Spatial and temporal variations of microbial community in a mixed plug-flow loop reactor fed with dairy manure

Microbial Biotechnology

Volumn 7, Issue 4, 2014, Pages 332-346

  Li, Yueh Fen ^a   Chen, Po Hsu ^a   Yu, Zhongtang ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VOLATILE FATTY ACID; FATTY ACID; MANURE;

ACTINOBACTERIA; ANAEROBIC DIGESTION; ARTICLE; BIFIDOBACTERIUM; CANDIDATUS NITROSOSPHAERA; CLOSTRIDIACEAE; CORIOBACTERIACEAE; CRENARCHAEOTA; DAIRY MANURE; DENATURING GRADIENT GEL ELECTROPHORESIS; EURYARCHAEOTA; GENE SEQUENCE; MANURE; METAGENOMICS; METHANOBACTERIUM; METHANOSAETA; MICROBIAL COMMUNITY; MICROBIOME; MIXED PLUG FLOW LOOP REACTOR; NONHUMAN; PH; PLANCTOMYCETES; PLUG FLOW REACTOR; POLYMERASE CHAIN REACTION; PYROSEQUENCING; ANIMAL; BIOREACTOR; BIOTA; BOVINE; MICROBIOLOGY; SPATIOTEMPORAL ANALYSIS;

ANIMALS; BIOREACTORS; BIOTA; CATTLE; FATTY ACIDS; HYDROGEN-ION CONCENTRATION; INDUSTRIAL MICROBIOLOGY; MANURE; METAGENOMICS; SPATIO-TEMPORAL ANALYSIS;

EID: 84901926148     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12125     Document Type: Article

References (49)

