메뉴 건너뛰기




Volumn 9, Issue 7, 2014, Pages

Genome sequence of Candidatus nitrososphaera evergladensis from group I.1b enriched from everglades soil reveals novel genomic features of the ammonia-oxidizing archaea

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; AMMONIA; CARBON; HEAVY METAL; NITROGEN; TERPENE;

EID: 84904279916     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0101648     Document Type: Article
Times cited : (81)

References (114)
  • 1
    • 33646260901 scopus 로고    scopus 로고
    • Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota
    • Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, et al. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLOS Biol 4: 0520-0536.
    • (2006) PLOS Biol , vol.4 , pp. 0520-0536
    • Hallam, S.J.1    Mincer, T.J.2    Schleper, C.3    Preston, C.M.4    Roberts, K.5
  • 2
    • 77952739182 scopus 로고    scopus 로고
    • Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
    • Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107: 8818-8823.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 8818-8823
    • Walker, C.B.1    De La Torre, J.R.2    Klotz, M.G.3    Urakawa, H.4    Pinel, N.5
  • 3
    • 83155173396 scopus 로고    scopus 로고
    • Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil
    • Jung MY, Park SJ, Min D, Kim JS, Rijpstra WI, et al. (2011) Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil. Appl Environ Microbiol 77: 8635-8647.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 8635-8647
    • Jung, M.Y.1    Park, S.J.2    Min, D.3    Kim, J.S.4    Rijpstra, W.I.5
  • 4
    • 84861212981 scopus 로고    scopus 로고
    • Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary
    • Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (2012) Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol 194, 2119-2120.
    • (2012) J Bacteriol , vol.194 , pp. 2119-2120
    • Mosier, A.C.1    Allen, E.E.2    Kim, M.3    Ferriera, S.4    Francis, C.A.5
  • 5
    • 84870692770 scopus 로고    scopus 로고
    • Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle
    • Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, et al. (2012a) Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. J Bacteriol 194: 6948-699.
    • (2012) J Bacteriol , vol.194 , pp. 6948-7699
    • Park, S.J.1    Kim, J.G.2    Jung, M.Y.3    Kim, S.J.4    Cha, I.T.5
  • 6
    • 84870702066 scopus 로고    scopus 로고
    • Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment
    • Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, et al. (2012b) Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment. J Bacteriol 194: 6940-96941.
    • (2012) J Bacteriol , vol.194 , pp. 6940-96941
    • Park, S.J.1    Kim, J.G.2    Jung, M.Y.3    Kim, S.J.4    Cha, I.T.5
  • 7
    • 84856577796 scopus 로고    scopus 로고
    • amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
    • Pester M, Rattei T, Fletchl S, Gröngröft A, Richter A, et al. (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14: 525-539.
    • (2012) Environ Microbiol , vol.14 , pp. 525-539
    • Pester, M.1    Rattei, T.2    Fletchl, S.3    Gröngröft, A.4    Richter, A.5
  • 8
    • 84859423097 scopus 로고    scopus 로고
    • Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges
    • Radax R, Hoffmann F, Rapp H, Leininger S, Schleper C (2012) Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges. Envirom Microbiol 14: 909-23.
    • (2012) Envirom Microbiol , vol.14 , pp. 909-923
    • Radax, R.1    Hoffmann, F.2    Rapp, H.3    Leininger, S.4    Schleper, C.5
  • 9
    • 70350052417 scopus 로고    scopus 로고
    • Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
    • Martens-Habbena W, Berube PM, Urakawa H, Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-979.
    • (2009) Nature , vol.461 , pp. 976-979
    • Martens-Habbena, W.1    Berube, P.M.2    Urakawa, H.3    Torre, J.R.4    Stahl, D.A.5
  • 10
    • 84872250001 scopus 로고    scopus 로고
    • Physiology and diversity of ammonia-oxidizing archaea
    • Stahl DA, de la Torre JR (2012) Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 66: 83-101.
