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Volumn 1, Issue , 2016, Pages

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; CARBON; RIBOSOME RNA;

EID: 84987667484     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2016.160     Document Type: Article
Times cited : (329)

References (56)
  • 1
    • 70349458100 scopus 로고    scopus 로고
    • The genomic basis of trophic strategy in marine bacteria
    • Lauro, F. et al. The genomic basis of trophic strategy in marine bacteria. Proc. Natl Acad. Sci. USA 106, 15527-15533 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 15527-15533
    • Lauro, F.1
  • 2
    • 84932197547 scopus 로고    scopus 로고
    • The physiology and ecological implications of efficient growth
    • Roller, B. R. K. & Schmidt, T. M. The physiology and ecological implications of efficient growth. ISME J. 9, 1481-1487 (2015).
    • (2015) ISME J. , vol.9 , pp. 1481-1487
    • Roller, B.R.K.1    Schmidt, T.M.2
  • 3
    • 0035917865 scopus 로고    scopus 로고
    • Cooperation and competition in the evolution of ATP-producing pathways
    • Pfeiffer, T., Schuster, S. & Bonhoeffer, S. Cooperation and competition in the evolution of ATP-producing pathways. Science 292, 504-507 (2001).
    • (2001) Science , vol.292 , pp. 504-507
    • Pfeiffer, T.1    Schuster, S.2    Bonhoeffer, S.3
  • 4
    • 84883327746 scopus 로고    scopus 로고
    • Availability of public goods shapes the evolution of competing metabolic strategies
    • Bachmann, H. et al. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl Acad. Sci. USA 110, 14302-14307 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 14302-14307
    • Bachmann, H.1
  • 5
    • 84941140948 scopus 로고    scopus 로고
    • RrnDB: Improved tools for interpreting rRNA gene abundance in Bacteria and Archaea and a new foundation for future development
    • Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K. & Schmidt, T. M. rrnDB: improved tools for interpreting rRNA gene abundance in Bacteria and Archaea and a new foundation for future development. Nucleic Acids Res. 43, D593-D598 (2015).
    • (2015) Nucleic Acids Res , vol.43 , pp. D593-D598
    • Stoddard, S.F.1    Smith, B.J.2    Hein, R.3    Roller, B.R.K.4    Schmidt, T.M.5
  • 6
    • 84868094960 scopus 로고    scopus 로고
    • Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    • Kembel, S. W., Wu, M., Eisen, J. A. & Green, J. L. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput. Biol. 8, e1002743 (2012).
    • (2012) PLoS Comput. Biol. , vol.8 , pp. 1002743
    • Kembel, S.W.1    Wu, M.2    Eisen, J.A.3    Green, J.L.4
  • 7
    • 84905661514 scopus 로고    scopus 로고
    • CopyRighter: A rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
    • Angly, F. E. et al. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome 2, 1-13 (2014).
    • (2014) Microbiome , vol.2 , pp. 1-13
    • Angly, F.E.1
  • 8
    • 0034074410 scopus 로고    scopus 로고
    • RRNA operon copy number reflects ecological strategies of bacteria
    • Klappenbach, J. A., Dunbar, J. M. & Schmidt, T. M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 1328-1333 (2000).
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 1328-1333
    • Klappenbach, J.A.1    Dunbar, J.M.2    Schmidt, T.M.3
  • 9
    • 8744259789 scopus 로고    scopus 로고
    • Life history implications of rRNA gene copy number in Escherichia coli
    • Stevenson, B. S. & Schmidt, T. M. Life history implications of rRNA gene copy number in Escherichia coli. Appl. Environ. Microbiol. 70, 6670-6677 (2004).
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 6670-6677
    • Stevenson, B.S.1    Schmidt, T.M.2
  • 10
    • 34247884431 scopus 로고    scopus 로고
    • Performance of the translational apparatus varies with the ecological strategies of bacteria
    • Dethlefsen, L. & Schmidt, T. M. Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol. 189, 3237-3245 (2007).
    • (2007) J. Bacteriol. , vol.189 , pp. 3237-3245
    • Dethlefsen, L.1    Schmidt, T.M.2
  • 11
    • 76749155783 scopus 로고    scopus 로고
    • The systemic imprint of growth and its uses in ecological (Meta)Genomics
    • Vieira-Silva, S. & Rocha, E. P. C. The systemic imprint of growth and its uses in ecological (Meta)Genomics. PLoS Genet. 6, e1000808 (2010).
