SEARCH

SEARCH BY CITATION

References

  • Allander T, Emerson SU, Engle RE, Purcell RH & Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. P Natl Acad Sci USA 98: 1160911614.
  • Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403410.
  • Beumer A & Robinson JB (2005) A broad-host range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria. Appl Environ Microb 71: 83018304.
  • Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F & Rohwer F (2002) Genomic analysis of uncultured marine viral communities. P Natl Acad Sci USA 99: 1425014255.
  • Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P & Rohwer F (2004) Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci 271: 565574.
  • Breitbart M, Haynes M, Kelley S et al. (2008) Viral diversity and dynamics in an infant gut. Res Microbiol 159: 367373.
  • Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann M-L & Brüssow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6: 417424.
  • Casas V & Rohwer F (2007) Phage metagenomics. Method Enzymol 421: 259268.
  • Chen F, Lu J-R, Binder BJ, Liu Y-C & Hodson RE (2001) Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR Gold. Appl Environ Microb 67: 539545.
  • Ghosh D, Roy K, Williamson KE, White DC, Wommack KE, Sublette KL & Radosevich M (2008) Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA. Appl Environ Microb 74: 495502.
  • Griffiths RI, Whiteley AS, O'Donnell AG & Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of Ribosomal DNA and RNA based microbial community composition. Appl Environ Microb 66: 54885491.
  • Helton RR, Liu L & Wommack KE (2006) Assessment of factors influencing direct enumeration of viruses within estuarine sediments. Appl Environ Microb 72: 47674774.
  • Joo J, Gunny M, Cases M, Hudson P, Albert R & Harvill E (2006) Bacteriophage-mediated competition in Bordetella bacteria. P Roy Soc B 273: 18431848.
  • Kulakov LA, McAlister MB, Ogden KL, Larkin MJ & O'Hanlon JF (2002) Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microb 68: 15481555.
  • Kulakov LA, Ksenzenko VN, Shlyapnikov MG, Kochetkov VV, Del Casale A, Allen CCR, Larkin MJ, Ceyssens P-J & Lavigne R (2009) Genomes of ‘phiKMV-like viruses’ of Pseudomonas aeruginosa contain localized single-strand interruptions. Virology 391: 14.
  • Mandilara GD, Smeti EM, Mavridou AT, Lambiri MP, Alkiviadis C, Vatopoulos AC & Rigas FP (2006) Correlation between bacterial indicators and bacteriophages in sewage and sludge. FEMS Microbiol Lett 263: 119126.
  • Manz W, Wagner M, Amann R & Schleifer K-H (1994) In situ characterization of the microbial consortia active in two wastewater treatment plants. Water Res 28: 17151723.
  • Miura Y, Noriko M, Hiraiwa N, Ito T, Itonaga T, Watanabe Y & Okabe S (2007) Bacterial community structures in MBRs treating municipal wastewater: relationship between community stability and reactor performance. Water Res 41: 627637.
  • Moebius K & Nattkemper H (1981) Bacteriophage sensitivity patterns among bacteria isolated from marine waters. Helgolander Meeresun 34: 375385.
  • Muyzer G, de Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb 59: 695700.
  • Myers RM, Fischer SG, Lerman LS & Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13: 31313145.
  • Otawa K, Lee SH, Yamazoe A, Onuki M, Satoh H & Mino T (2007) Abundance, diversity, and dynamics of viruses on microorganisms in activated sludge processes. Microb Ecol 53: 143152.
  • Parsley LC, Consuegra EJ, Thomas SJ et al. (2010) Census of the viral metagenome within an activated sludge microbial assemblage. Appl Environ Microb 76: 26732677.
  • Pascual C, Lawson PA, Farrow JAE, Gimenez MN & Collins MD (1995) Phylogenetic analysis of the genus Corynebacterium based on 16S rRNA gene sequences. Int J Syst Bacteriol 45: 724728.
  • Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Sander M & Schmieger H (2001) Method for host-independent detection of generalized transducing bacteriophages in natural habitats. Appl Environ Microb 67: 14901493.
  • Scholten JCM, Joye SB, Hollibaugh JT & Murrell JC (2005) Molecular analysis of the sulfate reducing and Archaeal community in a meromictic soda lake (Mono Lake, California) by targeting 16S rRNA, mcrA, apsA, and dsrAB genes. Microb Ecol 50: 2939.
  • Snaidr J, Amann R, Huber I, Ludwig W & Schleifer K-H (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microb 63: 28842896.
  • Tamura K & Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512526.
  • Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 15961599.
  • Thompson JD, Higgins DG & Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 46734680.
  • Thurber RV, Haynes M, Breitbart M, Wegley L & Rohwer F (2009) Laboratory procedures to generate viral metagenomes. Nat Protocol 4: 470483.
  • Tobe T, Beatson SA, Taniguchi H et al. (2006) An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. P Natl Acad Sci USA 103: 1494114946.
  • Wagner M & Loy A (2002) Bacterial community composition and function in sewage treatment systems. Curr Opin Biotech 13: 218227.
  • Wagner M, Amann R, Lemmer H & Schleifer KH (1993) Probing activated sludge with proteobacteria-specific oligonucleotides: inadequacy of culture-dependent methods for describing microbial community structure. Appl Environ Microb 59: 15201525.
  • Williamson SJ, Houchin LA, McDaniel L & Paul JH (2002) Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl Environ Microb 68: 43074314.