Erratum to Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers (Extremophiles, (2012), 16, (277-283), 10.1007/s00792-011-0428-6);Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers

Extremophiles

Volumn 16, Issue 2, 2012, Pages 277-283

  Kato, Shingo ^a,b   Nakawake, Michiyuki ^b   Ohkuma, Moriya ^a   Yamagishi, Akihiko ^b  

^a RIKEN BIORESOURCE CENTER   (Japan)

^b TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

Author keywords

Carbon fixation; cbbM gene; Chemolithoautotroph; Deep sea hydrothermal field; RubisCO form II

Indexed keywords

GAMMAPROTEOBACTERIA;

EID: 84857916925     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-014-0626-0     Document Type: Erratum

References (34)

1. Alfreider A, Vogt C, Hoffmann D, Babel W (2003) Diversity of ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit genes from groundwater and aquifer microorganisms. Microb Ecol 45: 317-328.
2. Alfreider A, Vogt C, Geiger-Kaiser M, Psenner R (2009) Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes. Syst Appl Microbiol 32: 140-150.
3. 2 acquisition by the CBB cycle. J Exp Bot 59: 1525-1541.
4. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
5. Elsaied H, Naganuma T (2001) Phylogenetic diversity of ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Appl Environ Microbiol 67: 1751-1765.
6. Elsaied H, Kimura H, Naganuma T (2007) Composition of archaeal, bacterial, and eukaryal RubisCO genotypes in three western Pacific arc hydrothermal vent systems. Extremophiles 11: 191-202.
7. Giri BJ, Bano N, Hollibaugh JT (2004) Distribution of RubisCO genotypes along a redox gradient in Mono Lake, California. Appl Environ Microbiol 70: 3443-3448.
8. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
9. Hara K, Kakegawa T, Yamashiro K, Maruyama A, Ishibashi J, Marumo K, Urabe T, Yamagishi A (2005) Analysis of the archaeal sub-seafloor community at Suiyo Seamount on the Izu-Bonin Arc. Adv Space Res 35: 1634-1642.
10. Higashi Y, Sunamura M, Kitamura K, Nakamura K, Kurusu Y, Ishibashi J, Urabe T, Maruyama A (2004) Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber. FEMS Microbiol Ecol 47: 327-336.
11. Hügler M, Sievert SM (2010) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann Rev Marine Sci 3: 261-289.
12. 2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol 73: 526-537.
13. Jordan DB, Ogren WL (1981) Species variation in the specificity of ribulose biphosphate carboxylase/oxygenase. Nature 291: 513-515.
14. Kato S, Kobayashi C, Kakegawa T, Yamagishi A (2009a) Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 2094-2111.
15. Kato S, Hara K, Kasai H, Teramura T, Sunamura M, Ishibashi J, Kakegawa T, Yamanaka T, Kimura H, Marumo K, Urabe T, Yamagishi A (2009b) Spatial distribution, diversity and composition of bacterial communities in sub-seafloor fluids at a deep-sea hydrothermal field of the Suiyo Seamount. Deep Sea Res Part I Oceanogr Res Pap 56: 1844-1855.
16. Kato S, Yanagawa K, Sunamura M, Takano Y, Ishibashi J, Kakegawa T, Utsumi M, Yamanaka T, Toki T, Noguchi T, Kobayashi K, Moroi A, Kimura H, Kawarabayasi Y, Marumo K, Urabe T, Yamagishi A (2009c) Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 3210-3222.
17. Kovaleva OL, Tourova TP, Muyzer G, Kolganova TV, Sorokin DY (2011) Diversity of RubisCO and ATP citrate lyase genes in soda lake sediments. FEMS Microbiol Ecol 75: 37-47.
18. Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Nishi S, Harada M, Matsuyama K, Takishita K, Kawato M, Uematsu K, Fujiwara Y, Sato T, Kato C, Kitagawa M, Kato I, Maruyama T (2007) Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr Biol 17: 881-886.
19. Lisa MN, Gary MK (2007) Disparate distributions of chemolithotrophs containing form IA or IC large subunit genes for ribulose-1, 5-bisphosphate carboxylase/oxygenase in intertidal marine and littoral lake sediments. FEMS Microbiol Ecol 60: 113-125.
20. Nakagawa S, Takai K (2008) Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 65: 1-14.
21. Nakagawa T, Ishibashi J, Maruyama A, Yamanaka T, Morimoto Y, Kimura H, Urabe T, Fukui M (2004) Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, izu-bonin arc, western Pacific. Appl Environ Microbiol 70: 393-403.
22. Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000.
23. Pichard SL, Campbell L, Paul JH (1997) Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities. Appl Environ Microbiol 63: 3600-3606.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
25. Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and red-like ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils. Appl Environ Microbiol 71: 175-184.
26. Sunamura M, Higashi Y, Miyako C, Ishibashi J, Maruyama A (2004) Two bacteria phylotypes are predominant in the Suiyo Seamount hydrothermal plume. Appl Environ Microbiol 70: 1190-1198.
27. Tabita FR (1988) Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol Mol Biol Rev 52: 155.
28. Tabita FR, Satagopan S, Hanson TE, Kreel NE, Scott SS (2008) Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J Exp Bot 59: 1515-1524.
29. Tivey MK (1995) The influence of hydrothermal fluid composition and advection rates on black smoker chimney mineralogy: insights from modeling transport and reaction. Geochim Cosmochim Acta 59: 1933-1949.
30. Tourova TP, Spiridonova EM, Berg IA, Kuznetsov BB, Sorokin DY (2005) Phylogeny of ribulose-1, 5-bisphosphate carboxylase/oxygenase genes in haloalkaliphilic obligately autotrophic sulfur-oxidizing bacteria of the genus Thioalkalivibrio. Microbiology 74: 321-328.
31. Tourova TP, Spiridonova EM, Berg IA, Kuznetsov BB, Sorokin DY (2006) Occurrence, phylogeny and evolution of ribulose-1, 5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium. Microbiology 152: 2159-2169.
32. Tourova TP, Kovaleva OL, Sorokin DY, Muyzer G (2010) Ribulose-1, 5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats. Microbiology 156: 2016-2025.
33. Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD, Hallam SJ (2009) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326: 578-582.
34. Watanabe K, Kajimura T (1993) Topography, geology and hydro- thermal deposits at Suiyo Seamount (in Japanese with English abstract). Proc JAMSTEC Symp Deep Sea Res 9: 77-89.