Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

ISME Journal

Volumn 7, Issue 12, 2013, Pages 2315-2329

  Rivers, Adam R ^a   Sharma, Shalabh ^a   Tringe, Susannah G ^b   Martin, Jeffrey ^b   Joye, Samantha B ^a   Moran, Mary Ann ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Deepwater Horizon; methane oxidation; oil degradation; transcriptomics

Indexed keywords

PETROLEUM; RNA 16S; TRANSCRIPTOME;

BACTERIOPLANKTON; BIODEGRADATION; COMMUNITY STRUCTURE; GENETIC ANALYSIS; MARINE ECOSYSTEM; METABOLISM; OIL SPILL; PETROLEUM; PLUME; SPECIES DIVERSITY; TAXONOMY;

ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MICROBIOLOGY; OIL SPILL; PHYLOGENY; PLANKTON;

BACTERIA; BIODIVERSITY; GENE EXPRESSION REGULATION, BACTERIAL; PETROLEUM; PETROLEUM POLLUTION; PHYLOGENY; PLANKTON; RNA, RIBOSOMAL, 16S; TRANSCRIPTOME; WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); CANDIDATUS NITROSOPUMILUS; GAMMAPROTEOBACTERIA;

EID: 84888199743     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.129     Document Type: Article

References (56)

1. Anders S, Huber W. (2010). Differential expression analysis for sequence count data. Genome Biol 11: R106
2. Anthony C. (1982). the biochemistry of methylotrophs. Academic Press: London, UK.
3. Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57: 289-300
4. Boden R, Ferriera S, Johnson J, Kelly DP, Murrell JC, Schäfer H. (2011). Draft genome sequence of the chemolithoheterotrophic, halophilic methylotroph Methylophaga thiooxydans DMS010 J Bacteriol 193: 3154-3155
5. Camilli R, Reddy CM, Yoerger DR, Van Mooy BAS, Jakuba MV, Kinsey JC et al. (2010). Tracking hydrocarbon plume transport and biodegradation at Deepwater Horizon. Science 330: 201-204
6. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics 25: 1972-1973
7. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336
8. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM et al. (2012). the MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742-D753
9. 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)
10. Eddy SR. (2011). Accelerated Profile HMM Searches. PLoS Comput Biol 7: e1002195
11. Falgueras J, Lara A. (2010). SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics 11: 38
12. Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA. (2011). Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 5: 461-472
13. Han M, Zmasek C. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10: 356
14. Hanson RS, Hanson TE. (1996). Methanotrophic bacteria. Microbiol Rev 60: 439-471 (Pubitemid 26170914)
15. 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
16. Jari O, GB F, Roeland K, Pierre L, Peter RM, BO R et al. (2013). Vegan: Community Ecology Package.
17. Joye SB, MacDonald IR, Leifer I, Asper V. (2011). Magnitude and oxidation potential of hydrocarbon gases released from the BP oil well blowout. Nat Geosci 4: 160-164
18. Kanehisa M, Goto S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30 (Pubitemid 30047706)
19. Katoh K, Misawa K, Kuma K, Miyata T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066 (Pubitemid 34851225)
20. Kelley D. (2013). Oce: Analysis of Oceanographic data. Kelly DP, Anthony C, Murrell JC. (2005). Insights into the obligate methanotroph Methylococcus capsulatus. Trends Microbiol 13: 195-198
21. 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
22. King GM, Smith CB, Tolar B, Hollibaugh JT (2012). Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern Gulf of Mexico. Front Microbio 3: 438
23. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D et al. (2009). Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645
24. Lamontagne RA, Swinnerton JW, Linnenbom VJ, Smith WD. (1973). Methane concentrations in various marine environments. J Geophys Res 78: 5317-5324
25. Le SQ, Lartillot N, Gascuel O. (2008). Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci 363: 3965-3976
26. Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. (2012). the metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J 6: 2257-2268
27. Li M, Jain S, Baker BJ, Taylor C, Dick GJ. (2013). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ Microbiol e-pub ahead of print Doi:10.1111/1462-2920.12182
28. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. (2011). UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172
29. 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
30. Martin J, BrunoVM, Fang Z, Meng X, BlowM, Zhang Tet al. (2010). Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 11: 663
31. Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL et al. (2012). Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6: 1715-1727
32. Matsen FA, Kodner RB, Armbrust EV. (2010). Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538
33. Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang XJ et al. (2005). the psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci USA 102: 10913-10918 (Pubitemid 41105967)
34. National Research Council. (2003). Oil in the Sea III: Inputs, Fates, and Effects. National Academies Press: Washington, DC.
35. Pitcher RS, Watmough NJ. (2004). the bacterial cytochrome cbb3 oxidases. Biochim Biophys Acta 1655: 388-399
36. Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. (2009). Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp 3: 1-6
37. 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 109: 20229-20234
38. Redmond MC, Valentine DL. (2012). Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci USA 109: 20292-20297
39. Redmond MC, Valentine DL, Sessions AL. (2010). Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl Environ Microbiol 76: 6412-6422
40. Reeder J, Knight R. (2010). Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669
41. Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ et al. (2010). Unlocking short read sequencing for metagenomics. PLoS ONE 5: e11840
42. Ryerson TB, Camilli R, Kessler JD, Kujawinski EB, Reddy CM, Valentine DL et al. (2012). Chemical data quantify Deepwater Horizon hydrocarbon flow rate and environmental distribution. Proc Natl Acad Sci USA 109: 20246-20253
43. Satinsky BM, Gifford SM, Crump BC, Moran MA. (2013). Use of internal standards for quantitative metatranscriptome and metagenome analysis. Meth Enzym (in press).
44. Stamatakis A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690 (Pubitemid 44642609)
45. Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative analyses of a universal rRNAsubtraction protocol for microbial metatranscriptomics. ISME J 4: 896-907
46. Suzuki T, Nakamura T, Fuse H. (2012). Isolation of two novel marine ethylene-assimilating bacteria, Haliea species ETY-M and ETY-NAG, containing particulate methane monooxygenase-like genes. Microbes Environ 27: 54-60
47. Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG et al. (2011). Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96 J Bacteriol 193: 6418-6419
48. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV et al. (2003). the COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41
49. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MSM, Klotz MG. (2011). A novel family of functional operons encoding methane/ammonia monooxygenase- related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3: 91-100
50. Tavormina PL, UsslerW, Joye SB, Harrison BK, Orphan VJ. (2010). Distributions of putative aerobic methanotrophs in diverse pelagic marine environments ISME J 4: 700-710
51. Trotsenko YA, Murrell JC. (2008). Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63: 183-229 (Pubitemid 351452251)
52. 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
53. 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: 5261-5267 (Pubitemid 47326658)
54. Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS et al. (2004). Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2: e303
55. Yvon-Lewis SA, Hu L, Kessler J. (2011). Methane flux to the atmosphere from the Deepwater Horizon oil disaster. Geophys Res Lett 38: L01602
56. ZhuW, Lomsadze A, Borodovsky M. (2010). Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38: e132.