Abstract
Composting is a useful technique that transforms livestock manure into stable organic fertilizer. In composting, the biodegradation of substrates is conducted by microbial communities of bacteria, archaea, and fungi. Bacteria are assumed to play an important role in the decomposition of organic substances. However, only a few studies have tracked bacterial communities throughout the composting process. Furthermore, the role of archaea in composting remains to be fully elucidated. To uncover the dynamics of these bacterial and archaeal communities, a variety of molecular biological methods like PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and clone library were utilized. A clone library constructed from bacterial 16S rRNA genes showed that the structure of the bacterial community changed dynamically with compost processing time. At first, phyla Firmicutes and Bacteroidetes were dominant. Phylum Firmicutes maintained abundance for 20 days, indicating that these bacteria may be active under high temperatures. In the final compost, the library consisted of sequences belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria.
A clone library constructed from archaeal 16S rRNA genes showed that the archaeal community was mainly comprised of methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA). During first 2 days, it was revealed that fecal methanogens could survive the early stage of composting. Thermophilic Methanosarcina spp. were present throughout the process, indicating that they may adapt to environmental changes such as high temperatures. Detecting AOA-like sequences showed that AOA could be actively involved in the nitrification of composting systems. Furthermore, the abundance of AOA varies markedly with the raw materials and composting technique used.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abdel-Mohsein HS, Sasaki T, Tada C, Nakai Y (2011) Characterization and partial purification of a bacteriocin-like substance produced by thermophilic Bacillus licheniformis H1 isolated from cow manure compost. Anim Sci J 82:340–351
Allgainer M, Reddy A, Park JI et al (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS ONE 5:e8812
Amon B, Amon T, Boxberger J, Alt C (2001) Emissions of NH3, N2O and CH4 from dairy cows housed in a farmyard manure tying stall (housing, manure storage, manure spreading). Nutr Cycl Agroecosys 60:103–113
Asano R, Sasaki T, Nakai Y (2007) Isolation and characterization of sulfur oxidizing bacteria from cattle manure compost. Anim Sci J 78:330–333
Asano R, Otawa K, Ozutsumi Y et al (2010) Development and analysis of microbial characteristics of an acidulocomposting system for the treatment of garbage and cattle manure. J Biosci Bioeng 110:419–425
Beck-Friis B, Pell M, Sonesson U et al (2000) Formation and emission of N2O and CH4 from compost heaps of organic household waste. Environ Monit Assess 62:317–331
Bernal MP, Alburquerque JA, Moral R (2009) Composting of animal manures and chemical criteria for compost maturity assessment. A review. Bioresour Technol 100:5444–5453
Bibby K, Viau E, Peccia J (2010) Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Water Res 44:4252–4260
Bintrim SB, Donohue TJ, Handelsman J et al (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA 94:277–282
Blanc M, Marilley L, Beffa T, Aragno M (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol Ecol 28:141–149
Böhm R (2002) What need for specific rules for composting of biowaste and catering waste. In: The biological treatment of biodegradable waste – Technical aspects, Brussels, 8–10 April 2002
Cahyani VR, Matsuya K, Asakawa S, Kimura M (2004) Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE. Soil Sci Plant Nutr 50:555–563
Cho KM, Lee SM, Math RK et al (2008) Culture-independent analysis of microbial succession during composting of swine slurry and mushroom cultural wastes. J Microbiol Biotechnol 18:1874–1883
Danon M, Franke-Whittle IH, Insam H et al (2008) Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiol Ecol 65:133–144
Dees P, Ghiorse W (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216
de Gannes V, Eudoxie G, Dyer DH, Hickey WJ (2012) Diversity and abundance of ammonia oxidizing archaea in tropical compost systems. Front Microbiol 3:1–16
