메뉴 건너뛰기




Volumn 6, Issue APR, 2015, Pages

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

Author keywords

Desulforudis; Evolution; Horizontal gene transfer (HGT); Population genomics; Single cell genomics; Terrestrial deep subsurface; Transposable phages; Transposases

Indexed keywords

RESTRICTION ENDONUCLEASE; TRANSPOSASE;

EID: 84930946066     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00349     Document Type: Article
Times cited : (54)

References (82)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S., Gish, W., and Miller, W. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.1    Gish, W.2    Miller, W.3
  • 2
    • 77955233623 scopus 로고    scopus 로고
    • Transposases are the most abundant, most ubiquitous genes in nature
    • Aziz, R. K., Breitbart, M., and Edwards, R. A. (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 38, 4207-4217. doi: 10.1093/nar/gkq140.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4207-4217
    • Aziz, R.K.1    Breitbart, M.2    Edwards, R.A.3
  • 4
    • 72649088719 scopus 로고    scopus 로고
    • Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm
    • Brazelton, W. J., and Baross, J. A. (2009). Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420-1424. doi: 10.1038/ismej.2009.79.
    • (2009) ISME J , vol.3 , pp. 1420-1424
    • Brazelton, W.J.1    Baross, J.A.2
  • 5
    • 4544321685 scopus 로고    scopus 로고
    • Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
    • Brüssow, H., Canchaya, C., and Hardt, W. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560-602. doi: 10.1128/MMBR.68.3.560-602.2004.
    • (2004) Microbiol. Mol. Biol. Rev , vol.68 , pp. 560-602
    • Brüssow, H.1    Canchaya, C.2    Hardt, W.3
  • 8
    • 53749096964 scopus 로고    scopus 로고
    • Environmental genomics reveals a single-species ecosystem deep within Earth
    • Chivian, D., Brodie, E., Alm, E., Culley, D., Dehal, P., DeSantis, T., et al. (2008). Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322, 275-278. doi: 10.1126/science.1155495.
    • (2008) Science , vol.322 , pp. 275-278
    • Chivian, D.1    Brodie, E.2    Alm, E.3    Culley, D.4    Dehal, P.5    DeSantis, T.6
  • 9
    • 84891787231 scopus 로고    scopus 로고
    • Ribosomal Database Project: data and tools for high throughput rRNA analysis
    • Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., et al. (2014). Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633-D642. doi: 10.1093/nar/gkt1244.
    • (2014) Nucleic Acids Res , vol.42 , pp. D633-D642
    • Cole, J.R.1    Wang, Q.2    Fish, J.A.3    Chai, B.4    McGarrell, D.M.5    Sun, Y.6
  • 10
    • 84879815524 scopus 로고    scopus 로고
    • Nature and extent of the deep biosphere
    • Colwell, F. S., and D'Hondt, S. (2013). Nature and extent of the deep biosphere. Rev. Mineral. Geochem. 75, 547-574. doi: 10.2138/rmg.2013.75.17.
    • (2013) Rev. Mineral. Geochem , vol.75 , pp. 547-574
    • Colwell, F.S.1    D'Hondt, S.2
  • 11
    • 65549163465 scopus 로고    scopus 로고
    • Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface
    • Coombs, J. M. (2009). Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface. Horiz. Gene Transf. 532, 413-433. doi: 10.1007/978-1-60327-853-9_24.
    • (2009) Horiz. Gene Transf , vol.532 , pp. 413-433
    • Coombs, J.M.1
  • 12
    • 40149103830 scopus 로고    scopus 로고
    • 'Biogeochemistry of aquifer systems'
    • eds C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach (Washington, DC: ASM Press)
    • Cozzarelli, I. M., Weiss, J. V, Hurst, C. J., Crawford, R. L., Garland, J. L., Lipson, D. A., et al. (2007). "Biogeochemistry of aquifer systems," in Manual of Environmental Microbiology, eds C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach (Washington, DC: ASM Press), 843-859.
    • (2007) Manual of Environmental Microbiology , pp. 843-859
    • Cozzarelli, I.M.1    Weiss, J.V.2    Hurst, C.J.3    Crawford, R.L.4    Garland, J.L.5    Lipson, D.A.6
  • 13
    • 84864453108 scopus 로고    scopus 로고
    • jModelTest 2, more models, new heuristics and parallel computing
    • Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9, 772. doi: 10.1038/nmeth.2109.
