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References

  • Agusti, G., F. Codony, M. Fittipaldi, B. Adrados, and J. Morato. 2010. Viability determination of Helicobacter pylori using propidium monoazide Quantitative PCR. Helicobacter 15:473476.
  • Alexander, T. W., J. L. Yanke, T. Reuter, E. Topp, R. R. Read, B. L. Selinger, et al. 2011. Longitudinal characterization of antimicrobial resistance genes in feces shed from cattle fed different subtherapeutic antibiotics. BMC Microbiol. 11:19.
  • Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol. Rev. 59:143169.
  • Arthurson, V. 2011. Storage conditions and animal source influence the dominant bacterial community composition in animal manure. World J. Microbiol. Biotechnol. 27:20132022.
  • Barkovskii, A. L., K. M. Manoylov, and C. Bridges. 2012. Positive and negative selection towards tetracycline resistance genes in manure treatment lagoons. J. Appl. Microbiol. 112:907919.
  • Barret, M., N. Gagnon, B. Morissette, E. Topp, M. Kalmokoff, S. P. J. Brooks, et al. 2012. Methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks. FEMS Microbiol. Ecol. 80:427440.
  • Burgmann, H., M. Pesaro, F. Widmer, and J. Zeyer. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods 45:720.
  • Dalkmann, P., M. Broszat, C. Siebe, E. Willaschek, T. Sakinc, J. Huebner, et al. 2012. Accumulation of pharmaceuticals, Enterococcus, and resistance genes in soils irrigated with wastewater for zero to 100 years in central Mexico. PLoS One 7:e45397.
  • Dineen, S. M., R. Aranda, D. L. Anders, and J. M. Robertson. 2010. An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil. J. Appl. Microbiol. 109:18861896.
  • Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rDNA-defined population inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340346.
  • Godon, J. J., E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta. 1997. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63:28022813.
  • Grewal, S. K., S. Rajeev, S. Sreevatsan, and F. C. Michel. 2006. Persistence of Mycobacterium avium subsp paratuberculosis and other zoonotic pathogens during simulated composting, manure packing, and liquid storage of dairy manure. Appl. Environ. Microbiol. 72:565574.
  • Hall, A. T., A. M. Zovanyi, D. R. Christensen, J. W. Koehler, and T. D. Minogue. 2013. Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples. PLoS One 8:e73845.
  • Heuer, H., and K. Smalla. 2007. Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ. Microbiol. 9:657666.
  • Iacovacci, G., A. Serafini, A. Berti, G. Lago, 2003. STR typing from human faeces: a modified DNA extraction method. Pp. 917920 in B. Brinkman, A. Carracedo, eds. Progress in forensic genetics 9: 917–920.
  • Knauth, S., H. Schmidt, and R. Tippkoetter. 2013. Comparison of commercial kits for the extraction of DNA from paddy soils. Lett. Appl. Microbiol. 56:222228.
  • Konstantinov, S. R., H. Smidt, and W. M. de Vos. 2005. Representational difference analysis and real-time PCR for strain-specific quantification of Lactobacillus sobrius sp nov. Appl. Environ. Microbiol. 71:75787581.
  • Lakay, F. M., A. Botha, and B. A. Prior. 2007. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. J. Appl. Microbiol. 102:265273.
  • Leung, K., and E. Topp. 2001. Bacterial community dynamics in liquid swine manure during storage: molecular analysis using DGGE/PCR of 16S rDNA. FEMS Microbiol. Ecol. 38:169177.
  • Lier, T., M. V. Johansen, S. O. Hjelmevoll, B. J. Vennervald, and G. S. Simonsen. 2008. Real-time PCR for detection of low intensity Schistosoma japonicum infections in a pig model. Acta Trop. 105:7480.
  • Lins, P., T. Schwarzenauer, C. Reitschuler, A. O. Wagner, and P. Illmer. 2012. Methanogenic potential of formate in thermophilic anaerobic digestion. Waste Manage. Res. 30:10311040.
  • Liu, F. H., S. B. Wang, J. S. Zhang, J. Zhang, X. Yan, H. K. Zhou, et al. 2009. The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J. Appl. Microbiol. 106:952966.
