Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater

Water Industry: Water-Energy-Health Nexus


To investigate the effects of temporal variations of process parameters on microbial community structures in the two types of full-scale anaerobic digester treating swine wastewater, three full-scale anaerobic digesters were monitored. An anaerobic filter (AF)-type digester located in Gong-Ju (GJ) showed the highest COD removal among three digesters and maintained stable efficiency. A digester in Hong-Seong (HS) was of the same type as it GJ and showed improved efficiency over the sampling period. A continuously stirred tank reactor (CSTR)-type digester in Soon-Cheon (SC) showed decreasing efficiency due to a high residual concentration of VFAs and NH4+. These process efficiencies were closely correlated to the Simpson indices of the methanogenic communities. Genera Bacillus, Methanosaeta, and Methanospirillum that have filamentous morphology were dominant in both AF-type digesters, but genera Acholeplasma, Methanosarcina, and Methanoculleus that have spherical or coccoid morphology were dominantly abundant in the CSTR-type digester. Correlation between populations suggests a possible syntrophic relationship between genera Desulfobulbus and Methanosaeta in digesters GJ and HS.


Full-scale, swine wastewater Digester type Anaerobic digestion Microbial community Multivariate analysis 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11356_2017_1103_MOESM1_ESM.pdf (2.8 mb)
ESM 1 (PDF 2.77 mb)