    • (2012) Nat. Methods , vol.9 , pp. 772
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 14
    • 0036606576 scopus 로고    scopus 로고
    • Fast algorithms for large-scale genome alignment and comparison
    • Delcher, A. L., Phillippy, A., Carlton, J., and Salzberg, S. L. (2002). Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478-2483. doi: 10.1093/nar/30.11.2478.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2478-2483
    • Delcher, A.L.1    Phillippy, A.2    Carlton, J.3    Salzberg, S.L.4
  • 15
    • 84861342496 scopus 로고    scopus 로고
    • Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
    • Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Richter, R. A., Valas, R., et al. (2012). Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6, 1186-1199. doi: 10.1038/ismej.2011.189.
    • (2012) ISME J , vol.6 , pp. 1186-1199
    • Dupont, C.L.1    Rusch, D.B.2    Yooseph, S.3    Lombardo, M.-J.4    Richter, R.A.5    Valas, R.6
  • 16
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 17
    • 84871367784 scopus 로고    scopus 로고
    • Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments
    • Engelhardt, T., Sahlberg, M., Cypionka, H., and Engelen, B. (2013). Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J. 7, 199-209. doi: 10.1038/ismej.2012.92.
    • (2013) ISME J , vol.7 , pp. 199-209
    • Engelhardt, T.1    Sahlberg, M.2    Cypionka, H.3    Engelen, B.4
  • 18
    • 84925045058 scopus 로고    scopus 로고
    • Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount
    • Field, E. K., Sczyrba, A., Lyman, A. E., Harris, C. C., Woyke, T., Stepanauskas, R., et al. (2015). Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J. 9, 857-870. doi: 10.1038/ismej.2014.183.
    • (2015) ISME J , vol.9 , pp. 857-870
    • Field, E.K.1    Sczyrba, A.2    Lyman, A.E.3    Harris, C.C.4    Woyke, T.5    Stepanauskas, R.6
  • 19
    • 0033542481 scopus 로고    scopus 로고
    • Marine viruses and their biogeochemical and ecological effects
    • Fuhrman, J. A. (1999). Marine viruses and their biogeochemical and ecological effects. Nature 399, 541-548. doi: 10.1038/21119.
    • (1999) Nature , vol.399 , pp. 541-548
    • Fuhrman, J.A.1
  • 20
    • 0036898759 scopus 로고    scopus 로고
    • Prokaryotic evolution in light of gene transfer
    • Gogarten, J., Doolittle, W., and Lawrence, J. (2002). Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226-2238. doi: 10.1093/oxfordjournals.molbev.a004046.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 2226-2238
    • Gogarten, J.1    Doolittle, W.2    Lawrence, J.3
  • 21
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010.
    • (2010) Syst. Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 22
    • 84857554632 scopus 로고    scopus 로고
    • Earthquake rupture at focal depth, Part I: structure and rupture of the pretorius fault, TauTona Mine, South Africa
    • Heesakkers, V., Murphy, S., and Reches, Z. (2011). Earthquake rupture at focal depth, Part I: structure and rupture of the pretorius fault, TauTona Mine, South Africa. Pure Appl. Geophys. 168, 2395-2425. doi: 10.1007/s00024-011-0354-7.
    • (2011) Pure Appl. Geophys , vol.168 , pp. 2395-2425
    • Heesakkers, V.1    Murphy, S.2    Reches, Z.3
  • 23
    • 84872436756 scopus 로고    scopus 로고
    • Microbial life under extreme energy limitation
    • Hoehler, T. M., and Jørgensen, B. B. (2013). Microbial life under extreme energy limitation. Nat. Rev. Microbiol. 11, 83-94. doi: 10.1038/nrmicro2939.
    • (2013) Nat. Rev. Microbiol , vol.11 , pp. 83-94
    • Hoehler, T.M.1    Jørgensen, B.B.2
  • 24
    • 80052549504 scopus 로고    scopus 로고
    • Integrative analysis of environmental sequences using MEGAN4
    • Huson, D. H., Mitra, S., Ruscheweyh, H., Weber, N., and Schuster, S. C. (2011). Integrative analysis of environmental sequences using MEGAN4. Genome. Res. 21, 1552-1560. doi: 10.1101/gr.120618.111.
    • (2011) Genome. Res , vol.21 , pp. 1552-1560
    • Huson, D.H.1    Mitra, S.2    Ruscheweyh, H.3    Weber, N.4    Schuster, S.C.5
  • 25
    • 80955177493 scopus 로고    scopus 로고
    • Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield
    • Itävaara, M., Nyyssönen, M., Kapanen, A., Nousiainen, A., Ahonen, L., and Kukkonen, I. (2011). Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield. FEMS Microbiol. Ecol. 77, 295-309. doi: 10.1111/j.1574-6941.2011.01111.x.