    • (2012) Annu Rev Microbiol , vol.66 , pp. 83-101
    • Stahl, D.A.1    De La Torre, J.R.2
  • 11
    • 0032804175 scopus 로고    scopus 로고
    • Improving nitrogen use efficiency for cereal production
    • Raun WR, Johnson GV (1999) Improving nitrogen use efficiency for cereal production Agron J 91: 357-363. (Pubitemid 29402893)
    • (1999) Agronomy Journal , vol.91 , Issue.3 , pp. 357-363
    • Raun, W.R.1    Johnson, G.V.2
  • 12
    • 0034775280 scopus 로고    scopus 로고
    • Ammonia-oxidizing bacteria: A model for molecular microbial ecology
    • DOI 10.1146/annurev.micro.55.1.485
    • Kowalchuk GA, Stephen JA (2001) Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology. Annu Rev Microbiol 55: 485-529. (Pubitemid 32978114)
    • (2001) Annual Review of Microbiology , vol.55 , pp. 485-529
    • Kowalchuk, G.A.1    Stephen, J.R.2
  • 15
    • 84899491578 scopus 로고    scopus 로고
    • Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea
    • doi:10.1038/ismej.2013.220
    • Stieglmeier M, Mooshammer M, Kitzler B, Wanek W, Zechmeister-Boltenstern S, et al. (2014) Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME J doi:10.1038/ismej.2013.220
    • (2014) ISME J
    • Stieglmeier, M.1    Mooshammer, M.2    Kitzler, B.3    Wanek, W.4    Zechmeister-Boltenstern, S.5
  • 16
    • 84861939476 scopus 로고    scopus 로고
    • Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil
    • Kim JG, Jung MY, Park SJ, Rijpstra WIC, Damsté JS, et al. (2012) Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 14: 1528-1543.
    • (2012) Environ Microbiol , vol.14 , pp. 1528-1543
    • Kim, J.G.1    Jung, M.Y.2    Park, S.J.3    Rijpstra, W.I.C.4    Damsté, J.S.5
  • 17
  • 19
    • 84894268023 scopus 로고    scopus 로고
    • Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats
    • Lebedeva E, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, et al. (2012) Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats. PLOS ONE 8: e80835.
    • (2012) PLOS ONE , vol.8
    • Lebedeva, E.1    Hatzenpichler, R.2    Pelletier, E.3    Schuster, N.4    Hauzmayer, S.5
  • 20
    • 84870486180 scopus 로고    scopus 로고
    • The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations
    • Spang A, Phoehlein A, Offre P, Zumbragel S, Haider S, et al. (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14: 3122-3145.
    • (2012) Environ Microbiol , vol.14 , pp. 3122-3145
    • Spang, A.1    Phoehlein, A.2    Offre, P.3    Zumbragel, S.4    Haider, S.5
  • 22
    • 0042853314 scopus 로고    scopus 로고
    • Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR
    • DOI 10.1046/j.1462-2920.2003.00476.x
    • Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5: 787-97. (Pubitemid 37056863)
    • (2003) Environmental Microbiology , vol.5 , Issue.9 , pp. 787-797
    • Ochsenreiter, T.1    Selezi, D.2    Quaiser, A.3    Bonch-Osmolovskaya, L.4    Schleper, C.5
  • 23
    • 76349125984 scopus 로고    scopus 로고
    • Global ecological patterns in uncultured Archaea
    • Auguet J-C, Barberan A, Casamayor E (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182-90.
    • (2010) ISME J , vol.4 , pp. 182-190
    • Auguet, J.-C.1    Barberan, A.2    Casamayor, E.3
  • 24
    • 84861220096 scopus 로고    scopus 로고
    • Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary
    • Mosier A, Allen E, Kim M, Ferriera S, Francis C (2012) Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol 194: 2121-2.
    • (2012) J Bacteriol , vol.194 , pp. 2121-2122
    • Mosier, A.1    Allen, E.2    Kim, M.3    Ferriera, S.4    Francis, C.5
  • 25
    • 84868333620 scopus 로고    scopus 로고
    • Intact polar and core glycerol dibiphytanyl glycerol tetrather lipids of Group I.1a and I.1b Thaumarchaeota in soil
    • Damsté JS, Rijpstra WIC, Hopmans EC, Jung MY, Kim JG, et al. (2012) Intact polar and core glycerol dibiphytanyl glycerol tetrather lipids of Group I.1a and I.1b Thaumarchaeota in soil. Appl Environ Microbiol 78: 6866-6874.
    • (2012) Appl Environ Microbiol , vol.78 , pp. 6866-6874
    • Damsté, J.S.1    Rijpstra, W.I.C.2    Hopmans, E.C.3    Jung, M.Y.4    Kim, J.G.5
  • 26
    • 84884242904 scopus 로고    scopus 로고
    • Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments
    • Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, et al. (2013) Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol 4: 104.
