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  • Abdul-Raouf, U.M., Beuchat, L.R. and Ammar, M.S. (1993) Survival and growth of Escherichia coli O157:H7 on salad vegetables. Appl Environ Microbiol 59, 19992006.
  • Acosta-Martinez, V., Dowd, S.E., Sun, Y. and Allen, V. (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40, 27622770.
  • Allende, A., Aguayo, E. and Artes, F. (2004) Microbial and sensory quality of commercial fresh processed red lettuce throughout the production chain and shelf life. Int J Food Microbiol 91, 109117.
  • Andersson, A.F., Lindberg, M., Jakobsson, H., Backhed, F., Nyren, P. and Engstrand, L. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3, e2836.
  • Babic, I., Roy, S., Watada, A.E. and Wergin, W.P. (1996) Changes in microbial populations on fresh cut spinach. Int J Food Microbiol 31, 107119.
  • Bhagwat, A.A. (2006) Microbiological safety of fresh-cut produce: where are we now? In Microbiology of Fresh Produce ed. Matthews, K.R. pp. 121165. Washington, DC: ASM Press.
  • CDC (2006) Update of multistate outbreak of Escherichia coli O157:H7 infections from fresh spinach. CDC website.
  • Chao, A., Chazdon, R.L., Colwell, R.K. and Shen, T.J. (2006) Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62, 361371.
  • Chatelut, M., Dournes, J.L., Chabanon, G. and Marty, N. (1995) Epidemiological typing of Stenotrophomonas (Xanthomonas) maltophilia by PCR. J Clin Microbiol 33, 912914.
  • Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, D141D145.
  • Cooley, M.B., Chao, D. and Mandrell, R.E. (2006) Escherichia coli O157:H7 survival and growth on lettuce is altered by the presence of epiphytic bacteria. J Food Prot 69, 23292335.
  • Delaquis, P., Bach, S. and Dinu, L.D. (2007) Behavior of Escherichia coli O157:H7 in leafy vegetables. J Food Prot 70, 19661974.
  • Delmotte, N., Knief, C., Chaffron, S., Innerebner, G., Roschitzki, B., Schlapbach, R., von Mering, C. and Vorholt, J.A. (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106, 1642816433.
  • Dowd, S.E., Callaway, T.R., Wolcott, R.D., Sun, Y., McKeehan, T., Hagevoort, R.G. and Edrington, T.S. (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8, 125.
  • Fierer, N., Bradford, M.A. and Jackson, R.B. (2007) Toward an ecological classification of soil bacteria. Ecology 88, 13541364.
  • Francis, G.A. and O’Beirne, D. (2001) Effects of vegetable type, package atmosphere and storage temperature on growth and survival of Escherichia coli O157:H7 and Listeria monocytogenes. J Ind Microbiol Biotechnol 27, 111116.
  • Gilbert, J.A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P.J., Huse, S. et al. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11, 31323139.
  • Hirano, S.S. and Upper, C.D. (2000) Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae– a pathogen, ice nucleus, and epiphyte. Microbiol Mol Biol Rev 64, 624653.
  • Huber, J.A., Mark Welch, D.B., Morrison, H.G., Huse, S.M., Neal, P.R., Butterfield, D.A. and Sogin, M.L. (2007) Microbial population structures in the deep marine biosphere. Science 318, 97100.
  • Hugenholtz, P., Tyson, G.W., Webb, R.I., Wagner, A.M. and Blackall, L.L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl Environ Microbiol 67, 411419.
  • Humblot, C. and Guyot, J.P. (2009) Pyrosequencing of tagged 16S rRNA gene amplicons for rapid deciphering of the microbiomes of fermented foods such as pearl millet slurries. Appl Environ Microbiol 75, 43544361.
  • Ibekwe, A. and Grieve, C. (2004) Changes in developing plant microbial community structure as affected by contaminated water. FEMS Microbiol Lett 48, 239248.
  • ICMSF (2005) Vegetables and vegetable products. In Microbial Ecology of Food Commodities ed. ICMSF pp. 277325. New York: Kluwer Academic/Plenum Publishers.
  • Jackson, E.F., Echlin, H.L. and Jackson, C.R. (2006) Changes in the phyllosphere community of the resurrection fern, Polypodium polypodioides, associated with rainfall and wetting. FEMS Microbiol Ecol 58, 236246.
  • Jesus, E.d.C., Susilawati, E., Smith, S.L., Wang, Q., Chai, B., Farris, R., Rodrigues, J.L.M., Thelen, K.D. et al. (2010) Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences. Bioenerg Res 3, 2027.
  • Johnston, M.A., Harrison, M.A. and Morrow, R.A. (2009) Microbial antagonists of Escherichia coli O157:H7 on fresh-cut lettuce and spinach. J Food Prot 72, 15691575.
  • Kadivar, H. and Stapleton, A.E. (2003) Ultraviolet radiation alters maize phyllosphere bacterial diversity. Microb Ecol 45, 353361.
  • Kanagawa, T. (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96, 317323.
  • Knief, C., Frances, L. and Vorholt, J.A. (2010) Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb Ecol 60, 440452.