    • (2010) PLoS Genet. , vol.6 , pp. 1000808
    • Vieira-Silva, S.1    Rocha, E.P.C.2
  • 12
    • 84904997234 scopus 로고    scopus 로고
    • Implications of streamlining theory for microbial ecology
    • Giovannoni, S. J., Thrash, J. C. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553-1565 (2014).
    • (2014) ISME J. , vol.8 , pp. 1553-1565
    • Giovannoni, S.J.1    Thrash, J.C.2    Temperton, B.3
  • 13
    • 79551492681 scopus 로고    scopus 로고
    • Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria
    • Eichorst, S. A., Kuske, C. R. & Schmidt, T. M. Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Appl. Environ. Microbiol. 77, 586-596 (2011).
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 586-596
    • Eichorst, S.A.1    Kuske, C.R.2    Schmidt, T.M.3
  • 14
    • 84875365733 scopus 로고    scopus 로고
    • Phylogenetic conservatism of functional traits in microorganisms
    • Martiny, A. C., Treseder, K. & Pusch, G. Phylogenetic conservatism of functional traits in microorganisms. ISME J. 7, 830-838 (2013).
    • (2013) ISME J. , vol.7 , pp. 830-838
    • Martiny, A.C.1    Treseder, K.2    Pusch, G.3
  • 15
    • 0029048945 scopus 로고
    • L rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation
    • Condon, C., Liveris, D., Squires, C., Schwartz, I. & Squires, C. L. rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J. Bacteriol. 177, 4152-4156 (1995).
    • (1995) J. Bacteriol. , vol.177 , pp. 4152-4156
    • Condon, C.1    Liveris, D.2    Squires, C.3    Schwartz, I.4    Squires, C.5
  • 16
    • 0015910716 scopus 로고
    • A theoretical study on the amount of ATP required for synthesis of microbial cell material
    • Stouthamer, A. H. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie Van Leeuwenhoek 39, 545-565 (1973).
    • (1973) Antonie Van Leeuwenhoek , vol.39 , pp. 545-565
    • Stouthamer, A.H.1
  • 17
    • 0031734090 scopus 로고    scopus 로고
    • Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp strain RB2256
    • Fegatella, F., Lim, J., Kjelleberg, S. & Cavicchioli, R. Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 64, 4433-4438 (1998).
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4433-4438
    • Fegatella, F.1    Lim, J.2    Kjelleberg, S.3    Cavicchioli, R.4
  • 18
    • 0027104840 scopus 로고
    • Translational accuracy and the fitness of bacteria
    • Kurland, C. G. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26, 29-50 (1992).
    • (1992) Annu. Rev. Genet. , vol.26 , pp. 29-50
    • Kurland, C.G.1
  • 19
    • 84904984023 scopus 로고    scopus 로고
    • Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea
    • Carini, P. et al. Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea. ISME J. 8, 1727-1738 (2014).
    • (2014) ISME J. , vol.8 , pp. 1727-1738
    • Carini, P.1
  • 20
    • 0001501897 scopus 로고
    • Production of B-group vitamins by mycorrhizal fungi and actinomycetes isolated from the root zone of pine (Pinus sylvestris L. )
    • Strzelczyk, E. & Leniarska, U. Production of B-group vitamins by mycorrhizal fungi and actinomycetes isolated from the root zone of pine (Pinus sylvestris L. ). Plant Soil 86, 387-394 (1985).
    • (1985) Plant Soil , vol.86 , pp. 387-394
    • Strzelczyk, E.1    Leniarska, U.2
  • 21
    • 84860511582 scopus 로고    scopus 로고
    • The black queen hypo thesis: Evolution of dependencies through adaptive gene loss
    • Morris, J. J., Lenski, R. E. & Zinser, E. R. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012).
    • (2012) Mbio , vol.3 , pp. e0003612
    • Morris, J.J.1    Lenski, R.E.2    Zinser, E.R.3
  • 22
    • 19544386268 scopus 로고    scopus 로고
    • The evolution of oligotrophy: Implications for the breeding of crop plants for low input agricultural systems
    • Raven, J. R., Andrews, M. & Quigg, A. The evolution of oligotrophy: implications for the breeding of crop plants for low input agricultural systems. Ann. Appl. Biol. 146, 261-280 (2005).
    • (2005) Ann. Appl. Biol. , vol.146 , pp. 261-280
    • Raven, J.R.1    Andrews, M.2    Quigg, A.3
  • 23
    • 84868220590 scopus 로고    scopus 로고
    • Trade-offs of chemotactic foraging in turbulent water
    • Taylor, J. R. & Stocker, R. Trade-offs of chemotactic foraging in turbulent water. Science 338, 675-679 (2012).