    • (2011) FEMS Microbiol. Ecol , vol.77 , pp. 295-309
    • Itävaara, M.1    Nyyssönen, M.2    Kapanen, A.3    Nousiainen, A.4    Ahonen, L.5    Kukkonen, I.6
  • 26
    • 84856659328 scopus 로고    scopus 로고
    • Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota
    • Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L., and Armbrust, E. V. (2012). Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335, 587-590. doi: 10.1126/science.1212665.
    • (2012) Science , vol.335 , pp. 587-590
    • Iverson, V.1    Morris, R.M.2    Frazar, C.D.3    Berthiaume, C.T.4    Morales, R.L.5    Armbrust, E.V.6
  • 27
    • 33750985359 scopus 로고    scopus 로고
    • Ecology. A starving majority deep beneath the seafloor
    • Jørgensen, B. B., and D'Hondt, S. (2006). Ecology. A starving majority deep beneath the seafloor. Science 314, 932-934. doi: 10.1126/science.1133796.
    • (2006) Science , vol.314 , pp. 932-934
    • Jørgensen, B.B.1    D'Hondt, S.2
  • 28
    • 84871364969 scopus 로고    scopus 로고
    • Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank
    • Jungbluth, S. P., Grote, J., Lin, H.-T., Cowen, J. P., and Rapp, É, M. S. (2013). Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. ISME J. 7, 161-172. doi: 10.1038/ismej.2012.73.
    • (2013) ISME J , vol.7 , pp. 161-172
    • Jungbluth, S.P.1    Grote, J.2    Lin, H.-T.3    Cowen, J.P.4    Rapp, ÉM.S.5
  • 29
    • 84867043272 scopus 로고    scopus 로고
    • Global distribution of microbial abundance and biomass in subseafloor sediment
    • Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., and D'Hondt, S. (2012). Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl. Acad. Sci. U.S.A. 109, 16213-16216. doi: 10.1073/pnas.1203849109.
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 16213-16216
    • Kallmeyer, J.1    Pockalny, R.2    Adhikari, R.R.3    Smith, D.C.4    D'Hondt, S.5
  • 30
    • 84863507534 scopus 로고    scopus 로고
    • Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data
    • Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., et al. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649. doi: 10.1093/bioinformatics/bts199.
    • (2012) Bioinformatics , vol.28 , pp. 1647-1649
    • Kearse, M.1    Moir, R.2    Wilson, A.3    Stones-Havas, S.4    Cheung, M.5    Sturrock, S.6
  • 31
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: quantification and classification
    • Koonin, E. (2001). Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55, 709-742. doi: 10.1146/annurev.micro.55.1.709.
    • (2001) Annu. Rev. Microbiol , vol.55 , pp. 709-742
    • Koonin, E.1
  • 32
    • 69649109364 scopus 로고    scopus 로고
    • Circos: an information aesthetic for comparative genomics
    • Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., et al. (2009). Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1345. doi: 10.1101/gr.092759.109.
    • (2009) Genome Res , vol.19 , pp. 1639-1645
    • Krzywinski, M.1    Schein, J.2    Birol, I.3    Connors, J.4    Gascoyne, R.5    Horsman, D.6
  • 33
    • 43449125894 scopus 로고    scopus 로고
    • Viruses in granitic groundwater from 69 to 450 m depth of the Aspö hard rock laboratory, Sweden
    • Kyle, J. E., Eydal, H. S. C., Ferris, F. G., and Pedersen, K. (2008). Viruses in granitic groundwater from 69 to 450 m depth of the Aspö hard rock laboratory, Sweden. ISME J. 2, 571-574. doi: 10.1038/ismej.2008.18.
    • (2008) ISME J , vol.2 , pp. 571-574
    • Kyle, J.E.1    Eydal, H.S.C.2    Ferris, F.G.3    Pedersen, K.4
  • 34
    • 23844509486 scopus 로고    scopus 로고
    • Retrons, msDNA, and the bacterial genome
    • Lampson, B. C., Inouye, M., and Inouye, S. (2005). Retrons, msDNA, and the bacterial genome. Cytogenet. Gen. Res. 110, 491-499. doi: 10.1159/000084982.
