Community structure and population dynamics of ammonia oxidizers in composting processes of ammonia-rich livestock waste

Systematic and Applied Microbiology

Volumn 36, Issue 5, 2013, Pages 359-367

  Yamada, Takeshi ^a,b   Araki, Shinya ^a   Ikeda Ohtsubo, Wakako ^a   Okamura, Keiko ^b   Hiraishi, Akira ^b   Ueda, Hideyo ^c   Ueda, Yasuichi ^c   Miyauchi, Keisuke ^a   Endo, Ginro ^a  

^a TOHOKU GAKUIN UNIVERSITY   (Japan)

^b TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

^c Japan Life Center Co   (Japan)

Author keywords

Ammonia oxidation; Ammonia oxidizing bacteria; AmoA; Compost; Livestock manure

Indexed keywords

AMMONIA; NITRATE; NITRITE;

AMMONIA OXIDIZING ARCHAEON; AMMONIA OXIDIZING BACTERIUM; ARTICLE; BEEF; BIODIVERSITY; COMMUNITY STRUCTURE; COMMUNITY SUCCESSION; COMPOSTING; DAIRY CATTLE; GENE DOSAGE; LIVESTOCK; MESOPHILE; MOISTURE; MULTIDIMENSIONAL SCALING; NITRIFICATION; PH; PHYSICAL CHEMISTRY; POPULATION DYNAMICS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; THERMOPHILE;

AMMONIA; ANIMALS; ARCHAEA; BACTERIA; BIOTA; LIVESTOCK; MANURE; OXIDATION-REDUCTION;

NITROSOMONADALES; NITROSOMONAS; SUIDAE;

EID: 84879606370     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2013.02.001     Document Type: Article

References (56)

1. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 1990, 56:1919-1925.
2. Amlinger F., Peyr S., Cuhls C. Green house gas emissions from composting and mechanical biological treatment. Waste Manage. Res. 2008, 26:47-60.
3. Anderson J.M., Ingram J.S.I. Tropical Soil Biology and Fertility: A Handbook of Methods 1993, Oxford University Press, Oxford, United Kingdom, pp 74-75. 2nd ed.
4. Arp D.J., Stein L.Y. Metabolism of inorganic N compounds by ammonia-oxidizing bacteria. Crit. Rev. Biochem. Mol. Biol. 2003, 38:471-495.
5. Bray J.R., Curtis J.T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 1957, 27:325-349.
6. Brochier-Armanet C., Boussau B., Gribaldo S., Forterre P. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 2008, 6:245-252.
7. Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 1987, 43:783-791.
8. Clarke K.R. Non-parametric multivariate analysis of changes in community structure. Aust. J. Ecol. 1993, 18:117-143.
9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
10. Flores-Mireles A.L., Winans S.C., Holguin G. Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots. Appl. Environ. Microbiol. 2007, 73:7308-7321.
11. Francis C.A., Roberts K.J., Beman J.M., Santoro A.E., Oakley B.B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA 2005, 102:14683-14688.
12. 4 emissions during swine manure composting without forced aeration - effect of compost pile scale. Bioresour. Technol. 2003, 89:109-114.
13. Good I.J. The population frequencies of species and the estimation of population parameters. Biometrika 1953, 40:237-264.
14. Hatzenpichler R., Lebedeva E.V., Spieck E., Stoecker K., Richter A., Daims H., Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA 2008, 105:2134-2139.
15. Herndl G.J., Reinthaler T., Teira E., van Aken H., Veth C., Pernthaler A., Pernthaler J. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 2005, 71:2303-2309.
16. Hiraishi A. Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett. Appl. Microbiol. 1992, 15:210-213.
17. Hirayama H., Takai K., Inagaki F., Yamato Y., Suzuki M., Nealson K.H., Horikoshi K. Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine. Extremophiles 2005, 9:169-184.
18. Hugenholtz P., Huber T. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int. J. Syst. Evol. Microbiol. 2003, 53:289-293.
19. 2O in a compost reactor treating organic household waste. J. Appl. Microbiol. 2009, 106:1502-1511.
20. Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
21. Jun Y., Wenfeng X. Ammonia biofiltration and community analysis of ammonia-oxidizing bacteria in biofilters. Bioresour. Technol. 2009, 100:3869-3876.
22. Junier P., Molina V., Dorador C., Hadas O., Kim O.-S., Juier T., Witzel K.-P., Imhoff J.F. Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Appl. Microbiol. Biotechnol. 2010, 85:425-440.
23. Koops H.P., Böttcher B., Möller U.C., Pommerening-Röser A., Stehr G. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov. and Nitrosomonas halophila sp. nov. J. Gen. Microbiol. 1991, 137:1689-1699.
24. Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J.I., Embley T.M., Woldendorp J.W. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 1997, 63:1489-1497.
25. Krümmel A., Harms H. Effect of organic matter on growth and cell yield of ammonia-oxidizing bacteria. Arch. Microbiol. 1982, 133:50-54.
26. Kruskal J.B. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 1964, 298:1-27.
27. Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques and Bacterial Systematics 1991, 115-117. Wiley, Chichester. E. Stackebrandt, M. Goodfellow (Eds.).
28. Lebedeva E.V., Alawi M., Fiencke C., Namsaraev B., Bock E., Spieck E. Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone. FEMS Microbiol. Ecol. 2005, 54:297-306.
29. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., König A., Liss T., Lüßmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.-H. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
30. Maeda K., Toyoda S., Shimojima R., Osada T., Hanajima D., Morioka R., Yoshida N. Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 2010, 76:1555-1562.
31. Magurran A.E. Measuring Biological Diversity 2004, Blackwell Publishing, Oxford, London.
32. Miller F.C., Macauley B.J. Odours arising from mushroom composting: a review. Aust. J. Exp. Agric. 1988, 28:553-560.
33. Miller J.J., Beaslev B.W., Larnev F.J., Olson B.M. Soil salinity and sodicity after application of fresh and composted manure with straw or wood-chips. Can. J. Soil. Sci. 2005, 85:427-438.
34. Nancy W. Determination of manure pH. Recommended Methods of Manure Analysis 2003, University of Wisconsin System, Wisconsin, USA, pp. 48-49. John Peters ed.
35. Okano Y., Hristova K.R., Leutenegger C.M., Jackson L.E., Denison R.F., Gebreyesus B., Lebauer D., Scow K.M. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl. Environ. Microbiol. 2004, 70:1008-1016.
36. Osada T., Fukumoto Y. Development of a new dynamic chamber system for measuring harmful gas emissions from composting livestock waste. Water Sci. Technol. 2001, 44:79-86.
37. Otte S., Schalk J., Kuenen J.G., Jetten M.S. Hydroxylamine oxidation and subsequent nitrous oxide production by the heterotrophic ammonia oxidizer Alcaligenes faecalis. Appl. Microbiol. Biotechnol. 1999, 51:255-261.
38. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glockner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
39. 2O): the dominant ozone-depleting substance emitted in the 21st century. Science 2009, 326:123-125.
40. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 1997, 63:4704-4712.
41. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
42. Schulze E.D., de Vries W., Hauks M., Rosén K., Rasmussen L., Tamm S.O., Nilsson J. Critical loads for nitrogen deposition on forest ecosystems. Water Air Soil Pollut. 1989, 48:451-456.
43. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (* and other methods), version 4 2002, Sinauer Associates, Sunderland, MA.
44. Takahashi M., Yamada T., Tanno M., Tsuji H., Hiraishi A. Nitrate removal efficiency and bacterial community dynamics in denitrification processes using poly (L-lactic acid) as the solid substrate. Microbes Environ. 2011, 26:212-219.
45. Treusch A.H., Leininger S., Kletzin A., Schuster S.C., Klenk H.P., Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 2005, 7:1985-1995.
46. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 1991, 173:697-703.
47. Wrage N., Welthof G.L., van Beusichem M.L., Oenema O. Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol. Biochem. 2001, 33:1723-1732.
48. Yamada T., Kikuchi K., Yamauchi T., Shiraishi K., Ito T., Okabe S., Hiraishi A., Ohashi A., Harada A., Kamataga Y., Nakamura K., Sekiguchi Y. Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 that cause bulking in methanogenic granular sludge. Appl. Environ. Microbiol. 2011, 77:2081-2087.
49. Yamada T., Miyauchi K., Ueda H., Ueda Y., Sugawara H., Nakai Y., Endo G. Composting cattle dung wastes by using a hyperthermophilic pre-treatment process: characterization by physicochemical and molecular biological analysis. J. Biosci. Bioeng. 2007, 104:408-415.
50. Yamada T., Sekiguchi Y., Imachi H., Kamagata Y., Ohashi A., Harada H. Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl. Environ. Microbiol. 2005, 71:7493-7503.
51. Yamada T., Suzuki A., Ueda H., Ueda Y., Miyauchi K., Endo G. Successions of bacterial community in composting cow dung wastes with or without hyperthermophilic pre-treatment. Appl. Microbiol. Biotechnol. 2008, 81:771-781.
52. Yamamoto N., Asano R., Yoshii H., Otawa K., Nakai Y. Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis. Appl. Microbiol. Biotechnol. 2011, 90:1501-1510.
53. Yamamoto N., Oishi R., Suyama Y., Tada C., Nakai Y. Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities. Microbes Environ. 2012, 27:519-524.
54. Yamamoto N., Otawa K., Nakai Y. Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting. Microb. Ecol. 2010, 60:807-815.
55. Yasuda T., Kuroda K., Fukumoto Y., Hanajima D., Suzuki K. Evaluation of full-scale biofilter with rockwool mixture treating ammonia gas from livestock manure composting. Bioresour. Technol. 2009, 100:1568-1572.
56. Zeng G., Zhang J., Chen Y., Yu Z., Yu M., Li H., Liu Z., Chen M., Lu L., Hu C. Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting. Bioresour. Technol. 2011, 102:9026-9032.