    • (2013) Front Microbiol , vol.4 , pp. 104
    • Zhalnina, K.1    De Quadros, P.D.2    Gano, K.A.3    Davis-Richardson, A.4    Fagen, J.R.5
  • 27
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
    • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-5.
    • (2009) Nucleic Acids Res , vol.37
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5
  • 28
    • 79952050667 scopus 로고    scopus 로고
    • Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
    • Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLOS ONE 6: 1-12.
    • (2011) PLOS ONE , vol.6 , pp. 1-12
    • Blainey, P.C.1    Mosier, A.C.2    Potanina, A.3    Francis, C.A.4    Quake, S.R.5
  • 31
    • 40449104806 scopus 로고    scopus 로고
    • DNA microarray analysis of central carbohydrate metabolism: Glycolytic/gluconeogenic carbon switch in the hyperthermophilic crenarchaeum Thermoproteus tenax
    • DOI 10.1128/JB.01524-07
    • Zaparty M, Zaigler A, Stamme C, Soppa J, Hensel R, et al. (2008) DNA microarray analysis of central carbohydrate metabolism: glycolytic/gluconeogenic carbon switch in the hyperthermophilic crenarchaeum Thermoproteus tenax. J Bacteriol 190: 2231-8. (Pubitemid 351355346)
    • (2008) Journal of Bacteriology , vol.190 , Issue.6 , pp. 2231-2238
    • Zaparty, M.1    Zaigler, A.2    Stamme, C.3    Soppa, J.4    Hensel, R.5    Siebers, B.6
  • 33
    • 78049356011 scopus 로고    scopus 로고
    • Both forward and reverse TCA cycles operate in green sulfur bacteria
    • Tang KH, Blankenship RE (2010) Both forward and reverse TCA cycles operate in green sulfur bacteria. J Biol Chem 285: 35848-35854.
    • (2010) J Biol Chem , vol.285 , pp. 35848-35854
    • Tang, K.H.1    Blankenship, R.E.2
  • 35
    • 84904320813 scopus 로고    scopus 로고
    • Metabolic reprogramming under microaerobic and anaerobic conditions in bacteria
    • Shan Y, Lai Y, Yan A (2012) Metabolic reprogramming under microaerobic and anaerobic conditions in bacteria. Subcell Biochem 64: 159-79.
    • (2012) Subcell Biochem , vol.64 , pp. 159-179
    • Shan, Y.1    Lai, Y.2    Yan, A.3
  • 36
    • 78649703098 scopus 로고    scopus 로고
    • Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria
    • Park BJ, Park SJ, Yoon DN, Schouten S, Sinninghe Damsté JS, et al. (2010) Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Microbiol 76: 7575-87.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 7575-7587
    • Park, B.J.1    Park, S.J.2    Yoon, D.N.3    Schouten, S.4    Sinninghe Damsté, J.S.5
  • 37
    • 27844507018 scopus 로고    scopus 로고
    • Unusual pathways and enzymes of central carbohydrate metabolism in Archaea
    • DOI 10.1016/j.mib.2005.10.014, PII S1369527405001700, Growth Development
    • Siebers B, Schönheit P (2005) Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol 8: 695-705. (Pubitemid 41643038)
    • (2005) Current Opinion in Microbiology , vol.8 , Issue.6 , pp. 695-705
    • Siebers, B.1    Schonheit, P.2
  • 38
    • 0015413829 scopus 로고
    • Isolation and properties of a fluorescent compound, factor 420, from Methanobacterium strain MoH
    • Cheeseman P, Toms-Wood A, Wolfe RS (1972) Isolation and properties of a fluorescent compound, factor 420, from Methanobacterium strain MoH. J Bacteriol 112: 527-531.
    • (1972) J Bacteriol , vol.112 , pp. 527-531
    • Cheeseman, P.1    Toms-Wood, A.2    Wolfe, R.S.3
  • 39
    • 84872783752 scopus 로고    scopus 로고
    • F420-dependent enzymes - Potential for applications in biotechnology
    • Taylor M, Scott C, Grogan G (2013) F420-dependent enzymes - potential for applications in biotechnology. Trends Biotechnol 31: 63-4.