    • (2005) Cytogenet. Gen. Res , vol.110 , pp. 491-499
    • Lampson, B.C.1    Inouye, M.2    Inouye, S.3
  • 35
    • 84987846822 scopus 로고    scopus 로고
    • Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships
    • Lau, M. C. Y., Cameron, C., Magnabosco, C., Brown, C. T., Schilkey, F., Grim, S., et al. (2014). Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. Front. Microbiol. 5, 1-17. doi: 10.3389/fmicb.2014.00531.
    • (2014) Front. Microbiol , vol.5 , pp. 1-17
    • Lau, M.C.Y.1    Cameron, C.2    Magnabosco, C.3    Brown, C.T.4    Schilkey, F.5    Grim, S.6
  • 36
    • 78651511845 scopus 로고    scopus 로고
    • Microbial seed banks: the ecological and evolutionary implications of dormancy
    • Lennon, J. T., and Jones, S. E. (2011). Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 9, 119-130. doi: 10.1038/nrmicro2504.
    • (2011) Nat. Rev. Microbiol , vol.9 , pp. 119-130
    • Lennon, J.T.1    Jones, S.E.2
  • 37
    • 0347126300 scopus 로고    scopus 로고
    • ACLAME: a CLAssification of Mobile genetic Elements
    • Leplae, R., Hebrant, A., Wodak, S. J., and Toussaint, A. (2004). ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res. 32, D45-D49. doi: 10.1093/nar/gkh084.
    • (2004) Nucleic Acids Res , vol.32 , pp. D45-D49
    • Leplae, R.1    Hebrant, A.2    Wodak, S.J.3    Toussaint, A.4
  • 38
    • 84874568717 scopus 로고    scopus 로고
    • Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer
    • Lerm, S., Westphal, A., Miethling-Graff, R., Alawi, M., Seibt, A., Wolfgramm, M., et al. (2013). Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer. Extremophiles 17, 311-327. doi: 10.1007/s00792-013-0518-8.
    • (2013) Extremophiles , vol.17 , pp. 311-327
    • Lerm, S.1    Westphal, A.2    Miethling-Graff, R.3    Alawi, M.4    Seibt, A.5    Wolfgramm, M.6
  • 39
    • 33750332574 scopus 로고    scopus 로고
    • Long-term sustainability of a high-energy, low-diversity crustal biome
    • Lin, L.-H., Wang, P.-L., Rumble, D., Lippmann-Pipke, J., Boice, E., Pratt, L. M., et al. (2006). Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314, 479-482. doi: 10.1126/science.1127376.
    • (2006) Science , vol.314 , pp. 479-482
    • Lin, L.-H.1    Wang, P.-L.2    Rumble, D.3    Lippmann-Pipke, J.4    Boice, E.5    Pratt, L.M.6
  • 40
    • 0242450079 scopus 로고    scopus 로고
    • Dating ultra-deep mine waters with noble gases and 36Cl, Witwatersrand Basin, South Africa
    • Lippmann, J., Stute, M., Torgersen, T., Moser, D. P., Hall, J. A., Lin, L., et al. (2003). Dating ultra-deep mine waters with noble gases and 36Cl, Witwatersrand Basin, South Africa. Geochim. Cosmochim. Acta 67, 4597-4619. doi: 10.1016/S0016-7037(03)00414-9.
    • (2003) Geochim. Cosmochim. Acta , vol.67 , pp. 4597-4619
    • Lippmann, J.1    Stute, M.2    Torgersen, T.3    Moser, D.P.4    Hall, J.A.5    Lin, L.6
  • 41
    • 82155173449 scopus 로고    scopus 로고
    • Geogas transport in fractured hard rock-correlations with mining seismicity at 3.54km depth, TauTona gold mine, South Africa
    • Lippmann-Pipke, J., Erzinger, J., Zimmer, M., Kujawa, C., Boettcher, M., Heerden, E., et al. (2011). Geogas transport in fractured hard rock-correlations with mining seismicity at 3.54km depth, TauTona gold mine, South Africa. Appl. Geochem. 26, 2134-2146. doi: 10.1016/j.apgeochem.2011.07.011.
    • (2011) Appl. Geochem , vol.26 , pp. 2134-2146
    • Lippmann-Pipke, J.1    Erzinger, J.2    Zimmer, M.3    Kujawa, C.4    Boettcher, M.5    Heerden, E.6
  • 42
    • 32644436207 scopus 로고    scopus 로고
    • Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface
    • Lollar, B. S., Lacrampe-Couloume, G., Slater, G. F., Ward, J., Moser, D. P., Gihring, T. M., et al. (2006). Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface. Chem. Geol. 226, 328-339. doi: 10.1016/j.chemgeo.2005.09.027.