1. Association of Official Analytical Chemists (1990) In Official Methods of Analysis, 15th edn. Arlington, VA, USA: AOAC.
2. Baker, G.C., Smith, J.J., and Cowan, D.A. (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
3. Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., and Knight, R. (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267.
4. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., etal. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
5. Chen, C.H. (2002) Generalized association plots: information visualization via iteratively generated correlation matrices. Stat Sin 12: 7-29.
6. Chen, S., Song, L., and Dong, X. (2006) Sporacetigenium mesophilum gen. nov., sp. nov., isolated from an anaerobic digester treating municipal solid waste and sewage. Int J Syst Evol Microbiol 56: 721-725.
7. Chouari, R., Le Paslier, D., Dauga, C., Daegelen, P., Weissenbach, J., and Sghir, A. (2005) Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl Environ Microbiol 71: 2145-2153.
8. De Vrieze, J., Hennebel, T., Boon, N., and Verstraete, W. (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Bioresour Technol 112: 1-9.
9. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., etal. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
10. 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.
11. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
12. Franke-Whittle, I.H., Goberna, M., and Insam, H. (2009) Design and testing of real-time PCR primers for the quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of uncultured methanogens. Can J Microbiol 55: 611-616.
13. 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: 285-290.
14. Goberna, M., Insam, H., and Franke-Whittle, I.H. (2009) Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl Environ Microbiol 75: 2566-2572.
15. Goberna, M., Gadermaier, M., García, C., Wett, B., and Insam, H. (2010) Adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37°C and 55°C. Appl Environ Microbiol 76: 6564-6571.
16. Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., etal. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
17. Hobson, P.N. (1990) The treatment of agricultural wastes. In Anaerobic Digestion: A Waste Treatment Technology. Critical Reports on Applied Chemistry 31. Wheatley, A. (ed.). New York, NY, USA: Elsevier Science Publishers, pp. 93-138.
18. Janse, I., Bok, J., and Zwart, G. (2004) A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis. J Microbiol Methods 57: 279-281.
19. Lansing, S., Botero, R.B., and Martin, J.F. (2008) Waste treatment and biogas quality in small-scale agricultural digesters. Bioresour Technol 99: 5881-5890.
20. Lerm, S., Kleyböcker, A., Miethling-Graff, R., Alawi, M., Kasina, M., Liebrich, M., and Würdemann, H. (2012) Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload. Waste Manag 32: 389-399.
21. Lozupone, C., and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
22. Namsree, P., Suvajittanont, W., Puttanlek, C., Uttapap, D., and Rungsardthong, V. (2012) Anaerobic digestion of pineapple pulp and peel in a plug-flow reactor. J Environ Manage 110: 40-47.
23. Nelson, M.C. (2011) An integrated investigation of the microbial communities underpinning biogas production in anaerobic digestion systems. PhD dissertation.
24. Nettmann, E., Bergmann, I., Pramschüfer, S., Mundt, K., Plogsties, V., Herrmann, C., and Klocke, M. (2010) Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 76: 2540-2548.
25. Nocker, A., Sossa-Fernandez, P., Burr, M.D., and Camper, A.K. (2007) Use of propidium monoazide for live/dead distinction in microbial ecology. Appl Environ Microbiol 73: 5111-5117.
26. Nocker, A., Richter-Heitmann, T., Montijn, R., Schuren, F., and Kort, R. (2010) Discrimination between live and dead cells in bacterial communities from environmental water samples analyzed by 454 pyrosequencing. Int Microbiol 13: 59-65.
27. Pelletier, E., Kreimeyer, A., Bocs, S., Rouy, Z., Gyapay, G., Chouari, R., etal. (2008) Candidatus Cloacamonas acidaminovorans': genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol 190: 2572-2579.
28. Peu, P., Brugère, H., Pourcher, A.M., Kérourédan, M., Godon, J.J., Delgenès, J.P., and Dabert, P. (2006) Dynamics of a pig slurry microbial community during anaerobic storage and management. Appl Environ Microbiol 72: 3578-3585.
29. Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
30. Reeder, J., and Knight, R. (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669.
31. Roy, C.S., Talbot, G., Topp, E., Beaulieu, C., Palin, M.F., and Massé, D.I. (2009) Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure. Water Res 1: 21-32.
32. Rudi, K., Moen, B., Sekelja, M., Frisli, T., and Lee, M.R. (2012) An eight-year investigation of bovine livestock fecal microbiota. Vet Microbiol 160: 369-377.
33. Shigematsu, T., Tang, Y.Q., Kawaguchi, H., Ninomiya, K., Kijima, J., Kobayashi, T., etal. (2003) Effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation. J Biosci Bioeng 96: 547-558.
34. Smith, R.C., and Oerther, D.B. (2006) Microbial community development in a laboratory-scale nitrifying activated sludge system with input from a side-stream bioreactor treating digester supernatant. Water Sci Technol 54: 209-216.
35. St-Pierre, B., and Wright, A.D. (2013) Metagenomic analysis of methanogen populations in three full-scale mesophilic anaerobic manure digesters operated on dairy farms in Vermont, USA. Bioresour Technol 138: 277-284.
36. Taskin, B., Gozen, A.G., and Duran, M. (2011) Selective quantification of viable Escherichia coli bacteria in biosolids by quantitative PCR with propidium monoazide modification. Appl Environ Microbiol 77: 4329-4335.
37. Ueki, A., Abe, K., Suzuki, D., Kaku, N., Watanabe, K., and Ueki, K. (2009) Anaerosphaera aminiphila gen. nov., sp. nov., a glutamate-degrading, Gram-positive anaerobic coccus isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol 12: 3161-3167.
38. Wang, L., Oda, Y., Grewal, S., Morrison, M., Michel, F.C., Jr, and Yu, Z. (2012) Persistence of resistance to erythromycin and tetracycline in swine manure during simulated composting and lagoon treatments. Microb Ecol 63: 32-40.
39. 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: 5261-5267.
40. Wu, H.M., Tien, Y.J., and Chen, C. (2010) GAP: a graphical environment for matrix visualization and cluster analysis. Comput Stat Data Anal 54: 767-778.
41. Yamamoto, N., Asano, R., Yoshii, H., Otawa, K., and Nakai, Y. (2011) Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis. Appl Microbiol Biotechnol 90: 1501-1510.
42. Yu, Z., and Morrison, M. (2004a) Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36: 808-812.
43. Yu, Z., and Morrison, M. (2004b) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70: 4800-4806.
44. Yu, Z., Michel, F.C., Hansen, G., Wittum, T., and Morrison, M. (2005) Development and application of real-time PCR assays for quantification of genes encoding tetracycline resistance. Appl Environ Microbiol 71: 6926-6933.
45. Yu, Z., García-González, R., Schanbacher, F.L., and Morrison, M. (2008) Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 74: 889-893.
46. Yu, Z., Morrison, M., and Schanbacher, F.L. (2010) Production and utilization of methane biogas as renewable fuel. In Biomass to Biofuels: Strategies for Global Industries. Vertès, A.A., Blaschek, H.P., Yukawa, H., and Qureshi, N. (eds). Hoboken, NJ, USA: John Wiley & Sons, pp. 403-433.
47. Zhou, Z., Meng, Q., and Yu, Z. (2011) Effects of methanogenic inhibitors on methane production and abundances of methanogens and cellulolytic bacteria in in vitro ruminal cultures. Appl Environ Microbiol 77: 2634-2639.
48. Zhu, C., Zhang, J., Tang, Y., Zhengkai, X., and Song, R. (2011) Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis. Microbiol Res 166: 27-35.
49. Zinder, S.H. (1993) Physiological ecology of methanogens. In Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. Ferry, J.G. (ed.). New York, NY, USA: Chapman & Hall, pp. 128-206.