    • (2012) Science , vol.338 , pp. 675-679
    • Taylor, J.R.1    Stocker, R.2
  • 25
    • 84870863360 scopus 로고    scopus 로고
    • Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
    • Redmond, M. C. & Valentine, D. L. Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc. Natl Acad. Sci. USA 109, 20292-20297 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 20292-20297
    • Redmond, M.C.1    Valentine, D.L.2
  • 26
    • 34548401606 scopus 로고    scopus 로고
    • Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession
    • Shrestha, P. M., Noll, M. & Liesack, W. Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession. Environ. Microbiol. 9, 2464-2474 (2007).
    • (2007) Environ. Microbiol. , vol.9 , pp. 2464-2474
    • Shrestha, P.M.1    Noll, M.2    Liesack, W.3
  • 28
    • 1542513850 scopus 로고    scopus 로고
    • Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota
    • Young, V. B. & Schmidt, T. M. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J. Clin. Microbiol. 42, 1203-1206 (2004).
    • (2004) J. Clin. Microbiol. , vol.42 , pp. 1203-1206
    • Young, V.B.1    Schmidt, T.M.2
  • 29
    • 84887221497 scopus 로고    scopus 로고
    • Global soil carbon projections are improved by modelling microbial processes
    • Wieder, W. R., Bonan, G. B. & Allison, S. D. Global soil carbon projections are improved by modelling microbial processes. Nat. Clim. Change 3, 909-912 (2013).
    • (2013) Nat. Clim. Change , vol.3 , pp. 909-912
    • Wieder, W.R.1    Bonan, G.B.2    Allison, S.D.3
  • 30
    • 84890387941 scopus 로고    scopus 로고
    • Bacterial growth efficiency varies in soils under different land management practices
    • Lee, Z. M. & Schmidt, T. M. Bacterial growth efficiency varies in soils under different land management practices. Soil Biol. Biochem. 69, 282-290 (2014).
    • (2014) Soil Biol. Biochem. , vol.69 , pp. 282-290
    • Lee, Z.M.1    Schmidt, T.M.2
  • 31
    • 0008467605 scopus 로고
    • Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes
    • Eagon, R. Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J. Bacteriol. 83, 736-737 (1962).
    • (1962) J. Bacteriol. , vol.83 , pp. 736-737
    • Eagon, R.1
  • 32
    • 0041996331 scopus 로고
    • The identity of Bacillus subtilis
    • Conn, H. J. The identity of Bacillus subtilis. J. Infect. Dis. 46, 341-350 (1930).
    • (1930) J. Infect. Dis. , vol.46 , pp. 341-350
    • Conn, H.J.1
  • 33
    • 33747333128 scopus 로고    scopus 로고
    • A set of recombineering plasmids for gram-negative bacteria
    • Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109-115 (2006).
    • (2006) Gene , vol.379 , pp. 109-115
    • Datta, S.1    Costantino, N.2    Court, D.L.3
  • 34
    • 0028610633 scopus 로고
    • Construction of ecocollection of paddy field soil bacteria for population analysis
    • Gorlach, K., Shingaki, R., Morisaki, H. & Hattori, T. Construction of ecocollection of paddy field soil bacteria for population analysis. J. Gen. Appl. Microbiol. 40, 509-517 (1994).
    • (1994) J. Gen. Appl. Microbiol. , vol.40 , pp. 509-517
    • Gorlach, K.1    Shingaki, R.2    Morisaki, H.3    Hattori, T.4
  • 35
    • 0027337265 scopus 로고
    • Isolation of typical marine bacteria by dilution culture: Growth, maintenance, and characteristics of isolates under laboratory conditions
    • Schut, F. et al. Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl. Environ. Microbiol. 59, 2150-2160 (1993).
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 2150-2160
    • Schut, F.1
  • 36
    • 0030778943 scopus 로고    scopus 로고
    • Isolation and characterisation of the marine ultramicrobacterium Sphingomonas sp strain RB2256
    • Schut, F., Gottschal, J. C. & Prins, R. A. Isolation and characterisation of the marine ultramicrobacterium Sphingomonas sp. strain RB2256. FEMS Microbiol. Rev. 20, 363-369 (1997).