    • (2006) Chem. Geol , vol.226 , pp. 328-339
    • Lollar, B.S.1    Lacrampe-Couloume, G.2    Slater, G.F.3    Ward, J.4    Moser, D.P.5    Gihring, T.M.6
  • 43
    • 51349136973 scopus 로고    scopus 로고
    • Isotopic signatures of CH4 and higher hydrocarbon gases from Precambrian Shield sites: a model for abiogenic polymerization of hydrocarbons
    • Lollar, B. S., Lacrampe-Couloume, G., Voglesonger, K., Onstott, T. C., Pratt, L. M., and Slater, G. F. (2008). Isotopic signatures of CH4 and higher hydrocarbon gases from Precambrian Shield sites: a model for abiogenic polymerization of hydrocarbons. Geochim. Cosmochim. Acta 72, 4778-4795. doi: 10.1016/j.gca.2008.07.004.
    • (2008) Geochim. Cosmochim. Acta , vol.72 , pp. 4778-4795
    • Lollar, B.S.1    Lacrampe-Couloume, G.2    Voglesonger, K.3    Onstott, T.C.4    Pratt, L.M.5    Slater, G.F.6
  • 44
    • 84922232638 scopus 로고    scopus 로고
    • The contribution of the Precambrian continental lithosphere to global H2 production
    • Lollar, B. S., Onstott, T. C., and Ballentine, C. J. (2014). The contribution of the Precambrian continental lithosphere to global H2 production. Nature 516, 379-382. doi: 10.1038/nature14017.
    • (2014) Nature , vol.516 , pp. 379-382
    • Lollar, B.S.1    Onstott, T.C.2    Ballentine, C.J.3
  • 45
    • 84859468966 scopus 로고    scopus 로고
    • Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
    • Lomstein, B. A., Langerhuus, A. T., D'Hondt, S., Jørgensen, B. B., and Spivack, A. J. (2012). Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484, 101-104. doi: 10.1038/nature10905.
    • (2012) Nature , vol.484 , pp. 101-104
    • Lomstein, B.A.1    Langerhuus, A.T.2    D'Hondt, S.3    Jørgensen, B.B.4    Spivack, A.J.5
  • 46
    • 84930392829 scopus 로고    scopus 로고
    • Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water
    • Magnabosco, C., Tekere, M., Lau, M. C. Y., Linage, B., Kuloyo, O., Erasmus, M., et al. (2014). Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water. Front. Microbiol. 5:679. doi: 10.3389/fmicb.2014.00679.
    • (2014) Front. Microbiol , vol.5 , pp. 679
    • Magnabosco, C.1    Tekere, M.2    Lau, M.C.Y.3    Linage, B.4    Kuloyo, O.5    Erasmus, M.6
  • 47
    • 84861898310 scopus 로고    scopus 로고
    • IMG: the Integrated Microbial Genomes database and comparative analysis system
    • Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., et al. (2012). IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, D115-D122. doi: 10.1093/nar/gkr1044.
    • (2012) Nucleic Acids Res , vol.40 , pp. D115-D122
    • Markowitz, V.M.1    Chen, I.-M.A.2    Palaniappan, K.3    Chu, K.4    Szeto, E.5    Grechkin, Y.6
  • 48
    • 69949116874 scopus 로고    scopus 로고
    • IMG ER: a system for microbial genome annotation expert review and curation
    • Markowitz, V. M., Mavromatis, K., Ivanova, N. N., Chen, I.-M. A., Chu, K., and Kyrpides, N. C. (2009). IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271-2278. doi: 10.1093/bioinformatics/btp393.
    • (2009) Bioinformatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1    Mavromatis, K.2    Ivanova, N.N.3    Chen, I.-M.A.4    Chu, K.5    Kyrpides, N.C.6
  • 49
    • 77249170201 scopus 로고    scopus 로고
    • CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    • Marraffini, L. A., and Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11, 181-190. doi: 10.1038/nrg2749.
    • (2010) Nat. Rev. Genet , vol.11 , pp. 181-190
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 50
    • 84355163060 scopus 로고    scopus 로고
    • High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
    • Martinez-Garcia, M., Swan, B. K., Poulton, N. J., Gomez, M. L., Masland, D., Sieracki, M. E., et al. (2012). High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J. 6, 113-123. doi: 10.1038/ismej.2011.84.