  • Kraft, A.A. (1992) Spoilage of dairy products, vegetables, fruits and other foods. In Psychrotrophic Bacteria in Foods Disease and Spoilage ed. Kraft, A.A. pp. 113120. Boca Raton, FL: CRC Press.
  • Krimm, U., Abanda-Nkpwatt, D., Schwab, W. and Schreiber, L. (2005) Epiphytic microorganisms on strawberry plants (Fragaria ananassa cv. Elsanta): identification of bacterial isolates and analysis of their interaction with leaf surfaces. FEMS Microbiol Ecol 53, 483492.
  • Kulichevskaya, I.S., Ivanova, A.O., Belova, S.E., Baulina, O.I., Bodelier, P.L., Rijpstra, W.I., Sinninghe Damste, J.S., Zavarzin, G.A. et al. (2007) Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands. Int J Syst Evol Microbiol 57, 26802687.
  • La Scola, B., Birtles, R.J., Mallet, M.N. and Raoult, D. (1998) Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 36, 28472852.
  • Lambais, M.R., Crowley, D.E., Cury, J.C., Bull, R.C. and Rodrigues, R.R. (2006) Bacterial diversity in tree canopies of the Atlantic forest. Science 312, 1917.
  • Liao, C.H. (2007) Inhibition of foodborne pathogens by native microflora recovered from fresh peeled baby carrot and propagated in cultures. J Food Sci 72, M134M139.
  • Liu, Z., Lozupone, C., Hamady, M., Bushman, F.D. and Knight, R. (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35, 120.
  • Lopez-Velasco, G. (2010) Molecular characterization of spinach (Spinacia oleracea) microbial community structure and its interaction with Escherichia coli O157:H7 in modified atmosphere conditions. Food Science and Technology. p. 258. Blacksburg: Virginia Tech.
  • Lopez-Velasco, G., Davis, M., Boyer, R.R., Williams, R.C. and Ponder, M.A. (2010) Alterations of the phylloepiphytic bacterial community associated with interactions of Escherichia coli O157:H7 during storage of packaged spinach at refrigeration temperatures. Food Microbiol 27, 476486.
  • Nguyen-the, C. and Carlin, F. (1994) The microbiology of minimally processed fresh fruits and vegetables. Crit Rev Food Sci Nutr 34, 371401.
  • Ragaert, P., Devlieghere, F. and Debevere, J. (2007) Role of microbiological and physiological spoilage mechanisms during storage of minimally processed vegetables. Postharvest Biol Technol 44, 185194.
  • Randazzo, C.L., Scifo, G.O., Tomaselli, F. and Caggia, C. (2009) Polyphasic characterization of bacterial community in fresh cut salads. Int J Food Microbiol 128, 484490.
  • Rheims, H., Sproer, C., Rainey, F.A. and Stackebrandt, E. (1996) Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiology 142(Pt 10), 28632870.
  • Rico, D., Martin-Diana, A.B., Barat, J.M. and Barry-Ryan, C. (2007) Extending and measuring the quality of fresh-fruit and vegetables: a review. Trends Food Sci Technol 18, 337386.
  • da Rocha, U.N., van Overbeek, L. and van Elsas, J.D. (2009) Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol Ecol 69, 313328.
  • Roesch, L.F., Fulthorpe, R.R., Riva, A., Casella, G., Hadwin, A.K., Kent, A.D., Daroub, S.H., Camargo, F.A. et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1, 283290.
  • Ronaghi, M. and Elahi, E. (2002) Pyrosequencing for microbial typing. J Chromatogr B Analyt Technol Biomed Life Sci 782, 6772.
  • Rudi, K., Flateland, S.L., Hanssen, J.F., Bengtsson, G. and Nissen, H. (2002) Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl Environ Microbiol 68, 11461156.
  • Schuenzel, K.M. and Harrison, M.A. (2002) Microbial antagonists of foodborne pathogens on fresh, minimally processed vegetables. J Food Prot 65, 19091915.
  • Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., Arrieta, J.M. and Herndl, G.J. (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103, 1211512120.
  • Thompson, I.P., Bailey, M.J., Fenlon, J.S., Fermor, T.R., Lillley, A.K., Lynch, J.M., McCormack, P.J., McQuilken, M.P. et al. (1993) Quantitative and qualitative seasonal changes in the microbial community from the phyllosphere of sugar beet. Plant Soil 150, 177191.
  • Urich, T., Lanzen, A., Qi, J., Huson, D.H., Schleper, C. and Schuster, S.C. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3, e2527.
  • 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, 52615267.
  • Whipps, J.M. (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52, 487511.
  • Yang, C.H., Crowley, D.E., Borneman, J. and Keen, N.T. (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci USA 98, 38893894.
  • Yang, J.H., Liu, H.X., Zhu, G.M., Pan, Y.L., Xu, L.P. and Guo, J.H. (2008) Diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases. J Appl Microbiol 104, 91104.
  • Yutthammo, C., Thongthammachat, N., Pinphanichakarn, P. and Luepromchai, E. (2010) Diversity and activity of PAH-degrading bacteria in the phyllosphere of ornamental plants. Microb Ecol 59, 357368.