  • Marti, R., P. Dabert, and A.-M. Pourcher. 2009. Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups. Appl. Environ. Microbiol. 75:49674974.
  • Marti, R., P. Dabert, C. Ziebal, and A. M. Pourcher. 2010. Evaluation of Lactobacillus sobrius/L-amylovorus as a new microbial marker of pig manure. Appl. Environ. Microbiol. 76:14561461.
  • McGarvey, J. A., W. G. Miller, S. Sanchez, and L. Stanker. 2004. Identification of bacterial populations in dairy wastewaters by use of 16S rRNA gene sequences and other genetic markers. Appl. Environ. Microbiol. 70:42674275.
  • McOrist, A. L., M. Jackson, and A. R. Bird. 2002. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J. Microbiol. Methods 50:131139.
  • Mieszkin, S., J.-P. Furet, G. Corthier, and M. Gourmelon. 2009. Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific bacteroidales 16S rRNA genetic markers. Appl. Environ. Microbiol. 75:30453054.
  • Moller, H. B., S. G. Sommer, and B. Ahring. 2004. Methane productivity of manure, straw and solid fractions of manure. Biomass Bioenergy 26:485495.
  • Peu, P., H. Brugere, A. M. Pourcher, M. Kerouredan, J. J. Godon, J. P. Delgenes, et al. 2006. Dynamics of a pig slurry microbial community during anaerobic storage and management. Appl. Environ. Microbiol. 72:35783585.
  • Plaza, C., D. Hernandez, J. M. Fernandez, and A. Polo. 2006. Long-term effects of amendment with liquid swine manure on proton binding behavior of soil humic substances. Chemosphere 65:13211329.
  • Ravva, S. V., C. Z. Sarreal, and R. E. Mandrell. 2011. Bacterial communities in aerosols and manure samples from two different dairies in central and Sonoma valleys of California. PLoS One 6:e17281.
  • Salonen, A., J. Nikkila, J. Jalanka-Tuovinen, O. Immonen, M. Rajilic-Stojanovic, R. A. Kekkonen, et al. 2010. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods 81:127134.
  • Spence, C., T. R. Whitehead, and M. A. Cotta. 2008. Development and comparison of SYBR Green quantitative real-time PCR assays for detection and enumeration of sulfate-reducing bacteria in stored swine manure. J. Appl. Microbiol. 105:21432152.
  • Tang, J.-N., Z.-G. Zeng, H.-N. Wang, T. Yang, P.-J. Zhang, Y.-L. Li, et al. 2008. An effective method for isolation of DNA from pig faeces and comparison of five different methods. J. Microbiol. Methods 75:432436.
  • Taskin, B., A. G. Gozen, and M. Duran. 2011. Selective quantification of viable Escherichia coli bacteria in biosolids by quantitative PCR with propidium monoazide modification. Appl. Environ. Microbiol. 77:43294335.
  • Techer, D., C. Martinez-Chois, M. D'Innocenzo, P. Laval-Gilly, A. Bennasroune, L. Foucaud, et al. 2010. Novel perspectives to purify genomic DNA from high humic acid content and contaminated soils. Sep. Purif. Technol. 75:8186.
  • Ufnar, J. A., D. F. Ufnar, S. Y. Wang, and R. D. Ellender. 2007. Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes. Appl. Environ. Microbiol. 73:52095217.
  • Vanysacker, L., S. A. J. Declerck, B. Hellemans, L. De Meester, I. Vankelecom, and P. Declerck. 2010. Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods. Appl. Microbiol. Biotechnol. 88:299307.
  • Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal dna amplification for phylogenetic study. J. Bacteriol. 173:697703.
  • Whitehouse, C. A., and H. E. Hottel. 2007. Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol. Cell. Probes 21:9296.
  • von Wintzingerode, F., U. B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213229.
  • Yankson, K. K., and T. R. Steck. 2009. Strategy for extracting DNA from clay soil and detecting a specific target sequence via selective enrichment and real-time (quantitative) PCR amplification. Appl. Environ. Microbiol. 75:60176021.
  • Zhou, J. Z., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316322.