Analysis of Archaeal Communities in Full-Scale Anaerobic Digesters Using 454 Pyrosequencing

454 Pyrosequencing을 이용한 실규모 혐기성 소화조의 아케아 군집구조 분석

  • Kang, Hyun-Jin (School of Civil, Environmental and Architectural Engineering, Korea University) ;
  • Kim, Taek-Seung (School of Civil, Environmental and Architectural Engineering, Korea University) ;
  • Lee, Young-Haeng (Water Research Center, Korea Institute of Science and Technology) ;
  • Lee, Taek-June (Water Research Center, Korea Institute of Science and Technology) ;
  • Han, Keum-Suk (Waterworks Research Institute, Seoul Metropolitan Government) ;
  • Choi, Young-Jun (Waterworks Research Institute, Seoul Metropolitan Government) ;
  • Park, Hee-Deung (School of Civil, Environmental and Architectural Engineering, Korea University)
  • 강현진 (고려대학교 건축사회환경공학부) ;
  • 김택승 (고려대학교 건축사회환경공학부) ;
  • 이영행 (한국과학기술연구원 물연구센터) ;
  • 이택준 (한국과학기술연구원 물연구센터) ;
  • 한금석 (서울특별시 상수도연구원) ;
  • 최영준 (서울특별시 상수도연구원) ;
  • 박희등 (고려대학교 건축사회환경공학부)
  • Received : 2011.06.16
  • Accepted : 2011.09.01
  • Published : 2011.09.30

Abstract

Archaeal communities were investigated using 454 pyrosequencing technology based on 16S rRNA gene in 11 samples collected from six different full-scale anaerobic digesters. Observed operational taxonomic units (OTUs) estimated from the archaeal 16S rRNA gene sequences were 13-55 OTUs (3% cutoff) which was corresponded to 29-89% of Chao1 richness estimates. In the anaerobic digesters there were archaeal sequences within the orders Thermoproteales, Thermoplasmatales, Desulfurococcales as well as within the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales, which are known to produce methane. Among these orders, Methanococcales known to produce methane using hydrogen was the predominant taxon and constituted 51.8-99.7% of total sequences. All samples showed a very similar community structure (Pearson correlation coefficient=0.99) except for one sample based on a heat map analysis. In addition, canonical correspondence analysis correlating archaeal communities to the environmental variables demonstrated that digester temperature and total solids removal rate were the two important explanatory variables. Overall results suggested that environmental and operational variables of anaerobic digester are important factors determining archaeal diversity and community structure.