  1. APHA-AWWA-WEF (2005) Standard methods for the examination of water and wastewater. American Public Health Association, Washington, D.C., 1167 ppGoogle Scholar
  2. Atkinson B, Mavituna F (1991) Biochemical engineering and biotechnology handbook. The Nature Press, New YorkGoogle Scholar
  3. Bittman R (1993): Mycoplasma membrane lipids chemical composition and transbilayer distribution. In: Rottem S, Kahane I (Editors), Mycoplasma cell membranes. Springer US, Boston, MA, pp. 29–52, DOI:  https://doi.org/10.1007/978-1-4615-2924-8_2
  4. Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37(1):911–917.  https://doi.org/10.1139/y59-099CrossRefGoogle Scholar
  5. Bouanane-Darenfed A, Fardeau M-L, Ollivier B (2014) The family Caldicoprobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: Firmicutes and Tenericutes. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 13–17Google Scholar
  6. Chen Y, Cheng JJ, Creamer KS (2008) Inhibition of anaerobic digestion process: a review. Bioresour Technol 99(10):4044–4064.  https://doi.org/10.1016/j.biortech.2007.01.057CrossRefGoogle Scholar
  7. Cheng P, Mueller RE, Jaeger S, Bajpai R, Iannotti EL (1991) Lactic acid production from enzyme-thinned corn starch using Lactobacillus amylovorus. J Ind Microbiol Biotechnology 7:27–34Google Scholar
  8. Cho K, Lee J, Kim W, Hwang S (2013) Behavior of methanogens during start-up of farm-scale anaerobic digester treating swine wastewater. Process Biochem 48(9):1441–1445.  https://doi.org/10.1016/j.procbio.2013.04.016CrossRefGoogle Scholar
  9. Choi EH, Yoon YM, Kim CH (2011) Generation and characteristics analysis of swine manure for introducing biogas system. 한국관개배수위원회 18:25–32Google Scholar
  10. Da Silva MLB, Cantão ME, Mezzari MP, Ma J, Nossa CW (2015) Assessment of bacterial and archaeal community structure in swine wastewater treatment processes. Microb Ecol 70(1):77–87.  https://doi.org/10.1007/s00248-014-0537-8CrossRefGoogle Scholar
  11. De Vrieze J, Hennebel T, Boon N, Verstraete W (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Bioresour Technol 112:1–9.  https://doi.org/10.1016/j.biortech.2012.02.079CrossRefGoogle Scholar
  12. Dubois M, Gilles M, Hamilton J, Godess P, Smith F (1956) Colorimetric method for determination of sugars related substances. Anal Chem 28(3):350–356.  https://doi.org/10.1021/ac60111a017CrossRefGoogle Scholar
  13. Falsen E, Collins MD, Welinder-Olsson C, Song Y, Finegold SM, Lawson PA (2005) Fastidiosipila sanguinis gen. nov., sp. nov., a new Gram-positive, coccus-shaped organism from human blood. Int J Syst Evol Microbiol 55(2):853–858.  https://doi.org/10.1099/ijs.0.63327-0CrossRefGoogle Scholar
  14. Gao S, Zhao M, Chen Y, Yu M, Ruan W (2015) Tolerance response to in situ ammonia stress in a pilot-scale anaerobic digestion reactor for alleviating ammonia inhibition. Bioresour Technol 198:372–379.  https://doi.org/10.1016/j.biortech.2015.09.044CrossRefGoogle Scholar
  15. George Garrity, Don J. Brenner, Noel R. Krieg, Staley JR (2005) Bergey’s Manual® of Systematic Bacteriology. Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria. Springer US, United States of AmericaGoogle Scholar
  16. Harmsen HJ, Akkermans AD, Stams AJ, de Vos WM (1996) Population dynamics of propionate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Appl Environ Microbiol 62(6):2163–2168Google Scholar
  17. Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann K-H (2011) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One 6(1):e14519.  https://doi.org/10.1371/journal.pone.0014519CrossRefGoogle Scholar
  18. Kim W, Cho K, Lee S, Hwang S (2013) Comparison of methanogenic community structure and anaerobic process performance treating swine wastewater between pilot and optimized lab scale bioreactors. Bioresour Technol 145:48–56.  https://doi.org/10.1016/j.biortech.2013.02.044CrossRefGoogle Scholar
  19. Kim W, Shin SG, Han G, Cho K, Hwang S (2015) Structures of microbial communities found in anaerobic batch runs that produce methane from propionic acid—seeded from full-scale anaerobic digesters above a certain threshold. J Biotechnol 214:192–198.  https://doi.org/10.1016/j.jbiotec.2015.09.040CrossRefGoogle Scholar
  20. Kita A, Suehira K, Miura T, Okamura Y, Aki T, Matsumura Y, Tajima T, Nishio N, Nakashimada Y (2016) Characterization of a halotolerant acetoclastic methanogen highly enriched from marine sediment and its application in removal of acetate. J Biosci Bioeng 121(2):196–202.  https://doi.org/10.1016/j.jbiosc.2015.05.018CrossRefGoogle Scholar
  21. Kovács E, Wirth R, Maróti G, Bagi Z, Rákhely G, Kovács KL (2013) Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition. PLoS One 8(10):e77265.  https://doi.org/10.1371/journal.pone.0077265CrossRefGoogle Scholar
  22. Li L, He Q, Ma Y, Wang X, Peng X (2015) Dynamics of microbial community in a mesophilic anaerobic digester treating food waste: relationship between community structure and process stability. Bioresour Technol 189:113–120.  https://doi.org/10.1016/j.biortech.2015.04.015CrossRefGoogle Scholar
  23. Li P, Wang Y, Wang Y, Liu K, Tong L (2010) Bacterial community structure and diversity during establishment of an anaerobic bioreactor to treat swine wastewater. Water Sci Technol 61(1):243–252.  https://doi.org/10.2166/wst.2010.807CrossRefGoogle Scholar
  24. Li W, Fu L, Niu B, Wu S, Wooley J (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings in BioinformaticsGoogle Scholar
  25. Lim JW, Chen CL, Ho IJR, Wang JY (2013) Study of microbial community and biodegradation efficiency for single- and two-phase anaerobic co-digestion of brown water and food waste. Bioresour Technol 147:193–201.  https://doi.org/10.1016/j.biortech.2013.08.038CrossRefGoogle Scholar
  26. Liu A-C, Chou C-Y, Chen L-L, Kuo C-H (2015) Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis. J Biotechnol 194:124–131.  https://doi.org/10.1016/j.jbiotec.2014.11.026CrossRefGoogle Scholar
  27. Lovley DR, Anderson RT (2000) Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface. Hydrogeol J 8(1):77–88.  https://doi.org/10.1007/PL00010974CrossRefGoogle Scholar
