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References

  • Bernal, M.P., Alburquerque, J.A. and Moral, R. (2009) Composting of animal manures and chemical criteria for compost maturity assessment. A review. Bioresour Technol 100, 54445453.
  • Canadian Council of Ministers of the Environment (CCME). (1996) Support document for compost quality criteria. National Standard of Canada (CAN/BNQ 0413-200). Available:http://www.compost.org/compostqualitydoc.pdf. Accessed: December 5, 2013.
  • 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.
  • Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 21942200.
  • Esty, W.W. (1986) The efficiency of Good's nonparametric coverage estimator. Ann Stat 14, 12571260.
  • Fernandes, L., Zhan, W., Patni, N.K. and Jui, P.Y. (1994) Temperature distribution and variation in passively aerated static compost piles. Bioresour Technol 48, 257263.
  • Flory, G.A. and Peer, R.W. (2010) Verification of poultry carcass composting research through application during actual avian influenza outbreaks. ILAR J 51, 149157.
  • Fuhrman, J.A. (2009) Microbial community structure and its functional implications. Nature 459, 193199.
  • de Gannes, V., Eudoxie, G. and Hickey, W.J. (2013) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresour Technol 133, 573.
  • Gihring, T.M., Green, S.J. and Schadt, C.W. (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14, 285290.
  • Good, I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40, 237264.
  • Guan, J., Chan, M., Grenier, C., Brooks, B.W., Spencer, J.L., Kranendonk, C., Copps, J. and Clavijo, A. (2010) Degradation of foot-and-mouth disease virus during composting of infected pig carcasses. Can J Vet Res 74, 4044.
  • Huang, H., Spencer, J.L., Soutyrine, A., Guan, J., Rendulich, J. and Balachandran, A. (2007) Evidence for degradation of abnormal prion protein in tissues from sheep with scrapie during composting. Can J Vet Res 71, 3440.
  • Huse, S.M., Welch, D.M., Morrison, H.G. and Sogin, M.L. (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12, 18891898.
  • Jessup, C.M., Kassen, R., Forde, S.E., Kerr, B., Buckling, A., Rainey, P.B. and Bohannan, B.J.M. (2004) Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19, 189197.
  • Jost, L. (2006) Entropy and diversity. Oikos 113, 363375.
  • Kalbasi, A., Mukhtar, S., Hawkins, S.E. and Auvermann, B.W. (2005) Carcass composting for management of farm mortalities: a review. Compost Sci Util 13, 180193.
  • Kim, M., Morrison, M. and Yu, Z. (2011) Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods 84, 81.
  • Kukolya, J., Nagy, I., Laday, M., Toth, E., Oravecz, O., Marialigeti, K. and Hornok, L. (2002) Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete. Int J Syst Evol Microbiol 52, 11931199.
  • Lee, Y., Kim, S., Kim, Y., Jeong, Y., Yun, M., Cho, J., Kim, J., Yun, H. et al. (2010) Archaeal diversity during composting of pig manure and mushroom cultural waste based on 16S rRNA sequence. J Korean Soc Appl Biol Chem 53, 230236.
  • Lozupone, C. and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 82288235.
  • Lykidis, A., Mavromatis, K., Ivanova, N., Anderson, I., Land, M., DiBartolo, G., Martinez, M., Lapidus, A. et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol 189, 24772486.
  • Maeda, K., Hanajima, D., Morioka, R. and Osada, T. (2010) Characterization and spatial distribution of bacterial communities within passively aerated cattle manure composting piles. Bioresour Technol 101, 9631.
  • Martin, A.P. (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68, 36733682.
  • Martins, L.F., Antunes, L.P., Pascon, R.C., de Oliveira, J.C.F., Digiampietri, L.A., Barbosa, D., Peixoto, B.M., Vallim, M.A. et al. (2013) Metagenomic analysis of a tropical composting operation at the São Paulo zoo park reveals diversity of biomass degradation functions and organisms. PLoS One 8, e61928.
  • Mitscherlich, E. and Marth, E.H. (1984) Microbial Survival in the Environment. Berlin: Springer.
  • Partanen, P., Hultman, J., Paulin, L., Auvinen, P. and Romantschuk, M. (2010) Bacterial diversity at different stages of the composting process. BMC Microbiol 10, 94.
  • Petrosino, J.F., Highlander, S., Luna, R.A., Gibbs, R.A. and Versalovic, J. (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55, 856866.
  • Pietronave, S., Fracchia, L., Rinaldi, M. and Martinottie, M.G. (2004) Influence of biotic and abiotic factors on human pathogens in a finished compost. Water Res 38, 19631970.
  • Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J. and Glockner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35, 71887196.
  • Quince, C., Lanzen, A., Davenport, R.J. and Turnbaugh, P.J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 3855.
  • Reuter, T., Xu, W., Alexander, T.W., Baker, B.C., Larney, F.J., Stanford, K. and McAllister, T.A. (2008) A simple method for temporal collection of tissue and microbial samples from static composting systems. Can Biosyst Eng 50, 6.176.20.
  • Reuter, T., Alexander, T.W. and McAllister, T.A. (2011) Viability of Bacillus licheniformis and Bacillus thuringiensis spores as a model for predicting the fate of Bacillus anthracis spores during composting of livestock mortalities. Appl Environ Microbiol 77, 15881592.
  • Ryckeboer, J., Mergaert, J., Coosemans, J., Deprins, K. and Swings, J. (2003a) Microbiological aspects of biowaste during composting in a monitored compost bin. J Appl Microbiol 94, 127137.
  • Ryckeboer, J., Mergaert, J., Vaes, K., Klammer, S., De Clercq, D., Coosemans, J., Insam, H. and Swings, J. (2003b) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53, 349410.
  • Schloss, P.D. (2008) Evaluating different approaches that test whether microbial communities have the same structure. ISME J 2, 265275.
  • Schloss, P.D., Hay, A.G., Wilson, D.B. and Walker, L.P. (2003) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46, 19.
  • Schloss, P.D., Hay, A.G., Wilson, D.B., Gossett, J.M. and Walker, L.P. (2005) Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl Microbiol Biotechnol 66, 457463.
  • Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75, 75377541.
  • Schloss, P.D., Gevers, D. and Westcott, S.L. (2011) Reducing the effects of PCR Amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6, e27310.
  • Senne, D.A., Panigrahy, B. and Morgan, R.L. (1994) Effect of composting poultry carcasses on survival of exotic avian viruses: highly pathogenic avian influenza (HPAI) virus and adenovirus of egg drop syndrome-76. Avian Dis 38, 733737.
  • Teixeira, L.C.R.S., Peixoto, R.S., Cury, J.C., Sul, W.J., Pellizari, V.H., Tiedje, J. and Rosado, A.S. (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4, 9891001.
  • Tiquia, S.M. (2005) Microbial community dynamics in manure composts based on 16S and 18S rDNA T-RFLP profiles. Environ Technol 26, 11011113.
  • Tkachuk, V.L., Krause, D.O., McAllister, T.A., Buckley, K.E., Reuter, T., Hendrick, S. and Ominski, K.H. (2013) Assessing the inactivation of Mycobacterium avium subsp. paratuberculosis during composting of livestock carcasses. Appl Environ Microbiol 79, 32153224.
  • Wang, K., Li, W., Guo, J., Zou, J., Li, Y. and Zhang, L. (2011) Spatial distribution of dynamics characteristic in the intermittent aeration static composting of sewage sludge. Bioresour Technol 102, 55285532.
  • Ward, B.B. (2002) How many species of prokaryotes are there? Proc Natl Acad Sci 99, 1023410236.
  • Xu, W., Reuter, T., Inglis, G.D., Larney, F.J., Alexander, T.W., Guan, J., Stanford, K., Xu, Y. et al. (2009) A biosecure composting system for disposal of cattle carcasses and manure following infectious disease outbreak. J Environ Qual 38, 437450.
  • Xu, W., Xu, Y., Reuter, T., Gilroyed, B., Jin, L., Stanford, K., Larney, F.J. and McAllister, T.A. (2010) An improved design for biocontained composting of cattle mortalities. Compost Sci Util 18, 3241.
  • Xu, W., Reuter, T., Xu, Y., Hsu, Y., Stanford, K. and McAllister, T.A. (2011) Field scale evaluation of bovine-specific DNA as an indicator of tissue degradation during cattle mortality composting. Bioresour Technol 102, 4800.
  • Yamamoto, N., Otawa, K. and Nakai, Y. (2009) Bacterial community developing during composting processes in animal manure treatment facilities. Aust-Asia J Anim Sci 22, 900905.
  • Yue, J.C. and Clayton, M.K. (2005) A Similarity measure based on species proportions. Commun Stat Theory Meth 34, 21232131.
  • Zucconi, F. and de Bertoldi, M. (1987) Compost specifications for the production and characterization of compost from municipal solid waste. In Compost: Production, Quality and Use ed. De Bertoldi, M., Ferranti, M.P., L'Hermite, P. and Zucconi, F. pp. 3050. New York: Elsevier.