Keywords

Methanococcales;anaerobic digestion;archaea;methanogenesis;pyrosequencing

References

  1. Angenent, L.T., S.W. Sung, and L. Raskin. 2002. Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste. Water Res. 36, 4648-4654. https://doi.org/10.1016/S0043-1354(02)00199-9
  2. Cole, J.R., B. Chai, R.J. Farris, Q. Wang, S.A. Kulam, D.M. McGarrell, G.M. Garrity, and J.M. Tiedje. 2005. The ribosomal database project (RDP-II): sequences and tools for highthroughput rRNA analysis. Nucleic Acids Res. 33, D294-D296.
  3. Collins, G., A. Woods, S. McHugh, M.W. Carton, and V. O'Flaherty. 2003. Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters. FEMS Microbiol. Ecol. 46, 159-170. https://doi.org/10.1016/S0168-6496(03)00217-4
  4. Cytryn, E., D. Minz, R.S. Oremland, and Y. Cohen. 2000. Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl. Environ. Microbiol. 66, 3269-3276. https://doi.org/10.1128/AEM.66.8.3269-3276.2000
  5. Delbes, C., R. Moletta, and J.J. Godon. 2000. Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction-single-strand conformation polymorphism analysis. Environ. Microbiol. 2, 506-515. https://doi.org/10.1046/j.1462-2920.2000.00132.x
  6. DeLong, E.F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685-5689. https://doi.org/10.1073/pnas.89.12.5685
  7. Demirel, B. and P. Scherer. 2008. The roles of acetotrophic and hydrohenotrophic methanogens during anaerobic conversion of biomass th methane: a review. Rev. Environ. Sci. Biotechnol. 7, 173-190. https://doi.org/10.1007/s11157-008-9131-1
  8. Gilliam, F.S. and N.E. Saunders. 2003. Making more sense of the order: A review of Canoco for Windows 4.5, PC-ORD version 4 and SYN-TAX 2000. J. Veg. Sci. 14, 297-304. https://doi.org/10.1111/j.1654-1103.2003.tb02155.x
  9. 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, 2802-2813.
  10. Grandin, U. 2006. PC-ORD version 5: a user-friendly toolbox for ecologists. J. Veg. Sci. 17, 843-844. https://doi.org/10.1111/j.1654-1103.2006.tb02508.x
  11. Harmsen, H.J.M., H.M.P. Kengen, A.D.L. Akkermans, A.J.M. Stams, and W.M. deVos. 1996. Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl. Environ. Microbiol. 62, 1656-1663.
  12. Huber, H. and K.O. Stetter. 2006. Desulfurococcales, pp. 52-68. In M. Dworkns (ed.), Prokaryotes: an evoling electron resource for the microbiological community, Springer, New York, NY, USA.
  13. Huber, H., M. Thomm, H. Konig, G. Thies, and K.O. Stetter. 1982. Methanococcus thermolithotrophilcus, a novel thermophilic lithotrophic methanogen. Arch. Microbiol. 132, 47-50. https://doi.org/10.1007/BF00690816
  14. Hwang, K., M. Song, W. Kim, N. Kim, and S. Hwang. 2010. Effects of prolonged starvation on methanogenic population dynamics in anaerobic digestion of swine wastewater. Bioresour. Technol. 101, S2-S6. https://doi.org/10.1016/j.biortech.2009.03.070
  15. Ince, B.K., I. Usenti, A. Eyigor, N.A. Oz, M. Kolukirik, and O. Ince. 2006. Analysis of methanogenic archaeal and sulphate reducing bacterial populations in deep sediments of the Black Sea. Geomicrobiol. J. 23, 285-292. https://doi.org/10.1080/01490450600760724
  16. Jones, W.J., J.A. Leigh, F. Mayer, C.R. Woese, and R.S. Wolfe. 1983. Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent Arch. Microbiol. 136, 254-261. https://doi.org/10.1007/BF00425213
  17. Kim, W., S. Lee, S.G. Shin, C. Lee, K. Hwang, and S. Hwang. 2010. Methanogenic community shift in anaerobic batch digesters treating swine wastewater. Water Res. 44, 4900-4907. https://doi.org/10.1016/j.watres.2010.07.029
  18. Kim, B.S., H.M. Oh, H. Kang, and J. Chun. 2005. Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. 43, 144-151.
  19. Klocke, M., E. Nettmann, I. Bergmann, K. Mundt, K. Souidi, J. Mumme, and B. Linke. 2008. Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass. Syst. Appl. Microbiol. 31, 190-205. https://doi.org/10.1016/j.syapm.2008.02.003
  20. Krober, M., T. Bekel, N.N. Diaz, A. Goesmann, S. Jaenicke, L. Krause, D. Miller, K.J. Runte, P. Viehover, A. Puhler, and et al. 2009. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J. Biotechnol. 142, 38-49. https://doi.org/10.1016/j.jbiotec.2009.02.010