    • (2013) Trends Biotechnol , vol.31 , pp. 63-64
    • Taylor, M.1    Scott, C.2    Grogan, G.3
  • 41
    • 84868092696 scopus 로고    scopus 로고
    • Marine archaea take a short cut in the nitrogen cycle
    • Kirchman DL (2012) Marine archaea take a short cut in the nitrogen cycle. Proc Natl Acad Sci U S A 109: 17732-17733.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 17732-17733
    • Kirchman, D.L.1
  • 42
    • 0036167265 scopus 로고    scopus 로고
    • Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria
    • DOI 10.1007/s00203-001-0369-z
    • Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing archaea. Arch Microbiol 177: 139-149. (Pubitemid 34143413)
    • (2002) Archives of Microbiology , vol.177 , Issue.2 , pp. 139-149
    • Norton, J.M.1    Alzerreca, J.J.2    Suwa, Y.3    Klotz, M.G.4
  • 43
    • 84864020137 scopus 로고    scopus 로고
    • The divergent AmoC subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea
    • Berube PM, Stahl DA (2012) The divergent AmoC subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. J Bacteriol 194: 3448-3456.
    • (2012) J Bacteriol , vol.194 , pp. 3448-3456
    • Berube, P.M.1    Stahl, D.A.2
  • 44
    • 0036038187 scopus 로고    scopus 로고
    • Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea
    • DOI 10.1007/s00203-002-0452-0
    • Arp D, Sayavedra-Soto L, Hommes N. (2002) Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol 178: 250-255. (Pubitemid 35025065)
    • (2002) Archives of Microbiology , vol.178 , Issue.4 , pp. 250-255
    • Arp, D.J.1    Sayavedra-Soto, L.A.2    Hommes, N.G.3
  • 45
    • 37249025200 scopus 로고    scopus 로고
    • Nitrifier genomics and evolution of the nitrogen cycle
    • DOI 10.1111/j.1574-6968.2007.00970.x
    • Klotz MG, Stein LY (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278: 146-156. (Pubitemid 350264573)
    • (2008) FEMS Microbiology Letters , vol.278 , Issue.2 , pp. 146-156
    • Klotz, M.G.1    Stein, L.Y.2
  • 46
    • 78349282589 scopus 로고    scopus 로고
    • Ammonia-oxidizing archaea-physiology, ecology and evolution
    • Schleper C, Nicol GW (2010) Ammonia-oxidizing archaea-physiology, ecology and evolution. Adv Microb Physiol 57: 1-41.
    • (2010) Adv Microb Physiol , vol.57 , pp. 1-41
    • Schleper, C.1    Nicol, G.W.2
  • 49
    • 84862668222 scopus 로고    scopus 로고
    • The dynamic roles of intracellular lipid droplets: From archaea to mammals
    • Murphy DJ (2012) The dynamic roles of intracellular lipid droplets: from archaea to mammals. Protoplasma 3: 541-585.
    • (2012) Protoplasma , vol.3 , pp. 541-585
    • Murphy, D.J.1
  • 50
    • 76849099236 scopus 로고    scopus 로고
    • Synthesis and production of polyhydroxyalkanoates by halophiles: Current potential and future prospects
    • Quillaguaman J, Guzman H, Van-Thuoc D, Hatti-Kaul R (2010) Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects. Appl Microbiol Biotechnol 85: 1687-1696.
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 1687-1696
    • Quillaguaman, J.1    Guzman, H.2    Van-Thuoc, D.3    Hatti-Kaul, R.4
  • 51
    • 0036795638 scopus 로고    scopus 로고
    • Crenarchaeol: The characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota
    • DOI 10.1194/jlr.M200148-JLR200
    • Damsté JS, Schouten S, Hopmans EC, van Duin AC, Geenevasen JA (2002) Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. J Lipid Res 43: 1641-1651. (Pubitemid 35168278)
    • (2002) Journal of Lipid Research , vol.43 , Issue.10 , pp. 1641-1651
    • Sinninghe, D.J.S.1    Schouten, S.2    Hopmans, E.C.3    Van Duin, A.C.T.4    Geenevasen, J.A.J.5
  • 52
    • 77955273494 scopus 로고    scopus 로고
    • Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    • Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, et al. (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
    • (2010) Trends Microbiol , vol.18 , pp. 331-340
    • Spang, A.1    Hatzenpichler, R.2    Brochier-Armanet, C.3    Rattei, T.4    Tischler, P.5
  • 53
    • 38549131184 scopus 로고    scopus 로고
    • Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
    • DOI 10.1111/j.1462-2920.2007.01506.x
    • de la Torre J, Walker C, Ingalls A, Könneke M, Stahl D (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Envirom Microbiol 10: 810-8. (Pubitemid 351160920)
    • (2008) Environmental Microbiology , vol.10 , Issue.3 , pp. 810-818
    • De La, T.J.R.1    Walker, C.B.2    Ingalls, A.E.3    Konneke, M.4    Stahl, D.A.5
  • 54
    • 77950043418 scopus 로고    scopus 로고
    • Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic group I.1b Archaeon
    • Pitcher A, Rychlik N, Hopmans E, Spieck E, Rijpstra W, et al. (2010) Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic group I.1b Archaeon. ISME J 4: 542-52.
