoilov VS, Khisametdinov MR, Sokolova DS, Babich TL, Tourova TP, Poltaraus AB, Belyaev SS, Ivanov MV (2013) Functional and phylogenetic microbial diversity in formation waters of a low-temperature carbonate petroleum reservoir. Int Biodeterior Biodegrad 81:71-81. doi:10.1016/j.ibiod.2012.07.008
40. Obuekwe CO, Al-Jadi ZK, Al-Saleh ES (2008) Comparative hydrocarbon utilization by hydrophobic and hydrophilic variants of Pseudomonas aeruginosa. J Appl Microbiol 105(6):1876-1887. doi:10.1111/j.1365-2672.2008.03887.x
41. Orphan VJ, Taylor LT, Hafenbradl D, Delong EF (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl EnvironMicrobiol 66(2):700-711. doi:10.1128/aem.66.2.700-711.2000 (Pubitemid 30082762)
42. Parkes J (1999) Cracking anaerobic bacteria. Nature 401(6750):217-218. doi:10.1038/45686
43. Pham VD, Hnatow LL, Zhang S, Fallon RD, Jackson SC, Tomb J-F, DeLong EF, Keeler SJ (2009) Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. EnvironMicrobiol 11(1):176-187. doi:10.1111/j.1462-2920.2008.01751.x
44. Puech V, Chami M, Lemassu A, Lanéelle M-A, Schiffler B, Gounon P, Bayan N, Benz R, Daffé M (2001) Structure of the cell envelope of Corynebacteria: importance of the non-covalently bound lipids in the formation of the cell wall permeability barrier and fracture plane. Microbiol 147(5):1365-1382. doi:10.1073/pnas.1112572108 (Pubitemid 32454654)
45. Ren H-Y, Zhang X-J, Z-y S, Rupert W, Gao G-J, S-x G, Zhao L-P (2011) Comparison of microbial community compositions of injection and production well samples in a long-term water-flooded petroleum reservoir. PLoS ONE 6(8):e23258. doi:10.1371/journal.pone.0023258
46. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406-425
47. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537-7541. doi:10.1128/aem.01541-09
48. Sen R (2008) Biotechnology in petroleum recovery: the microbial EOR. Prog Energy Combust Sci 34(6):714-724. doi:10.1016/j.pecs.2008.05.001
49. Singleton DR, Guzmán Ramirez L, Aitken MD (2009) Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl EnvironMicrobiol 75(9):2613-2620. doi:10.1128/aem.01955-08
50. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". PNAS 103(32):12115-12120. doi:10.1073/pnas. 0605127103 (Pubitemid 44215820)
51. Suflita JM, Davidova IA, Gieg LM, Nanny M, Prince RC (2004) Anaerobic hydrocarbon biodegradation and the prospects for microbial enhanced energy production. In: RafaelV-D, Rodolfo Q-R (eds) Studies in surface science and catalysis. Elsevier, New York, pp 283-305
52. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739. doi:10.1093/molbev/msr121
53. Tang Y-Q, Li Y, Zhao J-Y, Chi C-Q, Huang L-X, Dong H-P, Wu X-L (2012) Microbial communities in long-term, water-flooded petroleum reservoirs with different temperatures in the huabei oilfield, China. PLoS ONE 7(3):e33535. doi:10.1371/journal.pone.0033535
54. Thamdrup B, Rosselló-Mora R, Amann R (2000) Microbial manganese and sulfate reduction in black sea shelf sediments. Appl Environ Microbiol 66(7):2888-2897. doi:10.1128/aem.66.7.2888-2897.2000 (Pubitemid 30497596)
55. Vasconcellos SP, Angolini CFF, García INS, Martins Dellagnezze B, Silva CC, Marsaioli AJ, Neto EVS, Oliveira VM (2010) Reprint of: Screening for hydrocarbon biodegraders in a metagenomic clone library derived from Brazilian petroleum reservoirs. Org Geochem 41(9):1067-1073. doi:10.1016/j.orggeochem. 2010.08.003
56. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261-5267. doi:10.1128/aem.00062-07 (Pubitemid 47326658)
57. Wang L-Y, Mbadinga SM, Li H, Liu J-F, Yang S-Z Mu B-Z (2010) Anaerobic degradation of petroleum hydrocarbons and enlightenment of the prospects for microbial bio-gasification of residual oil. Microbiol 37(1):96-102 (in Chinese with English abstract)
58. Wang L-Y, Gao C-X, Mbadinga SM, Zhou L, Liu J-F, Gu J-D, Mu B-Z (2011) Characterization of an alkane-degrading methanogenic enrichment culture from production water of an oil reservoir after 274 days of incubation. Int Biodeterior Biodegrad 65(3):444-450. doi:10.1016/j.ibiod.2010.12.010
59. Wang L-Y, Dun R-Y, Liu J-F, Yang S-Z, Gu J-D, Mu B-Z (2012) Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures. Biogeosciences 9(11):4645-4659. doi:10.5194/bg-9-4645-2012
60. Watanabe K, Watanabe K, Kodama Y, Syutsubo K, Harayama S (2000) Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl Environ Microbiol 66:4803-4809. doi:10.1128/AEM.66.11.4803-4809.2000 (Pubitemid 32450122)
61. Watanabe K, Kodama Y, Kaku N (2002) Diversity and abundance of bacteria in an underground oil-storage cavity. BMC Microbiol 2:23. doi:10.1186/1471-2180- 2-23
62. Webster G, Rinna J, Roussel EG, Fry JC, Weightman AJ, Parkes RJ (2010) Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of the Severn Estuary, UK, revealed by stable-isotope probing. FEMS Microbiol Ecol 72(2):179-197. doi:10.1111/j.1574-6941.2010.00848.x
63. Zhang H, Kallimanis A, Koukkou A, Drainas C (2004) Isolation and characterization of novel bacteria degrading polycyclic aromatic hydrocarbons from polluted Greek soils. Appl Microbiol Biotechnol 65(1):124-131. doi:10.1007/s00253-004-1614-6 (Pubitemid 39044320)
64. Zhang X, Yue S, Zhong H, Hua W, Chen R, Cao Y, Zhao L (2011) A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis. Appl Microbiol Biotechnol 91(2):425-434. doi:10.1007/s00253-011-3296-1
65. Zhang F, She Y-H, Chai L-J, Banat IM, Zhang X-T, Shu F-C,Wang Z-L, Yu L-J, Hou D-J (2012) Microbial diversity in long-term waterflooded oil reservoirs with different in situ temperatures in China. Sci Rep 2:760. doi:10.1038/srep00760
66. Zhou L, Li K-P, Mbadinga SM, Yang S-Z, Gu J-D, Mu B-Z (2012) Analyses of n-alkanes degrading community dynamics of a hightemperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques. Ecotoxicology 21(6):1680-1691. doi:10.1007/s10646-012-0949-5