Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

Peter E. Larsen1, F. Collart1, Dawn Field2, Folker Meyer1, Kevin P. Keegan1, Christopher S. Henry1, John W. McGrath3, John P. Quinn3, Jack A. Gilbert4
1Argonne National Laboratory, 9700, S. Cass Ave, Argonne, Illinois, USA
2NERC Centre for Ecology and Hydrology, CEH Oxford, Mansfield Road, Oxford, OX1 3SR, UK
3School of Biological Science, Queens University, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
4Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago IL 60637, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Jørgensen BB, Boetius A: Feast and famine--microbial life in the deep-sea bed. Nat Rev Microbiol. 10: 770-81.

Buesseler KO, Lamborg CH, Boyd PW, Lam PJ, Trull TW, Bidigare RR, Bishop JK, Casciotti KL, Dehairs F, Elskens M, Honda M, Karl DM, Siegel DA, Silver MW, Steinberg DK, Valdes J, Van Mooy B, Wilson S: Revisiting carbon flux through the ocean's twilight zone. Science. 2008, 316 (5824): 567-70.

Paul Falkowski, Tom Fenchel, Edward Delong: The Microbial Engines That Drive Earth's Biogeochemical Cycles. Science. 2008, 320 (5879): 1034-1039. 10.1126/science.1153213.

Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, Somerfield PJ, Mühling M: The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A 'Multi-Omic' Study of Seasonal and Diel Temporal Variation. PLoS ONE. 2010, 5 (11): e15545-10.1371/journal.pone.0015545.

Gilbert JA, Meyer F, Joint I, Mühling M, Field D: Short Metagenome Report: Metagenomes and metatranscriptomes from the L4 long term coastal monitoring station in the Western English Channel. SIGS. 2010, 3 (2):

Mitra S, Gilbert JA, Field D, Huson DH: Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME J. 2010, 4: 1236-1242. 10.1038/ismej.2010.51.

Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield P, Huse S, Joint I: Seasonal succession of microbial communities in the Western English Channel using 16S rDNA-tag pyrosequencing. Env Microb. 2009, 11 (12): 3132-3139. 10.1111/j.1462-2920.2009.02017.x.

Bundy JG, Davey MP, Viant MR: Environmental metabolomics: A critical review and future perspectives. Metabolomics. 2009, 5: 3-21. 10.1007/s11306-008-0152-0.

Viant MR: Metabolomics of aquatic organisms: the new omics on the block. Mar. Ecol. Prog. Series. 2007, 332: 301-306.

Viant MR: Recent developments in environmental metabolomics. Molecular Biosystems. 2008, 4: 980-986. 10.1039/b805354e.

Lin C-Y, Viant MR, Tjeerdema RS: Metabolomics: Methodologies and Applications in the Environmental Sciences. J. Pestic. Sci. 2006, 31: 245-251. 10.1584/jpestics.31.245.

Wooley JC, Godzik A, Friedberg I: A Primer on Metagenomics. PLoS Comput Biol. 2010, 6 (2): e1000667-10.1371/journal.pcbi.1000667.

Heidelberg KB, Gilbert JA, Joint I: Review: The revolution in genomic approaches to describe environmental microbial diversity. Microb Biotechnol. 2010, 3 (5): 531-543. 10.1111/j.1751-7915.2010.00193.x.

Gilbert JA, Dupont C: Marine Metagenomics. Annual Review of Marine Science. 2011, 3: 347-371. 10.1146/annurev-marine-120709-142811.

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008, 9: 386-10.1186/1471-2105-9-386.

Pruitt KD, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, D61-5. 35 Database

Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27.

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P: KeggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 2010, D190-5. Database

Overbeek R, Begley T, Butler RM, Jomuna O, Choudhuri V, Chuang H, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005, 17: 5691-702.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res. 2008, D281-8. Database

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O: TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007, 35 (Database): D260-4. 10.1093/nar/gkl1043.

Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB: Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci USA. 2009, 106 (5): 1374-9. 10.1073/pnas.0808022106. Epub 2009 Jan 22

Field D, Joint I, Gilbert JA, et al: Towards a richer description of our complete collection of genomes and metagenomes: the "Minimum Information about a Genome Sequence" (MIGS) specification. Nat. Biotech. 2008, 6 (5): 541-7.

Ma HW, Aeng AP: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 2003, 19 (2): 270-277. 10.1093/bioinformatics/19.2.270.

Rao Y, Lee Y, Jarjoura D, Ruppert AS, Liu CG, Hsu JC, Hagan JP: A comparison of normalization techniques for microRNA microarray data. Stat Appl Genet Mol Biol. 2008, 7 (1): Article22. Epub 2008 Jul 21

Petković H, Cullum J, Hranueli D, Hunter IS, Perić-Concha N, Pigac J, Thamchaipenet A, Vujaklija D, Long PF: Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol Mol Biol Rev. 2006, 70 (3): 704-28. 10.1128/MMBR.00004-06.

Glöckner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R: Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. PNAS. 2003, 100 (14): 8298-8303. 10.1073/pnas.1431443100.

Sivakumar PM, Prabhawathi V, Doble M: Antibacterial activity and QSAR of chalcones against biofilm-producing bacteria isolated from marine waters. SAR QSAR Environ Res. 2010, 21 (3-4): 247-63. 10.1080/10629361003771009.

