Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

ISME Journal

Volumn 6, Issue 9, 2012, Pages 1715-1727

  Mason, Olivia U ^a,b   Hazen, Terry C ^a,c   Borglin, Sharon ^a   Chain, Patrick S G ^d,e   Dubinsky, Eric A ^a   Fortney, Julian L ^a   Han, James ^d,e   Holman, Hoi Ying N ^a   Hultman, Jenni ^a   Lamendella, Regina ^a   MacKelprang, Rachel ^e   Malfatti, Stephanie ^e,f   Tom, Lauren M ^a   Tringe, Susannah G ^e   Woyke, Tanja ^e   Zhou, Jizhong ^g,h   Rubin, Edward M ^e   Jansson, Janet K ^a,e  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

^e DOE JOINT GENOME INSTITUTE   (United States)

^f LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^g UNIVERSITY OF OKLAHOMA   (United States)

^h TSINGHUA UNIVERSITY   (China)

Author keywords

Deepwater Horizon; Gulf oil spill; metagenomics; metatranscriptomics; Oceanospirillales; single cell genomics

Indexed keywords

HYDROCARBON; RNA 16S; SEA WATER; TRANSCRIPTOME;

BACTERIUM; CHEMOTAXIS; DEEP SEA; DEEP WATER; GENOME; GENOMICS; HYDROCARBON SEEP; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MOTILITY; OIL SPILL; OXIDATION; PAH;

ARCHAEON; ARTICLE; BACTERIUM; BIODIVERSITY; GENETICS; GULF OF MEXICO; METABOLISM; METAGENOME; MICROBIOLOGY; OCEANOSPIRILLACEAE; OIL SPILL; PHYSIOLOGY; SINGLE CELL ANALYSIS;

ARCHAEA; BACTERIA; BIODIVERSITY; GULF OF MEXICO; HYDROCARBONS; METAGENOME; OCEANOSPIRILLACEAE; PETROLEUM POLLUTION; RNA, RIBOSOMAL, 16S; SEAWATER; SINGLE-CELL ANALYSIS; TRANSCRIPTOME;

ATLANTIC OCEAN; GULF OF MEXICO;

OCEANOSPIRILLALES;

EID: 84865318505     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.59     Document Type: Article

References (40)

1. Allgaier M, Reddy A, Park JI, Ivanova N, D'Haeseleer P, Lowry S et al. (2010). Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5: e8812.
2. Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, Yang DY et al. (2008). Identification of ancient remains through genomic sequencing. Genome Res 18: 1347-1353.
3. Camilli R, Reddy CM, Yoerger DR, Van Mooy BA, Jakuba MV, Kinsey JC et al. (2010). Tracking hydrocarbon plume transport and biodegradation at Deepwater Horizon. Science 330: 201-204.
4. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010a). QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335-336.
5. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. (2010b). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267.
6. Chao A. (1984). Non-parametric estimation of the number of classes in a population. Scan J Stat 11: 265-270.
7. Chao A, Lee SM, Jeng SL. (1992). Estimating population size for capture-recapture data when capture probabilities vary by time and individual animal. Biometrics 48: 201-216. (Pubitemid 23401166)
8. Chao A, Hwang WH, Chen YC, Kuo CY. (2000). Estimating the number of shared species in two communities. Stat Sinica 10: 227-246.
9. Colwell RK, Coddington JA. (1994). Estimating terrestrial biodiversity through extrapolation. Philos T Roy Soc B 345: 101-118.
10. Das N, Chandran P. (2011). Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011: 1-13.
11. DeAngelis KM, Silver WL, Thompson AW, Firestone MK. (2010). Microbial communities acclimate to recurring changes in soil redox potential status. Environ Micro-biol 12: 3137-3149.
12. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al. (2006). Greengenes, a Chimera-Checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072. (Pubitemid 44078840)
13. Dyksterhouse S, Gray J, Herwig R, Lara J, Staley J. (1995). Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 45: 116-123.
14. Federal Interagency Solutions Group. (2010). Oil Budget Calculator Science and Engineering Team. Oil Budget Calculator Technical Documentation.
15. Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
16. Grissa I, Vergnaud G, Pourcel C. (2007). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-W57.
17. Harayama S, Kishira H, Kasai Y, Shutsubo K. (1999). Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1: 63-70. (Pubitemid 129491926)
18. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N et al. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330: 204-208.
19. He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL et al. (2010). GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4: 1167-1179.
20. Kessler JD, Valentine DL, Redmond MC, Du M, Chan EW, Mendes SD et al. (2011). A persistent oxygen anomaly reveals the fate of spilled methane in the deep gulf of Mexico. Science 331: 312-315.
21. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. (2010). Wrinkles in the rare biosphere: pyrosequen-cing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
22. Lane DJ. (1991). 16S/23S rRNA sequencing. In: Stackenbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley: New York, pp 115-148.
23. Letunic I, Yamada T, Kanehisa M, Bork P. (2008). iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci 33: 101-103.
24. Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A et al. (2011). Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 6: 451-460.
25. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K Chu K, Dalevi D et al. (2008). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-D538. (Pubitemid 351149780)
26. Miller DN, Bryant JE, Madsen EL, Ghiorse WC. (1999). Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-4724.
27. Miller JR, Koren S, Sutton G. (2010). Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
28. Parks DH, Beiko RG. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
29. Reddy CM, Arey JS, Seewald JS, Sylva SP, Lemkau KL, Nelson RK et al. (2012). Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill. Proc Natl Acad Sci USA; e-pub ahead of print 3 February 2012; doi:10.1073/pnas.1101242108.
30. Redmond MC, Valentine DL. (2011). Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci USA; e-pub ahead of print 3 October 2011; doi:10.1073/pnas.1108756108.
31. Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. (2009). Whole genome ampli fication and de novo assembly of single bacterial cells. PLoS One 4: e6864.
32. Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Goly-shin PN. (2006). Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. J Bacteriol 188: 3763-3773. (Pubitemid 43825382)
33. Schneiker S, dos Santos VAPM, Bartels D, Bekel T Brecht M, Buhrmester J et al. (2006). Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotech 24: 997-1004. (Pubitemid 44215394)
34. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. (2007). CAMERA: A Community Resource for Meta-genomics. PLoS Biol 5: e75.
35. Simpson EH. (1949). Measurement of Diversity. Nature 163: 688-688.
36. Valentine DL, Kessler JD, Redmond MC, Mendes SD, Heintz MB, Farwell C et al. (2010). Propane respiration jump-starts microbial response to a deep oil spill. Science 330: 208-211.
37. Yakimov MM, Giuliano L, Gentile G, Crisafi E, Chernikova TN, Abraham W-R et al. (2003). Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. Int J Syst Evol Microbiol 53: 779-785. (Pubitemid 36681497)
38. Yakimov MM, Giuliano L, Denaro R, Crisafi E, Chernikova TN, Abraham WR et al. (2004). Thalassolituus oleivor-ans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 54: 141-148. (Pubitemid 38185772)
39. Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M et al. (2010). Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468: 60-66.
40. Zerbino D, Birney E. (2008). Velvet: algorithms for de novo short read assembly using De Bruijn graphs. Genome Res 18: 821-829. (Pubitemid 351645072)