    • (2012) ISME J , vol.6 , pp. 113-123
    • Martinez-Garcia, M.1    Swan, B.K.2    Poulton, N.J.3    Gomez, M.L.4    Masland, D.5    Sieracki, M.E.6
  • 51
    • 0038820050 scopus 로고    scopus 로고
    • Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure
    • Molin, S., and Tolker-Nielsen, T. (2003). Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14, 255-261. doi: 10.1016/S0958-1669(03)00036-3.
    • (2003) Curr. Opin. Biotechnol , vol.14 , pp. 255-261
    • Molin, S.1    Tolker-Nielsen, T.2
  • 54
    • 0347723719 scopus 로고    scopus 로고
    • Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine borehole following isolation
    • Moser, D. P., Onstott, T. C., Fredrickson, J. K., Brockman, F. J., Balkwill, D. L., Drake, G. R., et al. (2003). Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine borehole following isolation. Geomicrobiol. J. 20, 517-548. doi: 10.1080/713851170.
    • (2003) Geomicrobiol. J , vol.20 , pp. 517-548
    • Moser, D.P.1    Onstott, T.C.2    Fredrickson, J.K.3    Brockman, F.J.4    Balkwill, D.L.5    Drake, G.R.6
  • 55
    • 84355162254 scopus 로고    scopus 로고
    • De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
    • Narasingarao, P., Podell, S., Ugalde, J. A., Brochier-Armanet, C., Emerson, J. B., Brocks, J. J., et al. (2012). De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6, 81-93. doi: 10.1038/ismej.2011.78.
    • (2012) ISME J , vol.6 , pp. 81-93
    • Narasingarao, P.1    Podell, S.2    Ugalde, J.A.3    Brochier-Armanet, C.4    Emerson, J.B.5    Brocks, J.J.6
  • 56
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman, H., Lawrence, J., and Groisman, E. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304. doi: 10.1038/35012500.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.2    Groisman, E.3
  • 57
    • 33947312626 scopus 로고    scopus 로고
    • The origin and age of biogeochemical trends in deep fracture water of the Witwatersrand Basin, South Africa
    • Onstott, T. C., Lin, L.-H., Davidson, M., Mislowack, B., Borcsik, M., Hall, J., et al. (2006). The origin and age of biogeochemical trends in deep fracture water of the Witwatersrand Basin, South Africa. Geomicrobiol. J. 23, 369-414. doi: 10.1080/01490450600875688.
    • (2006) Geomicrobiol. J , vol.23 , pp. 369-414
    • Onstott, T.C.1    Lin, L.-H.2    Davidson, M.3    Mislowack, B.4    Borcsik, M.5    Hall, J.6
  • 58
    • 84890222423 scopus 로고    scopus 로고
    • Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?
    • Onstott, T. C., Magnabosco, C., Aubrey, A. D., Burton, A. S., Dworkin, J. P., Elsila, J. E., et al. (2014). Does aspartic acid racemization constrain the depth limit of the subsurface biosphere? Geobiology 12, 1-19. doi: 10.1111/gbi.12069.
    • (2014) Geobiology , vol.12 , pp. 1-19
    • Onstott, T.C.1    Magnabosco, C.2    Aubrey, A.D.3    Burton, A.S.4    Dworkin, J.P.5    Elsila, J.E.6
  • 59
    • 0028166469 scopus 로고
    • Comparison between geochemical and biological estimates of subsurface microbial activities
    • Phelps, T., Murphy, E., Pfiffner, S., and White, D. (1994). Comparison between geochemical and biological estimates of subsurface microbial activities. Microb. Ecol. 335-349. doi: 10.1007/BF00662027.
    • (1994) Microb. Ecol , pp. 335-349
    • Phelps, T.1    Murphy, E.2    Pfiffner, S.3    White, D.4
  • 60
    • 84864134721 scopus 로고    scopus 로고
    • SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes
    • Pruesse, E., Peplies, J., and Glöckner, F. O. (2012). SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829. doi: 10.1093/bioinformatics/bts252.
    • (2012) Bioinformatics , vol.28 , pp. 1823-1829
    • Pruesse, E.1    Peplies, J.2    Glöckner, F.O.3
  • 61
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter, M., and Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126-19131. doi: 10.1073/pnas.0906412106.
    • (2009) Proc. Natl. Acad. Sci. U.S.A , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 62
    • 0036966861 scopus 로고    scopus 로고
    • The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract
    • Scott, K. (2002). The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Cell. Mol. Life Sci. C 59, 2071-2082. doi: 10.1007/s000180200007.