  28. Lu L, Xing D, Ren N, Logan BE (2012) Syntrophic interactions drive the hydrogen production from glucose at low temperature in microbial electrolysis cells. Bioresour Technol 124:68–76.  https://doi.org/10.1016/j.biortech.2012.08.040CrossRefGoogle Scholar
  29. Madsen M, Holm-Nielsen JB, Esbensen KH (2011) Monitoring of anaerobic digestion processes: a review perspective. Renew Sust Energ Rev 15(6):3141–3155.  https://doi.org/10.1016/j.rser.2011.04.026CrossRefGoogle Scholar
  30. Miron Y, Zeeman G, van Lier JB, Lettinga G (2000) The role of sludge retention time in the hydrolysis and acidification of lipids, carbohydrates and proteins during digestion of primary sludge in CSTR systems. Water Res 34(5):1705–1713.  https://doi.org/10.1016/S0043-1354(99)00280-8CrossRefGoogle Scholar
  31. MoE (2013) Statistics of livestock wastewater treatment, Seoul, South KoreaGoogle Scholar
  32. Mulat DG, Jacobi HF, Feilberg A, Adamsen APS, Richnow H-H, Nikolausz M (2016) Changing feeding regimes to demonstrate flexible biogas production: effects on process performance, microbial community structure, and methanogenesis pathways. Appl Environ Microbiol 82(2):438–449.  https://doi.org/10.1128/AEM.02320-15CrossRefGoogle Scholar
  33. Oren A (2014a) The family Methanosarcinaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of bacteria and the archaea. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 259–281Google Scholar
  34. Oren A (2014b) The family Methanospirillaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of bacteria and the archaea. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 283–290Google Scholar
  35. Oren A (2014c) The family Methanomicrobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of bacteria and the archaea. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 231–246.  https://doi.org/10.1007/978-3-642-30197-1_257
  36. Oude Elferink SJWH, Vorstman WJC, Sopjes A, Stams AJM (1998) Characterization of the sulfate-reducing and syntrophic population in granular sludge from a full-scale anaerobic reactor treating papermill wastewater. FEMS Microbiol Ecol 27(2):185–194.  https://doi.org/10.1111/j.1574-6941.1998.tb00536.xCrossRefGoogle Scholar
  37. Pandey PK, Ndegwa PM, Soupir ML, Alldredge JR, Pitts MJ (2011) Efficacies of inocula on the startup of anaerobic reactors treating dairy manure under stirred and unstirred conditions. Biomass Bioenergy 35(7):2705–2720.  https://doi.org/10.1016/j.biombioe.2011.03.017CrossRefGoogle Scholar
  38. Parte A, Krieg NR, Ludwig W, Whitman W, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D (2011) Bergey’s Manual of Systematic Bacteriology: Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer New YorkGoogle Scholar
  39. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Meth 6(9):639–641.  https://doi.org/10.1038/nmeth.1361CrossRefGoogle Scholar
  40. Shin SG, Han G, Lim J, Lee C, Hwang S (2010) A comprehensive microbial insight into two-stage anaerobic digestion of food waste-recycling wastewater. Water Res 44(17):4838–4849.  https://doi.org/10.1016/j.watres.2010.07.019CrossRefGoogle Scholar
  41. Shin SG, Koo T, Lee J, Han G, Cho K, Kim W, Hwang S (2016) Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge. Bioresour Technol 214:711–721.  https://doi.org/10.1016/j.biortech.2016.05.021CrossRefGoogle Scholar
  42. Song M, Shin SG, Hwang S (2010) Methanogenic population dynamics assessed by real-time quantitative PCR in sludge granule in upflow anaerobic sludge blanket treating swine wastewater. Bioresour Technol 101(1):S23–S28.  https://doi.org/10.1016/j.biortech.2009.03.054CrossRefGoogle Scholar
  43. Vargas IT, Albert IU, Regan JM (2013) Spatial distribution of bacterial communities on volumetric and planar anodes in single-chamber air-cathode microbial fuel cells. Biotechnol Bioeng 110(11):3059–3062.  https://doi.org/10.1002/bit.24949CrossRefGoogle Scholar
  44. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman W (2009) Bergey’s Manual of Systematic Bacteriology: Volume 3: The Firmicutes. Springer New YorkGoogle Scholar
  45. Wan S, Sun L, Sun J, Luo W (2013) Biogas production and microbial community change during the co-digestion of food waste with Chinese silver grass in a single-stage anaerobic reactor. Biotechnol Bioprocess Eng 18(5):1022–1030.  https://doi.org/10.1007/s12257-013-0128-4CrossRefGoogle Scholar
  46. Xie Z, Wang Z, Wang Q, Zhu C, Wu Z (2014) An anaerobic dynamic membrane bioreactor (AnDMBR) for landfill leachate treatment: performance and microbial community identification. Bioresour Technol 161:29–39.  https://doi.org/10.1016/j.biortech.2014.03.014CrossRefGoogle Scholar
  47. Yu Y, Kim J, Hwang S (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 93(3):424–433.  https://doi.org/10.1002/bit.20724CrossRefGoogle Scholar
  48. Zhao B, Liu J, Frear C, Holtzapple M, Chen S (2016) Consolidated bioprocessing of microalgal biomass to carboxylates by a mixed culture of cow rumen bacteria using anaerobic sequencing batch reactor (ASBR). Bioresour Technol 222:517–522.  https://doi.org/10.1016/j.biortech.2016.09.120CrossRefGoogle Scholar
  49. Zhou L, Yu H, Ai G, Zhang B, Hu S, Dong X (2015) Transcriptomic and physiological insights into the robustness of long filamentous cells of Methanosaeta harundinacea, prevalent in upflow anaerobic sludge blanket granules. Appl Environ Microbiol 81(3):831–839.  https://doi.org/10.1128/AEM.03092-14CrossRefGoogle Scholar
  50. Ziganshin A, Schmidt T, Scholwin F, Il’inskaya O, Harms H, Kleinsteuber S (2011) Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles. Appl Microbiol Biotechnol 89(6):2039–2052.  https://doi.org/10.1007/s00253-010-2981-9CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Environmental Science and EngineeringPohang University of Science and TechnologyPohangRepublic of Korea
  2. 2.Department of Energy Engineering, Future Convergence Technology Research InstituteGyeongnam National University of Science and TechnologyJinjuSouth Korea
  3. 3.Center for Water Resource Cycle ResearchKorea Institute of Science and TechnologySeoulRepublic of Korea
  4. 4.Department of Environmental EngineeringKyungpook National UniversityDaeguRepublic of Korea

Personalised recommendations