    • (1997) FEMS Microbiol. Rev. , vol.20 , pp. 363-369
    • Schut, F.1    Gottschal, J.C.2    Prins, R.A.3
  • 38
    • 34247606048 scopus 로고    scopus 로고
    • Isolation and characterization of soil bacteria that define Terriglobus gen nov, in the phylum acidobacteria
    • Eichorst, S. A., Breznak, J. A. & Schmidt, T. M. Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum acidobacteria. Appl. Environ. Microbiol. 73, 2708-2717 (2007).
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 2708-2717
    • Eichorst, S.A.1    Breznak, J.A.2    Schmidt, T.M.3
  • 39
    • 0001003553 scopus 로고
    • Protein content and protein synthesis rates of planktonic marine bacteria
    • Simon, M. & Azam, F. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol. Prog. Ser. 51, 201-213 (1989).
    • (1989) Mar. Ecol. Prog. Ser. , vol.51 , pp. 201-213
    • Simon, M.1    Azam, F.2
  • 40
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: Back to metabolism in KEGG
    • Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205 (2013).
    • (2013) Nucleic Acids Res. , vol.42 , pp. D199-D205
    • Kanehisa, M.1
  • 43
    • 67650729745 scopus 로고    scopus 로고
    • The structural and biochemical foundations of thiamin biosynthesis
    • Jurgenson, C. T., Begley, T. P. & Ealick, S. E. The structural and biochemical foundations of thiamin biosynthesis. Annu. Rev. Biochem. 78, 569-603 (2009).
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 569-603
    • Jurgenson, C.T.1    Begley, T.P.2    Ealick, S.E.3
  • 44
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. D590-D596
    • Quast, C.1
  • 46
    • 79954466817 scopus 로고    scopus 로고
    • Release LTPs104 of the all-species living tree
    • Munoz, R. et al. Release LTPs104 of the All-Species Living Tree. Syst. Appl. Microbiol. 34, 169-170 (2011).
    • (2011) Syst. Appl. Microbiol. , vol.34 , pp. 169-170
    • Munoz, R.1
  • 48
    • 84898959182 scopus 로고    scopus 로고
    • A linear-time algorithm for Gaussian and non-Gaussian trait evolution models
    • Tung Ho, L. S. & Ane, C. A linear-time algorithm for gaussian and non-gaussian trait evolution models. Syst. Biol. 63, 397-408 (2014).
    • (2014) Syst. Biol. , vol.63 , pp. 397-408
    • Tung Ho, L.S.1    Ane, C.2
  • 49
    • 77749249761 scopus 로고    scopus 로고
    • MCMC methods for multi-response generalized linear mixed models: The MCMCglmm R package
    • Hadfield, J. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Statist. Software 33, 1-22 (2010).
    • (2010) J. Statist. Software , vol.33 , pp. 1-22
    • Hadfield, J.1
  • 50
    • 84867364321 scopus 로고    scopus 로고
    • J. Phytools: An R package for phylogenetic comparative biology (and other things)
    • Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217-223 (2012).
    • (2012) Methods Ecol. Evol. , vol.3 , pp. 217-223
    • Revell, L.1
  • 52
    • 4544340104 scopus 로고    scopus 로고
    • Scatterplot3d-an R package for visualizing multivariate data
    • Ligges, U. & Mächler, M. Scatterplot3d-an R package for visualizing multivariate data. J. Statist. Software 8, 1-20 (2003).
    • (2003) J. Statist. Software , vol.8 , pp. 1-20
    • Ligges, U.1    MäcHler, M.2
  • 53
    • 2542523843 scopus 로고    scopus 로고
    • ARB: A software environment for sequence data
    • Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363-1371 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1363-1371
    • Ludwig, W.1
  • 55
    • 72049108111 scopus 로고    scopus 로고
    • Phylogenetic logistic regression for binary dependent variables
    • Ives, A. R. & Garland, T. Phylogenetic logistic regression for binary dependent variables. Syst. Biol. 59, 9-26 (2010).
    • (2010) Syst. Biol. , vol.59 , pp. 9-26
    • Ives, A.R.1    Garland, T.2
  • 56
    • 84923369638 scopus 로고    scopus 로고
    • Habitat structure and the evolution of diffusible siderophores in bacteria
    • Kümmerli, R., Schiessl, K. T., Waldvogel, T., McNeill, K. & Ackermann, M. Habitat structure and the evolution of diffusible siderophores in bacteria. Ecol. Lett. 17, 1536-1544 (2014).
    • (2014) Ecol. Lett. , vol.17 , pp. 1536-1544
    • Kümmerli, R.1    Schiessl, K.T.2    Waldvogel, T.3    McNeill, K.4    Ackermann, M.5


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