    • (2002) Cell. Mol. Life Sci. C , vol.59 , pp. 2071-2082
    • Scott, K.1
  • 63
    • 0036159773 scopus 로고    scopus 로고
    • Mechanisms of killing spores of Bacillus subtilis by acid, alkali and ethanol
    • Setlow, B., Loshon, C. A., Genest, P. C., Cowan, A. E., Setlow, C., and Setlow, P. (2002). Mechanisms of killing spores of Bacillus subtilis by acid, alkali and ethanol. J. Appl. Microbiol. 92, 362-375. doi: 10.1046/j.1365-2672.2002.01540.x.
    • (2002) J. Appl. Microbiol , vol.92 , pp. 362-375
    • Setlow, B.1    Loshon, C.A.2    Genest, P.C.3    Cowan, A.E.4    Setlow, C.5    Setlow, P.6
  • 64
    • 0028868465 scopus 로고
    • Mechanisms for the prevention of damage to DNA in spores of Bacillus species
    • Setlow, P. (1995). Mechanisms for the prevention of damage to DNA in spores of Bacillus species. Annu. Rev. Microbiol. 49, 29-54. doi: 10.1146/annurev.mi.49.100195.000333.
    • (1995) Annu. Rev. Microbiol , vol.49 , pp. 29-54
    • Setlow, P.1
  • 65
    • 77956364248 scopus 로고    scopus 로고
    • Mobile DNA and evolution in the 21st century
    • Shapiro, J. A. (2010). Mobile DNA and evolution in the 21st century. Mob. DNA 1:4. doi: 10.1186/1759-8753-1-4.
    • (2010) Mob. DNA , vol.1 , pp. 4
    • Shapiro, J.A.1
  • 66
    • 58749113086 scopus 로고    scopus 로고
    • A diversity of uncharacterized reverse transcriptases in bacteria
    • Simon, D. M., and Zimmerly, S. (2008). A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Res. 36, 7219-7229. doi: 10.1093/nar/gkn867.
    • (2008) Nucleic Acids Res , vol.36 , pp. 7219-7229
    • Simon, D.M.1    Zimmerly, S.2
  • 67
    • 84868098266 scopus 로고    scopus 로고
    • Single cell genomics: an individual look at microbes
    • Stepanauskas, R. (2012). Single cell genomics: an individual look at microbes. Curr. Opin. Microbiol. 15, 613-620. doi: 10.1016/j.mib.2012.09.001.
    • (2012) Curr. Opin. Microbiol , vol.15 , pp. 613-620
    • Stepanauskas, R.1
  • 68
    • 34547492897 scopus 로고    scopus 로고
    • Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    • Stepanauskas, R., and Sieracki, M. E. (2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Natl. Acad. Sci. U.S.A. 104, 9052-9057. doi: 10.1073/pnas.0700496104.
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 9052-9057
    • Stepanauskas, R.1    Sieracki, M.E.2
  • 69
    • 0028972702 scopus 로고
    • Lithoautotrophic microbial ecosystems in deep basalt aquifers
    • Stevens, T. O., and McKinley, J. P. (1995). Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270, 450-455. doi: 10.1126/science.270.5235.450.
    • (1995) Science , vol.270 , pp. 450-455
    • Stevens, T.O.1    McKinley, J.P.2
  • 70
    • 80052479893 scopus 로고    scopus 로고
    • Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean
    • Swan, B. K., Martinez-Garcia, M., Preston, C. M., Sczyrba, A., Woyke, T., Lamy, D., et al. (2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296-1300. doi: 10.1126/science.1203690.
    • (2011) Science , vol.333 , pp. 1296-1300
    • Swan, B.K.1    Martinez-Garcia, M.2    Preston, C.M.3    Sczyrba, A.4    Woyke, T.5    Lamy, D.6
  • 71
    • 84879932140 scopus 로고    scopus 로고
    • Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
    • Swan, B. K., Tupper, B., Sczyrba, A., Lauro, F. M., Martinez-Garcia, M., Gonzalez, J. M., et al. (2013). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl. Acad. Sci. U.S.A. 110, 11463-11468. doi: 10.1073/pnas.1304246110.
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. 11463-11468
    • Swan, B.K.1    Tupper, B.2    Sczyrba, A.3    Lauro, F.M.4    Martinez-Garcia, M.5    Gonzalez, J.M.6
  • 72
    • 0035656111 scopus 로고    scopus 로고
    • Archaeal diversity in waters from deep South African gold mines
    • Takai, K. E. N., Moser, D. P., Flaun, M. D. E., Onstott, T. C., and Fredrickson, J. K. (2001a). Archaeal diversity in waters from deep South African gold mines. Society 67, 5750-5760. doi: 10.1128/AEM.67.21.5750-5760.2001.