    • (2010) ISME J , vol.4 , pp. 542-552
    • Pitcher, A.1    Rychlik, N.2    Hopmans, E.3    Spieck, E.4    Rijpstra, W.5
  • 55
    • 0033793828 scopus 로고    scopus 로고
    • Biosynthesis of isoprenoids via mevalonate in archaea: The Lost Pathway
    • Smit A, Mushegian A (2000) Biosynthesis of isoprenoids via mevalonate in archaea: The Lost Pathway. Genome Res 10: 1468-1484.
    • (2000) Genome Res , vol.10 , pp. 1468-1484
    • Smit, A.1    Mushegian, A.2
  • 56
    • 27844510004 scopus 로고    scopus 로고
    • Stress response by solute accumulation in archaea
    • DOI 10.1016/j.mib.2005.10.011, PII S1369527405001670, Growth Development
    • Muller V, Spanheimer R, Santos H (2005) Stress response by solute accumulation in archaea. Curr Opin Microbiol 8: 729-736. (Pubitemid 41643042)
    • (2005) Current Opinion in Microbiology , vol.8 , Issue.6 , pp. 729-736
    • Muller, V.1    Spanheimer, R.2    Santos, H.3
  • 57
    • 31944443146 scopus 로고    scopus 로고
    • Why do microorganisms have aquaporins?
    • DOI 10.1016/j.tim.2005.12.001, PII S0966842X0500332X
    • Tanghe A, Van Dijck P, Thevelein JM (2006) Why do microorganisms have aquaporins? Trends Microbiol 14: 78-85. (Pubitemid 43190737)
    • (2006) Trends in Microbiology , vol.14 , Issue.2 , pp. 78-85
    • Tanghe, A.1    Van Dijck, P.2    Thevelein, J.M.3
  • 58
    • 0035703118 scopus 로고    scopus 로고
    • Osmoadaptation in bacteria and archaea: Common principles and differences
    • Roesser M, Müller V (2001) Osmoadaptation in bacteria and archaea: common principles and differences. Envirom Microbiol 3: 743-754.
    • (2001) Envirom Microbiol , vol.3 , pp. 743-754
    • Roesser, M.1    Müller, V.2
  • 59
    • 84894369857 scopus 로고    scopus 로고
    • Survival of the fittest: Overcoming oxidative stress at the extremes of acid, heat and metal
    • Maezato Y, Blum P (2012) Survival of the fittest: overcoming oxidative stress at the extremes of acid, heat and metal. Life 2: 229-242.
    • (2012) Life , vol.2 , pp. 229-242
    • Maezato, Y.1    Blum, P.2
  • 60
    • 34547263402 scopus 로고    scopus 로고
    • Microbial extremophiles at the limits of life
    • DOI 10.1080/10408410701451948, PII 780669110
    • Pikuta EV, Hoover RB, Tang J (2007) Microbial extremophiles at the limits of life. Crit Rev Microbiol 33: 183-209. (Pubitemid 47134687)
    • (2007) Critical Reviews in Microbiology , vol.33 , Issue.3 , pp. 183-209
    • Pikuta, E.V.1    Hoover, R.B.2    Tang, J.3
  • 61
    • 70350596382 scopus 로고    scopus 로고
    • Do ammonia-oxidizing archaea respond to soil Cu contamination similarly asammonia-oxidizing bacteria?
