Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters

ISME Journal

Volumn 8, Issue 3, 2014, Pages 685-698

  Hollibaugh, James T ^a   Gifford, Scott M ^a,b   Moran, Mary Ann ^a   Ross, Meredith J ^a,c   Sharma, Shalabh ^a   Tolar, Bradley B ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

ammonia oxidation; diurnal; estuary; nitrification; nitrite; Thaumarchaeota

Indexed keywords

AMMONIA; NITROGEN; RNA 16S; SEA WATER;

ARCHAEON; ARTICLE; BACTERIUM; CLASSIFICATION; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; MICROBIOLOGY; PHYLOGENY; SEASON; UNITED STATES;

AMMONIA; ARCHAEA; BACTERIA; GENE EXPRESSION PROFILING; NITROGEN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; UNITED STATES;

EID: 84894338374     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.171     Document Type: Article

References (42)

1. Agogué H, Brink M, Dinasquet J, Herndl GJ. (2008). Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 456: 788-791.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
3. Biller SJ, Mosier AC, Wells GF, Francis CA. (2012). Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat. Front Microbiol 3: 252.
4. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. (2008). Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252. (Pubitemid 351256319)
5. DeLong EF. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
6. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C et al. (2012). Geneious. Biomatters Inc.: Auckland, NZ.
7. Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W. (2009). Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33: 855-869.
8. Francis CA, Beman JM, Kuypers MMM. (2007). New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 19-27. (Pubitemid 46717128)
9. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. (2005). Ubiquity and diversity of ammonia-oxidizing Archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688. (Pubitemid 41457116)
10. Fuhrman J, Hagström A. (2008). Bacterial and archaeal community structure and its patterns. in Kirchman DL editor. Microbial Ecology of the Oceans. John Wiley & Sons, Inc.: Hoboken, NJ, USA, pp 45-90.
11. Fuhrman JA, McCallum K, Davis AA. (1992). Novel major archaebacterial group from marine plankton. Nature 356: 148-149.
12. Gifford SM, Sharma S, Booth M, Moran MA. (2013). Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J 7: 281-298.
13. Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA. (2011). Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 5: 461-472.
14. Gomez-Alvarez V, Teal TK, Schmidt TM. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J 3: 1-4.
15. Hollibaugh JT, Gifford S, Bano N, Sharma S, Moran MA. (2011). Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME J 5: 866-878.
16. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755. (Pubitemid 32851390)
17. Kalanetra KM, Bano N, Hollibaugh JT. (2009). Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters. Environ Microbiol 11: 2434-2445.
18. Kelly S, Wickstead B, Gull K. (2010). Archaeal phyloge-nomics provides evidence in support of a methano-genic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc R Soc B Biol Sci 278: 1009-1018.
19. Kirchman DL, Elifantz HD, Ana I, Malmstrom RR, Cottrell MT. (2007). Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean. Limnol Oceanogr 52: 495-507. (Pubitemid 46972288)
20. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546. (Pubitemid 41613550)
21. Legendre P, Legendre L. (1998). Numerical Ecology, 2nd edn. Elsevier Science BV: Amsterdam, Netherlands.
22. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809. (Pubitemid 44258909)
23. Lund MB, Smith JM, Francis CA. (2012). Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea. ISME J 6: 1966-1977.
24. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. (2009). Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-979.
25. Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, DeLong EF. (2007). Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol 9: 1162-1175. (Pubitemid 46697272)
26. Nicol GW, Leininger S, Schleper C. (2011). Distribution and activity of ammonia-oxidizing Archaea in natural environments. In: Ward BB, Arp DJ, Klotz MJ (eds) Nitrification. ASM Press: Washington, DC, USA, pp 157-178.
27. Ouverney CC, Fuhrman JA. (2000). Marine planktonic archaea take up amino acids. Appl Environ Microbiol 66: 4829-4833.
28. Pitcher A, Wuchter C, Siedenberg K, Schouten S, Sinninghe-Damste JS. (2011). Crenarchaeol tracks winter blooms of ammonia-oxidizing Thaumarchaeota in the coastal North Sea. Limnol Oceanogr 56: 2308-2318.
29. Poretsky RS, Bano N, Buchan A, Hollibaugh JT, Moran MA. (2006). Environmental Transcriptomics: a method to access expressed genes in complex microbial communities. Molecular Microbial Ecology Manual, 3rd edn. Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Springer Verlag: Dordrecht, The Netherlands, pp 1892-1904.
30. Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. (2009). Analyzing gene expression from marine microbial communities using environmental tran-scriptomics. J Vis Exp 24: doi:10.3791/1086.
31. Prosser JI, Nicol GW. (2008). Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931-2941.
32. Robidart JC, Preston CM, Paerl RW, Turk KA, Mosier AC, Francis CA et al. (2011). Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. ISME J 6: 513-523.
33. Schleper C, Nicol GW. (2010). Ammonia-oxidising Archaea-genomes, physiology and ecology. Adv Microb Physiol 57: 1-41.
34. Simon JL. (1992). Resampling: The New Statistics. Resampling Stats: Arlington VA, USA.
35. Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E et al. (2010). Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
36. Teira E, Reinthaler T, Pernthaler A, Pernthaler J, Herndl GJ. (2004). Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean. Appl Environ Microbiol 70: 4411-4414. (Pubitemid 38969795)
37. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74. (Pubitemid 38451457)
38. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ et al. (2010). Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci 107: 8818-8823.
39. 2 pump. Limnol Oceanogr 49: 341-354. (Pubitemid 38536884)
40. Wang AZ, Cai W-J, Wang Y, Ji H. (2005). The southeastern continental shelf of the United States as an atmospheric CO2 source and an exporter of inorganic carbon to the ocean. Cont Shelf Res 25: 1917-1941. (Pubitemid 41414617)
41. Ward BB. (2011). Nitrification in the Ocean. In: Ward B, Arp DJ, Klotz MJ (eds) Nitrification. ASM Press: Washington, DC, USA, pp 325-345.
42. Zhang Z, Schwartz S, Wagner L, Miller W. (2000). A greedy algorithm for aligning DNA sequences J Comput Biol 7: 203-214. (Pubitemid 30412170)