Derikx PJL, de Jong GAH, Op den Camp HJM et al (1989) Isolation and characterization of thermophilic methanogenic bacteria from mushroom compost. FEMS Microbiol Lett 62:251–257
Diaz LF, Savage GM (2007) Factors that affect the process. In: Diaz L, de Bertoldi M, Bidlingmaier W, Stentiford E (eds) Compost science and technology, 1st edn. Elsevier B.V., Amsterdam, Netherlands, pp 49–66
Dilly O, Bloem J, Vos A, Munch JC (2004) Bacterial diversity in agricultural soils during litter decomposition. Appl Environ Microbiol 70:468–474
Fracchia L, Dohrmann A, Martinotti M, Tebbe C (2006) Bacterial diversity in a finished compost and vermicompost, differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes. Appl Microbiol Biotechnol 71:942–952
Franke-Whittle I, Klammer S, Insam H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Methods 62:37–56
Fujii C, Nakagawa T, Onodera Y et al (2010) Succession and community composition of ammonia-oxidizing archaea and bacteria in bulk soil of a Japanese paddy field. Soil Sci Plant Nutr 56:212–219
Fukumoto Y, Osada T, Hanajima D, Haga K (2003) Patterns and quantities of NH3, N2O and CH4 emissions during swine manure composting without forced aeration-effect of compost pile scale. Bioresour Technol 89:109–114
Gattinger A, Höfle MG, Schloter M et al (2007) Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil. Environ Microbiol 9:612–624
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63
Godden B, Penninckx M, Piérard A, Lannoye R (1983) Evolution of enzyme activities and microbial populations during composting of cattle manure. Eur J Appl Microbiol Biotechnol 17:306–310
Gong CH, Koshida J, Inoue K, Someya T (2005) Fluorescence direct count of bacteria in various manures and composts as compared with plate count. Jpn J Soil Sci Plant Nutr 76:401–410
Green S, Michel FJ, Hadar Y, Minz D (2004) Similarity of bacterial communities in sawdust- and straw-amended cow manure composts. FEMS Microbiol Lett 233:115–123
Guo Y, Zhu N, Zhu S, Deng C (2007) Molecular phylogenetic diversity of bacteria and its spatial distribution in composts. J Appl Microbiol 103:1344–1354
Haga K (1999) Development of composting technology in animal waste treatment. Asian-Aus J Ani Sci 12:604–606
Halet D, Boon N, Verstraete W (2006) Community dynamics of methanotrophic bacteria during composting of organic matter. J Biosci Bioeng 101:297–302
Hao X, Chang C, Larney FJ, Travis G (2001) Greenhouse gas emissions during cattle feedlot manure composting. J Environ Qual 30:376–386
Haruta S, Kondo M, Nakamura K et al (2002) Microbial community changes during organic solid waste treatment analyzed by double gradient-denaturing gradient gel electrophoresis and fluorescence in situ hybridization. Appl Microbiol Biotechnol 60:224–231
Hatzenpichler R, Lebedeva E, Spieck E et al (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 105:2134–2139
He Y, Inamori Y, Mizuochi M et al (2000) Measurements of N2O and CH4 from the aerated composting of food waste. Sci Total Environ 254:65–74
Hemmi H, Shimoyama T, Nakayama T et al (2004) Molecular biological analysis of microflora in a garbage treatment process under thermoacidophilic conditions. J Biosci Bioeng 97:119–126
Insam H, de Bertoldi M (2007) Microbiology of the composting process. In: Diaz L, de Bertoldi M, Bidlingmaier W, Stentiford E (eds) Compost science and technology, 1st edn. Elsevier B.V., Amsterdam, Netherlands, pp 26–48
Ishii K, Fukui M, Takii S (2000) Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J Appl Microbiol 89:768–777
Jäckel U, Thummes K, Kämpfer P (2005) Thermophilic methane production and oxidation in compost. FEMS Microbiol Ecol 52:175–184
Jarvis Å, Sundberg C, Milenkovski S et al (2009) Activity and composition of ammonia oxidizing bacterial communities and emission dynamics of NH3 and N2O in a compost reactor treating organic household waste. J Appl Microbiol 106:1502–1511
Kang CH, Oh KH, Lee MH et al (2011) A novel family VII esterase with industrial potential from compost metagenomic library. Microb Cell Fact 10:41
Kim YH, Kwon EJ, Kim SK et al (2010) Molecular cloning and characterization of a novel family VIII alkaline esterase from a compost metagenomic library. Biochem Biophys Res Commun 393:45–49
Klamer M, Bååth E (1998) Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis. FEMS Microbiol Ecol 27:9–20