    • Li X, Zhu YG, Cavagnaro TR, Chen M, Sun J, et al. (2009) Do ammonia-oxidizing archaea respond to soil Cu contamination similarly asammonia-oxidizing bacteria? Plant Soil 324: 209-217.
    • (2009) Plant Soil , vol.324 , pp. 209-217
    • Li, X.1    Zhu, Y.G.2    Cavagnaro, T.R.3    Chen, M.4    Sun, J.5
  • 62
    • 33746048460 scopus 로고    scopus 로고
    • Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2
    • DOI 10.1099/mic.0.28724-0
    • Ettema TJ, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, et al. (2006) Molecular characterization of a conserved resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2. Microbiology 152: 1969-1979. (Pubitemid 44070454)
    • (2006) Microbiology , vol.152 , Issue.7 , pp. 1969-1979
    • Ettema, T.J.G.1    Brinkman, A.B.2    Lamers, P.P.3    Kornet, N.G.4    De Vos, W.M.5    Van Der Oost, J.6
  • 63
    • 84875436722 scopus 로고    scopus 로고
    • Molecular characterization of copper and cadmium resistance determinants in the biomining thermoacidophilic archaeon Sulfolobus metallicus
    • doi:101155/2013/289236
    • Orell A, Remonsellez F, Arancibia R, Jerez CA (2013) Molecular characterization of copper and cadmium resistance determinants in the biomining thermoacidophilic archaeon Sulfolobus metallicus. Archaea doi:101155/2013/289236
    • (2013) Archaea
    • Orell, A.1    Remonsellez, F.2    Arancibia, R.3    Jerez, C.A.4
  • 64
    • 84881013236 scopus 로고    scopus 로고
    • A multicopper oxidase is required for copper resistance in Mycobacterium tuberculosis
    • Rowland JL, Niederweis M (2013) A multicopper oxidase is required for copper resistance in Mycobacterium tuberculosis. J Bacteriol 195: 3724-3733.
    • (2013) J Bacteriol , vol.195 , pp. 3724-3733
    • Rowland, J.L.1    Niederweis, M.2
  • 65
    • 30744445719 scopus 로고    scopus 로고
    • Copper tolerance of the thermoacidophilic archaeon Sulfolobus metallicus: Possible role of polyphosphate metabolism
    • DOI 10.1099/mic.0.28241-0
    • Remonsellez F, Orell A, Jerez CA (2006) Copper tolerance of the thermoacidophilic archaeon Sulfolobus metallicus: possible role of polyphosphate metabolism. Microbiology 152: 59-66. (Pubitemid 43092393)
    • (2006) Microbiology , vol.152 , Issue.1 , pp. 59-66
    • Remonsellez, F.1    Orell, A.2    Jerez, C.A.3
  • 66
    • 84869866788 scopus 로고    scopus 로고
    • Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea
    • Petitjean C, Moreira D, López-García P, Brochier-Armanet C (2011) Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea. BMC Evol Biol 12: 226.
    • (2011) BMC Evol Biol , vol.12 , pp. 226
    • Petitjean, C.1    Moreira, D.2    López-García, P.3    Brochier-Armanet, C.4
  • 67
    • 0033554650 scopus 로고    scopus 로고
    • Measurement of nitrate and ammonium uptake at ambient concentrations in oligotrophic waters of the North-East Atlantic Ocean
    • Rees A, Woodward M, Joint I (1999) Measurement of nitrate and ammonium uptake at ambient concentrations in oligotrophic waters of the North-East Atlantic Ocean. Mar Ecol Prog Ser 187: 295-300.
    • (1999) Mar Ecol Prog Ser , vol.187 , pp. 295-300
    • Rees, A.1    Woodward, M.2    Joint, I.3
  • 68
    • 77950912269 scopus 로고    scopus 로고
    • Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
    • Yin Y, Zhang H, Olman V, Xu Y (2010) Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome Proc Natl Acad Sci USA 107: 6310-5.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 6310-6315
    • Yin, Y.1    Zhang, H.2    Olman, V.3    Xu, Y.4
  • 71
    • 0034663575 scopus 로고    scopus 로고
    • Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea
    • DOI 10.1016/S0005-2728(00)00171-7, PII S0005272800001717
    • Whittaker M, Bergmann D, Arciero D, Hooper AB (2000) Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea. Biochim Biophys Acta 1459: 346-355. (Pubitemid 30612407)
    • (2000) Biochimica et Biophysica Acta - Bioenergetics , vol.1459 , Issue.2-3 , pp. 346-355
    • Whittaker, M.1    Bergmann, D.2    Arciero, D.3    Hooper, A.B.4
  • 72
    • 84870216095 scopus 로고    scopus 로고
    • The SLC10 carrier family: Transport functions and molecular structure
    • Döring B, Lütteke T, Geyer J, Petzinger E (2012) The SLC10 carrier family: transport functions and molecular structure. Curr Top Membr 70: 105-168.