    • (2001) Society , vol.67 , pp. 5750-5760
    • Takai, K.E.N.1    Moser, D.P.2    Flaun, M.D.E.3    Onstott, T.C.4    Fredrickson, J.K.5
  • 73
    • 0034919509 scopus 로고    scopus 로고
    • Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine
    • Takai, K., Moser, D. P., Onstott, T. C., Spoelstra, N., Pfiffner, S. M., Dohnalkova, A., et al. (2001b). Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int. J. Syst. Evol. Microbiol. 51, 1245-1256. doi: 10.1099/00207713-51-4-1245.
    • (2001) Int. J. Syst. Evol. Microbiol , vol.51 , pp. 1245-1256
    • Takai, K.1    Moser, D.P.2    Onstott, T.C.3    Spoelstra, N.4    Pfiffner, S.M.5    Dohnalkova, A.6
  • 74
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: a tool for genome-scale analysis of protein functions and evolution
    • Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36. doi: 10.1093/nar/28.1.33.
    • (2000) Nucleic Acids Res , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 75
    • 0032932428 scopus 로고    scopus 로고
    • Rapid microbial production of filamentous sulfur mats at hydrothermal vents
    • Taylor, C. D., and Wirsen, C. O. (1999). Rapid microbial production of filamentous sulfur mats at hydrothermal vents. Appl. Environ. Microbiol. 65, 2253-2255.
    • (1999) Appl. Environ. Microbiol , vol.65 , pp. 2253-2255
    • Taylor, C.D.1    Wirsen, C.O.2
  • 76
    • 84877004668 scopus 로고    scopus 로고
    • Transposable Mu-like phages in Firmicutes: new instances of divergence generating retroelements
    • Toussaint, A. (2013). Transposable Mu-like phages in Firmicutes: new instances of divergence generating retroelements. Res. Microbiol. 164, 281-287. doi: 10.1016/j.resmic.2013.01.008.
    • (2013) Res. Microbiol , vol.164 , pp. 281-287
    • Toussaint, A.1
  • 77
    • 0347915669 scopus 로고    scopus 로고
    • Complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage D3112
    • Wang, P. W., Chu, L., and Guttman, D. S. (2004). Complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage D3112. J. Bacteriol. 186, 400-410. doi: 10.1128/JB.186.2.400-410.2004.
    • (2004) J. Bacteriol , vol.186 , pp. 400-410
    • Wang, P.W.1    Chu, L.2    Guttman, D.S.3
  • 78
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07.
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 79
    • 20244380173 scopus 로고    scopus 로고
    • Microbial hydrocarbon gases in the Witwatersrand Basin, South Africa: implications for the deep biosphere
    • Ward, J. A., Slater, G. F., Moser, D. P., Lin, L. H., Lacrampe-Couloume, G., Bonin, A. S., et al. (2004). Microbial hydrocarbon gases in the Witwatersrand Basin, South Africa: implications for the deep biosphere. Geochim. Cosmochim. Acta 68, 3239-3250. doi: 10.1016/j.gca.2004.02.020.
    • (2004) Geochim. Cosmochim. Acta , vol.68 , pp. 3239-3250
    • Ward, J.A.1    Slater, G.F.2    Moser, D.P.3    Lin, L.H.4    Lacrampe-Couloume, G.5    Bonin, A.S.6
  • 81
    • 0036966971 scopus 로고    scopus 로고
    • The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes
    • Whittle, G., Shoemaker, N., and Salyers, A. (2002). The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes. Cell. Mol. Life Sci. C 59, 2044-2054. doi: 10.1007/s000180200004.
    • (2002) Cell. Mol. Life Sci. C , vol.59 , pp. 2044-2054
    • Whittle, G.1    Shoemaker, N.2    Salyers, A.3
  • 82
    • 55549133935 scopus 로고    scopus 로고
    • Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents
    • Williamson, S. J., Cary, S. C., Williamson, K. E., Helton, R. R., Bench, S. R., Winget, D., et al. (2008). Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J. 2, 1112-1121. doi: 10.1038/ismej.2008.73.
    • (2008) ISME J , vol.2 , pp. 1112-1121
    • Williamson, S.J.1    Cary, S.C.2    Williamson, K.E.3    Helton, R.R.4    Bench, S.R.5    Winget, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.