Cho JY, Kwon HC, Williams PG, Jensen PR, Fenical W: Azamerone, A Terpenoid Phthalazinone from a Marine-Derived Bacterium Related to the Genus Streptomyces. Actinomycetales. 2006, 8 (12): 2471-2474.

Motohashi K, Irie K, Toda T, Matsuo Y, Kasai H, Sue M, Furihata K, Seto H: Studies on terpenoids produced by actinomycetes. 5-dimethylallylindole-3-carboxylic Acid and A80915G-8"-acid produced by marine-derived Streptomyces sp. MS239. J Antibiot (Tokyo). 2008, 61 (2): 75-80.

Paytan A, McLaughlin K: The Oceanic Phosphorus Cycle. Chem. Rev. 2007, 107: 563-576. 10.1021/cr0503613.

Mikhail VS, Fuchs BM, Eilers H, Burkill PH, Amann R: Determination of Total Protein Content of Bacterial Cells by SYPRO Staining and Flow Cytometry. Appl Env Microbiol. 1999, 65 (7): 3251-3257.

Martin JH, Fitzwater SE: Iron-deficiency limits phytoplankton growth in the Northeast Pacific Subarctic. Nature. 1988, 331: 341-343. 10.1038/331341a0.

Martin JH, Coale KH, Johnson KS, Fitzwater SE, Gordon RM, Tanner SJ, Hunter CN, Elrod VA, Nowicki JL, Coley TL, Barber RT, Lindley S, Watson AJ, Van Scoy K, Law CS, Liddicoatp MI, Ling R, Stanton T, Stockel J, Collins C, Anderson A, Bidigare R, Ondrusek M, Latasa M, Millerostar FJ, Leestar K, Yao W, Zhangstar JZ, Friederich G, Sakamoto C, Chavez F, Buck K, Kolber Z, Greene R, Falkowski P, Chisholm SW, Hoge F, Swift R, Yungel J, Nightingale SP, Hatton A, Liss P, Tindale NW: Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature. 2002, 371: 123-129.

Martin JH: Glacial-interglacial CO2 change: The iron hypothesis. Paleoceanography. 1990, 5: 1-13. 10.1029/PA005i001p00001.

Street JH, Paytan A: Iron, phytoplankton growth, and the carbon cycle. Met Ions Biol Syst. 2005, 43: 153-93.

Blain S, et al: Effect of natural iron fertilization on carbon sequestration in the Southern Ocean. Nature. 2007, 446: 1070-1074. 10.1038/nature05700.

Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I: Potential for Phosphonate utilisation by marine bacteria in temperate coastal waters. Environmental microbiology. 2009, 11 (1): 111-25. 10.1111/j.1462-2920.2008.01745.x.

Kulakova AN, Wisdom GB, Kulakov LA, Quinn JP: The purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp Pal2. J Biol Chem. 2003, 278 (26): 23426-31. 10.1074/jbc.M301871200. Epub 2003 Apr 15

Quinn JP, Kulakova AN, Cooley NA, McGrath JW: New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling. Environmental Microbiology. 2007, 9 (10): 2392-2400. 10.1111/j.1462-2920.2007.01397.x.

Repeta DJ, Pantoja S, Johnson CG: Two chemically distinct pools of organic nitrogen accumulate in the ocean. Science. 2005, 308: 1007-1010. 10.1126/science.1108925.

Gooday GW: The ecology of chitin degradation. Edited by: Marshall KC. 1990, Advances in microbial ecology Plenum Press, Inc., New York, NY, 11: 387-429.

Jeuniaux C, Vossfoucart MF: Chitin biomass and production in the marine environment. Biochem. Syst. Ecol. 1991, 19: 347-356. 10.1016/0305-1978(91)90051-Z.

Keyhani NO, Roseman S: Physiological aspects of chitin catabolism in marine bacteria. Biochim Biophys Acta. 1999, 1473 (1): 108-22.

Cottrell MT, Kirchman DL: Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol. 2000, 66 (4): 1692-7. 10.1128/AEM.66.4.1692-1697.2000.

Cottrell MT, Wood DN, Yu L, Kirchman DL: Selected chitinase genes in cultured and uncultured marine bacteria in the alpha- and gamma-subclasses of the proteobacteria. Appl Environ Microbiol. 2000, 66 (3): 1195-201. 10.1128/AEM.66.3.1195-1201.2000.

Cottrell MT, Moore JA, Kirchman DL: Chitinases from uncultured marine microorganisms. Appl Environ Microbiol. 1999, 65 (6): 2553-7.

Svitil AL, Kirchman DL: A chitin-binding domain in a marine bacterial chitinase and other microbial chitinases: implications for the ecology and evolution of 1,4-beta-glycanases. Microbiology. 1998, 144 (Pt 5): 1299-308.

Southward AJ, Langmead O, Hardman-Mountford NJ, Aiken J, Boalch GT, Dando PR, Genner MJ, Joint I, Kendall MA, Halliday NC, Harris RP, Leaper R, Mieszkowska N, Pingree RD, Richardson AJ, Sims DW, Smith T, Walne AW, Hawkins SJ: Long-term oceanographic and ecological research in the Western English Channel. Adv Mar Biol. 2005, 47: 1-105.

Petković H, Cullum J, Hranueli D, Hunter IS, Perić-Concha N, Pigac J, Thamchaipenet A, Vujaklija D, Long PF: Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol Mol Biol Rev. 2006, 70 (3): 704-28. 10.1128/MMBR.00004-06.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-504. 10.1101/gr.1239303.