    • (2012) Curr Top Membr , vol.70 , pp. 105-168
    • Döring, B.1    Lütteke, T.2    Geyer, J.3    Petzinger, E.4
  • 75
    • 67549091828 scopus 로고    scopus 로고
    • Phosphate-dependent behavior of the archaeon Halobacterium salinarum Strain R1
    • Wende A, Furtwangler K, Oesterhelt D (2009) Phosphate-dependent behavior of the archaeon Halobacterium salinarum Strain R1. J Bacteriol 191: 3852-3860.
    • (2009) J Bacteriol , vol.191 , pp. 3852-3860
    • Wende, A.1    Furtwangler, K.2    Oesterhelt, D.3
  • 76
    • 79959326633 scopus 로고    scopus 로고
    • Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli
    • Leblanc SKD, Oates CW, Raivio TL (2011) Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli. J Bacteriol 193: 3367-3375.
    • (2011) J Bacteriol , vol.193 , pp. 3367-3375
    • Leblanc, S.K.D.1    Oates, C.W.2    Raivio, T.L.3
  • 77
    • 84864675114 scopus 로고    scopus 로고
    • The CopRS two-component system is responsible for resistance to copper in the cyanobacterium Synechocystis sp. PCC 6803
    • Giner-Lamia J, López-Maury L, Reyes JC, Florencio FJ (2012) The CopRS two-component system is responsible for resistance to copper in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol 159: 1806-1818.
    • (2012) Plant Physiol , vol.159 , pp. 1806-1818
    • Giner-Lamia, J.1    López-Maury, L.2    Reyes, J.C.3    Florencio, F.J.4
  • 78
    • 84873544862 scopus 로고    scopus 로고
    • Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli
    • Fried L, Behr S, Jung K (2013) Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. J Bacteriol 195: 807-815.
    • (2013) J Bacteriol , vol.195 , pp. 807-815
    • Fried, L.1    Behr, S.2    Jung, K.3
  • 79
    • 0035152738 scopus 로고    scopus 로고
    • Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system
    • DOI 10.1128/JB.183.2.451-460.2001
    • Tortosa P, Logsdon L, Kraigher B, Itoh Y, Mandic-Mulec I, et al. (2001) Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system. J Bacteriol 183: 451-460. (Pubitemid 32048102)
    • (2001) Journal of Bacteriology , vol.183 , Issue.2 , pp. 451-460
    • Tortosa, P.1    Logsdon, L.2    Kraigher, B.3    Itoh, Y.4    Mandic-Mulec, I.5    Dubnau, D.6
  • 80
    • 66249122044 scopus 로고    scopus 로고
    • Evolution of complex RNA polymerases: The complete archaeal RNA polymerase structure
    • Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, et al. (2009) Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PLOS Biol 7: 0001-0010.
    • (2009) PLOS Biol , vol.7 , pp. 0001-0010
    • Korkhin, Y.1    Unligil, U.M.2    Littlefield, O.3    Nelson, P.J.4    Stuart, D.I.5
  • 82
    • 79959307333 scopus 로고    scopus 로고
    • Phylogeny and evolution of the Archaea: One hundred genomes later
    • Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14: 274-281.
    • (2011) Curr Opin Microbiol , vol.14 , pp. 274-281
    • Brochier-Armanet, C.1    Forterre, P.2    Gribaldo, S.3
  • 83
  • 84
    • 78049291491 scopus 로고    scopus 로고
    • Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex
    • Kobayashi K, Kikuno I, Kuroha K, Saito K, Ito K, et al. (2010) Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex. Proc Natl Acad Sci USA 107: 17575-9.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 17575-17579
    • Kobayashi, K.1    Kikuno, I.2    Kuroha, K.3    Saito, K.4    Ito, K.5
  • 86
    • 0038202108 scopus 로고    scopus 로고
    • Archaeal DNA repair: Paradigms and puzzles
    • White MF (2003) Archaeal DNA repair: paradigms and puzzles. Biochem Soc Trans 31: 690-693.
