Erratum: Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling (ISME Journal (2013) 7 (1962-1973) DOI: 10.1038/ismej.2013.85);Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

ISME Journal

Volumn 7, Issue 10, 2013, Pages 1962-1973

  Baker, Brett J ^a   Sheik, Cody S ^a   Taylor, Chris A ^a   Jain, Sunit ^a   Bhasi, Ashwini ^a   Cavalcoli, James D ^a   Dick, Gregory J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Alteromonas; Archaea; Deep sea; Nitrification; Nitrospirae; Transcriptomics

Indexed keywords

BACTERIUM; CARBON CYCLE; DEEP SEA; EARTH; GENOME; GEOCHEMISTRY; MICROORGANISM; NITRITE; NITROGEN CYCLE; ORGANIC CARBON; OXIDATION; RECYCLING;

GUAYMAS BASIN; GULF OF CALIFORNIA; PACIFIC OCEAN;

ALTEROMONAS; ALTEROMONAS MACLEODII; ARCHAEA; BACTERIA (MICROORGANISMS); EURYARCHAEOTA; MARINE GROUP II; NITROSPIRAE;

EID: 84884670976     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.101     Document Type: Erratum

References (53)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215: 403-410
2. Baker BJ, Lesniewski R, Dick GJ. (2012). Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J 6: 2269-2279
3. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. (2010). Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908-917
4. Bazylinski DA, Wirsen CO, Jannasch HW. (1989). Microbial utilization of naturally occurring hydrocarbons at the Guaymas Basin hydrothermal vent site. Appl Environ Microbiol 55: 2832-2836
5. Bock E, Koops HP, Harms H, Ahlers B. (1991). In: Shively JM, Barton LL (eds) Variations in Autotrophic Life. Academic Press: London, pp 171-200
6. Boon B, Laudelout H. (1962). Kinetics of nitrite oxidation by Nitrobacter winogradskyi. Biochem J 85: 440-447
7. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Costello EK, Fierer N et al. (2010). QIIME allows analyses of high-Throughput community sequencing data. Nat Meth 7: 335-336
8. 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
9. Dick GJ, Tebo BM. (2010). Microbial diversity and biogeochemistry of the Guaymas Basin hydrothermal plume. Environ Microbiol 12: 1334-1347
10. Dore JE, Karl DM. (1996). Nitrite distributions and dynamics at station ALOHA. Deep-Sea Res II 43: 385-402
11. Ehrlich S, Behrens D, Lebedeva E, Ludwig W, Bock E. (1995). A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch Microbiol 164: 16-23
12. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW et al. (2008). Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805-3810
13. Frigaard NU, Martinez A, Mincer TJ, DeLong EF. (2006). Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850
14. Füssel J, Lam P, Lavik G, Jensen MM, Holtappels M, Gunter M et al. (2012). Nitrite oxidation in the Namibian oxygen minimum zone. ISME J 6: 1200-1209
15. Ivars-Martínez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J et al. (2008). Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J 2: 1194-1212
16. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. (2012). Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota. Science 33: 587-590
17. Jiao N, Zheng Q. (2011). The microbial carbon pump: From genes to ecosystems. Appl Environ Microbiol 77: 7439-7444
18. Karl DM, Church MJ, Dore JE, Letelier RM, Mahaffey C. (2012). Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation. Proc Natl Acad Sci USA 109: 1842-1849
19. Karner MB, DeLong EF, Karl DM. (2001). Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510
20. Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J et al. (2012). Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci USA 109: E1173-E1182. early edition
21. Koops H-P, Pommerening-Roser A. (2001). Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1-9
22. 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
23. Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S et al. (2011). Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol Ecol 75: 195-204
24. Lesniewski R, 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
25. Li H, Durbin R. (2009). Fast and accurate short read alignment with Burrow-Wheeler Transform. Bioinformatics 25: 1754-1760
26. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. (2004). ARB: A software environment for sequence data. Nuc Acids Res 32: 1363-1371
27. Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B et al. (2010). A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107: 13479-13484
28. Markowitz VM, Chen I-MA, Chu K, Szeto E, Palaniappan K, Grechkin Y et al. (2012). IMG/M: The integrated metagenome data management and comparative analysis system. Nucl Acids Res 40: D123-D129
29. Martin-Cuadrado A-B, Rodriquez-Valera F, Moreira D, Alba D, Ivars-Martínez E, Henn MR et al. (2008). Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic a]nalyses of bathypelagic plankton of different oceanic regions. ISME J 2: 865-886
30. Miller CS, Baker BJ, Thomas BC, Singer S, Banfield JF. (2011). EMRIGE: Reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Gen Biol 12: R44
31. 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
32. Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan L-K et al. (2012). Sizing up metatranscriptomics. ISME J 7: 237-243
33. Pester M, Schleper C, Wagner M. (2011). The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 14: 300-306
34. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al. (2007). SILVA: A comprehensive online resourse for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nuc Acids Res 35: 7188-7196
35. Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM et al. (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Meth 6: 639-641
36. Raven JA, Falkowski PG. (1999). Oceanic sinks for atmospheric CO2. Plant Cell Eviron 22: 741-755
37. Santoro AE, Buchwald C, McIlvin MR, Casciotti KL. (2011). Isotopic signature of N2O produced by marine ammonia-oxidizing Archaea. Science 333: 1282-1285
38. Santoro AE, Casciotti KL, Francis CA. (2010). Activity, abundance and diversity of nitrifying archaea and bacteria in the central California current. Environ Microbiol 12: 1989-2006
39. Schauer K, Rodionov DA, de Reuse H. (2008). New substrates for TonB-dependent transport: Do we only see the 'tip of the iceberg'? Trends Biochem Sci 33: 330-338
40. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: Opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541
41. Schmieder R, Lim YW, Edwards R. (2012). Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 28: 433-435
42. Schulz MH, Zerbino DR, Vingron M, Birney E. (2012). Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092
43. Shi YM, Tyson GW, DeLong EF. (2009). Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266-269
44. Shi YM, Tyson GW, Eppley JM, DeLong EF. (2011). Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5: 999-1013
45. Sorokin DY, Lucker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstr WI et al. (2012). Nitrification expanded: Discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J 6: 2245-2256
46. Stewart FJ, Ulloa O, DeLong EF. (2011). Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol 14: 23-40
47. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW et al. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790-794
48. Ward BB, Capone DG, Zehr JP. (2007). What's new in the nitrogen cycle? Oceanography 20: 101-109
49. Watson SW, Bock E, Valois FW, Waterbury JB, Schlosser U. (1986). Nitrospira marina gen. nov., sp. nov.: A chemolithotrophic nitrite-oxidizing bacterium. Arch Microbiol 144: 1-7
50. Wertz S, Leigh AKK, Grayston SJ. (2011). Effects of long-Term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers. FEMS Microbiol Ecol 79: 142-154
51. Wright J, Konwar KM, Hallam SJ. (2012). Microbial ecology of expanding oxygen minimum zones. Nature 10: 381-394
52. Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P et al. (2006). Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103: 12317-12322
53. Zehr JP, Kudela RM. (2011). Nitrogen cycle of the open ocean: From genes to ecosystems. Ann Rev Mar Sci 3: 197-225.