  21. Liu, W.T., O.C. Chan, and H.H.P. Fang. 2002. Microbial community dynamics during start-up of acidogenic anaerobic reactors. Water Res. 36, 3203-3210. https://doi.org/10.1016/S0043-1354(02)00022-2
  22. Madigan, M.T. and J.M. Martinko. 2006. Brock biology of microorganisms. 11th ed. Upper Saddle, Prentice Hall, USA.
  23. Metcalf and Eddy. 2003. Wastewater engineering: treatment and reuse. 4th ed. McGraw-Hill, New York, NY, USA.
  24. Metzker, M.L. 2010. Sequencing technologies-the next generation. Nat. Rev. Genetics 11, 31-46. https://doi.org/10.1038/nrg2626
  25. Qian, P.Y., Y. Wang, O.O. Lee, S.C.K. Lau, J.K. Yang, F.F. Lafi, A. Al-Suwailem, and T.Y.H. Wong. 2011. Vertical stratification of microbial communities in the Red sea revealed by 16S rDNA pyrosequencing. ISME J. 5, 507-518. https://doi.org/10.1038/ismej.2010.112
  26. Quince, C., A. Lanzen, T.P. Curtis, R.J. Davenport, N. Hall, I.M. Head, L.F. Read, and W.T. Sloan. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Meth. 6, 639-641. https://doi.org/10.1038/nmeth.1361
  27. Raskin, L., D.D. Zheng, M.E. Griffin, P.G. Stroot, and P. Misra. 1995. Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie van Leeuwenhoek 68, 297-308. https://doi.org/10.1007/BF00874140
  28. Rittmann, B.E. and P.E. McCarty. 2001. Environmental biotechnology: principles and applications. McGraw-Hill Higher Education, New York, USA.
  29. Schleper, C., G. Puehler, I. Holz, A. Gambacorta, D. Janekovic, U. Santarius, H.P. Klenk, and W. Zillig. 1995. Picrophilus gen. nov., fam. nov.: a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0. J. Bacteriol. 177, 7050-7059. https://doi.org/10.1128/jb.177.24.7050-7059.1995
  30. Schloss, P.D., S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, B.B. Oakley, D.H. Parks, C.J. Robinson, and et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. https://doi.org/10.1128/AEM.01541-09
  31. Schluter, A., T. Bekel, N.N. Diaz, M. Dondrup, R. Eichenlaub, K.H. Gartemann, I. Krahn, L. Krause, H. Kromeke, O. Kruse, and et al. 2008. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol. 136, 77-90. https://doi.org/10.1016/j.jbiotec.2008.05.008
  32. Shin, S., G. Han, J. Lim, C. Lee, and S. Hwang. 2010. A comprehensive microbial insight into two-stage anaerobic digestion of food waste-recycling wastewater Water Res. 44, 4838-4849. https://doi.org/10.1016/j.watres.2010.07.019
  33. Shin, S.G., B.W. Zhou, S. Lee, W. Kim, and S. Hwang. 2011. Variations in methanogenic population structure under overloading of pre-acidified high-strength organic wastewaters. Process Biochem. 46, 1035-1038. https://doi.org/10.1016/j.procbio.2011.01.009
  34. Tang, Y.Q., T. Matsui, S. Morimura, X.L. Wu, and K. Kida. 2008. Effect of temperature on microbial community of a glucosedegrading methanogenic consortium under hyperthermophilic chemostat cultivation. J. Biosci. Bioeng. 106, 180-187. https://doi.org/10.1263/jbb.106.180
  35. Ter Braak, C.J.F. 1988. CANOCO - an extension of decorana to analyze species-environment relationships. Vegetatio 75, 159-160.
  36. Vissers, E.W., P.L.E. Bodelier, G. Muyzer, and H.J. Laanbroek. 2009. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol. Lett. 298, 193-198. https://doi.org/10.1111/j.1574-6968.2009.01718.x
  37. Wagner, A.O., C. Malin, P. Lins, and P. Illmer. 2011. Effects of various fatty acid amendments on a microbial digester community in batch culture. Waste Management 31, 431-437. https://doi.org/10.1016/j.wasman.2010.10.020
  38. Whitman, W.B., E. Ankwanda, and R.S. Wolfe. 1982. Nutrition and carbon metabolism of Methanococcus voltae. J. Bacteriol. 149, 852-863.
  39. Whitman, W.B. and C. Jeanthon. 2006. Methanococcales, pp. 257-273. In M. Dworkns (ed.), Prokaryotes: an evolving electron resource for the microbiological community, Springer, New York, NY, USA.
  40. Yu, Y., C. Lee, J. Kim, and S. Hwang. 2004. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 89, 670-679.