    • (2003) Biochem Soc Trans , vol.31 , pp. 690-693
    • White, M.F.1
  • 87
    • 78149449833 scopus 로고    scopus 로고
    • Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples
    • Snyder JC, Bateson MM, Lavin M, Young MJ (2010) Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples. Appl Environ Microbiol 76: 7251-7258.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 7251-7258
    • Snyder, J.C.1    Bateson, M.M.2    Lavin, M.3    Young, M.J.4
  • 88
    • 74249095519 scopus 로고    scopus 로고
    • CRISPR/Cas, the immune system of bacteria and archaea
    • Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167-170.
    • (2010) Science , vol.327 , pp. 167-170
    • Horvath, P.1    Barrangou, R.2
  • 89
    • 77249170201 scopus 로고    scopus 로고
    • CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    • Marraffini L, Sontheimer E (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181-90.
    • (2010) Nat Rev Genet , vol.11 , pp. 181-190
    • Marraffini, L.1    Sontheimer, E.2
  • 91
    • 25644435673 scopus 로고    scopus 로고
    • Isolation of an autotrophic ammonia-oxidizing marine archaeon
    • DOI 10.1038/nature03911, PII N03911
    • Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546. (Pubitemid 41613550)
    • (2005) Nature , vol.437 , Issue.7058 , pp. 543-546
    • Konneke, M.1    Bernhard, A.E.2    De La, T.J.R.3    Walker, C.B.4    Waterbury, J.B.5    Stahl, D.A.6
  • 96
    • 0030814870 scopus 로고    scopus 로고
    • The ammonia monooxygenase structural gene amoa as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations
    • Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 4704-12. (Pubitemid 27524201)
    • (1997) Applied and Environmental Microbiology , vol.63 , Issue.12 , pp. 4704-4712
    • Rotthauwe, J.-H.1    Witzel, K.-P.2    Liesack, W.3
  • 97
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng Y, Leung HC, Yiu S-M, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.2    Yiu, S.-M.3    Chin, F.Y.4
  • 98
    • 3042631307 scopus 로고    scopus 로고
    • Genome sequence assembly using trace signals and additional sequence information
    • Chevreux B, Wetter T, Suhai Sn (1999) Genome sequence assembly using trace signals and additional sequence information. In: German conference on Bioinformatics 45: 56.
    • (1999) German Conference on Bioinformatics , vol.45 , pp. 56
    • Chevreux, B.1    Wetter, T.2    Suhai, Sn.3
  • 100
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • DOI 10.1101/gr.2289704
    • Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403. (Pubitemid 39029237)
    • (2004) Genome Research , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 101
    • 40549120596 scopus 로고    scopus 로고
    • The RAST Server: Rapid Annotations using Subsystems Technology
    • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75.
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1    Bartels, D.2    Best, A.A.3    DeJongh, M.4    Disz, T.5
  • 102
    • 69949116874 scopus 로고    scopus 로고
    • IMG ER: A system for microbial genome annotation expert review and curation
    • Markowitz VM, Mavromatis K, Ivanova NN, Chen I, Chu K, et al. (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25: 2271-2278.
    • (2009) Bioinformatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1    Mavromatis, K.2    Ivanova, N.N.3    Chen, I.4    Chu, K.5
  • 107
    • 34547579396 scopus 로고    scopus 로고
    • CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats
    • Grissa I, Vergnaud G, Poucel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-W57.
    • (2007) Nucleic Acids Res , vol.35
    • Grissa, I.1    Vergnaud, G.2    Poucel, C.3
  • 108
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 109
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • DOI 10.1080/10635150701472164, PII 780704285
    • Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577. (Pubitemid 47171631)
    • (2007) Systematic Biology , vol.56 , Issue.4 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 110
    • 80055104018 scopus 로고    scopus 로고
    • MorePhyML: Improving the phylogenetic tree space exploration with PhyML 3
    • Criscuolo A (2011) MorePhyML: improving the phylogenetic tree space exploration with PhyML 3. Mol Phylogenet Evol 61: 944-948.
    • (2011) Mol Phylogenet Evol , vol.61 , pp. 944-948
    • Criscuolo, A.1
  • 112
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126-19131.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 113
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.