Kohda C, Ando T, Nakai Y (1997) Isolation and characterization of anaerobic indole- and skatole-degrading bacteria from composting animal wastes. J Gen Appl Microbiol 43:249–255
Könneke M, Bernhard AE, de la Torre JR et al (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546
Kowalchuk GA, Naoumenko ZS, Derikx PJ et al (1999) Molecular analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in compost and composted materials. Appl Environ Microbiol 65:396–403
Kunihiro T, Veuger B, Vasquez-Cardenas D et al (2014) Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments. PLoS ONE 9:e96219
Lämmle K, Zipper H, Breuer M et al (2007) Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 127:575–592
Lee YH, Kim SK, Kim YH 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 53:230–236
Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809
Lu J, Sanchez S, Hofacre C et al (2003) Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers. Appl Environ Microbiol 69:901–908
Lyngsø FH, Flotats X, Blasi AB et al (2011) Inventory of manure processing activities in Europe. Technical Report No. I concerning “Manure Processing Activities in Europe” to the European Commission, Directorate-General Environment.
Mackie R, Stroot P, Varel V (1998) Biochemical identification and biological origin of key odor components in livestock waste. J Anim Sci 76:1331–1342
Maeda K, Morioka R, Hanajima D, Osada T (2009) The impact of using mature compost on nitrous oxide emission and the denitrifier community in the cattle manure composting process. Microb Ecol 59:25–36
Maeda K, Toyoda S, Shimojima R et al (2010) 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 76:1555–1562
Martins LF, Antunes L, Pascon RC 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
Mayumi D, Akutsu-Shigeno Y, Uchiyama H et al (2008) Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome. Appl Microbiol Biotechnol 79:743–750
McGarvey JA, Miller WG, Sanchez S, Stanker L (2004) Identification of bacterial populations in dairy wastewaters by use of 16S rRNA gene sequences and other genetic markers. Appl Environ Microbiol 70:4267–4275
Ministry of Agriculture, Forestry and Fisheries (MAFF) (2015) The circumstances surrounding livestock environment. [in Japanese] http://www.maff.go.jp/j/chikusan/kikaku/lin/l_hosin/pdf/kankyo_2701.pdf Accessed 8 Feb 2016
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966–2978
Niisawa C, Oka S, Kodama H et al (2008) Microbial analysis of a composted product of marine animal resources and isolation of bacteria antagonistic to a plant pathogen from the compost. J Gen Appl Microbiol 54:149–158
Ntougias S, Zervakis G, Kavroulakis N et al (2004) Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Syst Appl Microbiol 27:746–754
Oishi R, Tada C, Asano R et al (2012) Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations. Microb Ecol 63:787–793
Ozutsumi Y, Hayashi H, Sakamoto M et al (2005) Culture-independent analysis of fecal microbiota in cattle. Biosci Biotechnol Biochem 69:1793–1797
Pang H, Zhang P, Duan CJ et al (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol 58:404–408
Pedro M, Haruta S, Hazaka M et al (2001) Denaturing gradient gel electrophoresis analysis of microbial community from field-scale composter. J Biosci Bioeng 91:159–165
Pell AN (1997) Manure and microbes, public and animal health problem? J Dairy Sci 80:2673–2681
Peters S, Koschinsky S, Schwieger F, Tebbe C (2000) Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936
Ryckeboer J, Mergaert J, Vaes K et al (2003) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53:349–410
Sasaki H, Maruyama G, Suzuki H et al (2004) Distribution of ammonia assimilating bacteria in the composting process. Compost Sci Util 12:108–113
Sasaki H, Nonaka J, Otawa K et al (2009) Analysis of the bacterial community in the livestock manure-based composting process. Asian-Aus J Ani Sci 22:113–118
Schloss PD, Hay AG, Wilson DB, Walker LP (2003) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46:1–9
Schloss PD, Hay AG, Wilson DB et al (2005) Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl Microbiol Biotechnol 66:457–463
Sonthiphand P, Limpiyakorn T (2011) Change in ammonia-oxidizing microorganisms in enriched nitrifying activated sludge. Appl Microbiol Biotechnol 89:843–853
Sundh I, Rönn S (2002) Microbial succession during composting of source-separated urban organic household waste under different initial temperature conditions. In: Insam H, Riddech N, Klammer S (eds) Microbiology of composting. Springer, Berlin, Heidelberg, pp 53–64
Takaku H, Kodaira S, Kimoto A et al (2006) Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and -independent approaches. J Biosci Bioeng 101:42–50
Tang J, Kanamori T, Inoue Y et al (2004) Changes in the microbial community structure during thermophilic composting of manure as detected by the quinone profile method. Process Biochem 39:1999–2006
Thummes K, Kämpfer P, Jäckel U (2007a) Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Syst Appl Microbiol 30:418–429
Thummes K, Schäfer J, Kämpfer P, Jäckel U (2007b) Thermophilic methanogenic Archaea in compost material, occurrence, persistence and possible mechanisms for their distribution to other environments. Syst Appl Microbiol 30:634–643
Tourna M, Freitag TE, Nicol GW, Prosser JI (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10:1357–1364
Treusch A, Leininger S, Kletzin A et al (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995
United States Environmental Protection Agency (USEPA) (2013) Literature review of contaminants in livestock and poultry manure and implications for water quality. EPA 820-R-13-002. USEPA, Office of Water, Washington, D.C.
Wells G, Park H, Yeung C et al (2009) Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor, betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 11:2310–2328
Weon H, Lee S, Kim B et al (2007) Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov, isolated from livestock manure composts. Int J Syst Evol Microbiol 57:2908–2911
Yamada T, Miyauchi K, Ueda H et al (2007) Composting cattle dung wastes by using a hyperthermophilic pre-treatment process, characterization by physicochemical and molecular biological analysis. J Biosci Bioeng 104:408–415
Yamada T, Suzuki A, Ueda H et al (2008) Successions of bacterial community in composting cow dung wastes with or without hyperthermophilic pre-treatment. Appl Microbiol Biotechnol 81:71–81
Yamamoto N, Asano R, Yoshii H et al (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
Yamamoto N, Asano R, Otawa K et al (2014) Microbial community dynamics during composting process of animal manure analyzed by molecular biological methods. J Integr Field Sci 11:27–34
Yamamoto N, Ohishi R, Suyama Y et al (2012) Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities. Microb Environ 27:519–524
Yamamoto N, Otawa K, Nakai Y (2009) Bacterial communities developing during composting processes in animal manure treatment facilities. Asian-Aus J Ani Sci 22:900–905
Yamamoto N, Otawa K, Nakai Y (2010) Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting. Microb Ecol 60:507–815
Zhang T, Jin T, Yan Q et al (2009) Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants. J Appl Microbiol 107:970–977
Acknowledgements
This work was supported, in part, by the Foundation of the Ministry of Education, Culture, Sports, Science and Technology, Japan, as a “Project of Integrated Compost Science” and by a grant from the Livestock Technology Association, Japan.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Ethics declarations
Funding
This study was funded by the Foundation of the Ministry of Education, Culture, Sports, Science and Technology, Japan, as a “Project of Integrated Compost Science” and by a grant from the Livestock Technology Association, Japan.
Conflict of Interest
Nozomi Yamamoto declares that she has no conflict of interest. Yutaka Nakai declares that he has no conflict of interest.
Ethical Approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Yamamoto, N., Nakai, Y. (2019). Microbial Community Dynamics During the Composting Process of Animal Manure as Analyzed by Molecular Biological Methods. In: Hurst, C. (eds) Understanding Terrestrial Microbial Communities. Advances in Environmental Microbiology, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-030-10777-2_6
Download citation
DOI: https://doi.org/10.1007/978-3-030-10777-2_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-10775-8
Online ISBN: 978-3-030-10777-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)